Experimental Error

OccuBus

2011-11-21T05:24:00.001-08:00

I've been participating in the Occupy Wall Street movement over the past two months. It's been exciting and worthwhile. In case you're wondering "What is the movement about?" or "What is the movement saying?", I'd like to lay that out in a couple of short sentences.

OWS's central message is that money has taken over the government, and that shouldn't be the case. We should be more democratic than oligarchic. Just because you're rich your voice shouldn't carry more weight.

While there are a host of other causes floating about, and there's also a general surge of diverse political opinion and discussion (something I've relished over these past two months), that's the central message that everyone -- from anarchists, socialists, progressives, Democrats, libertarians, Republicans, and so on -- agrees on.

That being said, our local chapter of this movement is trying to buy a bus. But we're broke. There are a lot of good reasons to own a bus, all central to the ideals of the occupy movement, which revolve around 1) presence of our movement, 2) mobilization of the occupiers to important areas, and 3) ability to carry around supplies and people to actions. If you have a little extra and like the idea of a group of spirited activists driving around doing community service and demonstrating against corruption in the government, then this is the group to donate to.

See us at www.occubus.org

Naturally, it's also just fun to give an update on life and what's come out of the Wichita chapter of the occupy movement, so if you don't have money, at least tell me if you think this is a cool idea or not.

A life update

2011-11-08T15:57:00.000-08:00

The previous month I've been busy with the local section of the "Occupy..." movement. Things seem to be starting to branch into definite groups with select progressive goals, at least by my lights. We'll see how these goals carry on. Hopefully well.

In either case, though, the movement has provided some excellent practical lessons on the art of organizing people. I've also gotten in contact with several local activists that I hadn't known before, which is nice.

Some take-away lessons:

1. Anarchy isn't all bad. While I agreed with the overall message, the anarchic approach had me nervous. But benefits to the anarchic approach kept on cropping up, especially with respect to either a) convincing people to come out, or b) responding to those who weren't going to come out anyways. While order has progressively been built up, and fractions have resulted from that order, I found the anarchic approach more refreshing than I had initially anticipated.

2. The consistent application of principles is more important than overtly emotional appeals, or passionate justifications. There's nothing wrong with these, of course, but the problem with the latter is that they make it difficult to organize if these are your sole motivations, justifications, or arguments. These things in conjunction I think are best, but one needs to be able to consistently make appeals to the means and ends they're going to use in order to bring about order.

3. Protest is a perfectly good reason to organize! You don't need a super-involved project, such as a newspaper, political party, platform, or other event. You can organize people around something as simple as handing out flyers, holding signs, or simply talking to people on the streets. The thing missing isn't that there isn't something to do, but that people are largely socially uncertain in unfamiliar settings. This asociality is a larger barrier to organizing than the need for a project. (I had always thought that the project was important, but really now I think having similar-ish goals and someone with a little social gusto and willingness to listen is probably enough to get people out)

4. Though anarchy isn't all bad, I have recieved confirmation on my hypothesis that in order to get things done, you need some kind of social rules at play. Anarchy can provide these, understood in the right way. But a stricter order, IMV, would still be nice. I don't mind hierarchy. It seems a necessary feature of society. I only mind it when the leaders are ignoble.

5. There are a lot more left-leaning people in Kansas than I had presumed.

6. If you schedule a protest, make sure you have some musicians. People get bored, and this is usually a good source of morale.

7. Literature is important. The importance of street literature isn't a thesis-level writing, but simple bullet points which get your message across. Having presence is the important aspect.

Other than that, I've tried to organize a union at work but to no avail. People think it sounds good-ish, but not good enough to actually do anything about it. So I've taken the liberty of mentioning unionization every time someone complains about work. I'm probably hated by everyone. ;)

Lastly, I'm considering looking at different graduate programs from chemistry. In particular, I'm considering going to some softer sciences because they're more interesting and complex. Either that, or philosophy. If I have the guts to bite the bullet and try to do philosophy of science as an occupation. (And I don't know what the heck people mean by the golden rays of industry in science. Industry is boring as fuck. And, they fuck you over like any other industry -- academic or otherwise -- would. Seems to me that it's pretty much just another job: you hate it, but heck, it pays the bills, and you have time off to do things you like)

Free Philosophy journal!

2011-07-30T10:08:00.000-07:00

So I was poking around looking for stuff on ordinary language philosophy, and I came across http://commons.pacificu.edu/eip/ which is an online bi-annual philosophy journal which publishes their work for free. Very cool!

Chemistry Union

2011-07-21T17:54:00.001-07:00

At the new job I work at I often hear complaints about wages, treatment, and working conditions. The Chemistry field looks precarious, at times. While this field is by no means the worst field to work within, I have taken to mentioning the benefits of unionism where I work to other workers.

Politics tends to be a "no-no" topic, from what I can tell about the atmosphere so this makes it somewhat difficult to broach. But I don't think a Chemists union would have to restrict itself to a single plant, or a single company, and in fact I think would be better if it did not restrict itself to a plant or company. In a sense Chemists already have a professional organization to help workers keep in touch with the chemistry field -- the ACS (though that only applies to Americans). But this is a wholly unbalanced relationship. It keeps a pool of ready and willing workers in contact with companies who may pick and choose, but we don't have bargaining rights outside of our resumes and references. I think that the chemistry employees would benefit greatly by forming a union -- and not just a union which is embedded within a given company, but a union formed by and operated by the workers themselves. This would give us, as employees, bargaining power in the labor market of chemistry. This is beneficial because it would aid us in bringing more stability to our jobs so that we can pursue the things in life that are worthwhile outside of work, such as family, projects, politics, and so forth. Further, it would make the working field equatable, as currently we are all disjointed which is beneficial only to those with collective bargaining power: our employers.

But it's a hard sell. I live in a conservative state, and conservative values tend to weigh against unionism on the basis of principle, and on the basis of fear. I mention fear because when I mentione unionizing, the responses are not of the sort, "I do not believe..." but "Such activities couldn't succeed", so I think there's at least some motivational fear which stops unionism from working. The sad thing is that rural, conservative states would benefit most from unionism. They tend to be the poorest!

Job!

2011-06-16T15:26:00.000-07:00

While I may not have been accepted by any universities for graduate programs, I have been hired on as a quality control chemist right out of college. This is, more or less, a good thing. So far everyone is dorky, which means we get along, and while I've had to read a bajillion and have a Megabajillion more little papers and procedures to read, I'll actually be doing chemistry to support myself. This should include, in the main, wet lab techniques and HPLC. This also means that I'll have the opportunity to really hone my lab skills to perfection, including lab notebook keeping techniques. While I'm good with theory and have an ability to communicate complex ideas, I've always been a little. . . disorganized. Here, that is not an option, and since I like the idea of remaining employed, I'll actually work on that rather than simply say, "I should, but haven't yet"

Also, they have an R&D department in house, so there's opportunity to move into research, eventually. Great news!

My Diagram of Kant's mind

2011-06-08T09:20:00.000-07:00

I'm placing this here mostly so that I may share it with others in an online reading group I'm participating in. But, hey, if you like this sort of thing, maybe you'll get a kick out of it. It can be read as a "flow of information" diagram, where the stuff on the right has information flowing in, and hte stuff on the left is information flowing inward as well, but from some high-falutin' seat of rockem'-sockem thought, and the stuff we experience is right in the middle where it says "The Categories, temporalized" -- or the Schema.

EDIT: And it looks like I'll need another diagram for his theory of perception, so I'm putting that here too.

"We"-Intentionality

2011-05-06T18:00:00.000-07:00

Recently I've been taken with the notion of "we"-intentionality. I'm not sure if it's the greatest solution just yet, but it's a cool concept that helps explain at least one thing -- why people say "we" when they address an audience.

First, intentionality. Intentionality is that feature of our minds that "refers", or has aboutness. To explain this: Suppose your imagine a picture of your car. The "aboutness", or that which refers your thought to your car is the intentionality of that thought. This would be an example of "I"-intentionality -- you're talking about yourself and yourself only in thinking about your car. "We"-intentionality would be something like "We believe that vegetables are good for you". The "we" would mean that you and others that you are a part of believe. That which allows you all to believe together is "we"-intentionality. It's a little weird to think in these terms, at first, because we're used to thinking of thoughts as "private". But think about a close friend or lover you've had. Usually people can tell if something is wrong with them, or predict what they're going to say next if the friends know each other enough. I know that I've had this experience. I would say that this is an instance of "we"-intentionality: It's actually not too uncommon to know what peers in an organization, or even other people within a given community that only passingly know each other think and feel. Surely we can be mistaken, and corrected, but we can also be correct, so I'd say that this is at least a proof of concept of "we"-intentionality.

What does this explain? Well, I've noticed that in conversation when sharing beliefs or explaining concepts to a group of people, the pronoun "we" is often used. A person may jeer if they disagree, "Are you two people?" -- but the language can also float by without notice. This would be an instance of correctly inferring that "we"-intentionality applies in that situation. In either instance, however, "we"-intentionality explains a feature of communication: it is an act of agreeing with one another, or checking to see if we agree with each other (feel free to interject, here ;) ). By saying "We think..." it brings attention to the fact that agreement is needed in this instance for an argument to continue, or it checks to see if a group is indeed still in line with one another. No "royal perspective" is no longer necessary to explain why people say "we" when speaking to others -- we have "we"-intentionality.

Placing Consciousness in a Biological Context

2011-04-30T17:24:00.000-07:00

In biology, I think that form is ontologically prior to function. By this I mean that a change in form implies a change in function, but that a change in function does not imply a change in form. By form I mean phenotype. So, a proper biological ontology would be:

Genotype -- Phenotype -- Function

Phenotypic expression is causally determined by environmental constrains on the ability to reproduce genotypes to the next generation. Natural selection, in this case, is the hard-stop of genotype reproduction -- those who do not pass their information on will stop passing their information on. As such, environment is actually wider than natural selection, and natural selection only plays a role at the level of genotype. Natural drift would also fall in at the level of genotype. Sexual selection, however, would be ontologically separate from natural selection because it is a selection for phenotypes which then causes a selection for some genotypes.

In most biological species function can only be changed by phenotype, and phenotype by the three preceding mechanisms.

"Consciousness" is a separate evolutionary mechanism which operates on function in the limits of phenotypic expression -- or in some extreme cases, such as cloning, acts on genotypic expression. As a mechanism of evolution, it operates in the realm of function – the brain runs on functions and this mechanism of evolution is a function of genotypic reproduction and selection. This isn’t to say that consciousness isn’t more than this – this would just be the way one could explain consciousness in a biological context. More detailed explanations of consciousness would supervene on this general sketch.

I think this ontology accounts for the biological nature of consciousness, as well as its special place in nature while staying in the bounds of an ontological naturalism. These would be the reasons for adopting it.

A quick and unconsidered take on foundationalism

2011-04-25T15:08:00.000-07:00

According to OxfordDictionaries.com on April 25, 2011, there exists in the English language…
Total Words:	171,476
Nouns:	85738
Adjectives:	42869

Suppose the Sentence "'noun' is 'adjective'"

Then for each noun, there are 42869 possible sentences
Given this, there are 85,738 x 42,869 possible sentences of this form, giving some
leeway for creative embellishments, and the fact that we aren't counting verbs
or modifiers or articles etc etc.
This amounts to…
3675502322
or…
3.676E+09
About 3.6 billion sentences of this form

Now compare the number of sentences which we use to describe the world
This, I believe, gives a strong reason to believe that ….
	1) Our perceptions are similar
	2) Our world is structured by us

Which implies, in a metaphorical sense, that empiricists and rationalists are both wrong.


THE END!	lulz

Experts

2011-04-17T15:31:00.000-07:00

Some time ago I had posited that a good problem to solve in the philosophy of science would be to answer, "How should we treat experts?" The problem arises because one doesn't want to just take a person's word on the truth of some claim, yet there are disciplines in modern society which require a a restrictive amount of time to become "expert" in -- and therefore one must rely upon the truth claims of others in certain domains. This may not seem to be a problem, but suppose the recent bank scandal: The experts were the bankers, and they used their expertise to gain. As such, the trust which "expert" status was broached. Even more than this "expert" status is always potentially abusive, not only socially but also personally. The solution to the problem should treat this: How does one minimize potential abuse while still having experts in a given domain, a thing which surely is useful?

A few possible solutions:
1. Remove expertise status. No expertise status, no problem of experts. This has some potentially undesirable consequences, however, as we surely enjoy our brain surgeons to be trained as brain surgeons before doing brain surgery. This solution is still viable in some sense, however, because we could restrict expert status to a few occupations which we deem as acceptable (Doctor, Lawyer, Scientist for example) This would minimize the potential for abuse. However, this is already largely done on a social level, so there isn't much of a problem being solved here.

2. Ethics: If we were all ethical, then there wouldn't be abuse of expertise status. This would require a certain level of trust between members in a society which would be earned by our acting in proper ways. This is an ideal solution. By ideal I mean, totally impractical in every way because we don't take ethics terribly seriously on a social-wide level. It's a "personal" thing. So to implement this solution we would first have to start revising what our social ethics amounts to, which would likely push aside some of our other social values.

3. Trust Experts: This is a common solution to the problem. The value of experts is held above the potential for abuse to the point that we all agree to trust experts despite this potential for abuse.

4. I have a possible rule that might be adopted, and I would think of this as a sort of middle path between 2 and 3. It would be "Require experts to be able to teach". This indicates that when an expert makes a claim, a non-expert is allowed to question that claim. Naturally there are good and bad ways of going about this. If a non-expert states "Well, fuck you buddy!" this will likely not facilitate proper or positive communication between either party. Instead, he could state something along the lines of, "I do not believe you. Could you explain yourself further?" This would require something of a social change, as well -- that we be socially allowed to civilly disagree, even on potentially hostile topics. This would require a form of training which would help persons to express their disagreements in a succinct and communicable manner. The best discipline for this, I feel, is philosophy. So, solution 4 really boils down to not just a rule, but a change in our education by requiring philosophy be learned by everyone in High School. However, it does have the advantage of engendering trust between persons as they come to understand one anothers' position more, and thereby allowing experts to exist, while placing them subject to the possibility of a willing "student" asking questions.

It's likely apparent which solution I prefer.

Incommensurability

2011-02-24T19:05:00.000-08:00

Incommensurability is the thesis that world-views which scientific practice has posed throughout the ages are fundamentally different, or not comparable. An example often used a comparison between Einsteinian, Newtonian, and Quantum physics. Newton stated that mass is an entity separate from energy. Einstein's physics posits that mass is a manifestation of energy -- a possible property for energy to take on. Quantum physics, contra both Newtonian and Einsteinian physics, posits (in its first form, at least) that causality is a probabilistic construct, instead of an infinitely deterministic construct.

Usually the incommensurabile thesis is defended by pointing out dramatic changes between scientific systems. Naturally there is wiggle room for what constitutes "dramatic". Generally I take this to mean that the ontological construct of science has changed. So, we have an atomic theory, for instance, and it would not change the ontological structure of chemistry to posit another atom, or another molecule, or even a new way of bonding. There exists atoms and bonds. However, were we to posit that the universe is not composed of atoms, but waves of energy and waves of energy only, and that the atoms we reference are tools in the same sense that a meter is a tool (whereas "length" would be the ontic unit of a meter), then we'd have an instance of incommensurability. " "The universe is atoms and only atoms" and "The universe is energy waves and only energy waves" "can not be true. You have to choose one or the other, or make an adjustment that allows for both.

In playing with the incommensurability thesis, I broke open my Aristotle and wrote the following thought experiment where I interpreted spectroscopic data using Aristotle's theories.

Spectroscopic analysis would be conceived of in an entirely different way within the Aristotelian framework. Nature abhors a void so there aren't any atoms, and... (From Book II of De Anima)

"...to explain what light is.

Now there clearly is something which is transparent, and by 'transparent' I mean what is visible, and yet not visible in itself, but rather owing its visibility to the colour of something else; of this character are air, water, and many solid bodies. Neither air nor water is transparent because it is air or water; they are transparent because each of them has contained in it a certain substance which is the same in both and is also found in the eternal body which constitutes the uppermost shell of the physical Cosmos. Of this substance light is the activity-the activity of what is transparent so far forth as it has in it the determinate power of becoming transparent; where this power is present, there is also the potentiality of the contrary, viz. darkness. Light is as it were the proper colour of what is transparent, and exists whenever the potentially transparent is excited to actuality by the influence of fire or something resembling 'the uppermost body'; for fire too contains something which is one and the same with the substance in question. "

So, the differences one can obtain from a spectroscope could be explained by this transparent substance in activity with different proportionate mixtures of the elements, which is something Aristotle references often in explaining why different things are what they are (I'm just taking a guess here. But I don't think it's fair to infer, using Aristotle's work in a scientific manner, that reference to quantum energy states modeled by operator algebra explains lines on a given spectroscopic measurement). But, even more importantly, this would be the mere material cause, reflecting a samples potentiality. The actuality could only be garnered from what that material would be used for. Suppose it is a medicine. The ratio of elements would be the potential within the substance, and the shape of the sample at the time of the spectroscope would be during its coming-to-be. For the end of medicine is getting well, and when it is used would be its actuality. (I'm pulling from ideas in Aristotle's Physics and Metaphysics as well, here)

In using Aristotle, while I can find a common referent, and I even think that modern theories are better with respect to truth-value, one can come to understand the incommensurability thesis best, I think. This is because science works by inferring to the best explanation within a certain explanatory framework, and inferences, contra arguments, are actions. It's in the use of science that one understands incommensurability best, and not the "logic" of science.

Tractatus Logico-Philosophicus

2011-02-15T10:26:00.000-08:00

I have been re-engaging Wittgenstein's Tractatus logico-philosophicus. It is one of the most difficult books I've read, and now reread, and even translated to get a bearing on my reading. With the most difficult thinkers I engage, I enjoy stopping in the middle of my writing and drawing a diagram of the argument/metaphysic in order to have a visual representation of the argument as I go along that I can modify, reconnect, and have at the end to remind myself of key points. The list of thinkers that had been on that list is now expanded by one, and Wittgenstein's diagram is the messiest version (though Kant is still the one that has forced me to start from scratch more than any other).

Last night I believe I obtained an important key to understanding this work: It ought to be read as a lament. The book claims to have solved all the problems of philosophy in its introduction, and to claim that the size of the Tractatus shows how insignificant these problems are. And so he begins:

1. The World is everything that is the case

which lays a foundation, of sorts, upon which the Tractatus digs into. I think it important to understand this as a digging downward, because the emotional feel of this work is best understood as a negative plot: the sharpness of this descent can first be sharply felt within section 3. Section 2 begins to outlay the connection between "the case", "objects", "facts", "atomic facts/states of affairs", and other common-place things which are talked of "in the world".

In 3 one can feel the descent because this is where one understands in what way we understand the world. 4 displays how thinking is connected with itself, and this is why the serious logic begins here. The outline of propositions is significantly different from the outline of atomic facts and objects. We can only mention atomic facts and objects, as we can only mention atomic propositions and their truth values. 5 shows how truth values are derived. I think the nadir occurs around proposition 5.5, but I'm being somewhat arbitrary about that. That I have a feeling for this text, now, is a significant leap forward in understanding it. I can not explain all of the text, but I have an idea of its predominant thrust.

The end of 5, right before 6, signifies an upward slope. But it isn't a hopeful upward slope. It's the beginning of building back upwards from the hole that has been dug into the foundations lain in the beginning.

6 begins to show in what way this digging and explicating, while part of what philosophy has been doing, doesn't answer what philosophy asks -- the world is understandable, but the whole is tautologous. It places mathematics and natural science in a "place" within understanding, and reflects that while some persons think these things are ultimately true that this is a sort of superstition. Science, causality, and so on is logical, and all we can know is logic. And, even more than that, I think a very important proposition for understanding the catharsis/melancholy of the ending is:

6.4 All propositions are of equal value.

From this it follows that the important questions, important to Witty at least, can not be answered. They have no sense. Or that this is the answer to the important questions: That the question, having no answer, can't even be sensibly formulated -- and so the secret to immortality and happiness lies not in philosophical speculation, but in a mental nowness: Which is entirely unsatisfying.

This is why I think one needs to read Wittgenstein's "correct method" as sort of tongue-in-cheek preperation for his final proposition. If "correct philosophy" consists in correcting the errors of metaphysical speculation, and others feel that they are not then learning philosophy, then how is philosophy philosophy? Why is it that philosophy is, correctly done, unphilosophical?

Naturally the ending is a bit enigmatic, but I think the final proposition in 6 can be understood in that all what has been said is senseless -- in Wittgenstein's specific way of using this word. The outline that the Tractatus is has no reference. As the entire thing does not refer to "the case", and one finds that out by the time they begin to build "the world" back into a whole from which it has been disassembled, there can't actually be a sense to any of these propositions. However, if we, after having crawled through, on, and over these propositions, one would be wise, having reached the limit of our world at the barrier of language, to throw the ladder down. What has been taken apart is no longer needed -- it is senseless, and with that understanding of senselessness, the world is made right.

However, There is proposition 7. I get the feeling that Wittgenstein did not take his own advice. He did not "see the world right". The entire book is a detailed struggle to understand ethics and related philosophical problems, and it ends in failure. It's horribly dissapointing, and with 7 we see that Wittgenstein will not give up that chase -- he will simply remain silent, and melancholy.

Man, I'm probably going to reread the Tractatus, as I'm not entirely certain on what everything in it means -- but the effort I've spent in reading and rereading this book has been well worth it. Once I seemed to "Get it"... it was an absolutely incredible feeling.

Egypt is an Inspiration

2011-01-30T13:27:00.000-08:00

I've been watching Al-Jazeera to catch up on the Egyptian uprising link

The images are an amazing sight to behold because they're of regular men and women standing up in protest to change their government. They're persons that want freedom. They're an example of how people can bond together to affect political change, and it is change of this nature that the United States could benefit from. They want democracy. I am not against democracy. But our politics do not account for the political nature of economics, and as economic power becomes intertwined in political power this is a poor interpretive stance. The economic is the political. With this message in mind, everyday persons in the United States could bind together in a general union ran by workers. Those who stock shelves, wait tables, and tend bars could have a political voice. At present there is no labor-left party within the United States, not one with power. But there could be one. The images of Egypt, of regular persons wanting freedom for themselves, give examples of how regular persons can stand up against the social constructs to make a better tomorrow. It makes one think that political struggle isn't an entirely depressing affair.

Rationality

2011-01-28T16:42:00.000-08:00

I've stated on here that I believe rationality ought to be part of politics. I go so far as to say that I am a sort of rationalist. I say "sort of" because "Reason", "rationality", and so on, don't mean the same thing to everyone. Not only do people disagree with the meaning and implications of rationalism, they also feel divided on the issue. My "sort of" is rhetorical: I mean to say "reserve your judgment for after you hear me out"

I believe that rationality can be summed up with a single, simple maxim: Find reasons for your beliefs which are logically consistent. When you can no longer do this, acknowledge this, but continue to reflect on this hinge proposition.

There are no appeals to a universal "making-sense-ness" within the heads of reasonable persons. There is no pointing at the unreasonable, or routing out the irrational, or exercise of epistemic chauvinism. That isn't to say that rationality can't or hasn't been used for these or other negative ends. It certainly can. However, rationality is, in the end, a loose position. It is this looseness that I wish to point out.

Suppose I claimed that I believed in God. If someone then asked why, I would say, "Because I experience his existence every day" If they retorted, "Why don't I experience this, if he is so wonderful?" I would reply, "I am ignorant. I wish he made this known to me, but I'm afraid that I can't say"

This is a rational position. It is a position I disagree with, but it is a rational position. It is epistemically rational. There is a difference between rationality and proof. Having reasons for your beliefs, finding warrant, and applying these constitently is all that is required to be rational. "Proof" is the deduction of a position from axioms. However, argument, and reasons for positions, are much more varied than deductive systems. One may only use deductive systems to justify their position, but it's not necessary for rationality.

I chose "God" because I'm mostly speaking to that group of persons who think that concluding that God does not exist is the only conclusion a rational person who is honest or not arguing for "Feel-good" constructs could come to. Rationality is not so restrictive that the atheist/agnostic/materialist/whatever world-view is a for-ordained conclusion. Beliefs as divergent as "There is no purpose in the world" or "There is a God" or "The World is nothing but Mind" can be justified underneath the rubric of rationality . We can rationally disagree and discover where, and possibly why, we diverge.

This doesn't reflect on the "truth" of either claim, or any claim within rationality. Rationality and "truth" are two separate issues: At base, if it were true that irrationality is "true", then rationality would be against "truth". All this is intended to do is point out that "rationality" really, really, really doesn't say that much, and that therefore theism, disagree with it or no, can be rational.

THE experiment of my undergraduate career

2011-01-20T19:28:00.001-08:00

... is making a standard curve. Today I came into lab, and we were prepping yet another standard curve. I wonder to myself: Is this what Chemists do? Are we always interested in identifying either the identity or concentrations of some substance? Is this only specific to analytical chemistry, or does it translate elsewhere?

Not that I would really mind, if that were the case. I'm really good at it, now. R^2 values are regularly .999whatever. Standard deviations are regularly quite tolerable, and this is all by hand. But I also keep on thinking: What can I do with these tools? What can I explain within chemistry with this experimental-theoretical framework? Is there really much left in chemistry to pursue outside of explaining things outside of itself, or improving the apparatusus to be more automated, more precise, more accurate, but not novel?

At conferences I've seen a lot of interesting computer modeling projects, where the standard parameters determined experimentally are shown to be able to be calculated from basic quantum mechanically based algorithms -- stuff like the change in gibbs, enthalpy, or energy contributions from solvents, solvent structures, and other modular neatness. But I can't help but think that there has to be some greater theoretical project than simply increasing the resolution of our models, improving the efficiency for identifying substances, or making more accurate estimations of important physical parameters. These would be termed core chemical projects. All other projects seem to involve elucidation of other systems for some other purpose, whether it be interest in a biochemical system, or improvement of some industrial practice.

But I'm stuck as to where, or if I tried something new if it'd even be interesting or desirable to try; PhD's earned in respected fields are likely more marketable, after all. I suppose I could memorize a few more reactions, and what they look like, to be better prepared to identify oddities when I see them, or have a handle on unexpected events at a more intuitive level. But I wonder: What novel thing can chemistry do today?

For Accommodationism

2011-01-13T09:56:00.000-08:00

There is a current amongst the atheist blogs I read regarding accommodationist vs. confrontationalist stances. This is my argument for accommodationism as the superior position of the two.

Confrontationalism lacks any credible epistemic basis to discredit religion at large, and this is, from what I can tell, what it tries to do. If it does not do this, then the following is incorrect. When I say religion at large, I mean all the predominant religious positions within culture today. We'll say Christianity, Islam, Buddhism, Judaism, and Hinduism. Further, it lacks the moral basis to discredit religion at large. These are the two main issues brought against religion by confrontational atheists. I think that these positions are the product of arguing against weak positions, positions I also stand against, but when generalized to all religions then atheism is making too dogmatic a claim. At that point we're talking politics. If politics, then there are more important issues than atheism to discuss, like war, class, capitalism, genocide, health care, gay rights, science education, and so on. Further, there are religious allies to these political causes, and so if politics, then accommodationism is better for supporting these political points, as well as building a healthy pluralistic environment.

On epistemology: The central claim here is that religions are false. The basis that religions are evaluated to be false are scientific claims. However, there exist scientists who are religious. To relegate these scientists to the special, no-counter example corner of "Their beliefs are contradictory" is to play the no true Scotsman card. As such, I have good reason to believe that science does not prove religion false.

To know and to believe are two separate things. To know something requires an argument, whether it be a "negative claim" or not. On "Negatives":I can prove a negative, such as the square root of 2 is not rational. Negatives can be proven via the modus tollens inference, or the proof by contradiction. In fact, the often used problem of evil builds itself on the proof by contradiction. However, I don't think the problem of evil works to prove that God does not exist, but only that God is not in this exact way that some rationalist theists thought he was. But, for the major world religions, you didn't need such a proof by contradiction -- God's nature is explicated in far greater detail within the religious tracts than some simple, vague Three-O reference.

Lastly, there is an emphasis on evidence based claims. Why, and what does it even mean? If all we mean is, "Well, it's nice to have data", then I have no problem. If what we mean is ,"the existence of pH meters proves that God does not exist", then I'm claiming that this is a little senseless. The whole "evidence based claims" meme sounds great as a talking point, works fine against creationism, but could really do with a little more ground work to support it.

On moral claims: Atheists are personally moral, as are many theists. To point to the Catholic abuses of children, the crusades, and so on doesn't say anything. You need to show that religion is the causal culprit. Without a causal argument one must admit that atheism leads to mass murder, as the USSR performed mass murder. Clearly no one in the atheist community believes this, so one should admit that the correlation between theism and child molestation doesn't follow causally.

Further, if the atheists lack an epistemic basis to claim that religion is false, and continue to claim that religion is false for epistemic reasons, then the atheists are loosing moral credibility with respect to truth-claims in that they are demonstrating an inability to self-reflect, which is an important part of moral deliberation.

As neither epistemic or moral claims counter religion as a whole very well, we should get down to the brass tacks of politics. Accommodationism is a superior politic to confrontationalism because it's more honest about our epistemic certainty, it allows bridges to be built between the atheist community and theist communities who are friendly towards the same political end goals, such as gay rights and science education, and it plays a better PR role. In fact, accommodationism is the correct position, not the weak and scared position that's too afraid to "say anything". Accommodationists are skeptical of strong negative claims, and find things outside of metaphysical speculation, such as science education vs. thoughts on the existence of god, to be more important. As the confrontationlists have said, let us not mince words. Religion, at large, can stand on its own two feet, and atheists don't have a good basis to claim that it doesn't do so in its entirety. The confrontationalist position is poorly thought out, lacks self reflection, and the conclusions it purports to prove are simply wrong if it's swinging its rhetoric at religion as a whole. As such, accommodationism is the only position that is epistemically and morally worthwhile, whether or not confrontationalists are angry about this fact or not. While there are some religions that deserve scorn and derision, the claim that all major religions are false is simply an unsupported belief.

Weighing in on a national tragedy in an uncomfortable way

2011-01-10T12:29:00.000-08:00

There has been much talk about the shooting of Representative Giffords and the death of innocent bystanders. Many causal sources have been proposed:

CSM reports that Europe believes that the political climate in general is at fault, and this is due to America's decline in power and its failure in two world wars. link
Sarah Palin and extreme Right-wing rhetoric link
Public School systems link
Ayn Rand, Mein Kampf, Das Kapital, and George Orwell link
Some "They do it, too!" from the right link
Some point to gun laws link

As long as we're weighing in political opinions, I might as well take a swing: the shooters actions are a clear indictment of capital. Capitalism encourages news sources to instead offer flash, fiction, and meta-commentary that conform to our predispositions -- this brings in a larger market share of viewers. The need for counter-factuals, scientific inquiry, and criticism is abolished. All that matters in every walk of life is profit. This drive for profit increases the number of persons, which, due to our limited capacity as thinkers, increases the number of sub-cultures which develop. Capitalism, in pursuit of the greater spectacle, further exacerbates these sub-groups so that they lose more and more common pragmatic rules of communication that are a necessary precondition for rational discourse. Each sub-group obtains its own epistemic values and assigns a differing distribution of weight to facts presented, which creates discontinuities between large groups of people. These discontinuities are further exacerbated when we attempt rational discourse, and noise is generated.

The internet is not to blame. This internet is to be praised for making this reality more apparent.

With noise, misinformation, confusion, political turmoil, meta-commentary, and economic hardship comes a climate that generates a person willing to shoot a politician for unknown, indistinct, un-rational reasons. And, for those thinking this a ridiculous causal hypothesis, I couldn't agree more. But I ask you this: Is this a better explication than anything offered so far?

If we were really interested in causal factors, then we'd likely wait on police reports or turn to the field of psychology. Everything offered in the news thus far has been sociology/politics. We're using the event to construct a narrative which argues for our politics -- we have a political axe to grind. I don't think this is even necessarily a bad thing. Perhaps we should reevaulate our rhetoric in light of having what that rhetoric means being shown to us. We should certainly reevaluate the role capitalism plays in everything complained of so far, such as irrational political discourse. However, as I am a proponent of rationality within political discourse, I think it best to understand that the news presented thus far has been political speculation -- like metaphysical speculation, but less structured.

The Central Dogma

2011-01-09T19:21:00.000-08:00

In Biochemistry, the above is known as "The Central Dogma". It used to be the case that we thought RNA, once transcribed as RNA stayed as RNA and that it could never be the case that RNA became DNA. Whether this was the case for reasons of convenience or it was genuinely thought to be impossible, I have no clue, but such a statement does have a "dogmatic" feel to it and so I always took that to be a reason why it was called a Dogma.

The other reason, which is related to it being a central dogma, is that it forms the conceptual basis for a basic biochemical analysis of DNA expression. First one learns what DNA, RNA, and Protein are, and then one learns that this is the general outline by which DNA is expressed into RNA, and the general outline of protein tranlsation from RNA. As has oft been repeated, DNA can be thought of as a code which expresses a sequence of RNA bases, which in turn generates proteins through a well modulated and specific chemical reaction. There are four RNA bases, each of which has a complement on DNA. These four bases form "codons", which are the basis of the genetic code for all life known to date.

A Codon is a sequence with three bases in it. AUG, for example, forms an RNA codon. As there are four bases and three "slots" for each codon, there are 4^3 possible codons, or 64. These 64 possible codons only code for 20 amino acids, which are the building blocks of proteins.

Proteins perform many, many functions within the body, and so understanding how proteins are made and transferred through reproduction forms a strong basis for understanding life at the chemical level. There are many, many details to get lost in, and some of the nitty-gritty details are really only known by people in that specific research field. This is why the central dogma is of so much importance: It gives a foundational biochemical reference point to which we can connect all of our other knowledge to.

I said earlier that it used to be thought that DNA makes RNA, end of story. That, now, has changed -- it turns out that we've found enzymes which help to reintegrate RNA back into DNA sequences. This enzyme is called "reverse transcriptase", and it is through mechanisms such as these that viruses infect us. Although, to them, it's not an infection: It's their method of reproducing themselves. A greater understanding of this purely theoretical mechanism can yield practical results in the field of AIDS treatment, which goes to show how a general theoretical question like ,"How does a cell operate at the chemical level?" can possibly lead to practical benefits. Surely this isn't the motivation behind such research, as such research is intrinsically interesting, but it does go to show how intrinsically interesting questions which have no perceived benefit are often connected to practical benefits.

The other thing that the central dogma shows is that even scientific "dogma" can undergo revision. As far as I can tell, whether it was for heuristical reasons or judged to be this way, the central dogma was taken very seriously. Yet, over time, we've had to revise our models given a long series of inquisitive arguments. It can't be emphasized enough that even our most basic scientific descriptions are taken as fallible constructions -- not to dissuade persons from the credibility of scientific work, but to make persons aware of how far a scientific argument can go. The word "science" has often been used to legitimize, and pointing out how actual science is full of qualifiers -- like "may", "could be", "might", "I suspect", coupled with complex arguments from difficult to obtain and possibly faulty data to likely rejectable conclusions, at least in so far as it's only a published paper -- can only help the public to critically evaluate scientific claims.

Or, in short, even the most stalwart of scientific constructs have hesitancy involved: If a company or politician may gain by your acceptance of their scientific claims, and they lack this hesitancy, you might want to turn your bologna alarm on and check some alternate sources.

Feminism and Labor Politics

2011-01-04T20:51:00.000-08:00

This month's IWW had an excellent article covering the intersection of labor politics and feminism. In particular, it asks some excellent questions for men within the labor movement in a direct, firm, and non-threatening manner. I highly recommend checking it out on the bottom of page 4:

IWW Jan/Feb 2011 Issue

I was very excited to see this issue, because I feel that many disparate left-leaning causes are in many ways fighting the same battle, and it's great to see this sort of crossover. After all, Marx expressed radical feminism, desiring to dismantle family structures and marriage because of their inherent tendency to enslave one class of persons as property to property owners.

Atheism: A Basis

2011-01-01T03:25:00.000-08:00

A recent theme that has re-emerged in my life, mostly due to the holidays, has been the philosophic basis for atheism.

Skipping definitions and relying upon common uses for words, the standard question I receive is, "Why don't you believe in God?" As I use the big A word as opposed to the little A word, the question is more earnest, if rarely an attack. The simplest reply that doesn't ruffle feathers is, "I don't have a reason to do so"

But this isn't the entire reason for my atheism. Within my life the God hypothesis has been "falsified", in any sense of the word that this can be meaningful. This isn't to say that God can't be, as clearly falsification isn't the end-all and be-all of enquiry (Or even scientific enquiry). This is only to say that I have always been interested in theology, have prayed, have meditated, have read holy books, have attended several services, and have even had experiences that mirror what others describe as God. If all that one means by "God" is "A feeling of warmth one may experience when at calm or in a particularly beautiful or sublime aesthetic experience which helps guide one to a moral walk in life, albeit confusedly" then sure -- I'm a theist. I felt this long ago in acting, in having sex, in looking at works of art, in philosophy, in science, and so on.

The problem I tend to encounter within countering atheists as well as in speaking with theists is a singular assumption that atheism implies material reductionism: Physics and Determinism are the basis of all reality, and those namby-pamby feelings are merely illusions to which you are a slave to!But are they?What exactly is meant by "Real"? What does this word connote, denote, mean, and why is the scientific description of the world MORE real than, say, a person’s theological standpoint? Does "Reality" admit of degrees? Is the one "noumenally Real", and the other merely "Phenomonon"? I certainly do not think this is the case. Further, on the basis of "Occam's Razor" no dualisms are permittable (though I have other reasons to stand against dualism). If an atheist rejects Occam's razor, but is still a material reductionist, that would be a person whom I'd be interested in having a discussion with. The first question in this paragraph will be my starting point for arguing contra material reductionism.

So, why atheism? While theism can mean many, many, many things, and I'm certainly open to this sort of a discussion, theism, within America, still has a very simplistic basis that has a very strong influence on American culture. To those theists that find the atheists out of bounds: I encourage you to speak. You should be more offended by this simplistic theism that is easily refuted, thereby inspiring the hubris of atheists, than atheists are -- yet it is the atheists who are speaking.

What do I mean by simplistic theism? A theism unconsidered, that uses an elementary notion of faith as a shield against questioning. A theism whose only recourse to scientific argument is to reference the infallibility of the Bible. A theism that is tied to Republican politics (as opposed to a theist who is also a Republican). A theism that can't find a love in their heart for homosexuality. A theism that claims to know God. These are simplistic theisms, and in comparison to the high-and-mighty self proclaimed horse of the atheists, the atheist position, while not merely negative and thereby in need of argumentation, comes across as stronger.

As for my argument: I don't think God is either non-falsifiable or incomprehensible, in the same way that I don't think that matter is incomprehensible or non-falsifiable. What I do think, however, is that arguments for God tend to put the cart before the horse -- they are decided beforehand. Now, this can mean one of two things, as far as I can tell: One, God is simply a metaphor for understanding the world, an interpretive lens that provides categories through which one may communicate on a pragmatic basis with other believers, or interpret certain contexts such as morality and judgment to pragmatic ends. Two: God is a presupposition which one believes in not by choice, but is "triggered" by background, environment, and personal characteristics. I find neither condition blameworthy, mutually exclusive, nor does either actually negate the possibility of the standard metaphysical God. But such descriptions of theism and God are the reasons why I am an atheist. Theistic culture, from my perspective, confusedly shifts the referent of God from the culture and values themselves to a grand metaphysical system of rewards and punishment that has, in my interpretation, immoral implications. If there were no metaphysical construct giving these moral precepts an infallibility, then there may be room for discourse to change them in light of new contexts. But there is no such device within the theism which influences a large number of Americans.

Epistemically, I have no argument contra theism. I have no problem with hinge propositions. However, with Kant, I argue that God is implicated by morality -- yet the morality of our modern Gods is immoral, and I refuse to consent to such a Kingdom of Ends. Ergo, I am not a mere epistemic agnostic; though epistemically I have qualms here and there with the atheists, to me ethics is a stronger compulsion for acting than epistemology. As far as I can tell, to make an argument from an internal perspective, the first commandment has been broken: other Gods have been placed before God -- God, the symbol, for the culture of men. And so Atheism, not as a simple pondering of the Problem of Evil (which, if one accepts God, I don't think is a problem; Leibniz's Best of All Possible Worlds and all that razzle-dazzle), is a moral choice against a deeply Christian nation. I have no desire to abolish all of God, though I don't believe in him. But I certainly wish to negate those who use what could be a beautiful concept for some towards alienating homosexuality, promoting patriarchy and militarism, creating an Other in Islam, supporting Capitalism, and generally promoting right-wing politics. And, as things sit, a large enough number of theists make the atheist camp more worthwhile.

Additionally, I just find sleeping in on Sunday and premarital sex to be more holy than falling asleep on a hard wooden pew and lying about not having premarital sex.

Kinetics

2010-11-30T11:39:00.001-08:00

I've written a bit in the past on equilibrium expressions in chemistry, and have also noted how thermodynamics (i.e. equilibrium) is one of the two foundational concepts in all of chemistry, while kinetics is the other foundational concept. A reaction can be characterized as favorable through thermodynamic expressions, but because said reaction can take forever to take place, it can, for all intents and purposes, be considered as not taking place. This is all related to the energy diagram of a reaction:

The distance between the starting point on the left and the ending point on the right gives the change in energy of a system or species. This is the thermodynamic aspect of a reaction, and is directly related to equilibrium. The center portion, where the energy is changing in all kinds of ways, is related to the kinetics of a reaction.

Think about a trampoline. When you jump high into the air on a trampoline, it took a considerable amount of energy to get you up there (from the trampoline, from your legs). This is similar to the high points on the reaction diagram above. The molecule undergoing reaction needs to change its shape in order to become a new compound, but in order to get there it has to "jump up" into a shortly lived shape, much like jumping on a trampoline will only propel you into the air for a short amount of time. The amount of energy it takes to change a molecules shape is what slows a reaction down.

In the above diagram, we have two high points. The first high point, because of how much energy the molecule starts with, takes more energy to be put into the molecule in order to get the molecule to that energetically packed shaped. This would be termed the "slow step" of a reaction. The molecule briefly takes a more comfortable shape before having to undergo one more energetically unfavorable conformation change, and then it drops back down to the final product. However, because the molecule already has a lot of energy gained from the previous conformation, this step is much faster since it only requires a little shove to get going over the final hill.

This is the theoretical picture of a reaction, but kinetic relationships are usually represented with equations. Deriving these equations will be the topic of my next blog post.

Graduate School

2010-11-29T12:25:00.000-08:00

I finished up the GRE this past weekend, and the preliminary results look good. After having paid for the GRE, however, the capital necessary to finance the application process is lacking. Seriously, this shit is bookoo expensive. As such, plans include:

1) Decrease the number of schools to which I'm applying. Shame, since I had researched several

2) Call the schools this week and beg them to waive the application fee

if not 2, then 3) Don't apply, but move to favorite graduate school area, take a class next year, and solicit myself in person for one year.

Option three actually doesn't look too bad from my vantage point, since having a year of not-school would likely increase my motivation going in. Not that I have major motivational problems at the moment, I just figure that it would have this effect. Option three is bad, however, in that I know I'll forget a lot of information in that year, and would be playing catch-up for the first semester rather than coming in fresh.

Seriously, how do people find the money for this? It's ridiculous that the "standard" bill shelled out (advice says to pick ~5 schools), including the GRE, is approximately 500-1000 dollars (depending on how many schools you apply to) just to hear "Yes" or "No" back from the school.

Turkey-Day, 2010

2010-11-25T23:26:00.000-08:00

An interesting point came up at the Turkey feast today. For most of my life I've dined with the fam, which of course means that I do not drink wine, I do not use bad words, and I remain mostly quiet and polite.

However, since my family has moved away from our used-to-be-home base, I've been celebrating Thanksgiving with a close friend of mine and his wife. I bring pie over, they cook everything else. It's very kind of them.

The additional benefit to this, however, is that we're all opinionated atheists, and as such I can get drunk, swear like no other, and bray on about Socialism. In that sense, everything is actually more SOP, and thereby "filial" in the classic sense where one can expect to "be themselves and not worry about it". Honestly, I can't "be myself and not worry about it" around the family -- I know that it would hurt their feelings, and so I simply abstain. I feel no resentment for this fact, but it's still nice to find a place where you can be worry-free of what you say when you aren't exactly part of the mainstream of popular opinions.

Here's to a great Turkey day. Maybe in the future we'll forgo the turkey. Ya'know, just to make the holiday that much more sacrilegious.

Skepticon III

2010-11-21T18:31:00.000-08:00

I just arrived back from Skepticon III to my small abode and I am exhausted. This was three days of skepticism, atheism, science, feminism, gay rights, sexuality, late night conversations, and reference-trading [I love references]. Talk about a fantastic venue. (It's also free due to the work of a lot of cool volunteers that I'd like to thank)

Perhaps my favorite aspect of these events is what seemed to be a large cross-over between the afformentioned groups: Feminism, LGBT rights, and general strong stance against right-wing religious movements. I hope these political trends continue to be introduced. It would be great to unify a sort of left-political force within the United States that aren't as blatantly not-left as the Democratic Party. Though I doubt everyone will agree with my particular politics, I'm tired of two blatantly bourgeois options.

Of those who spoke my favorite to listen to was PZ Myers. I like science things, and I thought his poker game analogy for evolution was a wonderful tool that I'm going to shamelessly steal.

Again, while this may not reach those organizers, thanks

Points of Conflict in Evolution

2010-11-17T08:01:00.000-08:00

Last night at the Socrates Cafe (hosted by our university's Philosophy Club!) the topic was "Can religion be reconciled with evolution?" Overall it was an interesting discussion, but what I was most interested in were points of conflict between evolutionary theory and religious views. I thought I'd gather up these ideas here. From memory, it seemed there were four clear points of conflict:

A Sense of Purpose
Literal interpretations vs. Alegorical interpretations of The Bible
The relation between Man and Animal set out in The Bible.
Knowledge of man vs. Knowledge of God

Naturally this all depends on what one means by religion, what one means by God, and what a specific religion denotes. The focus was upon mainstream Christianity, though, because this is the predominant religion in our region, and therefore it is here that we were most familiar with conflict arising. I'll first explain the conflicts, then move onto possible resolutions. To explain the conflicts --

A sense of purpose: The Bible, especially in the New Testament (I'm a little sketchy on the theological backing for this statement, however) states that man is on this earth for a special purpose. This gives meaning to an individual's life as they fit into a plan of some kind that a benevolent being has orchestrated for them. The conflict arises because evolution carries a purely materialistic connotation with it -- not as a necessity, but human existence and some of its traits are explicable in material terms. More than this, we thought that the word "random chance" tends to carry the connotation that man has no purpose, and therefore no meaning within an evolutionary context.

Literal vs. Allegorical: If one takes the Biblical account of the origin of man and the universe as a literally descriptive event, then clearly evolution and The Bible conflict. According to The Bible, man was created in God's image exactly as he is now. According to evolution, he was one of many species who made it to this point.

The relation between Man and Animal: According to The Bible, Animals were set upon the earth for men to use and take care of. This places man above animal. There comes a conflict with evolution when man is taken to be an Animal, because this relation is, at least in part, dissolved.

Knowledge: Some religious traditions claim to have knowledge of a superior or different kind. Because evolution is a man-made construct that admits itself of being tentative always, and because Godly knowledge is necessarily perfect, a conflict between scientific claims and religious claims arises in that a religious individual who believes to have a superior kind of knowledge will simply dismiss evolution tout court. In addition to this, the teaching of evolution might be frowned upon as it introduces a different way of looking at the world that may influence their children away from the perfect knowledge that the believer has.

Resolutions

Purpose: This one is complex to resolve because it is highly dependent upon how one interprets evolution and how one interprets their religion at a metaphysical level. However, one clear resolution seemed to be pointing out the meaning of the word "Random". Random can be easily confused because it has several meanings, and in the context of biology it has a specific meaning that probably doesn't reflect what one would consider "Truly Random". In the context of biological evolution, randomness isn't necessarily stochastic so much as it is unpredictable. An example may help here:

Mutations to genes can be introduced by a number of inputs. An example of a random input would be the molecular machinery making a mistake in transcribing DNA into RNA. Instead of the base that the machinery is supposed to pass along, another is put into place. This piece of RNA will then express another amino acid, which can change the function of the protein which is being made. This change of function almost always leads to a decrease in an organisms function -- it is unable to reproduce, whether it be because of death or some other reason. However, it is possible for this mutation to make a positive contribution to an organisms function, in that it is better able to reproduce than its fellow creatures. In either direction, this is a "Random" mutation. It may not be "Truly Random", but this is what the term is meant to imply -- that some changes are able to be accounted for, but are not predictable at the level of predictability that one tends to expect in a scientific theory. As such, evolution isn't "Random" in the sense that we don't have a purpose. I used the term function on purpose. There is an interesting analogue here.

When Adam and Eve leave the Garden their purpose becomes to have a family. In a sense, this is their function. They must plow the earth and work in order to procreate and be happy. Similarly in biology an organisms fitness can be simplified to their ability to procreate. The function of life is to create more life. If one doesn't take the Bible too literally, the parallels between these supposedly disparate disciplines are interesting, which leads me into the next resolution.

Literal vs. Allegorical: A literal interpretation is clearly irreconcilable with evolution. I won't get into whether a literal or an allegorical interpretation is better, but I will note that allegorical interpretations are in almost all cases reconcilable with evolution.

Some interesting parallels exist between the creation story of the Bible and currently accepted scientific cosmology. While God separated the light from the darkness, the current model on the universe's beginning is the Big Bang. The Big Bang doesn't explain the question of being in the least, but it does start with a large conflagration where all being was mixed. With time the light was parsed from space. In the second creation story within Genesis there is a parallel between what is created on Earth and what currently cosmological models describe. First came the waters, then came the plants, then came the animals, and then came man. The Knowledge of Good and Evil corresponds to man's birth of consciousness. The innocence of species-hood without higher cognitive functions was a sort of bliss. A new perceptive ability brought about the realization of pain in this world, work for our bread, and a longing for a heavenly existence. I didn't come up with that story, but I think it's neat.

Between Man and Animal: This is something of a specific problem, since not everyone will think that their religious background gives them right over animals. However, supposing that man is greater than animals -- If one accepts the doctrine that man is fallen, then there shouldn't be a problem in accepting that Man is an animal. Man can still be greater than other animals, in that he prefers those rationally inclined, but it seems to run parallel with theological teachings to assume that we actually have an animality. In Christianity this animality is to be overcome, something which I can't say I agree with, but the existence of animality seems to go with, not against, religion.

Knowledge of Man vs Knowledge of God: Here I don't think there is a resolution. I only think it important to point out that in "Knowledge of Man" (i.e. Science) class that we should stick to the subject matter of "Knowledge of Man". I have some theological problems with revealed knowledge, but that is outside the scope of this post. Still, it seems unreasonable to be worried about knowledge of man infecting a child's knowledge of God if the knowledge of God is perfect. There shouldn't be much worry at all here.

Evolution, Science, and Politics

2010-11-15T20:05:00.000-08:00

Tonight I saw a film at my university titled Kansas vs. Darwin, with the filmmaker present, Q&A session, dinner, the works. It was very nice. While I've always maintained a certain fascination with Creationism, et al., I wasn't quite aware to how widespread beliefs in Creationism are. After watching the film, I decided to investigate what Gallup had to say:

2004 Gallup Poll on Americans beliefs: link
2007 Gallup Poll, coupled with some healthy Republican bashing, which reveals a similar trend: link

Now, I'm no social scientist, so I wouldn't say that I have the theoretical backing to interpret this data as well as it could be. But the trend is strong, in that Approximately 1/2 of Americans believe that God created man in his present form. This lies in contradistinction to the 1/3 of Americans which reject Evolution as a theory. I think this disparity is explainable in light of creationist beliefs that there is a difference between micro and macro evolution.

The percentage numbers on this are staggering, however. I'm from Kansas, and so from the filter of popular culture, news, as well as some personal experience (organically flavored with personal bias) I knew that there existed quite a few individuals who rejected the theory of evolution. From reading creationist websites, however, I gained the impression that this was a fairly fringe group of individuals due to the nature of the claims, and that I just so happened to be lucky enough to live in a blood-Red state, where bouts of insanity are viewed as acceptable (I'm more joking than serious). Clearly, however, these suppositions are wrong. The shear percentage of individuals refutes my supposition that "Creation Science" is a fringe movement, politically speaking, and the film above stated there was... somewhere around 27 other states going through similar struggles? I can't remember the exact number, but it was greater than Kansas + Texas, the two likely candidates.

From the dinner and the video viewing, it seemed that this widespread belief could be explained on the basis of what possible philosophical implications the theory of evolution entails. There is certainly a movement of persons who believe that the theory of evolution entails materialism, atheism, a loss of moral value, and/or the loss of human dignity and specialness. I am not of this group of individuals.

However, it seems that there is this perception, and it may best be explained by two notions: The notion that Animals are inferior to Humans, and the notion that God created Man in his own image.

If man is an animal, then the inference from evolution is that man is not special. This contradicts our notion that man is a special being with a special purpose above that of the animals. Therefore, evolution must be wrong, because it animalizes man. On the face, outside of arguments for evolution, this is a convincing argument -- one may look at animals in the zoo and conclude that there is a world of difference between us, and because we value ratio-emotional-linguistic expressions that happen to communicate well with us, one may conclude that man is a special sort of creature above the animals. This explains the large number, at least in part.

The second notion: If man was generated by natural processes, then he was not always in the shape that he currently is in, and this contradicts Biblical teaching. If Biblical teaching, supposedly incontrovertible, is wrong in one instance, and The Bible must be taken as a literal whole, and The Bible is the basis for moral beliefs, then the theory of evolution threatens not only the historical myths upon which moral beliefs are found, but the moral beliefs themselves.

It seems to me that, for the regular individual involved, they aren't interested in scientific truth. The individuals involved are interested in a spiritual truth. However, on top of this layer of worry about materialism and the decay of moral values in a Godless society predicated upon natural selection there seems to be a strong political current. The 2007 Gallup Poll suggests that Republicans are catering to this sort of audience. This is pretty much standard fare tactics for the Republican party (promising empty metaphysical maybes to convince rural districts to vote against their economic advantage), so I wouldn't be surprised if a large section of this percentage is explicable in terms of political clout. Something else mentioned at the film was the divisiveness of the topic of evolution, and the fact that those against evolution bond together socially over their non-belief in evolution. It would seem plausible, given the Gallup poll above, that the Republican party is cashing in politically on this movement, which would explain why it is widespread -- it would certainly explain where funding for the institutions which pump out creationist literature come from.

To ask these social bonds to be dissolved is to ask too much. But, simultaneously, to ask people to believe in the strongest scientific conclusions within a Western society isn't asking very much. This hints at another source of the problem: Science Education being horrible, and science education being horrible not just because we live in an anti-intellectual culture that values funding imperialistic ventures for its stockholders (though that doesn't help). There is a disconnect between the scientific communities expectations of scientific literacy, and their willingness to put effort into educating the public on scientific matters. This is natural, given that careers are built on publications and patents (which, coincidentally, happen to be the things which support the Market). But if the scientific community wants the public to be educated, and given that the public funds the scientific community they honestly have a right to know what's going on, they need to change their attitude towards outreach programs and the value of popular science work. If these become worthwhile career enhancers (though that shouldn't be the bottom line in choosing who popularizes and who doesn't) then we're likely to see a rise in scientific literacy.

ACS Conference

2010-10-08T12:20:00.000-07:00

My poster was admitted to the regional ACS conference this coming October! Results are pending on a single experiment (it was done once, but the data was difficult to interpret so we're subbing some expensive taq for the not-as-expensive taq we used initially), but they looked promising from the first run. Either way, my undergraduate research requirement will be satisfied, and if the results are positive then they should be publishable.

Which brings me to a point I often question about the scientific process: Why don't negative results get publishing, at least, more often? I'm assuming that it's more of a principle of parsimony in publishing than a fascination with positive results, but sometimes I wonder... is there a database where one could at least throw up negative results? Maybe it wouldn't count as publishing, but something like this would be great because... well, it could potentially stop other research groups from traveling down the same avenue, thereby limiting the amount of resources wasted on the same question. This, at least on its face, sounds like a good thing.

Some Possible phil-o-sci Problems I want to solve

2010-10-05T19:08:00.000-07:00

How do you properly disseminate scientific information?

Problem 1: The expert, and consensus. Consensus can be achieved amongst the respected scientific community on controversial (whether that controverys be manufactured or no) issues. The obvious topics here are evolution and global warming. However, the problem isn't with the scientific community achieving consensus. The problem is disseminating that consensus, and determining when one can claim scientific consensus such that it is acceptable to use this term in popular discourse. I take it at face value in this blog post that both evolution and global warming are issues upon which consensus is reached. The problem here isn't with the science; it's with our vision of the expert. A society unequipped with the rational equipment to distinguish between good and bad scientific claims -- and not in an immediate way. The research can take time -- is exactly the sort of society one would expect to see if it that society relied upon the image of the expert. The problem of the expert isn't that experts shouldn't speak; quite the contrary. The problem is that theatrical devices can achieve the image of the expert without the substantial mental effort necessary to become an expert. Additionally, the problem of the expert lies in the fact that experts will disagree, yet we lowly types not in the public sphere still need to be able to distinguish which expert is the better expert. This is particularly relevant in issues of basic scientific theory which happen to apply to political issues; because one can find a person with credentials who is willing to adopt a viewpoint, and use their expert status to back it up, we have a culture wherein we can easily select for the expert that happens to make us feel comfortable with our viewpoint. This is confirmation bias at work.

I state the problem of the expert because it is my opinion that this is a more basic question in the philosophy of science than the problem of demarcation. All solutions for demarcation have, at present, only excluded things which most individuals who have chosen rationality already excluded for basic, philosophic reasons. The problem of demarcation is, itself, a problem. If, instead, the philosophy of science concentrated on generating thought-technology for the lay man to integrate scientific knowledge, and to do so without excluding the majority of viewpoints already held dear, then the problem of demarcation would be swept away as an interesting question, in the same way that the problem of being is an interesting question in metaphysics. The problem of consensus is something of an ejaculatory beginning to a question I have that may or may not produce anything -- it may just be an intellectual curiosity. But it seems that one should at least have an idea when consensus is obtained if one wishes to integrate scientific knowledge into a population that, itself, does not practice science, and may not be interested in science enough to be educated in science.

Problem 2: What to integrate? As I'm heavily influenced by Dewey in my educational philosophy, I am interested in teaching methods to knowledge. In the context of science the problem with this is that science doesn't have a method, or rather that the method itself is also constantly evolving and changing with what is judged good by those practicing science, and is better learned by doing science than by formalization, but simultaneously one needs to "catch-up" with the facts before this process can begin. This is a necessity for the progress of science, but it does leave one contemplating the educational question in a quandary: What do you teach the public? Just the facts? But the facts change. The method? Again, so does this. That which is relevant to policy decisions? But here we run into the problem of the expert, and setting ourselves up as experts, which appears, in a theatrical sense, exactly like any expert. (Relevant side note: this highlights just how important Aesthetics are, or can be)

Problem 3: Alienation. While the wonders of science are wonderful to those in the in, the wonders of science appear mechanistic and destructive to a large fraction of the population. And this isn't totally unfounded -- the scientific community should never play apologist to the atom bomb, for example. I think it is in the problem of alienation that one is best able to explain the reaction against evolution, for example. Our cultural understanding of spatio-temporal explanations fall on the logical side of the divide, while our values fall on the extra-scientific side. And, what's more, the scientific community doesn't actually question itself on questions of the ethical impact of disseminating scientific knowledge. Scientific knowledge needs be known -- the end. While I'm sympathetic to the need to disseminate knowledge, we also need to question How it is disseminated, and in what way it ought to be disseminated. Several viewpoints which seem to be working great for a large section of the population on their quest towards happiness (the real point of life) run counter to scientific knowledge. As Bertrand Russell said in What I Believe, you need knowledge in addition to love. The problem of alienation arises through our pursuit of the first and our negligence of the second. An answer to this question of alienation is the active integration of scientific viewpoints with existing, followed, and practiced philosophies that seem to work and don't run counter to being able to participate within this rational process. The ethic of this type of work should be -- if a worldview can be justified, then it should be justified. As I've become accustomed to a virtue-theory ethic, this can be justified by our cultural value of pluralism.

An epistemic reason for religious tolerance

2010-09-24T08:14:00.000-07:00

Yesterday evening just before I left campus I received a phone call from the local LDS representative assigned to myself by the church. My father always forwards my address when I move because he cares about my eternal salvation. It makes sense when you consider his perspective, and usually I don't really mind the occasional visit from those who love God because I find the conversations fun. However, last night was not the best night for myself. I tried to intimate that, but he offered tonight, so I was all "Yeah, sure, come over, whatever" Being somewhat on edge due to a busy schedule, and not really feeling like putting up with the fellow, I decided to pour myself a double before he came over. Unlike other times when he'd come over to share the word, where I would attempt to politely but firmly point out my objections, I was not quite so polite this time around. There's a sense in which I feel bad about this, 'cause the guy's an old retired man, and really, of all the times in a person's life this might be the worst time to start edging in on their religion, God, and all that. They lived the life, they might as well receive some sort of comfort compensation when coming near the end of it. So, hey, I can't say I'm proud of it. But I did come up with an interesting insight from the conversation none-the-less (This is probably the least inflammatory comment, which just goes to show me that polemics are better comedy than philosophy).

Of those religions that I am familiar with, and seem to be wildly popular (Christianity, Judaism, Islam), all of them claim that God is in some way infinite. There are interesting philosophical developments in the understanding and concept of God, and some theologians come-with, but when approaching the usual basics of these religions (and I fully admit here that I'm at a loss when it comes to "Eastern" traditions), and the beliefs of what seems to be canon to these religions, God possesses infinite properties (to some, within the scopes of logic, to others, not so, and so much the worse for logic).

Additionally, from what I have seen within these religions, it seems that man's finitude, at the least as a moral being, is central to their system of understanding the world. Yet, despite this finitude, these religions will often have claims wherein this religion is the true religion amongst religions. While this is a common objection amongst non-believers (adopting, at least temporarily, intersubjective agreement as truth), what I did not realize before was the contrast between the infinitude of God, the finitude of man, and how this directly contradicts any religion's claim to the one true path to God. It is not that, granting God, we can't understand a segment of God or experience the divine. It's that many people make this claim of perfect or nearer-perfect knowledge of God, and yet the doctrine of God's infinitude and man's finitude necessarily leads one to conclude that man can't understand God, as he can't understand the infinite. As such, one ought to conclude that one's religion is but a path to the divine, something that a given individual thinks is correct, but is itself not the best, or at the very least possibly not the best, description of God and his will. To think so is to adopt a religious chauvinism that abuses God for one's religion when one is supposed to instead revere him; clearly, a contradiction. It is for this reason that we should reject faiths that proclaim themselves True.

Ontology and Science

2010-09-16T13:45:00.000-07:00

Last I blogged I mentioned that building an ontology on top of scientific models currently strikes me as a bad idea. Here's why.

A rough outline of what ontology is is the study or question of that which exists. It includes exploring the meaning of "Being", "Essence", and questions such as "How can anything exist at all?", "How do you know if something exists?", the existence of God, or universal laws, or questions which reflect upon the meaning and nature of time and matter. I wrote this in order of seeming increasing relevance to scientific questions to give the impression as to why it is one might seek the answers to the questions of ontology in scientific investigations. Surely, scientific investigations use concepts of matter, time, natural law, and attempts to elucidate the mechanism and relation between all that is posited as is to give a cohesive picture of existence. There is an attendant epistemology, and supposedly, there isn't a reference to ethics outside of the confines of this epistemology (things like "Don't fake data", etc.)

What is posited as is, in science, is posited as is not on the basis of asking what is, but on the basis
of asking a general research question. This research question is formulated on the information already present from previous generations scientific careers. The information generated previously was generated not to find what is (usually), but to also answer questions that seemed relevant on the basis of what was passed onto that scientific generation. In short, science progresses towards seemingly relevant research questions generated upon data that was generated on previous research questions. This process can be directed towards other things than asking what is, especially given that one's career depends upon their publications, and the citations to these publications. This process of information generation seems to be predominantly directed towards economic benefit for those who are able to invest, military applications, and the health of those who are able to afford care. So, the process of science, current science, whilst I won't deny the position of scientific realism, isn't trying to answer questions one would prima facie think belongs to a scientific realist's set of questions -- instead, a good demarcating point for scientific knowledge is the knowledge which assists in humanities power over nature, and due to our economic situation, this power of humanity over nature becomes the power of the rich over that which isn't rich.

I will note that this isn't a necessary evil. It just makes science non-ontological, at least in the sense where one attempts to answer ontological questions primarily. Since science doesn't usually answer ontological questions, it follows from this that referencing science in answering ontological questions can be faultier than one might first assume.

Another good reason to not mix these two disciplines is that if one were to mix ontological questions with the scientific enterprise, the scientific enterprise would likely come to a halt -- if one runs a quick probability calculus on the history of ontological questions, one could easily conclude that it is highly probable that ontological questions are insoluble. Based upon this, we wouldn't even want to build an ontology on science for the fear that science wouldn't operate, at least if it is the case that we want science to operate as most people who build ontology on science do. Instead, science assumes an ontology (A formal, universal ontology based in the concept of "energy", and thereby an ill-defined sort of physicalism, upon which general principles of other disciplines that are supposedly "smaller" are loosely attached to), and then gets to work attempting to describe the universe with that ontology, as well as with a ever-morphing epistemology. I can't stress enough that these are good things for the scientific enterprise, so long as the scientific enterprise continues to value producing knowledge which generates support from governments and industry.

Approaching science from the questions of ontology, one realizes that science isn't the "objective" viewpoint that ontology looks for, as is often thought. It's an approach to ontological questions that tends to beg the ontological questions with a rough rational-empirical epistemology of some kind (and even this varies with the discipline, the scientist, and with history). If one is not a scientist but wishes to build a scientific ontology, then one will often employ a half-hearted Popper reference. Science seems to operate underneath a value-set, in the same way that Popper's Scientific Logic operates underneath a value-set, and proclaims this value-set as a methodology to mask the fact that it is, indeed, a value-set. Now, I have no problem with mixing my epistemology with my values -- but I'll mention that my value-set doesn't include falsifiability, numerical accuracy, and prediction-of-outcomes as prime. There likely somewhere down the line, but my prime values include compassion and equality far before what experimental parameters supposedly require, and it would do so whether or not the current psychological theory proclaimed that this should be so.

This leads into my final point on why I, on a personal level, have stopped attempting to build an ontology on top of science: politics. While this process is more self-correcting in my view, the scientific enterprise would mirror some religious power structures in an uncomfortable way the moment that science starts proclaiming ontological truth to individuals not trained in the abstract difficulties of scientific knowledge. It seems to me that a better approach is to relegate science as an epistemic approach to solving abstract puzzles related to power-over-nature, an end that is valuable unto itself, but not valuable as ontological constructs -- at least, not as ontological constructs to anyone outside of the scientific community. If one is able to retort to a scientific argument, then I don't have a political problem with a scientific approach to ontological questions. However (and note that this is with good reason -- the problem isn't with the scientific enterprise, only with mixing science and ontology) the majority of the population can't reject scientific claims because they lack the background. Any structure that can proclaim uncriticized truth (to those who aren't in the community) is just asking to become a political structure. This would likely destroy the scientific enterprise.

Seeing as I don't want science to become a political entity, and seeing that both ontology and science seem to mutually destruct one another, it seems wise to me to perhaps allow each to inform the other, but to keep them separate in some sense... I'm not sure exactly how to succeed in doing that, however. Science jumps out as a source of answers to some pretty basic ontological questions, and it answers these in a pretty successful manner. I just don't think importing this ontology to ontology, or other areas of life, academic and otherwise, seems to be pertinent at all -- science doesn't have a general epistemic approach (unless one wishes to interpret it teleologically), and it really only deals with pre-defined description problems that themselves are highly oriented towards control over nature. Honestly, this has about zilch to do with what's important in life, excepting the fact that scientific exploration is interesting unto itself for some people and therefore important to some lives.

After summer thoughts on Science

2010-09-09T17:13:00.000-07:00

*cough, cough, bleh, blewy* I have been resurrected! Indeed, the summer was full of research fun and things very un-blog-related. But now, a few weeks into the semester, I return to my little patch of the internet to update.

And, with that in mind, I've recently come to the realization that I've forgotten a lot of science. Over the summer I focused in on a single research project, and became very good at the processes' that guided that project. I'm still a little fuzzy on the details (i.e., I need to run a few more experiments to get some results), but overall I'm confident I understand this little piece of science that I can call my own. However, as I return for my senior year as a chemistry major, I'm sort of blown away by what, of the general theoretical chemical understanding, I have to remind myself of. There is a sense in which I've integrated a large number of facts into a process, but it still kind of freaks me out. I'm certain that, were I more dedicated to the sciences, and cared less for things like literature, philosophy, theatre, and all the varied "unrelated" disciplines which constitute my hobbies, that I wouldn't need reminding. I would have reminded myself through biographies, pop-sci publications, and so on. In short, if I cared more about science I'd be a better scientist. But I don't care so much about science that I want to dedicate my whole being to it. It's an interest amongst interests, and it happens to be better funded both academically and industrially, so I pursue it.

After this summer I've begun to think that science (at least of the physical variety) is just fun- there are more important things in the world than it. And I'm more hesitant of basing an ontology on scientific pronouncements. Lastly, I've come to think that the theory of evolution is probably the strongest scientific theory, which is counter-intuitive to the usual "Heirarchy of the Sciences!" I may just write an essay on it, if I get around to it.

I think all these altered thoughts on science came from actually doing the research itself. Somehow, in the process of learning the models of physical science, the education itself seems to lull one -- sure the models are good, and the training rigorous, but the models are set. There isn't as much "critique" as one might think, at least at the undergraduate level. Having some experience in this, now, it's hit me how much of science is. . . made up? At least in praxis. Not that this is a bad thing. I've always defended art. It's just struck me how much science, while awesome, beautiful, and fun, really isn't the holy grail of epistemology like I thought. It's an approach amongst approaches, and a rather nice one at that. But I'm hesitant, now, to place it even at the top of the epistemological food chain. It's robust, but not superior. It's good, but not the best. It's worthwhile, but not to a singular point. I think that expresses what I mean fairly well, without getting into the nitty-gritty of an argument (something which, at the moment, I'm still formulating to be honest. But I know I've hit upon something here. It's just. . . wider and more disjointed than what this blog post can express)

Process: Work

2010-05-13T08:16:00.000-07:00

The first law is concerned with the internal energy change of a system. This is what ΔU represents. As I admitted earlier U is an odd concept to me. I think this primarily arises because, at least chemically speaking, we're mostly interested in the changes in U. Changes in energy I am comfortable with, and the way in which they change is what the right hand side of the equation describes: namely, q and W. These two symbols designate every process that could possibly change the internal energy of a given system.

"W" stands for work. Work can encompass a large number of things. Work, mechanically speaking, is defined as
In a mathematical context, and in one dimension. This simply states that a Force (From Newton's 2nd Law F = ma) applied over a distance equals the amount of work done. If you happen to be unfamiliar with integration, the long squiggly sign is the mathematical way of saying "from point A to point B", and "dx" means the change in position x (like a Cartesian grid, such as you learn about in algebra class). Work can come from more than mechanics, though: It can be performed by electric circuits, or chemical reactions (cell phones, vehicles), or some other type. In the end, however, it's still work.

Thermodynamics is largely used to describe gas phase systems. This doesn't have to be the case, but the gas phase is effected by thermodynamics more so than solid and liquid phases, at least with respect to the phases we normally encounter. As such, work is not defined in the mechanical sense. Instead the concepts of pressure, volume, and temperature are used, and work is defined as
Where P is Pressure and dV is the change in volume. The reason for the negative sign, in this context, is a matter of definition. When "negative" work is performed, this indicates that the system of interest (in this case, a gas) is loosing energy (or releasing energy, as an equivalent expression) to the surroundings. If the integration produces a positive sign (by having a negative PV), then this indicates that energy is entering the system. This is actually analogous to the above definition as mechanical work almost always gives energy to the system: A force applied to a ball from point a to point b will give energy to that ball. But in the context of gas description the application of a force would decrease the volume of a system, which mathematically would give a negative "PV", which goes against the convention of negative = release energy from system, and positive = give energy to system.

Looking at this, the "process" part doesn't seem to be coming into play at all. If you go from point A to point B, won't the distance between these points be the same regardless? As stated so far, it seems that way, but there's one other aspect of integration that works into the idea of "Process" here. An equivelent way to look at integration is that it gives you the area underneath a curve on a Cartesian grid. For example, this:

would integrate to give the area of the black shaded block here:
As such, integrating a function like this:

Would give a much larger area in comparison to the first one, as can be seen here:Sorry for the math digression, but I think it's important to understanding the concept of processes. When I took Chem I, the whole "you can go different ways to the top of a mountain" shpeal only served to confuse me further.

The great thing is there is such a function that describes gases and relates to our function for work. It is known as the ideal gas law: PV = nRT. In most thermodynamic cases, n is constant (and stands for the number of particles), and in all cases, R is constant (Specifically, named "The Gas Constant). Rearranging this algebraically gives
Which states that P is a function of T and V, or P(T, V). We can plot this in three dimensions, but there's no need: If you have two of the numbers from above, whether it be pressure, temperature, or volume, then you can find the third as n and R are held constant. Also, since we're interested in work, we might as well label one axis and pressure and the other as volume since those are the two variables that determine work. I'm not sure why this is the case, but I've never seen it otherwise, so I'll state that "By convention" the x axis is volume, and the y axis is pressure, thereby giving

Now, analogously to the Cartesian plane of algebra, every point on here is defined by some number, but here the number has a unit, or a meaning, attached to it: Namely, the pressure or the volume associated. Also analogously to the Cartesian plane above, if you "integrate" from one point to another on this plane, you will obtain the area associated with it. If you recall, integration from "Point A to Point B" [Or, rather, from point (Vo, Po) to point (V, P)] was also the definition of work. In other words, the area of a block you would obtain by moving from one point on the plane to another is equal to the amount of work performed. The actual path that one takes is the process one uses to get from one point on this plane to another. Therefore, the process described by this path:

Takes (or releases, depending on which point you start with) less energy than this path:

That is why work depends upon the process taken: Because it is the area underneath the curve which would be drawn from one point on the Cartesian Plane of Pressure-Volume to another point. If you were to decrease pressure and then increase volume, you'd be doing less work. If you instead increased pressure before increasing volume, you'd be doing more work.

Each of these paths have special names attached to them that designate what's happening. The first PV-integration example is called "isothermal", meaning that temperature does not change in the process, and the second is "isobaric" meaning that pressure does not change in the process. Some other processes I can think of are "isochoric", which means that volume is held constant (No work done), and "adiabatic" which means that energy is not lost or gained through the other process involved in determining the change in internal energy: Heat (q). I'd go into heat, but I think this one is long enough as it is, so I'll reserve that for next time around.

Penny Experiment, trial 1

2010-05-07T10:42:00.000-07:00

When I was in middle/high school (I don't remember which) we dropped pennies into sulfuric acid to watch them react. I remembered this to be a lot of fun, and at the beginning of this semester I thought I'd try an "at-home" version with vinegar to see if dilute acetic acid would do the same thing. I expected it to, as hydronium should still be present in solution, but I expected the kinetic to be severely limited since there wouldn't be as much hydronium in solution.

So, run 1: I filled a ceramic coffee mug with "5% acidity" vinegar, and placed a penny (post 1984) into the acid and let it sit. Two months or so later (I probably should have documented this more rigorously, but it was just a curiosity on my part), water had evaporated but the penny appeared to be identical aside from some black grime (whatever that grime is made of) that was more easily removed. So, I had a shiny penny.

Run 2: I'm trying to stick with the "easily in reach within your home" type chemicals for pop-experimental purposes. It was suggested to me that I add salt in order to form a little HCl in solution. Seeing as the other experiment didn't work at all I thought why not, give it a try and see what happens.

I filled the coffee cup with fresh vinegar, and then poured salt to fill the coffee cup ~ 1/2 way. This would ensure a saturated solution of salt in vinegar, thereby possibly driving the reaction to form HCl. Then I dropped the same penny in. ~ 2 weeks after I started the experiment, I noticed that some dark splotches were forming on the salt. When I pulled the penny out to examine it, I thought I saw some zinc, but I wasn't positive if it was just me looking for it, so I through the penny back in. Just today (some odd 2 weeks after the last check) I pulled the penny out and sure enough: holes had been eaten through the copper, and some of the copper surrounding the holes was easily removed as the zinc underneath had been oxidized.

Very neat! The salt certainly sped up the reaction (though I'm not sure if it's acting as a catalyst), from my rough qualitative memory watching an at-home experiment when the fancy strikes me. There was also a pretty cool crystal layer that had formed as the vinegar had evaporated again. I think the evaporation likely helps in reacting with the penny, as the concentration of acid is increasing as water evaporates. I'm somewhat curious about the composition of the crystals (Sodium acetate? Sodium Chloride? Sodium Iodide, as it was iodized salt?). The primary thing that's mystifying me at the moment is: Why did the salt actually help in this reaction? HCl, being a strong acid, would dissociate completely, and so would likely not form to an appreciable amount -- I would expect this to hold even in a saturated solution of NaCl. If anything, I would think that the ionic atmosphere would play a larger role in interfering with the equilibrium. Of course, I also used the same penny after the last one, so I'm thinking I need to redo all this with a new penny at least. And, so that I don't have to use a pH meter (or titration... but for this I'd likely deal with the error in the meter) to find how much hydronium I have at the end, I'm going to try covering the coffee mug so that no water evaporates. Still, kind of some interesting preliminary results.

Thermodynamics: The Uno Law

2010-05-05T09:57:00.000-07:00

Beyond the basic chemical equilibrium context, to understand Gibbs free energy you need to understand thermodynamics in a "ground up" fashion. The thing is, I'm not sure even I understand thermodynamics in a ground up fashion. This was part of my motivation to start blogging on it: To keep me thinking about the concepts such that they might eventually click.

The thermodynamic approach I was taught started with quantum mechanics, moved into statistical mechanics, and ended on thermodynamics. What's nice, from a chemist's perspective, about this approach is that the quantum model of the atom elucidates a lot of qualitative understanding of the atom you pick up in earlier courses, such as bond strengths, aromaticity, and IR spectra (or spectroscopy in general). Then statistical mechanics utilizes the energy levels found in quantum mechanics to make macroscopic predictions from the quantum model through statistics (ergo: statistical mechanics).

However, when approaching thermodynamics, then, outside of the basic chemical approach linked to equilibrium, I found the study to be very odd. I have been acquainted with explaining macroscopic observations through microscopic models, so it was hard to think "Macroscopically", even though the mathematics was simpler. So, in approaching general thermodynamics I think it's important to remember what it is thermodynamics is trying to describe, as that is where I lost a conceptual foot-hold in the race (and resorted to math to get me through, as opposed to understanding the concept behind the math)

Literally, thermodynamics is describing the movement of heat. But more is involved than heat: there is also work. So the name isn't exactly the best. What helped me was in emphasizing the macroscopic nature of thermodynamics. It models a large system of particles within some kind of surrounding environment. We are free to define the system, so the system is chosen such that something interesting can be measured or for conveniences sake.

In this case, the system is a beaker with a piston. The little green dots are supposed to be particles of gas floating around inside the beaker. The system stops where the beaker begins, and the surroundings begin just after the system stops. This allows measurements of the gaseous behavior alone to be recorded.

Thermodynamically speaking, there are three quantities that define this system: Pressure, Temperature, and Volume. Of these three, you only need know two to know the third as they are related through the ideal gas law. (Note: There are more "equations of state", as they are called, than the ideal gas law. But it's the simplest and gets the point across)

However, the ideal gas law isn't enough. That just defines the "State" of the system. It doesn't tell us very much about how much energy is transferred from or to the system in going from one state to another. And that, I think, is the best way to think about thermodynamics: the amount of energy transferred in moving from one state to another in a macroscopic system. Macroscopic states can be defined by the three variables of P, V, and T, and the movement between these states requires energy to enter or leave the system. How much energy enters or leaves depends upon the way in which one moves from one state to another.

That leads to the first law of thermodynamics. There are many ways of stating this law, but when trying to understanding how much energy passes into or out of a system due to a process the following is used:

ΔU = W + q

Where "U" is the "Internal Energy", W is work, and q is heat. Internal energy, to me, is a weird concept. It's this energy that's.... there?... inside the system 'n stuff? Yes. That's exactly it. Personally, I'm still wrapping my head around the concept -- the best I can do is to say that it represents every shred of energy that is within the system, from the vibration of bonds, the momentum of molecules, the mass of the atoms, the potentials of fields, EVERY source of energy that happens to be within the system. That.... I think is it. And, frankly, we don't even care about the total internal energy, but rather the changes in internal energy, because those are much easier to measure than absolute internal energies. (ergo: Δ)

So, changes occur in internal energy, and those changes are equal to work and heat. These are the processes by which energy is removed from or added to a system. They both transfer energy, but they do so in different ways. For now it is enough to understand that the changes in internal energy occur through the two processes (or mechanism, or "How-to", if that makes more sense?) of work and heat. What those processes encompass I'll blog about later.

Free Energy

2010-04-25T17:58:00.000-07:00

A point I found difficult in studying thermodynamics as a chemist is that the concept of Free Energy is much more important to chemical study -- but it is a more deeply derived concept based upon thermodynamics and energy transfer in general. I often try and think of ways to build a conceptual framework within chemistry without referencing the physics that it is based upon, because in the end, the physics isn't totally necessary for gaining an understanding of the chemical picture. This is why I began blogging this month from the "end-point" of thermodynamics with respect to chemistry: Equilibrium. If you can understand equilibrium in general, then one should be able to understand chemical equilibrium. And, hopefully from this, one should be able to understand Free Energy.

In the previous two posts I attempted to explicate equilibrium as a general model and as a model for chemical systems. This works if you think about atoms as "billiard balls" connected to one another through "Bonds". When a chemical reaction occurs, the bonds in the reactants are broken and the bonds in the products are formed through some kind of process. To deduce an equilibrium expression the step-by-step process does not necessarily need to be known: All that need be known are the ending concentrations of the products and the reactants. The reason that these concentrations are constant is not that the chemicals stop moving due to some mystical equilibrium constant that brings out the golden tablet of concentration stating "Thou shalt not react!" Instead, the chemical species continue to react both in the forward direction (Towards products) and the backward direction (from products to reactants), it is just that at equilibrium these processes occur at the same rate. What those rates are is another story -- but what those concentrations are when the rates are equal is driven by Free Energy.

Free Energy, as a concept, is simple enough to understand from the words alone. It's the amount of energy available to do stuff. The reason why we need this concept is a more difficult issue, and is directly related to the second law of thermodynamics. However, the concept itself can be understood in stating that there is some quantity we call energy, and of this quantity we can not use all of it because of the second law. That quantity which can be used in a process, however, is called Free Energy.

I skip around the second law because I myself found it hard to understand, there are several ways of explaining it, and with reference to chemical thermodynamics I don't know which is the best way to go about explaining it. In fact, I think it unnecessary to understand the second law when first approaching chemical phenomena so long as we conceive that there is this concept that limits the amount of energy that can be obtained from any process, and that concept is the second law of thermodynamics.

The way in which Free Energy applies to equilibrium is through a relation (or equation, expression, what-have-you) of a certain type of Free Energy, that is conveniently defined for standard laboratory conditions. This type of free energy is called "Gibbs Free Energy", because it was invented by Josiah Willard Gibbs. This is the energy available to do work when the system is under constant pressure (or nearly so), such as you find in a laboratory at a given height above the earth. In a chemical reaction taking place in a beaker, the change in free energy can be measured with a simple thermometer. Further, the change in free energy is directly related to the equilibrium constant at a given temperature through:

ΔG = -RT ln (K)

One thing you can notice from this relationship is that if the change in free energy is positive, then raising e to the power of a negative number will give you a number less than one. Similarly, raising e the power of a positive number will give you a number greater than one. This indicates that negative changes in Gibbs Free Energy are indicative of chemical reactions where products are favored more than reactions. The converse of this is also true: Positive changes in Gibbs Free Energy are indicative of chemical reactions that favor reactants.

Naturally, one needs to know how one measures Gibbs Free Energy. The above equation is not what one would call the definition of Gibbs, or give someone a good way of measuring the change in Gibbs free energy, but only its relation to the equilibrium constant. However, I think I'll save that discussion for later. Currently what is more important to grasp is that Free Energy and equilibrium and linked together, and that Free Energy is a thermodynamic concept which is why questions of equilibrium and answered through the concepts of thermodynamics. However, in first understanding chemical reactions, one need not have the grounding principles of thermodynamics down: One need only understand equilibrium as a ratio of products of reactants in a chemical reaction, and that this ratio of equilibrium is governed by the concept of available free energy in a chemical system. That, I think, is the basic beginning to understanding the thermodynamics of chemistry without basing that understanding in the thermodynamics proper.

Equilibrium as a General Model

2010-04-12T09:54:00.000-07:00

I think I'm going to have a series of posts on the basics of thermodynamics and its application to chemistry because, well, it's so darn interesting.

In the previous post I outlined some basic concepts of chemical equilibrium. But the case that I gave was very specific and would only apply to a system that operates in a similar manner -- namely, that one molecule of X would combine with one molecule of Y to form one molecule of XY. This is not always the case. But before going into specific chemical equilibrium, I think it better to look at where the model for equilibrium comes from.

A model for physical systems can be constructed from the concept of a system and surroundings. Both are selected by the modeler, usually specifically selected for convenience of calculation, and in that sense are arbitrary. The system is simply what you are interested in. The surroundings includes everything else, but usually only the immediate surroundings are all that are taken into account -- a chemical example would be what is in a beaker for a system, and the lab that the beaker is in for the surroundings.

In designating a system/surroundings, you have some quantities that can describe both: Energy, Pressure, Temperature, Volume, and moles of gas. Any of these quantities can be exchanged between the system and the surroundings, and which quantities can be exchanged often describe the type of system that you are looking at.

A common example from physics is the mechanical equilibrium of a spring represented by the following force diagram.
(Do forgive my Paint abilities). According to Newton's Second Law

ΣF = Fs + Fg
Fs = -kx
Fg = mg
And, because this system is in equilibrium ΣF = 0
Therefore, Fs + Fg = 0, and Fs = -Fg, which means by substitution kx = mg

Which happens to usually be a highly convenient situation. In particular, note that the previous solution had no reference to time. This is something unique to equilibrium solutions: There is no reference to time, only to what each respective variable is at when no variable of interest is changing.

However, when dealing with the system/surroundings model, usually forces aren't the variables of interest. A close analogue. A common example of pressure equilibrium would be a balloon which has been tied off. The gas within the balloon would have a higher pressure than the exterior pressure, but pressure would not be exchanged between the system (the gas in the balloon) and the surroundings (the room the balloon is in).

This situation can occur between any variables of interest -- Pressure, Volume, Temperature, Energy, and chemical concentration. The final one is the one that chemists are first introduced to. This is, ultimately, just the application of thermodynamics/statistical mechanics to chemical systems. Ergo, the study of the model of equilibrium is actually the study of thermodynamics, which is one of the main branches of chemistry. The above explication of equilibrium should also clarify why it is that kinetics, despite being related to energy just as thermodynamics is related to energy, is a separate case of study: The concept of equilibrium requires things to not change with time, and the concept of equilibrium is the model within thermodynamics most often used to model chemical systems as, regardless of the time it takes, the system will tend towards concentrations which satisfy the equilibrium constant.

I think this is done mostly to simplify predictions: thermodynamics, I must admit, is still a bit of an impenetrable thick fog as it is. Not having to worry about time-dependence makes things a little easier.

Equilibrium, Basic Chemical Approach

2010-04-11T14:48:00.000-07:00

In a previous post I mentioned that there are two things one must consider in analyzing a chemical reaction: thermodynamics and kinetics. The model of equilibrium covers the first of these.

Equilibrium, in its most basic sense, is the ratio between what is created in a chemical reaction and what was used in a chemical reaction. Suppose the following general chemical reaction:

This reads as "Chemical X and Chemical Y react to yield Chemical XY in equilibrium" Many chemical reactions will include a simpler notation for their "react to yield" symbol such as "→" because most reactions that one is introduced to in a general chemistry course fully react to products. The vast majority of chemical reactions do not have this feature, however, and the double arrow symbol above is used to indicate that both products and reactants are being formed when the system has reached chemical equilibrium.

However, the relative amounts of product and reactant can be predicted through the use of an equilibrium constant. Each chemical system has its own equilibrium constant, but the equilibrium constant remains the same for systems prepared with the same chemicals and under the same surrounding conditions. This constant can be found from the following:

This states that the concentration of chemical XY divided by the product of the concentrations of chemical X and Y equals a constant -- specifically, the equilibrium constant. This means that given a certain reaction and its equilibrium constant, one should be able to predict the concentrations each species will have when equilibrium is reached -- and you can do so. This is a very tidy result because chemists have to model ~10^23 particles all interacting at once. This allows one to predict effects in the physical world while ignoring things such as electric fields, momentum, and position. For example, if one has the equilibrium constant one can be a qualitative prediction about the relative concentrations of products to reactants. If the equilibrium constant is greater than one, then products are highly favored. This is the case with many introductory chemical systems one studies, which is when the symbol → is used since products are so highly favored. However, if the equilibrium constant is smaller than one, then reactants are more favored than products in this particular chemical reaction.

This equilibrium relationship governs the reverse reaction as well: if one where to look at the reaction , then the equilibrium constant for this reaction would be the reciprocal of the previous reaction. This is easily proven if you simply place the concentration of the products of this reaction multiplied together over the concentration of the reactant.

Of course, it also has its own set of limitations. The equilibrium constant is only constant for a given temperature. It can also be somewhat difficult to actually obtain the equilibrium constant, though there are several methods of doing so. Further, as I've previously mentioned, the equilibrium constant says nothing about the kinetics of the reaction: Only the relative energy of the products and reactants, or how favorable the reaction is thermodynamically. This can be important in synthesizing chemicals as two different products could be likely to form, but because of one product is slow to form, the other product is the major chemical created.

Choosing a Method

2010-02-12T20:19:00.000-08:00

Every field has a methodology. Adhering to a methodology may seem the best way of retaining objectivity, but last night I found experienced methodologies, arriving at valid conclusions within the reference frame of their method, that conflicted. This was the result of a philosophical discussion after watching a debate on whether or not the resurrection of Jesus is true. Now, the conflict is not irreconcilable on either side -- both sides could explain the other in their own terms -- so there wasn't a want of consistency on either party. But there was a lack of a definitive answer, as is often the case in philosophical questions.

Though this is not, by necessity, a philosophical question. The answer can require a philosophical method, but it does not necessitate it. The Pro side used a historical method. I can't meaningfully comment on the historical method, but I can say that it seeemed the Pro side should be treated as an expert. The argument, to my philosophical knowledge, was valid. The case that his argument failed, and I knew that it failed, was in my knowledge of the scientific method. Resurrection, to the best of our knowledge, is highly unlikely to be possible. The best inference, at this point, is to conclude that Resurrection can not happen. Naturally this doesn't mean that it can't happen. But I would also point out that nothing has brought us closer to knowledge than the method of science. However, in the case of historical details, that remains problematic -- thereby the need for a historical method.

I would place the scientific method above the historical method in its ability to ascertain the truth due to my experience with the method. But, supposing that your world-view allowed resurrection, and you apply the historical method, everything seemed to fall well into place. So, in some sense, the debate becomes an argument of metaphysics -- hardly the appropriate place for truth-determination.

So, in what way does one choose a method? The whole point of creating method is to become as objective as possible. Yet there is a multiplicity of methods. While, normally, the choice of method is obvious (Are you investigating the world? (science) Are you investigating the past? (history) Are you investigating wisdom? (philosophy).), there can come a point where two individuals can come to an impasse on some questions, such as the resurrection example, and both think their method is the most objective way to truth, yet come to different conclusions. I believe that both debaters were making good-faith efforts for their position, as opposed to playing polemics to "win", so I don't think an ego-driven hypothesis resolves the question. Surely anyone interested in proper conclusions can admit that they don't want the ranking of methods to be dictated by how comforting we find their conclusions, or how well they justify everything we already believe -- that would entirely defeat the point of method!

How do you rank methods, and why?

The Scientist and Society

2010-01-22T09:58:00.001-08:00

I have politics on the brain, with the state of the union address coming up, and as such have been lead back to what Cassidy's "Uncertainty" started: The interplay between science, scientists, and politics.

On the face of things it seems that the best a scientific minded individual to do is affect apolitical attitudes. This is what scientific organizations tend towards, and I think it's a good thing. We want our society to make decisions based upon the world we live in, so the best way to have this political influence is to not discuss or make statements about standard political questions. In some sense this is problematic, as we currently see debates on religion in public education, or we have a single political party that primarily speaks against global warming, but in these cases there are firm scientific reasons for taking a position: 1) Religion ain't science. 2) Data and the mainstream interpretation of that Data. In short, the success of the scientific method.

I can't agree more than with this position for scientific societies. It is in this way that they can best help society, in general. However, I wonder if this attitude is best for the scientific individual. Given I live in the United States, I would infer that the usual reply would be "No. The individual can express whatever they wish, so long as they, personally, take credit for said comment, and do not speak in the name of X organization". But, as it is in this way that scientific communities can better help direct their communities, if said individual is attached to such-and-such a cause in popular culture, it could put political question on any scientific pronouncement said individual has. In conflict with this is the premise that, as individuals, we ought to have the freedom to express our political affiliations outside of any other affiliations that we may harbor. However, people don't operate in said manner. They can attempt to separate the individual from their various affiliations, and even make a good faith effort to do so -- but we still retain knowledge of an individuals full social affiliations. And if we do, indeed, wish to effect society in the most positive way that a scientist can, it may be the case that we ought to forgo public political opinions in favor of public scientific pronouncements.

I don't pretend to have an answer to the question, I am only raising it as a question to be thought and ranted about. The converse of this position is, of course, the life of Werner Heisenberg. He's an extreme case, however, and we do not currently live in quite as extreme a time as he did, so I do not think his life example is a good example to base current opinions off of. However, I think most will agree that his example definitively states that there is, in the case where one accepts keeping quiet about political opinions, a point (line, plane?) somewhere when that person should stop playing the apolitic become publicly political. But under what circumstances is that the case, and can one even determine those circumstances during the times that those circumstances exist?

I wish there was a journal or forum for ethical discussions amongst the scientific community -- though that may violate the "Objective"-ness of the scientist on the political landscape.

K-INBRE Symposium

2010-01-17T15:43:00.001-08:00

I just got back from a weekend conference hosting individuals to present their research in speech format. I've gone to one symposium before, but in this one I actually had a poster to present. And... it was not anywhere near as bad as I had thought it would be. I used to do performance art, so perhaps I shouldn't have been nervous, but the subject matter was different. In performance art you have a role to play, to entertain people. With a poster... I thought it would be different. But then I ended up just telling jokes and playing the role of "elucidator of research" -- sort of in the same fashion that I try and tutor people. All of the people who looked at the poster probably had a better knowledge of biochemistry than I, as I've just been learning biochemical terms specifically related to my organism and I'm a chemistry undergraduate who has yet to take biochem, but everyone seemed pretty generous and forgiving. If they asked a specific question, sometimes I would and sometimes I would not know, and I would be blunt and let them know if it were the case that I was ignorant. They nodded and let me finish the "shpiel" I prepared in explaining the poster, and some of them even taught me things. It was a very positive experience, and hopefully next year I'll have a better working knowledge of biochem and, please oh please may this year yield presentable results.

Significant Figures

2010-01-15T09:00:00.000-08:00

Oi! Well, the winter break is over (which is my excuse for Winter mute-ness), and I've hit the ground running again. As the Cake is a Lie, Syllabus Day is a myth.

Today I heard the best formulation for what significant figures are:

The mathematical method for keeping track of the least accurate measurement.

From this least accurate measurement in a series of measurements, you can tell just how well you know the "true" value of a given measurement. I don't know if this just went over my head in early chemistry classes, but I'll remember it now because it solidified all the abstruse rules I've been utilizing to no purpose aside from it being something... necessary... because, like, yeah...

It's not as if the rules are terribly difficult, unto themselves, but I don't recall ever knowing why I was using them. Obviously they were significant (harhar), but to what end... eh. However, this helps me understand why the addition of significant figures only depends upon the number with the least decimal places. If you add what you measure to be 2.5 Liters to a measured .0532 Liters, the relatively large uncertainty in the first measurement will "wash out" the relatively finer accuracy in the second measurement, giving you "'bout 2.6 Liters".

This leads perfectly into Uncertainty in measurements, which is related but something we utilize in the more formal sense in our everyday life. If you're getting off the clock in 16.3 minutes, you'll likely think of it as "15 minutes". And, for the purposes at hand (having a feeling for when you're going to get off), that level of accuracy is perfectly acceptable. If, then, someone asks you to stay for 5, you'll probably realize they don't mean "5.00 minutes", but rather there is some variance (or whatever it might mean in your particular social context). This is us utilizing the uncertainty in their measurement (their feeling for how long it will take until an extra task is done) that can be modeled mathematically: This could take plus or minus such-and-such an amount of time. "5 minutes" doesn't mean " 5.00 minutes", but maybe 5.0 plus or minus .5 minutes (or whatever). While you know from the clock that you have 16.3 minutes, the most number of significant figures you can keep is determined by their measurement of 5.0 minutes plus or minus .5 minutes, so you add the two measurements together and obtain that you could be on the clock from 21 minutes to 22 minutes after rounding off with significant figures. Perhaps a better model of conversation and on the fly estimates would actually use 5 plus or minus 4 minutes. From this you could conclude that you could be on the clock between 20 to 30 minutes, because then you would only have 1 significant figure. I mean, sure we don't actually go through the step-by-step analysis, but we tend to have a "feeling" for these things in conversation despite not knowing how we can conclude that our "feeling" may or may not be correct. I think the above expressed well what I always intuited about significant figures but never concretely expressed.

The Two Pillars of Chemistry

2009-12-07T13:32:00.000-08:00

It's that time of the semester where time spent outside of finishing projects and preparing for finals is scarce, but I wanted to get a quick post in. I've been wanting to do this post for awhile, so it should come fairly easily:

I remember well my days in Chem II where I learned that there chemical reactions were reducible to two major concepts: Kinetics and Thermodynamics. The first deals with how fast a reaction proceeds, and the second deals with what is energetically favorable. And the great thing is that this can all be displayed using only one graph:

This is a reaction energy diagram that I nabbed from here. The energy being referred to is the Potential Energy of the main molecules under study in a chemical reaction: What you start with and what you finish with. In this particular diagram, the starting molecule (labeled Reactants) only undergoes one quick change before becoming a new molecule (labeled Products). You'll notice that in this reaction the products have a lower Potential energy than the Reactants. Because of the Law of Conservation of Energy, this energy doesn't just disappear, but is released into the environment (Which, as far as chemists are concerned, is "Not the Molecule). An everyday example of this happens if you have a gas-burning stove, or inside your car engine. The energy is released and heats up your food, or drives the piston down. The comparison between the Potential energy of your starting products to your ending products is what chemists use to gauge whether or not a reaction is "Thermodynamically favorable", and entails Pillar One of chemistry: Thermodynamics. In this particular reaction diagram, the reaction is thermodynamically favored because the products have a lower potential energy than the reactants -- this works, in a lot of ways, like gravity. Objects "like to" get closer the center of the earth, and molecules like to have a lower potential energy.

I actually often give chemicals personalities and say "Likes to do..." more often than may be healthy, but personification helps in simplifying the theory.

And now: THE SECOND PILLAR OF CHEMISTRY

(OK, I fess up: these aren't official pillars, I'm just raising a big hullabaloo)

Deals with the section of the graph where the Potential Energy raises temporarily. The maximum of this curve is termed the "Transition State", because... well, to sound redundant, it's very transitory, and it's in transition from one molecule to another. The higher this maxima is in comparison to the starting Potential Energy of the Reactants, the slower the rate is going to be.

So, really, the two pillars of chemistry tie back to the most fundamental concept of dynamics: Energy. But one quick look at Diamond tells you that it's important to separate Energy into Kinetics and Thermodynamics -- it is thermodynamically favorable for Diamond to spontaneously decompose into Graphite. However, the transition state is so high, this is very... very... slooooowwwww.....

Feminist Man in the Midwest

2009-11-24T17:38:00.001-08:00

That sentence describes me. I can not say that this was always the case, but I can say that I've acquired the wisdom to call myself a feminist for a couple years now. I don't particularly feel like describing my journey into feminism, but after a brief conversation at the skeptical conference I want to outline why I'm a feminist.

In the first place feminism is not some monolithic man-hating organization. Anyone reading this probably already knows that, but I frequently here it described that way. There is a considerable amount of diversity within feminism and what it means to be a feminist. I honestly can't even claim to have an expert understanding of all feminist positions. I can only claim that I think strict gender roles and expectations can be harmful to individuals, and that I choose to help establish gender equality in my day-to-day life (as that's where it really begins).

So what does all that entail? For me, it just involves speaking up and asking questions. There are a lot of mores and folkways that strike me as silly and outmoded, but I would like to replace those social constructions with better ones. So I question norms in the hopes of finding better answers. Feminism encompasses some moral positions that anyone ought to defend, like rape prevention, access to birth control, and pay equality. Nobody argues against these things (well, OK, there are a few who argue against birth control, but it's nonsensical). I've argued against feminism without realizing the contradiction. But feminism, as a philosophical position, is beneficial to both men and women: It puts our social expectations in human terms, general terms that can be fulfilled by anyone in spite of their sex. I think that this more general formulation helps us to respect each other as humans, which is really what I think feminism is all about. There may be general sexual trends within a population, but we ought to also find ways to encompass those who don't follow those trends. Feminism is one of those answers.

Feminism can cover a host of issues and topics, none of which I am an expert on, but most of which I find interesting and enjoy discussing and reading about. I tend to approach feminism more from a male perspective, and think that the social expectations of men can be harmful and should therefore be questioned. (shocking, I know, seeing as I'm male).

Skepticon II

2009-11-22T15:38:00.000-08:00

For the longest time I found the notion of an atheist movement to be odd. While I have been an atheist for a long time now, I thought people found meaning in religion, and it didn't seem like to nicest thing in the world to go around removing people's meaning. Further, it seemed odd to form organizations around the idea that God Is Dead. I wasn't always as certain of this as I am now, but I figured that anyone who bothered to actually continue looking for truth would at least be able to rationalize one way or the other, and while I was sure that Atheism was the right conclusion, at least theism offered a structure for individuals to tackle moral problems.

I no longer feel this way. At least entirely. I still don't feel terribly great about poking holes in people's beliefs, but there are good reasons to believe things and bad reasons to believe things. Further, while I am intrigued in continuing the philosophical debate on the existence and nature of God, as well as everything that might entail, I am certain now that a movement for atheists is a good thing. I was convinced of this by Skepticon II.

The main problem, as I hinted to above, that I had with the New Atheists was that I perceived it as a destructive movement as opposed to a generative movement. I knew that God did not equate to goodness, and took offense when someone thought I couldn't be good because I didn't believe in God, but it seemed supremely silly to me to gather together to destroy the beliefs of others. Quite simply, this isn't the case. If Skepticon II is a good sampling of what the New Atheism has to offer, then while I disagreed with individual's that spoke there, that was a common theme amongst many people. And my impression was that this sort of disagreement and debate was encouraged. This means that, while we all agree on the non-existence of God, there are still questions and problems that we all still have and disagree on.

So, while it seems that Atheism would be destructive, it was the exact opposite: It was generative to the point that everyone had a point of contention with something which was a widely positive experience to myself -- especially because everyone there never once listed "The Bible" as a good reason to do something.

Further, while I have a group of atheist friends that I generally hang around, I'm a fairly quiet and complacent fellow who doesn't speak out to many people. While I enjoy and very greatly value this group of friends, it was also fun just to hang around people who are relatively similar to myself in their general metaphysical world view and to feel that I wasn't fundamentally alone. There was a community of people who wanted to bullshit about science, literature, music, politics, teaching, philosophy, alcoholic drinks, often all in the same conversation. This was something else that wasn't stated explicitly, but that seemed I noticed: The New Atheism is an intellectual movement. The speakers all had an intellectual discipline, and they shared their specialty in their speeches -- something I highly enjoyed. I especially enjoyed seeing science being shared glibly with anyone who chose to show up. Further, the science was embraced by those who attended (at least, those whom I talked to). It was not shunned as some hum-drum boring routine you have to go through in order to pass a class. (Sorry for the minor bias towards the science, but it is what I study. I also enjoyed the philosophers and historians, as well as the debate on the existence of God)

So, it is a generative movement, and it is a movement that actually values intellectual labor (something desperately lacking in my experience). Further, it's filled with enthusiastic individuals who enjoy finding like-minded people (which, really, who doesn't?). I find that hard to object to. Thank you to all who set it up and all the speakers who came.

Research for Killing

2009-11-18T20:45:00.000-08:00

I just returned from a presentation given by a man who works for the US Army in developing better ordinance. The primary reason for my visit was to ask him about his ethical justifications on doing research to further the cause of war. His primary reasons were:

1) For the people in uniform, so that they can come back home.
2) A human in a democracy follows the will of that democracy even if he disagrees with the democracies stances, and attempts to make political change if he does disagree with those stances, but still supports all political decisions.

I can't accept these as good ethical reasons, but I'm glad he answered without hesitation, and he acknowledged that it was actually a difficult quandary -- so he was aware that there was a gray boundary.

As I interpret his ethical justification the reason is "Patriotism!" which fits well with the zeitgeist of our times, but I fail to see that as a good ethical argument for just about anything. If all actions that are patriotic are justifiable so long as they're vindicated by some form of democratic unity, then the south was right to own slaves. I find any justification on the weapons industry hard to justify because you're dealing with something that's pretty fundamental, ethically -- you're furthering man's ability to kill people. And if the 20th century tells us anything, furthering that ability doesn't really deter use. It just makes as that much better at killing people, exactly as the research intended.

Plus there's this whole side to it that makes me think that they're taking the easy way out: It's friggen' easy to destroy things. It's much, much harder to actually produce something useful or interesting.

I think I'm going to be a curmudgeon when I grow up. *grumble, grumble, grumble...*

Unpacking Equations

2009-11-12T11:36:00.000-08:00

Equations are poetry. In the abstract they signify shapes, in science we add the significance with units and measurements. It is the cross-over between shape and meaning that creates the poetry of equations. Looking at a common example:

The poetic meter of equations comes from the standard method of algebra. It helps in unpacking the meaning. This reads: The gravitation force between two objects is the mass of object one multiplied by the mass of object two multiplied by a constant, divided by the square of the distance between those objects. This is really just a first step in understanding, as that it a lot of information to process. Actually, I think the reason we use equations is because they help us to process massive amounts of information with less effort. Plus they're all objective 'n shit, which Scientists happen to think is a good way to stay hip with the kids.

The first reading is akin to substitution. You have mathematical symbols that can be translated into words, and stating those relationships using words helps in understanding what an equation is saying in the grand scheme of things. In this case I understand that the mass of both objects can differ, so if the mass of either object changes, so will my force. In this case, it has a positive correlation between the force, whereas an increase in distance has a negative one -- or, in more accessible language, the heavier the objects involved are the greater the gravitational force between them, and the further apart they are the lesser the gravitational force is between them. Something else to note is the fact that the decrease happens at a squared rate, where mass is only linear (unless, of course, you increase the mass of both objects under consideration by the same amount). All that's left is big "G" which never changes. It's actually just something that's determined by measuring, and it's a factor that makes this equation work.

So, the equation states a relationship between things we observe. But if they're an actual relationship, we can also determine other parts from the Force, such as the mass of an object in space, without actually measuring that mass on a scale. Or, for this same equation, we can determine the Potential Energy of an object.

The definition of energy is a Force applied across a distance, or for the above:

dF = G((m*M)/r^2) dy

where "m" is the mass of any object on the earth, and M is the mass of the earth. I put it in y so that it will appear more familiar in the end. In this, we simply integrate from point zero (the ground) to whatever point above the ground we're interested in, and thus obtain:

PE = (m*M) [(-1/r)] from 0 to y = -GmM/y

And so we have a statement about the universe from the above equation that required a little digging to see. Big M and G do not change, and the potential energy is the negative of an inverse relationship between the mass of the object on earth and the distance that object is moved away from the surface of the earth. Not only did this require a little digging, if you haven't had a background in Calculus then it probably didn't make as much sense. While it is preferable to be lucid, I'm trying to make a point: That math is a language. The meter of a poem and the conventions of language bring out the meaning in lines. The operators in math is this meter that creates the poem describing what we see, and thereby, letting us as humans understand at a deeper level than once we did. While what I use and look for in poetry might differ, the experience is largely the same. You read an equation over and over again, looking for the implicit relationship and meaning, and make connections over time that reveals a deeper truth -- in the case of poetry, about the emotion, and in the case of equations, about the universe.

Infinity and Electron Probability

2009-11-10T12:38:00.001-08:00

A thought today from Pchem:

Infinity is a relative term. One meter away from the nucleus of an atom is infinity, and 10 billion billion kilometers away from the sun is infinity. Since infinity is a general concept, rather than a number, it can be defined anywhere. So, if we consider the probability of finding an electron such-and-such a distance from the nucleus, we can find the probability that it will be from that point inwards, or the probability of finding the electron between two points by doing the same method but subtracting the smaller value. We know that the probability of finding the electron converges to 0 at infinity, but infinity can be anywhere we set it to be. Supposing you want to find the probability of finding the electron on Mars (as was the example given today), you can find the probability between "Nucleus and Mars" (A very high number), and you can then find the probability between"Just beyond Mars and Infinity". Then you can subtract "Nucleus and Mars" probability from "Just beyond Mars and Infinity" to get a real probability of finding the electron on Mars. I think this all arises because we can set infinity anywhere we want (which is necessary for the concept of infinity to be of any use).

It ain't that weird

2009-11-03T10:32:00.000-08:00

For all the hullabaloo I've read in popular science books and the strong emphasis my physical chemistry text book places on the differences between classical and quantum mechanics, half-way through the semester I'm sitting here saying to myself: It ain't that weird. I half-way wonder if the only reason it seemed weird initially was because everyone told me how friggen' weird quantum mechanics are. Sure, an electron doesn't behave like a baseball. Is there really any reason why we think that it should? Even in Physics 1, whenever dealing with real objects we would make it clear that we were inventing a point that made all the classical laws apply (Center of Mass), but that this point wasn't a real point, so that if the object were destroyed mid-flight, the center of mass would still continue due to inertia. And, actually, the originators of quantum mechanics knew that it would be absurd to propose a physical system that entirely violated what had already been observed, so they built equations around the idea that as you took the limit of them that you would get classical results. So what gives? Why does every voodoo mystic and half-baked spiritualist in the world think the deep secret of the universe lies in quantum mechanics? I certainly acknowledge that I'm going at this at the depth of Chemistry, and not at the depth of physics (half way through and we've just started spectroscopy. I'm told that physicists tend to finish their first semester of quantum with solving the hydrogen atom), but all the quantum "Weirdness" is still there.

Really, the quantum concept can be introduced utilizing series and sequences. And seeing as we don't exactly live at the size of electrons and can only interpret spectroscopic data to make inferences about what's going on, it makes perfect sense that the wave equation is an abstract description of what's going on, and we need observable values that we in the macroscopic world actually can see. In fact, it almost makes MORE sense than trying to plot out the trajectory of electrons and protons, because we can't actually see these things, and testing what we can see is exactly what science is all about.

Maybe it's the shift from determinism to the "probabilism" (no, not a real word) that really gets people, but half-way through, and fully realizing that quantum mechanics aren't yet entirely complete... I seriously enjoy learning about and thinking about them, but I'm just not quite grasping what's so weird about them. Difficult? Certainly. Abstract? Yes. But the same held (and still holds) true in my classes on chemistry, physics, and mathematics.

"Why Evolution is True" by Jerry Coyne

2009-11-02T07:54:00.000-08:00

I enjoy pop-sci books written by those qualified to write them. Jerry Coyne certainly meets that criteria on "Why Evolution is True", but he also fulfills the other part of why I enjoy reading pop-sci: I learn in an entertaining and easy sort of way. The majority of the time Coyne reviews a good chunk of data collected thus far that supports the theory of evolution while demonstrating the basics of how the scientific method works. However, despite doing this, one does not need a background in science to understand the arguments for evolution -- everything is straightforward and fairly easy to comprehend. There is some occasional ribbing of theism involved, but the ribbing is directed towards the current creationist movement that biologists have to contend with more than the grand philosophical questions of theism. This approach shows that Coyne is more concerned about the scientific stance of evolution and the reasons for its truth rather than any particular over-arching metaphysical stance. Some reviews term this ribbing as "Preaching to the choir", but Coyne never lets on what his particular religious stance is. Instead his overall concern isn't the existence or non-existence of God, but the lack of proper scientific argument from self-described creationists and the Intelligent Design community.

What I found particularly enjoyable was his treatment of the debates on evolution within the biological community. Not being a biologist, and having taken all of a single college course on biology, I found it refreshing to be able to review the variations on evolution currently being debated. Overall, Coyne presents the truth of evolution in an entertaining way with references to boot. I would recommend the book to those not in biology but wanting to have a clearer understanding of why the theory of evolution is on par with the atomic theory, as well as a deeper understanding of the social issues at hand (the last chapter covers these) from the standpoint of a biologist who is currently working in the field. We need more popular science books just like this.

The Second Law of Thermodynamics

2009-10-22T15:58:00.000-07:00

The Second Law clicked today. It took two hours of work at a chalk board along with conversations with a professor (who happens to be very generous with his time), but it clicked in my head, and the interpretation that helped it click was the statistical formulation of the Second Law. So, for me, the most confusing part of the second law is NOT how esoteric it is -- it's far from esoteric. It makes perfect sense and matches up with what we observe. To me, describing the Second Law
as "In spontaneous processes the entropy of the universe tends to increase, where entropy is the measure of disorder" is the confusing part. This statement makes sense, but only if you're familiar with the jargon. And even then, I was still left with wondering "So... why is this, again...?" While you can always ask why (and one ought to), the statistical interpretation satiates the confusing "Why?" for the "Hm, I wonder Why?" kind of why -- bridging the gap from frustrating unfamiliarity to curiosity.

But stating the statistical formulation takes a lot more room. I'll still take a go at it, however.

Suppose you have a chunk of energy. You split that energy into 10 equal parts to observe how it behaves, and you have two metal blocks that can absorb that energy. Placing all 10 equal parts into one of the metal blocks (We'll say so that the energy heats up the block, since I am referring to thermodynamics here) and sitting it next to the other metal block, you sit and wait to see what happens. The heat from the first block should heat up the second block until they're about the same temperature. For our purposes, this is no different than when you let your soup cool off to room temperature, or your ice melts in a glass of water, or when you cuddle up with someone when you feel cold. Eventually heat will be transferred until you reach the same temperature. At this point, heat transfer seems to stop. Ice does not later boil, the soup does not freeze, and you and your partner remain at about the same temperature (though there are some extra complications involved with cuddling, since human bodies produce their own heat, but for rough analogy and everyday experience, it works). Something stops the transfer of heat from continuing in the same direction that is initially observed. Something also stops the transfer of heat from going back to where it used to be (Hot soup, ice cubes, you stay cold). This "Something" is the Second Law of Thermodynamics. From the 10 pieces of energy analogy above:

You have two blocks of metal. However, those blocks of metal have places to store this energy -- atoms. Everything has atoms that it can store energy in. The question really becomes which atoms hold what amount of energy. This is a question that can be addressed mathematically with a concept termed "Multiplicity". Multiplicity is the number of ways you can store those 10 units of energy in however many atoms are present in the metal block. You can place all 10 in the first atom you touch, or spread them out in 10 different atoms, or put 5 in one atom and 5 in another. These are all different ways to arrange this amount of energy. Even so, if all 10 of the energy units are still in the first block, this would mean that the block is at the same temperature (if you'll recall that our energy units tell us how hot our blocks are) no matter how they are arranged within the individual atoms that make up the block. This is something called a "Macrostate" -- a mathematical description of what we observe, namely, the temperature of the block. However, the "Microstate", or the mathematical description of how the energy units are distributed amongst the individual atoms in the block, still plays a crucial role. See, if we take into consideration the second block of metal we just touched to the first block (Let's suppose that both of the blocks are the same size), we essentially double the number of atoms our 10 units of energy can spread between. We also increase the number of macrostates from the single one before (Where our block stayed at the temperature of 10 units of energy that we placed there) to 11 different possible macrostates -- 9 units of energy in the first block, 1 unit of energy in the second block, or 8 units of energy in the first block and 2 units of energy in the second block, so on and so forth.

So the question becomes: Which macrostate is the most likely one to observe? From common experience, we know that things tend to have the same temperature as one another if given enough time, such as the soup cooling off in a room example above. So we should expect that what we observe will be 5 units of energy in the first and 5 units of energy in the 2nd block, given enough time. But why? That is where the term for "Microstates" comes in. It turns out that when you have 5 in the first and 5 in the second, you have more possible ways of distributing the energy throughout the different atoms than you do with any other macrostate. So, it just becomes a statistical issue: There are more possible ways for the Macrostate 5/5 to be observed, therefore it is the one most often observed. There may be some oscillations about this point, but we still observe this more often than anything else.

Now the real kicker is that when dealing with the real world, one deals with more than 10 energy units. We deal with billions upon billions of energy units. And, as atoms are awfully small, we also deal with billions upon billions of atoms. So, with such large numbers the oscillations about the midpoint become immeasurable. So, while oscillations are dictated by probability to occur, as every possible way to arrange the energy in the atoms is just as likely as any other way, we don't notice them due to the sheer improbability of that happening. Like, much more than 10^23. I'm not sure how to express how improbable it is to feel an object heat up without anything heating it up(as it is REALLY FRIGGEN IMPROBABLE), but as you've never experienced it in your life, and I am confident in saying that, you too can feel confident that the 2nd Law is pretty sound stuff! Cool factoid: another common experience unrelated to heat, table salt dissolving in water is an entropy driven process, which is to say that without the 2nd Law of Thermodynamics, table salt wouldn't dissolve.

The Stories of Problems, and visuals

2009-10-15T11:33:00.000-07:00

While visualizability is far from a necessary component in a physical system, I still find fictional visualizations beneficial to working problems. I imagine energy as a sinusoidal beam, heat as a cloud of these beams, and electron probabilities as a static mist. I think it helps me to create a narrative of the events, which can make arranging appropriate questions to ask myself easier in the mental array of problem solving techniques. I have recently started developing a visualization for circuits by using water pipes. Except, not. I imagine they're large, already filled pipes that require motors to both pull and push the water, because the fluid is just that dense; or, I try to think of it as a steam like substance under pressure, but so high in mass that it's very stubborn to move, so it just needs two motors. I try to avoid thinking about liquid water, because water is blue, and I imagine that electrons are blue, so I'm trying to keep the visual for the flow of positive charge separate from the visual of electrons that I use, say, when comparing electronegativities, because their stories are different. Maybe something more "Yellow"-like

I highly recommend it. Even if the visualizations are somewhat false, I've found them to be helpful in the problem-solving area.

Teaching Experience, 3

2009-10-14T16:14:00.000-07:00

This is an experience I've noticed over my tutoring that happens with most students, in general.

If you ever ask someone, "Does that make sense?" they will always, always, always answer "Uh-huh" (or "Yes", or another general colloquial affirmation). I could say "the delta G favors dissociation" to someone memorizing the solubility rules, and they'll only start to nod their heads, look a little confused, but they will answer "Yes" with at least a .99 probability -- I haven't tested that, but I hypothesize that it would happen.

I wouldn't say that I suddenly get the pass on this one, either. If I'm struggling with a concept, I'll often just blurt the first thing that comes to mind to see if it sticks and see if I'm anywhere near the right track. If someone asks if I understand, I'll say "Yes", wait a minute, and then ask a question directly related to what I was just told. Sometimes the answer will be the exact same thing that they just said.

So this got me to thinking about a general possible maxim for teaching: Never ask your students if they understand. Always assume that they do not understand. When they look bored, then that is the point at which they understand.

This isn't always necessary, as sometimes an individual's body language will let you know whether or not they understand the concept. But some people, including myself, are tricky at hiding it... in the hopes that they don't embarrass themselves (at least, that's my personal motivation), and in the hopes that something later will make it all click together.

I am going to start testing this tomorrow.

EDIT: The phrase is a habit. I totally fail.

"Uncertainty" by David Cassidy

2009-10-12T06:18:00.000-07:00

Last night I finished Cassidy's biography on Heisenberg, and so wanted to write a brief review.

The author is a scientist-turned-historian writing a biography on a great scientist. As such, the book is really writing three stories that all occur simultaneously. The obvious one is the life that Heisenberg led. You also get a brief synopsis of his scientific achievements as they were developed and published. To put both of these stories in context, however, the third story being told is a pseudo-personal history of Germany. To give the reader a better understanding of this history, Cassidy will give brief anecdotes about the figures that appear in Heisenberg's life that Heisenberg would not have known, such as the activities of Oppenheimer during the second world war, or the actions of influential Nazi party individuals that, entirely unknown to Heisenberg, essentially saved his life.

There is a historical controversy about Heisenberg dealing with his actions during World War II. The author takes great pains to tread around this with tact, and succeeds at doing so while giving information around the controversial events. He lays out why certain pieces of evidence are suspect, historically speaking, but because these pieces of evidence seemed wrapped up in the controversy, he gives the evidence and its subsequent argument.

While I do not mean to denigrate the efforts of historians, as a scientist-in-training I personally think that the interest in those controversial events lies not in the exact truth of them, but rather in the ethical implications attached either way. If this book can be said to have a theme outside of the main subject matter, the "ethics of science" is the most prominent. This is far from surprising, as World War II really encompasses that question as a whole. I honestly don't think the question was considered before the fall of Nazi Fascism and the bombing of Hiroshima and Nagasaki. However one falls on the question of ethics, the life of Heisenberg is an excellent first stepping stone for addressing the intersection between ethics and science, and as such, this is a book any scientist (or ethical philosopher) ought to be interested in reading.

Undergraduate Research

2009-10-05T12:43:00.001-07:00

While it may be a pain in the ass for the professor involved, I have to say that I'm happy that this class is a required part of my undergraduate degree. Especially when put in contrast to the upper-level science courses I am currently taking, which half the time cease to have a lab component complementing the theory -- not that theoretical classes are bad unto themselves, as there's a lot of material out there from which one has to play catch-up with. But I've been forced to learn about a subject I've never had a class in by way of teaching myself from current literature. I haven't done a single experiment, I've only given myself a beginning background in an area. And the ability to utilize things like scifinder or pubmed or the ACS website, and teach yourself (with a little help from my advisor, I must admit) about a topic... I can't help but think these are invaluable skills for work that I hope to be doing in the future. And they aren't skills I ever used in a class room setting, because their you're more concerned with problem solving, memorization, and finding answers in your text-book index.

Additionally, there's an emotional satisfaction to it all -- becoming familiar with an area in order to do original research. But I wouldn't argue that is prime reason for including things in curriculum.

Hydrogen Bonding

2009-10-04T12:59:00.000-07:00

Last I mentioned wanting to go over the reason why drinking alcohol, despite being heavier, has a lower boiling point than water. The explanation lies not just in chemical bonding, but in a specific type of chemical bond: The hydrogen bond. In order to understand hydrogen bonding, however, I think one needs to understand chemical bonding in general.

A chemical bond is what holds molecules together. When you have something like H2O, a chemical bond holds the two hydrogen atoms to the oxygen atom. By this definition a hydrogen bond isn't strictly a chemical bond, as it does not hold molecules together, but rather is a way to describe the interaction between a large group of molecules. However, they are related, as a sort of "Bonding" occurs between multiple molecules. Behold, the molecular shape of water!

You'll notice that, with respect to the atoms involved, it has what is called a "Bent" shape that resembles the shape of the letter "V". The four dots around the oxygen atom represent electrons that the oxygen carries around with it. The important thing to know about those electrons in this case is that they are negatively charged, like magnets, which have both a positive and a negative side.

Or a North and South side, as in this picture. Same idea. In fact, if you've played with magnets, water behaves in much the same way: The negative side of water is attracted to the positive side of water. The negative side of water is the side with the oxygen, because oxygen "likes" to carry around electrons (relative to hydrogen). The positive side of water is around the two hydrogen atoms for two reasons: Hydrogen atoms are single protons, which have a positive charge, and as stated before, the oxygen atom "likes" to carry around negative charge much more than hydrogen does. So the oxygen atom not only has the four electrons that it normally carries around, but it will also carry both hydrogens' electrons around. This causes the entire water molecule to become "polar" in the same way that the bar magnets above are polar: With a North and a South side.

Hydrogen bonding is this sort of interaction: Where one side of a molecule will have hydrogen atoms attached to atoms, like Oxygen, which will carry much more negative charge than hydrogen will. This causes a polarity on the molecule, and then large groups of that molecule will interact with itself, where the negative side will be attracted to the positive side. This won't cause true chemical bonds, as they aren't new molecules, but the interaction is enough to have an effect on macroscopic observations, such as boiling point.

To relate this back to the post on distillation: you'll notice from the diagrams in the previous post that drinking alcohol also happens to have an oxygen atom with a hydrogen atom attached to it, which makes it suspiciously similar to alcohol. In fact, this is the case, and some hydrogen bonding occurs in drinking alcohol. However, you'll also notice that there are two hydrogen atoms attached to the oxygen in water, and only one in the case of drinking alcohol. This allows for multiple hydrogen bonds to form, which makes water more attracted to itself than alcohol is to itself. Because water is attracted to itself than alcohol is to itself, it takes more energy (and hence a greater temperature) to cause it to boil. So in the distillation process, alcohol will evaporate before water because of the effects of hydrogen bonding are greater on boiling point than the molecular weights.

This sort of explanation is the essence of chemistry. There are a number of physical things one can measure. There are a number of attributes to a given compound. But the desired end goal is to find a molecular explanation for a macroscopic observation -- something that the hydrogen bond easily does in this case. Also, for further reading, check out the effects of the hydrogen bond on DNA configuration and the density of ice. It has a great deal of explanatory power across several differing areas of study, as well as theoretical justification in physics. These are all the makings of great scientific facts.

Distillation

2009-09-09T16:05:00.000-07:00

This apparatus is what a chemist uses to distill things. There is a long cylindrical tube connected to a flask that sits on a heat source. The tube connects to another, similarly shaped tube that sticks out from its side, and is pointed downward. This tube, called the "condenser" has water running through a cavity between the inside and outside of the glass -- sort of like having a glass tube within a slightly larger glass tube. This tube ends in a spout, where some sort of receptacle is placed for collection. In the picture above, the receptacle is a graduated cylinder with a red plastic bottom.

What occurs macroscopically in a distillation is pretty common to everyday experience: You add heat to some liquid, and the liquid evaporates up the tube and eventually travels through the condenser, where the water quickly cools the vapor, and drips out of the spout and into the receptacle. In particular, this is how liquor companies obtain higher concentrations of alcohol. When you make alcohol, the alcohol is fully dissolved in water -- like beer, or wine. The trick to higher alcohol content lies in... Chemistry!

So, suppose a beaker full of recently made alcohol -- it will be clear, and from appearances look to be the same liquid. This is because alcohol is miscible in water, which is the opposite of what happens when you mix oil and water. No matter how much water and alcohol you mix together, they will always freely intermingle. So, you're left with a beaker of water and alcohol molecules:

Behold the power of paint! The blue atoms with two red atoms coming off of them is a water molecule. The other one is a molecule of the drinking variety of alcohol. It has a blue atom as well because both water and alcohol have Oxygen in them.

How would you separate these?

A quick look at ethanol's MSDS sheet tells us that the alcohol has a boiling point of 78 degrees Centigrade. Water's boiling point is 100 degrees centigrade. Attempting to boil the mixed liquid seems like a good idea. And, in fact, this is how alcohol and water are separated -- first the alcohol evaporates and is collected, then the water will stop evaporating. If you want to keep them separate, you stop the distillation once you have collected the majority of your alcohol. How does one tell when that happens?

You'll notice in the photograph a thermometer. If we plot a graph of the amount of liquid collected on the x-axis versus the temperature of the vapor (which corresponds to the liquid's temperature) on the y-axis, you'll see something like this:

I chose this image on purpose because it displays the two types of distillation on the same graph -- simple and fractional. They both have roughly the same shape, only fractional distillation has a much larger spike in its temperature. We'll come back to this sh0rtly.

Note also that alcohol, which evaporates first, has a lower boiling point than the water. Also note that the temperature in the graph climbs as the distillation occurs. This is because the vapor evaporating has an increasing number of water molecules, which require a higher temperature to vaporize. So, you know that you have collected as much alcohol as you can when you reach a mid-point on the graph, which you can determine experimentally by running the whole distillation once through.

Also note in this graph that the fractional distillation has a much sharper jump in temperature. This is because, initially, you are evaporating mostly alcohol and leaving most of the water, but then suddenly you only have water. In the simple distillation, the rate of change of the ratio of alcohol to water is much more gradual (prepositional phrase glory, right there). That is because...

*fan-fare!*

The fractional distillation simulates doing a simple distillation hundreds of times over! Well, I'm uncertain about the actual factor, but it does simulate it going over and over again. The photograph above shows a set up for fractional distillation. If it were a simple distillation, the flask carrying the mixture wouldn't be connected to a long vertical tube, but would be next to the condenser. In the vertical tube are placed several glass beads. As the vapor rises, it condenses on the beads (since the beads are cooler than the vapor), and the heat from more vapor gradually warms up the bead until the condensate evaporates again. This occurs time and time again, with some of the liquid pouring back down into the initial flask. Each time this occurs, the mixture becomes a little more concentrated in the chemical with the lower boiling point -- in this case, the drinking alcohol. With a simple distillation, this occurs only once, but the beads essentially simulate many simple distillations in a row.

Now, an oddity here -- you'll notice from the Paint drawn beaker diagram above that the alcohol molecules are actually larger than the water molecules. The molecular weight of alcohol is, roughly, 46 grams per mole. Water's molecular weight is 18 grams per mole. Yet, despite having more mass (thereby giving the impression that it will need more heat, which can be roughly thought of as energy, to turn into a gas), the alcohol has a lower boiling point. Stay tuned for this explanation next time! Whenever next time is. This is a busy semester.

Derivations

2009-09-05T16:00:00.000-07:00

Two years over and done with, and I have a good feeling for reading equations. This isn't always the case -- I'm still unpacking things as complex as, say, the Schrodinger equation, but give me something along the lines of chemical kinetics, a classical mechanics problem, or the ideal gas law: Yeah, I feel pretty good about reading the relationship. Just as I feel comfortable with reading equations, this year has a new angle being thrown at me: Deriving equations from other equations.

Holy shit, derivations are difficult. So far, I have no real "feel" for where to begin in deriving. I just write down two or three related equations, isolate some variables, do some substitutions, and play with the rules of logarithms hoping that all my random math play will, in the end, give me the equation that I'm looking for. To say the least, this doesn't help. I've been walked through deriving the ideal gas law using classical mechanics, and the derivation itself makes complete sense. But now, left on my own, I feel entirely stuck.

The current problem: Derive P^gamma V = constant from PT^f/2 = constant, where gamma = f+2/2, and f is the degrees of freedom. So, I have both forms of the ideal gas law, the first law of thermodynamics, a definition for work, and the equipartition theorem of energy... I think I could google something up, but this wouldn't help me in knowing how to actually derive equations, rather than follow arguments.

If you have any kind of method for deriving equations, then this is my desperate cry for help. In the end, I'll get it. But it'd be nice to see what other people do if and when they derive equations.

EDIT: In solving, I found a new "method" for derivations. Working backwards. By playing with the "end" result in the same way that I played with the beginning result, I was able to see a familiar form that I knew I could convert the beginning result to. Other than that... no method, really. More intuition.

Teaching Experience, 2

2009-09-03T19:39:00.000-07:00

Alright, so teaching is much much more complicated than tutoring, granted, but it's where I get my practice in the craft at this point in time. And as it's easier, it's a good place to practice, because I get to directly see results. It probably also helps that the people I tutor come willingly and are paying for their classes. So, it's like baby-teaching. Nevertheless, it's a good field to practice and develop my teaching skills, so I'm still labeling it "Teaching Experience"

Today, we covered Unit Conversions and basic chemical nomenclature. Nomenclature is hard to teach because there aren't any real patterns to pick out, and there is quite a bit of data to memorize. As such, you just have to memorize by use, so the best way to teach it is to do it. In a tutoring session, that seems difficult, but upon reflection now, I think naming drills may have been the ideal solution. Must pocket this idea for the future.

Unit Conversions are fairly simple, but they still stump a lot of people. So, like most people, I use the picket-fence method, AKA Dimensional Analysis -- However, I've found in teaching that the use of big unfamiliar words gets in the way of the concept, so it's usually better to introduce the concept first, and then the big unfamiliar word attached to that concept. There isn't a real reason I can think of why, other than the big unfamiliar word sounds scary, so those who are low on confidence (like those who like to go to tutoring sessions) will often shoot themselves down before the concept is introduced. Further, something else that I've found great for tutoring is to start doing the work on the board, but only write what is stated by the students. That way they have to do the thinking, and you're not stuck there giving another lecture that the students have already heard. It's a bit silly to do that in a tutoring session, especially when the lecture didn't get through to them. Sometimes I throw hints in there, or to make things easier I'll explain a single step and do it so they don't become frustrated, but overall I find letting students do the work teaches them better than doing it for them.

Also,I love having more than one student at tutoring. I haven't experienced this until recently, as I'm only recently in a position where we have open tutoring. But today, when one student understood the problem and the other didn't, the first student jumped right in to answer the other students question: So the first student was reviewing the material while the second student was having it explained in a way that maybe is a little simpler than I'm explaining it -- I'm used to dimensional analysis, as well as Chemistry in general, so the terms I'm used to working in may in fact be above the head of those taking Freshman Chemistry. In fact, not just may, but ARE. That is one of the great difficulties in teaching -- you become proficient in a subject, but it becomes difficult to explain the subject because in becoming proficient you generally forget some of the simple steps in between that you used to have to take consciously in order to solve problems. Or you just assimilate simple terms into more complex terms in order to store a greater amount of information. Then you have to unpack all that knowledge, and lead people along step by step from the beginning while not intimidating them, entertaining them, and being there friend while still maintaining a position of authority and respecting their values and way of thinking but modifying it in such a way that they become better thinkers and learn the actual subject matter.

Fascinating. Difficult. Rewarding. Undervalued.

Heisenberg

2009-09-02T19:19:00.000-07:00

I'm currently reading "Uncertainty" by David Cassidy in conjunction with my P-chem class. While I can't currently write a review of the book, as I haven't finished yet, I do have to say that reading about his early life is a serious motivator for myself. He learned how to apply Calculus to Physics during his high school years through self-study. I'm in my mid-twenties, and while I've progressed in that direction to a point that I'm feel pretty confident with it now, man! I did that with the help of professors lecturing me on that very topic. Looking at the educational ability of the greats around the turn-of-the-century is humbling and inspiring.

Also, interesting fact: Max Plank, Albert Einstein, and Werner Heisenberg all graduated from the same "Gymnasium" -- early 20th century German equivalent to our High Schools. Implicated reason for this: the rich ensured that the best teachers were teaching at their Gymnasium by way of spending money on them. This isn't pointed out to denigrate the ability of these great men, but it does make you wonder about those who think teachers are already payed enough. (Totally anecdotal evidence reinforcing my personal bias in action)

Math and Science: Dehumanizing?

2009-08-31T15:26:00.000-07:00

An interesting article reviewing Harper's magazine (I tried to get to the original article, but no such luck without money, and I just so happen to be a student) article "Dehumanizing: When math and science rule the school" -- link to CJR, I got this via Symmetry Mag.

I have no problem with liberal arts studies -- in fact, I encourage them and enjoy them myself. The problem I have with the above is: In what way are the sciences dehumanizing? If the point is more to speak up in favor of a liberal arts education, I would be in full support. But it strikes me as particularly silly to claim that math and science are dehumanizing, setting them up as some sort of Human anti-Human dichotomous interaction where one or the other wins out, and we have to set out to find the mean between them. Was I always as interested in math and science as I currently am? Far from. But I was also a 19 year old wanna-be artist. I would expect someone in the humanities, whose grown up a bit, to realize that the conflict between the two isn't intrinsic to the subjects, but a skewing of national culture values being directed towards the things that have "Practical" value or economic returns, which is something that scientists also have to deal with.

Because they are useful...

2009-08-26T14:15:00.000-07:00

I ran into an interesting paragraph today. It stated the equation F = ma is used because... it's the fundamental equation in classical mechanics, and it helps to describe a lot of physical phenomena. Essentially, because it is useful. This was described in conjunction with a correlative equation in quantum mechanics that I can't begin to explain, so I'm not typing it out. There was a similar statement made in my Heat and Thermodynamics class that I'm taking: It claimed that Energy was THE fundamental concept of all of physics, and as such, evaded definition. This all brought home to me how much the philosophy of science is seriously influenced by Descartes and all the early modern philosophers: I've personally read that fundamental things escape definition being propagated by Descartes, Locke, and Hume. This shouldn't come up as much of a surprise, seeing as Descartes laid down fundamental work for calculus, and Hume is credited with seriously developing the philosophy behind the scientific method (Taking empiricism to its logical conclusions and inadvertently making a reductio ad absurdum argument for the existence of induction as a separate logical system, in my humble opinion). But this still surprises me.

The process of first principles in logical systems is arational, granted. But the idea that we use concepts in science simply because they are useful for describing the physical world seems, to me, to be a bit off from the idea that we are, indeed, understanding the physical world. I'm fine with stating that science only describes things in useful ways, and that is why we use them, but this description really gives little reason why we would choose one scientific explanation over another, or why even differing disciplines would, indeed, come to the same conclusions. I mean, by this, I could essentially adopt Aristotelian teleology in my description, claim that it's useful for understanding, and stand back satisfied with that use. However, just try and publish a scientific paper today where you ascribe purpose to your explanation, and I sincerely doubt it'll fly. To me, it seems that the "use" approach for validating the logical beginnings of scientific descriptions falls flat. I think the reason for this statement is to cut down the number of assumptions one has to make in making scientific pronouncements (which I would claim is a good thing) -- but unless there is some other validation method, I'm thinking that we are indeed still assuming that our minds are interpreting truth about the physical universe, but we're post hoc attempting to erase the fact that we're making this assumption.

So, sure, they're useful, and that's great. Maybe I'll change my mind when I realize there are other criteria that can be applied to first principles. However, I think it's a far more elegant solution to just admit that we're making something up that sounds like it might be right, then validating it empirically, and assuming all the while that our minds have some connection to the truth of the universe.

The Photoelectric Effect

2009-08-20T17:32:00.001-07:00

You cover this topic in your first semester of Freshman chemistry. But at the time I have to say that I failed to grasp the weirdness (and pure scientific genius) of Einstein's nobel prize winning experiment dealing with the photoelectric effect. I don't pretend to be able to condense a good 50 years of scientific inquiry into one blog post, so I'm just going to focus on the single part of the photoelectric effect that I seriously missed in Freshman chem, and am only now beginning to grasp in Physical Chemistry.

The energy of an electron ejected from a metallic surface depends not on how much light is hitting said metallic surface, but rather how often the light hits the metallic surface. To illustrate this odd phenomena, suppose a ball being hit by another ball (in a perfectly elastic collision for ease of explanation):

Now, in mechanics (and if you're familiar with pool) we would expect the ball to hit the other ball, stop, and for the second ball to continue in motion, like so:

This would happen no matter how hard we shoved the original ball. As long as there was still kinetic energy in the initial ball when it hit the second ball, then the second ball will be sent away. This is somewhat still the case with regards to the photoelectric effect, but not exactly. The photoelectric effect deals mainly with light waves and electrons. The electrons are in a metal, which if you've ever opened anything electronic, you'll notice that it's filled with metal wires. That's because electrons easily move through metals, which is why metals can carry a current. This also makes the electrons easily knocked away from the metal by a source of energy like, say, light.

There's one more very important thing to consider -- at the time of this experiment, light was thought to be a wave (For some very good reasons, explained at Built on Facts). The energy transmitted from light was thought to be dependent upon a given light beams "Intensity", which was determined by the wave's Amplitude. This is important because the electrons held in the metal have 1) a certain amount of energy they need to absorb in order to knock whatever force is holding them in place away, as well as 2) however much more energy is added to the electron to get it moving. However, when Einstein flashed both bright and dim lights on his sheet of metal, there was no change in how many electrons were ejected. This means that the amount of energy from a light beam was not dependent upon its intensity. Further, there was a given Frequency where electrons were no longer ejected. So, the energy from light must be dependent upon how frequent each wave hit the metal, as opposed to how many waves hit the light in a given time. To illustrate this:

In these two drawings, the light with one "wave", but more frequency (illustrated by the shorter wave lengths, as all light travels at a constant speed) has a GREATER amount of energy than the drawing on the left with four "waves" hitting the metal plate all at the same time. Now, in everyday life, supposing you throw four balls at an equal amount of Force at a target and they all hit at the same time, you're going to transfer all of the energy in each of those those balls into the target at the same time -- which will give you a greater overall impact. If you were to throw them separately, but more frequently, the net energy transfered to the target would be the same, but the impact would be 1/4 of the initial example each time you threw the ball. In the case of the light waves, not only is the energy transfer greater with frequency, but so is the overall impact! This is completely contrary to everyday intuition (which is fine, as physical systems aren't actually supposed to do anything. we just observe what they do, then describe them). This all ALSO resulted in confirming a separate experiment by Planck that stated the same thing, but came from different angles -- which gave further support that the energy in a light wave is not dependent upon intensity, but instead on frequency. The end all equation to this all was:

E = hν

Where E is energy, h is a physical constant (called Plank's Constant), and nu (ν) is the frequency of a given wave.

Now... OK... admittedly, here's where things are still shady for myself... but the photoelectric effect also demonstrates the dual nature of light: That light exhibits both wave-like and particle-like features. The best formulation I can come up with here is that, supposing we have a wave, like above, and we know the frequency that the wave needs to be at in order to knock electrons loose (as frequency corresponds to energy). We set that frequency to just above what is required to detect electrons being knocked loose. Now, we spread that light beam out with a lens over an entire metallic surface. What is observed? Whether the light is spread out or focused on a single point, the same number of electrons are ejected. If we had a wave, the entire wave would be spread out over the surface, and we would then also have less energy transferred to the plate, and we would expect electrons to not be knocked loose. However, since we still observe electrons not only be knocked loose, but the exact same number of electrons being knocked loose, we have to conclude that light energy comes in packets. And THAT is the beginning of quantum (meaning "piece") mechanics.

Holy. Fuckin'. Shit.

(apologies for any bungling to actual history of this discovery, or even misrepresentation of the theory. Really, I'm just beginning to grapple with these concepts. Someday, this stuff'll make even more sense)

Conceptual Question of the Day

2009-08-19T16:42:00.000-07:00

Classes started today. Also, I think I'm going to try to treat this more like a traditional blog, which means more frequent updates with less thought out content. Sweet. Though I'd like to also throw in some good content when I feel I have the time. For now, however, my semester is lookin' hella busy, and I don't think I have the time to write an end-of-the-week recap of my thoughts on science. Instead, I'm just blundering along and pushing out junk, hoping that something sticks to the inner walls of knowledge.

So, of all the questions I raised to myself today, this is the one I remember as the most interesting: Suppose a ball is coming towards you. You do not know the origin of the ball. Before the ball looks like it's going to hit, how do (or can?) you distinguish between a) a ball coming towards you, and b) a 4 dimensional "sphere" entering the familiar 3 dimensions.

Teaching Experience, 1

2009-08-04T11:24:00.000-07:00

Let it be known that I want to be a teacher. It isn't what I want to do when I first graduate, but it is what I want to become in the end. So, I try to explain things to people as well as keep up on my philosophy of teaching. The other week I had a good teaching experience, and have recently read Whitehead's "Aims of Education", which has me thinking about teaching in general. The experience went like so:

My brother visited me. He has recently graduated from High School and is currently working some low income jobs before he goes to college. In conversation he made a comment where he felt uncertain about evolution. I asked what, and specifically he thought that random mutation was an odd concept. Particularly, he found it difficult to believe that random mutation could create viable species over time, because he found the idea of "Random" to be arbitrary, and he thought that if a species mutates that it would be more likely to die. I explained what "Random mutation" actually meant -- not that it just happens, that there are explanations for the mutations, but the causes are out of anyone's control and therefore are labeled "random" -- and that he was completely correct in his assumption that a mutation is more than likely kill an animal. It was only in the rare cases where a mutation actually helped a species pass on its genetic code and survive better than its peers that the mutation is passed on. I also noted that there was more to speciation than random mutation, such as sexual selection or dramatic geographic separation, etc. Later we visited my campus' museum of rocks, and the museum of stuffed birds. We saw fossil records of now extinct species, and stuffed animals of species still alive. Later we visited our towns' zoo. Once we reached the zoo, my brother would comment about certain features of an animal, how these features helped that animal survive, and essentially out-compete other animals in certain ways.

So, in an afternoon, he had the groundwork of a theory given to him, and then he was able to make deductions from that theory about actual animals that he experienced. I'm sure Rousseau would be proud right now, but I'm a little uncertain about Dewey (of whom I am a large admirer of). My brother obviously learned something, and started applying that knowledge to what he saw in the everyday world. Which is awesome, and for a passing incident where I hadn't really prepared anything of the sort and we were just hanging out, very awesome from my perspective, as he's grasped the foundations accepted by the scientific community. These are all important. However, as teaching should be about process, what I taught him was not the process of science. He learned how to make logical conclusions from a given framework of knowledge. Which is, in fact, a fantastic skill, and of great use in the scientific method. However, there was no induction that occurred -- we didn't have a large sampling of animals from which we induced the hypothesis of natural selection, but rather, we walked amongst the animals looking for positive confirmation of a generally accepted hypothesis. This is all well and good, but it's not scientific, and it's not teaching the scientific method, but rather the analytic method.

But then there's the practical side of things: Most places have access to zoos. But do they have access to wildlands that easily show speciation? We could substitute in photographs, but that would certainly not be what Whitehead would agree to, as he's seems to be more of a mixture of a Romantic/Utilitarian educator. I don't know if I agree with him entirely, but I certainly saw something awesome occur while we visited the zoo -- the application of accepted theory, and the acceptance of accepted theory. It wasn't the whole method of science, but analytics is certainly an important part of science. Perhaps the scientific method, as a whole, could be spread out amongst the various sciences? Leave the Null-Hypothesis to the physical sciences, as physical objects are in easy supply to any school budget?

Arational Process

2009-07-23T15:39:00.000-07:00

I am currently fascinated by the process by which one selects a hypothesis to test over other hypotheses, and that one can't test a hypothesis all unto itself. Funnily enough, even that is a hypothesis.

We have some concept of the universe we want to test -- a hypothesis -- and we select to test it out of several others. It all seems to match up after observations are made, but that matching may only be us looking for positive reinforcement of our own idea. So you also test a second hypothesis at the same time, the Null Hypothesis. The Null Hypothesis states what evidence would prove our initial hypothesis conclusively false.

But still, in the midst of this, there isn't a step by step process by which we choose a hypothesis -- there is no mechanism, no real way of knowing how to choose the best hypothesis. There are guidelines, but ultimately, science doesn't care how one chooses an idea to test. All science really is is a method for testing the "soundness" of an idea.

And even when the idea is validated, we often later will recount, reform, and rephrase our understanding of the universe. And... well, that fascinates me. It drives the point home that science is, while a rational process, is also an arational process at its heart. And it makes me wonder: Are all bodies of knowledge similarly arational? Euclid didn't have a method for choosing his postulates. Aristotle didn't have a method for distinguishing between his "Causes" -- it was essentially just really smart people pulling stuff out of their ass. If not math, science, or philosophy, what is fully rational? Logic?

Knowing your Audience

2009-07-09T14:12:00.000-07:00

One ought to "Know Your Audience", as they say in all general composition classes. But doing this is harder than it sounds. It is a difficulty I've run into in tutoring, TA'ing, attempting to understand popularization with this blog, and just general explanation of science in conversation. I do not think this is as hard with fiction as it is with non-fiction, in particular, with science. There's a certain amount of distinction that comes with scientific understanding, but simultaneously, so long as we're not talking about the popularly held HARD sciences, or a specialization of the harder sciences, I've come across the notion that it ought to be "Common Sense for Common People" -- at least in my attempted explanations of chemistry.

Generally, I figure people know what atoms are, and molecules, and that the entire universe is composed of them. However, beyond that and the existence of the periodic table, I grow uncertain about the layman's knowledge, as anything beyond that was what I learned in my college courses. I recall specifically going into an explanation about water, one time, and thought it necessary to go over the shapes of molecules, but this gave insult to the person I was talking to, who thought I was just trying to show off my knowledge, and also who thought I, being the "Science Major of Awesome", was trying to belittle him, who was a "Liberal Arts" major (Though I really, honestly wasn't. I value knowledge as a whole, and find competitive distinction between the two classes of knowledge as trivial and silly)

So, through this experience I realized that one has to assume some knowledge, otherwise people take insult, and then they'll shut you out. But on the other side of what I perceive to be a thin line is assuming too much knowledge. You get blank looks, but no one wants to admit that they're ignorant, which I think is especially reinforced by this notion of "Common Sense"-ness that comes with the basic physical sciences (which I would define as anything not commonly associated with hardness, ie, not quantum mechanics, string theory, space related, or drug related). Everything else, from my anecdotal and probably somewhat off perspective, and I am mostly referring to information I learned in my general chemistry and my Physics I class, is treated as if one should just know this common sense stuff, when in fact there's no way one could know all of this "Common Sense" stuff without taking the time to learn it.

So, where do you err? It would seem talking "above" people would be better, because then at least, if they are so inclined, can look things up they don't understand. This under the assumption that the alternative shuts everyone off to learning, which isn't the best of assumptions -- I'm sure some people are patient with reviewing things they already know. It just seems a difficult problem to surmount in determining which path to lean towards (as, ideally, you'll just find that happy medium on the thin line) when you "Know Your Audience", especially when your audience can have varying amounts of technical knowledge.

Because I try to avoid the "Ivory Tower" feel of science, and encourage people to keep up with scientific progress, I think leaning towards the "Insult your Audience" side is better. However, as I am also often still learning things myself, and an explaining them in order to better understand them, I think I unintentionally lean towards the "Mystify your Audience" approach.

Assumptions in Science

2009-06-29T06:41:00.001-07:00

It is a hobby of mine to collect assumptions in the scientific method as I have a personal interest in philosophy in general, and the philosophy of science in specific. I try to keep them to a bare minimum and disprove assumptions, usually analytically. So, in this blog post, I am going to list some assumptions general to the scientific method that I do not think the method would work without, and give some commentary. I would appreciate input on the assumptions listed, as well as suggestions for further assumptions.

If there are Laws in nature, then those laws do not change with respect to time or space.

I don't think its necessary to assume that Laws do, in fact, exist, because science is a inductive process based in empiricism. So, if Laws exist, we will observe them -- they are not assumed to exist. However, because of the nature of science to build on the work of others, and because it sometimes takes time to fully understand the limits of a theory (Look at Newton)
, we assume that the Laws do not change from one time to another. They are, in this sense, eternal. I think it is better to state the assumption like this than to say that "Time Exists" or
"Space Exists" or "Laws Exist", because these are things that are either difficult to define outside of empirical definitions, or they are things that we do not know exist. If Time does not exist, then of course the laws won't change with respect to time, because a non-existent entity can't effect an existing one. It also doesn't presuppose that we will actually find order in the universe. We hope to find order, sure, but we can't say that we will find order without performing an experiment.

Our Physical World is Deterministic

This is an assumption that I've come to question as of late. I state "Physical World" because science only deals with the physical world. Further, the scientific method does not deal with any other possible physical world, but the one in which we live, because that is the only one which we can empirically verify, which is the highest form of verification in scientific inquiry. However, the term "Deterministic" is one that requires a bit of elucidation.

If by "Deterministic" all we mean is "Physical Laws can not be violated" then I am fine with the assumption of Determinism as an assumption (or, really, that's more of a definition). However, philosophically speaking, Determinism has a much wider meaning. Generally it means that every event from the beginning of time was determined before all events occurred. This can be demonstrated with a Thought Experiment: Supposing we know the physical laws of a photon, and we are present to observe the beginnings of the universe, then we can determine, through a long series of calculations, exactly where the photon is going to go.

However, I do not think we assume Determinism. I think by saying that Determinism is a major assumption in the scientific method, we're putting the cart before the horse. Rather, the evidence amassed through the scientific method suggests that our physical universe is a deterministic one. However, even within the confines of Monism (that the universe does not have any parrelel realities that act in different ways. Generally compared to Dualism, which is generally attributed to Descartes), and that Monism is our Physical Universe, things aren't necessarily deterministic in the grand sense that everything is predetermined before it happens. Rather, it is deterministic in the sense that physical laws can not be violated, and so action is limited, but only within the confines of physical laws, not completely Deterministic as it is usually defined.

There is a Truthful connection between our mind and the Universe

This is a recent one I came upon, so I haven't thought about it as much. It basically assumes that science, in general, is coming closer to the truth about things, rather than the truth about the way we think about things. There is no logical reason for assuming this, but it seems to be working so far. It's the sort of assumption one makes if they either believe in Dualism, or are not purely empirical, such as that demonstrated by David Hume. Science, dealing with Induction to understand data, and Deduction as means for formulating Hypothesis's and understanding of several Induction's, does not only deal with pure empiricism. Rather, it hops between "Types". These types are somewhat separate unto themselves and can be regarded as "Methods to Knowledge".

EDIT: Going through these posts again, I've realized that I've changed the most on this post. I fully disagree assumption 1 and 2, and I think "assumption" 3 can be well argued for, and therefore doesn't count as an assumption -- though it may have to be argued for in a "philosophic" sense, so it may still be an assumption within the domain of science if one accepts that these things are distinctly different at this point.

Colloids

2009-06-03T14:37:00.000-07:00

With summer comes employment, and with employment comes less learning, and with less learning comes less blogging. In addition, my summer studies are centering around broader philosophical studies than what is topical for this blog, so expect a decrease in posting for the summer months.

However, during a pub-crawl with my friends a few weeks ago, the subject of colloids came up. I poured the beer out too fast, and it foamed over. I knew foam to be a colloid, I knew alloys to be colloids, but I had no recollection of what distinguished a colloid from a solution. Both are heterogeneous mixtures of substances with molecules dispersed fairly regularly throughout a medium. Generally, solutions are liquids that have solids dissolved in them, though they can also have a combination of liquids. Colloids don't have a specified state: In fact, the type of colloid depends upon the states of the dispersion medium (analogous to the solvent) and the thing being dispersed through that medium (analogous to the solute). So, really, in a prima facie way, it seems that colloids are just a more general terminology for solutions.

So I broke out my gen-chem book, and found out I was mistaken -- the difference between colloids and solutions is the size of the molecules, or groups of molecules. In both, a molecule or ion is solvated, or completely surrounded by the solution. But in a colloid, the groups of molecules are much larger, between 1 * 10^3 pm to 1 * 10^6 pm (picometers). For comparison, the bond length of a Helium to Helium molecule is 300 picometers. Another common example of a colloid is found in soap -- when soap molecules interact with grease, they embed into the grease while keeping a single part of the soap molecule on the outside of the grease. The part embedded in the grease is attracted to oily things, and the part on the outside of the grease is attracted to water -- so running water will then push the grease along. This is a colloid composed of a clump of molecules attracted to each other, but dispersed in another medium, and much larger than a molecule in a solution. Another good day-to-day example of colloids can be seen if you go for a walk at the park. If you've seen light streaming through the branches, this is because the light is reflecting off of dust in the air. In fact, this is a common way to distinguish between colloids and solutions, and is known as the Tyndall effect (this picture demonstrates a colloid of a solid in a liquid). The molecules in a solution are so small that they don't interfere with the visible light spectrum, but the molecules or groups of molecules in a colloid are large enough to do so.

So this brought me to another question regarding chemical philosophy: While we can observe the Tyndall effect to distinguish between colloids and solutions, do the sizes of the molecules matter very much aside from the fact that they interact with visible light? I've done kinetics experiments revolving around a solutions ability to absorb light. So, even though we can't observe the interaction with our eyes, the molecules do still interact with light, don't they? Is the terminology of solutions a bit too simplistic? After all, there is a point in solutions where you have to ask, what is the solvent and what is the solute? What if you have more than two liquids and a solid? Proteins can grow to reach sizes like this, and yet they are only one molecule solvated by water. Does that make our DNA colloidal, and what point does this distinction elucidate? After all, we could also just say that solutions with really big particles in them interact with the visible light spectrum and be done with it. But then we'd be expanding the terms of solution to include things that are clearly not mixed in the same way that salt water is mixed, such as mayonnaises, or beer foam. But they are also slightly different from a solid block of, say, iron. But just because there seems to be this odd in between zone where we're uncertain about how to classify and understand given solutions, it seems rather ad-hoc to just make up a term and rationalize a distinction. So, what's the point of colloids, and what terms should we use in distinguishing between types of solutions, if indeed we ought to revise them at all? I'm going with the ambiguous and open-ended ending.

Just one little drop...

2009-05-16T19:59:00.000-07:00

A chemist stands, swirling an Erlenmeyer flask with a small sample of liquid in the bottom, holding the flask up to a Buret that drips liquid into it. It drips at a rate of about 1 drop every 2 seconds, and Oddly, the two liquids combining are clear, but each time the liquid from the Buret comes into contact with the liquid in the Erlenmeyer flask, a bright pink liquid evolves, and disappears in the swirling motion of the chemicals. Then, the chemist notices how the pink liquid dissipates at a slower rate, so he slows the rate in order to observe the reaction of every drop. One drop is added. The chemist swirls, and the pink disappears. Another drop is added. The solution in the Erlenmeyer begins to fully turn pink, but with a little swirling, it slowly goes clear. Almost there, the chemist allows half of a bead of liquid to form, and stops the rate entirely. He pulls out a stirring rod, and grabs the half-bead with it, then swirls it into the Erlenmeyer solution. The solution turns a mild shade of pink, but does not dissipate. The experiment is over -- but what just happened, and why was the chemist interested in it?

This was a description of a Titration experiment. This is an analytical tool for determining how much chemical stuff is dissolved in a known amount of liquid, and the bane of students in General Chemistry II. It combines the ideas of atoms, ions, dissolution, chemical reactions, and moles -- that's a lot of theory, and while I realize everyone knows what an atom is, I don't know if everyone will remember what an ion is, or why salt dissolves in water. Nonetheless, I don't think its absolutely necessary to fully understand these concepts to get the gist of what a Titration is all about.

Take some baking soda (do it!), and put some of it into two different cups -- I put 1/2 teaspoon into two coffee cups. Then fill one of the cups with water halfway, and the other one quarter of the way up with water. Break out the household vinegar, and a tablespoon, and drop one tablespoon of vinegar into each glass, and watch what happens. Keep doing this. (this can get messy, so it might be best to do this in the sink) This is a little rough, but when I did it at home, it seemed to illustrate the point -- you'll notice that bubbles stop forming with roughly equal amounts of vinegar, even though one cup has twice the amount of water in it. This suggests that the water has nothing to do with the reaction, just the baking soda and the vinegar.

That's because it's true -- the water is the medium through which the chemical reaction takes place, or in chemical parlance the "solvent". It's where the chemicals you're interested in float around, find each other, and react.

Just so you know, there is a chemical reaction going on between the water and the chemicals you're interested in, but it has nothing to do with the one that evolves the bubbles, and is called "Dissolution". Basically, it's what happens when you put sugar in your milk, or when you mix salt and water. The water molecule separates all the molecules packed together in that grain of sugar or salt and surrounds them, which is what renders them "invisible", since molecules are too small to see all by themselves.

Now, back to titration -- that's basically what you performed in the kitchen! But there are a few differences.For starters, chemist's use instruments that are known to produce better accuracy and precision. This is primarily a quantitative experiment, which leads to the next point of difference: Normally, the liquid in the Erlenmeyer flask has an unknown amount of chemicals you're interested in in it. You usually know that it's in water, or can easily tell, and you can tell what type of chemical you need to react with it with litmus paper. Further, when preparing a chemical to react with the unknown, you have complete control: You can measure the amount of chemical you dissolve into water. Then, you react a known amount of chemical with an unknown amount of chemical, and when the reaction doesn't happen anymore, you know that all of the unknown amount has reacted and that that unknown amount is equal to the amount of chemical you prepared to react with it.

One other little snag in this is, how do you know when a chemical reaction is complete? Most of them aren't as dramatic as the reaction between baking soda (Sodium Bicarbonate) and Vinegar (Acetic Acid). This is what the pink color was all about in the story above -- this is another chemical present in the mixture. It doesn't interfere with the reaction between the two chemicals you're interested in, but it changes color whenever your prepared chemical comes into contact with it. This way, if the pink disappears, you know that all of your prepared chemical reacted with the unknown chemical, and you continue. If pink stays, even just a little bit, then you know you've reached what is generally termed the "Equivalence Point" -- the point where a solution's pH changes dramatically from acidic to basic with the addition of a small amount of either an acid or a base.

This is why the chemist was taking so much care near the end of his experiment. It doesn't take a lot to accidentally go past the equivalence point. Even one little drop can add too much of your prepared chemical, and then your calculation for how much chemical amount was added will be off far enough that you'll have only a very rough idea of how much chemical amount was in the unknown, rather than a good idea.

Now, this can get much more complex, but the general idea holds: You have some unknown amount of molecules floating around in some water, and you want to know how many molecules are there. So you throw in a chemical that will react with those molecules, and when they're done reacting, you do a little math and figure out the unknown -- pssh, who says chemistry is hard to understand? It's just colors, numbers, and bubbles.

Crystals

2009-05-08T12:43:00.001-07:00

So, the end of semester is here, and summer looms at me with its tasty treats of indolence and self-education. With that, I'm looking back over the past semester, and trying to think of the most important things I learned. While actually comparing knowledge in terms of importance is, IMO, somewhat meaningless, it's good to think back about what you learned, and answering this question is an excellent catalyst for that type of intellectual probing. It's a toss-up between my physics course, and my organic course. In my physics course chemical theory suddenly clicked. Working problems starting from the basic SI units helped me understand what I was talking about when I was talking about the energy in a system, or in understanding the derivation of the gas laws. Still, while theory is important to understand, and this helped clarify chemical theory for me, I have an even more difficult time in connecting theory to experience -- in lab I often feel like I'm just pouring two liquids together, and shit happens, while in a lecture exam, some Grignard reagent attacks a ketone which is then protonated in a second step by a dilute acid. It's a world of imaginary particles and rationalized diagrams, where the lab is a world of color changing liquids. I have to actively think about theory after an experience to connect the two together, so because of that, I think the most important discovery I made was a personal fascination with crystals.

In organic chemistry, in most labs, we would combine liquids to form crystals. Place a liquid with some sort of chemical dissolved in it contained within a beaker into a water-ice bath, and observe. Initially, pure liquid. Then, slowly, small specks of a solid begin to form, barely noticeable. Without poking or prodding, the specks grow larger, clumping together, forming uniform shapes, even though they form independently of each other. These uniform shapes depend on the exact compound being created, but indeed, they are uniform. Look at common table salt -- each cube looks, more or less, as if they're a uniform shape. The same thing would happen in lab, only in different shapes, and it would happen by virtue of being surrounded by a cold source.

One day while recrystalizing a certain product, I made the connection to atoms. Small particles slowly clumping together in a uniform shape -- similar to crystals. Essentially, watching crystals form gave me an experiential understanding of atoms and compounds. It was the closest I could get, with the naked eye, to seeing atoms and compounds interacting. Now, the naked eye type of experience isn't necessary in understanding a given scientific concept, but I think it helped in my lab skills and in my understanding of an experiment. Suddenly, liquids weren't turning brown, but simple sugars were reacting with copper ion in Benedict's Reagent, Double bonds were attacking bromine, and esters were being cleaved by basic solutions to form soap. I felt more confident in using the framework of theoretical knowledge in order to understand an experimental situation. I saw the atoms reacting with one another, forming new compounds, and solidifying in energetically favorable positions. I watched crystals grow, and beheld the beauty and simplicity in the atomic theory of matter.

It's a sublime moment for me when theory is understood in experiental and experimental terms, and I sit back watching nature and feel like I actually understand what's going on. All the work involved in understanding the material -- my retraction from having as much of a social life, neglection of my hobbies, interruption of a normal sleep schedule, as well as the actual intellectual labor -- suddenly becomes worthwhile.

And to think I came back to school just to get a better job than working in a warehouse; I never thought I'd love science this much. But, there you have it -- I love crystals. I think they're the coolest things ever, and the purification of compounds by recrystalization has become my favorite process in lab. It reminds me of Primo Levi's description of distillation -- there's a certain elegance to the application of theory, and observing that elegance in action will always fascinate me.

The Simplest Solution

2009-05-04T08:34:00.000-07:00

Due to end-of-semester busyness, I was not able to update over the weekend. But, I want to try and stay on my self-assigned blog schedule, and now I'm just studying for finals, so a day late is better than a week, right?

I already had the idea that science tried to break things apart. But, generally, I always thought this was to find the most basic understanding of the universe -- to be able to explain causation from understanding the way that everything works. I think this is still a part of it, but there's another part to it too.

The human mind can only compute so much.

To demonstrate, see the following physics problem (and if you've had Physics I before, I'm sure you've solved this problem before):

A 1 kg rock is suspended by a massless string from one end of a 1 meter measuring stick. What is the mass of the measuring stick if it is balanced by a support force at the .25 meter mark?

I always find pictures to be useful when solving physics problems, so the first things first:

Really, that's about as complex as I normally draw, just to help me visualize a given scenario. In this problem, there is the word "Massless", which is just a fancy way of saying that the string that connects the rock to the meter stick doesn't have to be accounted for, so we're really just dealing with the rock, the meter stick, and the fact that the meter stick isn't moving even with the rock attached to it and the fact that the balancing point is located .25 meters away from where the rock is connected.

The main concept that needs to be applied here is the concept of Torque. Torque can be written in a number of ways, mathematically, but conceptually it's fairly simple, and related to my previous post talking about Force. When talking about Force, the examples and problems usually use cannon balls, footballs, or cars. That's because they easily relate to something called Translational Motion -- which is just the movement of an object from Point A to Point B. You throw a ball, it goes from your hand, Point A, to some spot on the ground, Point B, and there are a host of equations one can use to predict where that point will be based upon how hard you throw the ball, what angle you throw the ball at, and what the ball interacts with on the way there. These equations all have analogous equations that relate to another type of motion: Rotational Motion. Rotational motion is still motion, but it behaves differently than Translational Motion -- not so different that the Laws of the Universe are different, but we have to model them differently because their Translational motion would be a lot harder to model mathematically than it would if we were to just measure the motion of spinning things by the angles they travel through. So, really, it's still Point A to Point B motion, but instead of measuring things in meters, where the direction would constantly be changing, you measure things in Θ (Theta), a generic symbol meaning "Angle".

Torque is the rotational analogue to Force. But instead of F = ma, you have τ = Iα. τ is the Greek letter Tau, and it stands for Torque, which is rotational Force. α is the Greek letter alpha, and it stands for rotational acceleration (with units of radians/second^2, instead of meters/second^2).

This leaves "I". "I" stands for "Moment of Inertia", which does not explain itself as well as "Mass" does, so it requires a bit of explanation itself. Similarly to mass, if the Moment of Inertia is greater, it takes more Torque to gain a greater angular acceleration. But with rotational motion, you have to take more into account than the mass of an object. You also have to take into account how far away a mass is from the center of rotation. And, as you're actually dealing with a large number of particles all revolving around a single point (we'll call this point the "axle"), all of which may have different masses than each other, and most likely are at different lengths from the axle, this can easily get pretty complex. To be technically correct, you would have to find the distance a single particle is from the axle, find its mass, and compute its individual Moment of Inertia -- which is easy enough when you have only one particle. The equation for the Moment of Inertia of a single particle is "I=mr^2", where m is the mass and r is the distance from the axle. So, you square the distance of the particle from the axle, and multiply it by its mass. But when you're dealing with, say, a wheel, there are a lot of particles.

The way to then tackle a problem like the one above is the realize "Hey, this thing basically has an axle at .25 meters, and it has Torque being applied to that axle due to the Force of gravity. Even better than that, the thing isn't moving, so we know that the Torques are equal on both sides. So, the Torque of Left side is equal to the Torque of Right side, so I'll set their equations equal to one another. I know the mass of the rock, if I can figure out the Moment of Inertia for the Left side and the Moment of Inertia for the Right side, then I can find the mass of the meter stick".

Or, mathematically speaking, Iα(left) = Iα(right) from τ = Iα

This is where I made a mistake in tackling the above problem. There is a way to get around having to add up each individual particle, and in fact this simplification at least makes the moment of inertia calculable by hand. For example, when looking at pulleys (another favorite of physics problems) First, you assume that the particles are, more or less, the same mass, as the object is made of the same material -- a good assumption. Then, because the shape of a wheel is a regular shape where the outside of the wheel is equidistant from the axle, you can actually say "Hey! That pulley's a hellalot like a cylinder!", and make another assumption that is more or less correct: that the pulley will behave as if we had a perfect cylinder. The equation for the Moment of Inertia of a perfect solid cylinder is well known, so you can just plug it into the above equation and work away. It's 1/2mr^2, in case you're curious.

The problem is, the above problem is NOT a perfect cylinder, nor is it anywhere close to one. So, my first instinct was to go back to the basic definition for "I", where you can find "I" for any solid object (as that's what I'm dealing with). This involves integrating the volume of an object with respect to its mass which, quite honestly, is a pain in the ass -- at least for me. And actually, this is what I learned: It's not that there is anything wrong with taking the above approach, but you want to simplify the problem to make it easy, digestible, and understandable. And there is such a solution to the above problem, I just didn't see it initially.

It deals with a concept known as "Center of Mass". Center of Mass lets you treat a whole object as if it were a point particle. You mathematically find some fictional point near the object that the object will follow in motion, so you can use the equations you normally use for a point -- which are easier to deal with than whole objects. It also deals with how you define your system. Before I was looking at the system as "Left Side" and "Right Side", but that combines the mass of the meter stick on the left side, which itself is unknown, and I would have to use more algebra to find the unknown. Instead, if I look at the above problem as "Rock" and "Meter stick", then I at least have less algebra to do.

So, applying the idea of "Center of Mass" to the above problem, I have the rock. The objects weight is concentrated at the left end of the meter stick, due to the massless string, so I can treat the rock like a point at the left end of the meter stick. Then I have the meter stick. By itself, the meter stick, assuming that the mass of the meter stick is more or less spread out evenly (a good assumption), has a Center of Mass at its center. In relation to the axle we're dealing with, that puts the point particle .25 meters away on the right side of the axle, which is the exact distance of the rocks center of mass. So, the above picture can now be drawn as:

I put the circle and arrows in to emphasize the fact that we're really dealing with Torque here, even though this isn't a wheel. What can be seen in the picture is the two torques we're dealing with are in opposite angular direction, and are equidistant from the axle. The beauty to this solution lies in the fact that I is easy to find (mr^2, because now they're points). Also note, because the sum of the Torques are equal to one another, we have no angular acceleration to deal with (which means, technically, we wouldn't have any torque, but the above Torque equation is ACTUALLY written as "The sum of the Torques" with a Σ before τ to denote "Add Torques up" and differs slightly from the mathematical definition of Torque. I just wanted to tie the idea of Torque into Force from before)

So, we substitute "τ" for "Iα", then drop α because there isn't any, and are left with I = I. Substitute mr^2, and you're left with mr^2 = mr^2, and looking at the picture, you see that the Center of Mass is equally distant, so it follows that the masses of the two particles must be the same.

Had I started with Center Mass, I would've realized that the points were equally distant from one another, and that the meter stick wasn't going anywhere, so they'd have to be equal in mass too, and I could have solved this in less than 1 minute.

And that's when it dawned on me -- we can really make things as complex as we want. It's not the complexity in science that we even want. It's the simplicity. We're dealing with a highly complex universe that takes time to understand, and there's no way we'd understand it if all we do is take the clunkiest path to understanding. We want to break things apart and find the root cause of phenomena, sure, but in addition to that we just want to be able to understand the phenomena themselves without going through a huge and sometimes difficult to follow line of thinking (as I did above).

So, that's why you look for the simplest solution -- because we can only compute so much in our head at once, and there's a certain satisfaction that comes with a simple explanation if that little bit explains a whole lot.

Physics vs Chemistry: Fight!

2009-04-22T09:29:00.001-07:00

I often contemplate the differences between these two areas of study. Also, I hear fellow undergrads argue for one or the other, usually divided along the lines of their respective major. Anymore, I think they're so interrelated that I find it hard to find a difference between the two, except for the phases of matter that they most often deal with.

Back in the days when science was new, Physics dealt with understanding the fundamental laws of the universe, and it was Chemistry that was making the attempt at understanding the fundamental pieces that the universe was composed of. Both of these fields also grew out of a long standing philosophical tradition that can be traced back to the days of the pre-Socratics, and exemplified by Aristotle. Buuuut... that's going a bit further back than I think is necessary to understand what's different, anymore, about these two sciences, if indeed they ever really were different.

Physics, as a science, really began with Newton. It could be traced back further to Galileo, Kepler, and Ptolemy, but he's the big man that laid out a comprehensive scientific theory. Chemistry, likewise, has a big man on campus -- Dalton. Dalton's atomic theory brought back the idea that the universe is composed, at its smallest level, of indivisible particles called "Atoms", and was proposed around the same time as Newton's theory. Likewise, work done by Boyle, Cavendish, and Lavoisier contributed to Chemistry, but Dalton's the guy who proposed the first scientific theory of the atom. (Though mad props must be given to Cavendish, who isolated Hydrogen, Oxygen and created the "element" water -- of four elements fame -- from two different elements of "Air", thereby disproving the idea that four elements created everything and paving the way for the atomic theory)

Newton's theory can be summed up as such:
1) An object at rest remains at rest. An object in motion will stay in motion

2) Momentum is related to Force directly, and is related to mass inversely (F/m=a, from the previous post, except Newton did propose his law in terms of Momentum, a concept accounting for both the mass of an object, and the movement it's currently undergoing)

3) If two objects interact, the force exerted by object A on object B is equal in magnitude and opposite in direction to the force exerted by object B on object A.

And now, Dalton's Atomic Theory:

1) All matter is made of atoms. Atoms are indivisible and indestructible.

2) All atoms of a given element are identical in mass and properties

3) Compounds are formed by a combination of two or more different kinds of atoms.

4) A chemical reaction is a rearrangement of atoms

From these two rough outlines, while both are attempting to deal with fundamental pieces of the universe, it seems that initially Physics dealt with a macro-world: How whole objects interact, how cannonballs fly, how wheels spin. Conversely, Chemistry dealt with a micro-world: Fundamental pieces that make up all things, what is actually happening in the micro world, and understanding what effect that has in the macro world.

How things seem to change. Now its the physicists attempting to delve deep into the universe, and the Chemists sit content at the atomic level. Actually, this history makes sense when you think about the things that inspired these two progenitors of the physical sciences. Newton created calculus to better understand astronomy. Dalton collected weather data on a daily basis for 57 years. Newton watched objects moving far away that he had no hopes of understanding without attempting to understand how all objects move. Dalton watched condensation, evaporation, clouds -- a macro world understood through a micro-world of millions of particles interacting with one another.

It's all the physical universe, but when, say, researching a cell, I haven't broken out the quantum equations to understand how it works. I applied concepts traditionally assigned to the realm of chemistry (and, of course, Biology). But, those ideas are in turn heavily influenced by physics (and math), which itself is heavily influenced by math. At present, we don't have a cohesive enough physics model to build towards understanding all biological science, and if we did, it would match up with the findings of biology. It would just be another way to explain it, and the same would happen in building a physics theory of chemistry. Chemistry knowledge, which may one day be obsolete, would serve as the bridge of knowledge between physics and biology, if such a theory is possible.

So, the question still remains, what's the difference? Size? Well, in a sense, yes: I think size is it, in its own way. Not that physicists don't study classical physics anymore, far from. There are still people researching and applying classical physics for purposes other than engineering. But rather, in the number of particles we each deal with. As a chemist, we deal with "System" models most of the time. The "system" model is a method of understanding something, and it's something you define yourself -- generally, chemists define systems as "What's in the beaker". We talk about the energy of a system. We talk about "How Often" a collision between atoms occurs -- not that we really know how often it occurs, exactly, but we do have a way of quantifying it. Physicists deal with points: Displacement of an object, energy transferred from one object to another, the behavior of a single electron. Even with an object of oddly displaced mass, there is an acknowledgment that many particles are moving: But they use the concept of an imaginary representative particle (called the center of mass) in order to apply point-particle models to the object. This isn't always the case, but I have yet to come across having to deal with systems of billions and billions (may Carl Sagan rest in peace) of particles explained by the characteristics of the fundamental particles in my physics studies.

But then you have the physics of condensed matter, dealing with 10^23 particles, and physical chemistry, dealing with the size of a single nucleus. So, the interplay between the two is muddied even further. Which is better? Neither. What's the difference? No idea. It may be the reason Chemistry is given the definition of "The Study of Change" -- it's hard to distinguish what's really different between the two, when we both deal with the physical world at a basic level, sometimes modeled as single points, sometimes billions of points, sometimes a beaker of chemicals, sometimes a ball of mass. In essence, they're really the same: It's the approach that is different. The chemist's explanation can stop at the point we relate a phenomena to an element or compounds composition of elements. The physicist's explanation stops at the point where they have a general rule that can be applied to anything in the universe. Beyond that -- well, I'm still figuring it out.

Dembski's Argument for Intelligent Design

2009-04-17T14:42:00.001-07:00

This is a little off-topical from what I want to blog about, as it relates to biology, but I recently read Dembski's paper "Intelligent Design as a Theory of Information". It's an older paper (1998), but it attempts to justify Intelligent Design as a proper scientific theory of biology. Now, I am no biologist -- I have a general working knowledge of biology, but far from in depth -- but I am a scientist (in training), and have a more firm, if not complete, grasp of science, the scientific method, and the philosophy behind science, and my critique of Dembski's paper relies on these concepts.

I don't expect everyone to read the entire paper, but the critique makes more sense if you're at least passingly familiar with it. As such, I present the abstract here:

For the scientific community intelligent design represents creationism's latest grasp at scientific legitimacy. Accordingly, intelligent design is viewed as yet another ill-conceived attempt by creationists to straightjacket science within a religious ideology. But in fact intelligent design can be formulated as a scientific theory having empirical consequences and devoid of religious commitments. Intelligent design can be unpacked as a theory of information. Within such a theory, information becomes a reliable indicator of design as well as a proper object for scientific investigation. In my paper I shall (1) show how information can be reliably detected and measured, and (2) formulate a conservation law that governs the origin and flow of information. My broad conclusion is that information is not reducible to natural causes, and that the origin of information is best sought in intelligent causes. Intelligent design thereby becomes a theory for detecting and measuring information, explaining its origin, and tracing its flow.

Dembski is essentially setting out to scientifically prove two points, all the while using those two points to "Science-ify" ID.

Next Dembski defines information as "...the actualization of an event to the exclusion of other events". He compares this to the common sense definition, namely, that information is "the transmission of signals across a communication channel". He references two philosophers whose work, related to this paper, is in the philosophy of the mind. And, yes: The mind, when presented with information, has to tune out of the majority of the massive amount of information being presented to it by the senses in order to properly function and focus. At the end of this section, Dembski states:

"Information needs to [be] referenced not just to the actual world, but also cross-referenced with all possible worlds."

He builds to this subtly, all the while making, more or less, low-key insightful definitions of what information is, and what we may need to consider when considering how information behaves. But this is the first statement that bespeaks the nature of Dembski's argument; it is philosophical, not scientific. Namely, the reference to all possible worlds, as concieved in Anslem's ontological argument for the existence of God, is in no way scientific, or even related to science. No matter what may have happened in our world, one core assumption in science is that the natural universe is deterministic: the entire natural world follows laws, and those laws are immutable. We may not know, exactly, what those laws are, but that doesn't change the laws' status with regards to existence. In addition, just because we have a model of probability, that does not change the determinist assumption core to scientific inquiry. For example: The Heisenberg Uncertainty Principle states that we can never know both the location and momentum of an electron, and the quantum model of the atom relies upon the idea that an electron exists in more than one location at one time, and uses probability to describe how likely an electron will be at one location at a certain time. That does not change the idea of the universe being deterministic. These are models of the physical world -- a statement of "is", a model attempting to understand an absolute certainty of how probable the electron will be present at a certain location, and the ability to predict how the atom will behave based upon that probability. It's still determinist -- it's just unfamiliar to how we usually think of determinism. Secondly, in the grand metaphysical sense there are other possible worlds: But there is no way of understanding those worlds, no matter how close they relate to ours, in a scientific way. Science delves into the natural world, and the natural world only. The natural world is the one we live in, the one where the things that happen in the realm of our senses is the only one we study. Even in a possible world where, everything else being the same as ours, a quarter flipped a year ago lands heads up instead of tails up is a world that science does not and can not understand, as we have no way to sense that world.

The next two sections of the paper delve into more definitions that are attempting to link information theory to the study of biology. First, Dembski derives a method of measuring information, as measurements are necessary to science. He uses the analogy of a deck of cards and poker hands. His example states two possibilities: a royal flush, and all other possible hands. He then goes through some probability mathematics and applies information theory concepts to show that there is more information in knowing that we obtained a royal flush than there is in knowing we obtained one of the other possibilities. The argument follows. Intuitively, if you have a hand of "one of every other possibility", there are any number of hands you could possibly have, while the specifications of "Royal Flush" require exact cards, so you actually have more information by knowing you have a royal flush as opposed to a set consisting of several possibilites. There is also a definition integral to his argument, namely, "Complex Information". Complex information is information similar to the Royal Flush -- it has a larger magnitude of information than "Simple Information", and that complexity indicates some sort of correlation between possible events. Dembski states at the end of the first section:

This notion of complexity is important to biology since not just the origin of information stands in question, but the origin of complex information.

He has yet to establish the connection between complex information and the study of biology. Earlier in the paper, he quotes the honorable Biophysical Chemist Manfred Eigen (Who is a Grade A scientific bad ass):

In Steps Towards Life Manfred Eigen (1992, p. 12) identifies what he regards as the central problem facing origins-of-life research: "Our task is to find an algorithm, a natural law that leads to the origin of information." Eigen is only half right. To determine how life began, it is indeed necessary to understand the origin of information. Even so, neither algorithms nor natural laws are capable of producing information.

But that still doesn't establish the link between information theory and biology. Also note that Steps Towards Life is a popular science book which, while probably insightful, can easily be taken out of context. In addition, it is the opinion of a man that, while blazingly brilliant, can still be wrong, and also has not established the link between information and biology, scientifically speaking. I don't mean to demean Manfred Eigen in any way with this -- but, that's the process. Opinions are wonderful to debate in a philosophical sense, and can often inspire people in many ways, both scientifically and otherwise, but opinion does not equate to science.

The next portion distinguishes between "Specified Complex Information" and "Unspecified Complex Information". He uses the example of an archer shooting at a wall so large that he can not miss, but gives two pertinant scenarios: One in which the archer paints the target before he shoots and hits a bulls eye, and one in which the archer paints a target after the arrow hits the wall and makes it look like a bulls eye. He covers some other possibilities, but essentially, the scenario where the archer shoots the arrow and then hits a bulls eye is equatable to "Specified Complex Information", and it is the type of information that can lead us to scientifically understand that the archer is a good archer.

Dembski then continues by generalizing the above scenario: Basically, that patterns established before they are tested, but then verified by tests, are the type of patterns one knows to be linked to causality. The patterns established after having witnessing an event may be causally related, but they may also be fabrications, similar to the scenario with the archer painting a target around his arrow. He then compares this generalization to the study of life, as life obviously can't formulate a hypothesis about itself before it exists. In this paragraph, he states:

But what about the origin of life? Is life specified? If so, to what patterns does life correspond, and how are these patterns given independently of life's origin?

Which needs more clarification as to what exactly he's asking for. How is it conceivable to separate the patterns of life from their origin, and why is that necessary? Dembski seems to be critiquing all of scientific inquiry here because it is formulated a posteriori -- but that's what all scientific inquiry is based upon. It is only through experience that we gain ideas of how the world works, then through experimenting with those ideas that we confirm that they are, indeed, good scientific ideas. Newton was inspired by the movement of planets. Dalton was inspired by the formation of storms. While a fair amount of theoretical reasoning has to go into science, theory is nothing without experimentation -- which Dembski acknowledges, but he's rejecting the thought of basing theory upon experience on the sole basis that then the theory is more likely to be favored. It's a great question to pose, for the philosopher of science, but it is this subjectivity that the scientific method attempts to overcome. Bringing up a difficulty in performing scientific inquiry to critique a theory derived from performing that scientific inquiry is, still, not scientific, but philosophical. Dembski is free to reject the confines of the scientific method, but if he does so, he can not then claim to have a scientific theory, as he did not reach that theory through the process of science.

The next paragraph, which I will quote in full, is where Dembski argues for the link between information theory and biology, as well as science in general:

Information can be specified. Information can be complex. Information can be both complex and specified. Information that is both complex and specified I call "complex specified information," or CSI for short. CSI is what all the fuss over information has been about in recent years, not just in biology, but in science generally. It is CSI that for Manfred Eigen constitutes the great mystery of biology, and one he hopes eventually to unravel in terms of algorithms and natural laws. It is CSI that for cosmologists underlies the fine-tuning of the universe, and which the various anthropic principles attempt to understand (cf. Barrow and Tipler, 1986). It is CSI that David Bohm's quantum potentials are extracting when they scour the microworld for what Bohm calls "active information" (cf. Bohm, 1993, pp. 35-38). It is CSI that enables Maxwell's demon to outsmart a thermodynamic system tending towards thermal equilibrium (cf. Landauer, 1991, p. 26). It is CSI on which David Chalmers hopes to base a comprehensive theory of human consciousness (cf. Chalmers, 1996, ch. 8). It is CSI that within the Kolmogorov-Chaitin theory of algorithmic information takes the form of highly compressible, non-random strings of digits (cf. Kolmogorov, 1965; Chaitin, 1966).

So, essentially, Dembski is claiming that all science can be modeled by information theory. But he has no scientific basis for this -- only a philosophical argument, which, again, is not science. It's true that science deals with information, mathematical models, and computer programs to better understand the world. But that still does not establish a direct scientific connection between information theory and all other areas of science. Furthermore, if a scientific connection were established between information theory and, suppose, just biology, then unless there was a reason to reject the theory of evolution and replace it with information theory, then information theory's model of biology would conform to the model of evolution. By analogy, we don't have a sub-atomic particle model of how an animal behaves at the moment, but unless evolution were somehow disproven, then the sub-atomic model of population shifts would conform to the evolutionary model.

What Dembski claims is that information theory is superior to all other sciences, and thereby claiming that any law formulated in information theory will trump all other scientific laws. This, also, goes against a basic philosophy of science concept: Theories are not proven, only disproven. Unless we have a reason to reject a scientific theory, we continue working with it. There is no superior science -- the natural world is deterministic, we study the natural world, so all conclusions, no matter what facet of that natural world we study, will, in the end, match each other. In science, one does not see all the theories before them, and then start a new theory that needs to be worked out. The scientific world would forever be reformulating ideas and starting the work of Newton over again if that were the case. One builds upon the ideas that have so far shown to be good scientific ideas. One is right to question assumptions or ideas that have come before them, but if there is not scientific evidence, or, essentially, a reason to reject those ideas, then those ideas are assumed to be correct for the purposes of building a body of knowledge related to the natural world.

The next section is titled "Intelligent Design". Here, Dembski states:

In this section I shall argue that intelligent causation, or equivalently design, accounts for the origin of complex specified information.

He continues to describe how a psychologist determines whether or not a rat has learned how to navigate a maze. The maze must be complex, in order to eliminate the chance of the rat solving the maze by shear luck, and the rat then must demonstrate that it has memorized the series of turns it takes to get to the other end of the maze. This is a method for determining if the rat has learned, and thereby, demonstrate that it has made an intelligent choice. There is also an analogy drawn to the difference between writing a sentence, and spilling a bottle of ink on paper. In one case, someone directs the pen, in the other, the ink randomly spills out. For further clarification, Dembski also references a story about an American listening to someone speak Chinese: There is design, but it is incomprehensible to the American, simply because he lacks the knowledge of the Chinese language. But this does not stop it from being an Intelligent choice. Then Dembski states:

The actualization of one among several competing possibilities, the exclusion of the rest, and the specification of the possibility that was actualized encapsulates how we recognize intelligent causes, or equivalently, how we detect design. Actualization-Exclusion-Specification, this triad constitutes a general criterion for detecting intelligence, be it animal, human, or extra-terrestrial. Actualization establishes that the possibility in question is the one that actually occurred. Exclusion establishes that there was genuine contingency (i.e., that there were other live possibilities, and that these were ruled out). Specification establishes that the actualized possibility conforms to a pattern given independently of its actualization.

Dembski then states that this pattern for recognizing intelligent causation exactly matches up to the criteria for recognizing CSI. Implicitly, because of Dembski's claim to linking CSI to to all of science, and because the confirmation of CSI follows exactly how psychologists confirm that an acting being intelligently makes a choice, it follows that then what science studies, CSI, is generated from an intelligent cause.

The problem with this argument is that he has not properly established a link between CSI and all other science. Further, he has not established even a philosophical argument for the link between a psychologist determining whether a mouse has learned, and the determination of CSI. Technically, if the confirmation of CSI were grounded in scientific inquiry, then it's painstakingly obvious that it would follow the same pattern that a psychologist uses to determine if a mouse has learned a maze: They'd both be scientific. In addition, just because a process can be formulated in such a way that they are seemingly the same, does not mean they pertain to the same things -- in one example, a psychologist determines how a mouse learns, and attempts to generalize those findings to other mice and, ultimately, other animals. This has nothing to do with an intelligent causation to explain the existence of life, and everything to do with how animals learn. Dembski fails to establish a philosophical bridge, as well as a scientific one, from mouse to, essentially, God. So, his conclusion does not follow from his premises, a textbook non sequitur error.

Further, the first statement demonstrates how this argument is not a scientific one: That intelligent causation accounts for CSI. Even if his argument had followed, it would not matter. One can rationalize a good many things with complete validity, and still be wrong. An argument can have validity, but no experimental support. Here Dembski presents an a priori rationalization for an intelligent causation to the origins of life. Even had it validity, it would not have experimental support, which is essential to the process of science.

The final paragraph outlines Dembski's postulated Conservation Law. In it, he critique's Eigen for attributing the origin of CSI to natural causes, because, in his opinion it can not be explained by natural causes. He then claims, because he has proposed a law of conservation, that information theory as applied to biology is a scientific theory. He continues to argue that pure chance -- the type of randomness proposed by Epicurus, where the universe follows no law other than randomness -- can not account for CSI. He continues to argue that neither can a Darwinian approach account for the existence of CSI (and, hence, life) because Darwin's theory only deals with how life changes over time, not how it was initially generated. Finally, because of this, Dembski concludes that natural causes can not account for the existence of CSI, and goes on to expound upon the implications this holds for scientific inquiry. Namely, in analyzing the origins of CSI, Dembski uses a systems-surroundings model, defines his system as the natural universe, which contains CSI that can neither be generated or destroyed. Because CSI can neither be generated or destroyed, it must have come from somewhere which, in Dembski's view, is the surroundings: The intelligent causation.

This parellels both Paley's watchmaker argument, as well as Aquinas' first cause argument for the existence of God. I, personally, disagree with both arguments, but that is irrelevant. What is relevant is that Dembski continues to make a priori rationalizations for the existence of an intelligent cause, all the while claiming that his argument is a scientific one. This is patently false. There is no method, there is no experiment, there is only suppositions. As beautiful as philosophy is to study, masking it as science because you disagree with the conclusions of science is not science. The fact that Dembski spends roughly half the paper talking about probability mathematics and another third of the paper referencing basic psychology and some concepts related to information theory does not change the fact that Dembski is, essentially, making an ontological argument for the existence of an intelligent designer. Dembski demonstrates this when he claims that the origin of life can not be explained through natural causes, as science only deals with natural causes.

Also, I want to briefly address a philosophical point: Namely, the social implication that science and religion are somehow at odds. I claim that they are in no way related. As I critique Dembski for attempting to apply the scientific method to the existence of God, I similarly critique Dawkins. Not that this necessarily bolsters my argument, I'm only claiming consistency. God is a metaphysical question. Science is an epistemic method to understanding the natural world, and only the natural world. God, by most definitions, is somehow outside the natural world. Therefore, science can say nothing about God, or, as Dembski puts it, an intelligent designer. If God is, by definition, the natural world, then and only then can science interpret God, and those conclusions will be unaltered by this Spinozan derived definition of God.

Because science has nothing to do with God, you can go on believing whatever it is you will with regards to God no matter the conclusions of science. Just realize that making claims about the natural world because of supernatural reasons, such as dating the world 6000 years old because of biblical record, will not be taken seriously by anyone who accepts the scientific method. After all, as the scientific method has nothing to say about God, God has nothing to say about the natural world, aside, possibly, as an a priori rationalization for the existence of it.

Basically, I'm just stating that questions of science and questions of God mix like oil and water. It is your personal conviction that determines their relative densities.

Approximations of Truth

2009-04-15T19:56:00.000-07:00

The question of how to know Truth is a fundamental question of philosophy. Truth with a capital T has been debated and sought after by every philosopher pretty much ever. In everyday life we do this too. The joke, "I saw it on TV, it must be true!", or simply asking how somebody knows what they're talking about. In arguing politics, God, or various other uncouth dinner conversations we'll reference a class, a life experience, a book we read. We'll talk about how we were raised, what's acceptable, and why it's acceptable. This is the every day man's search for Truth, and it's similar to any philosopher's search for Truth, it's just not published (though I don't want to denigrate the expertise of those who study philosophy -- I just think we, on a day-to-day basis, loose contact with the fact that we're essentially answering the same questions, only in different ways, and possibly at different levels of understanding).

So, how do we know Truth? That is the spawn of a lengthy discussion and inner dialogue, one in which I am still looking for. However, there is a misconception about science that I think is very important to understanding it -- that science is truth. Or, more importantly, the misconception that scientists think science is truth, but the rest of the world knows it's just science. So, without further ado, here's a quick run-down of what I think of the interplay between science and truth.

1) "Just" Science

To be clear, I am not speaking out against the scientific method in the least. It is, in my opinion, the most surefire epistemic method for understanding the natural world. There are a few assumptions made in scientific inquiry, but that's alright -- we need to make assumptions in order to come closer to truth. In the days of Euclid, mathematicians were trying to go about proving everything, and it was he who said, "Fuck proving that lines are straight -- they just are" (roughly). He said a number of other things related to geometry, but aside from his enormous contribution to mathematics, he also made an enormous contribution to logic: Not everything can be proven. In fact, one has to accept certain propositions in order to move on and build. That's what science does -- makes a few assumptions that really are not terribly controversial, and builds a knowledge of the natural world using them.

EDIT: I need to admit a mistake. Aristotle actually points out that one needs to start from some point in order to build a system, and he is dated older than Euclid. I'm not sure if any Pre-Socratics pointed this out, as well, but this at least pushes the date further back, and as Aristotle is the first person to give a strictly formal account of logic, it wouldn't be surprising if he's the first to point out this feature.

2) Science, and truth

So, we gain a knowledge of the natural world. But what exactly does this knowledge entail? How do we KNOW (in uber-skeptic parlance) that what we deduce in scientific inquiry is true? Well, strictly speaking, we don't. Science proves nothing. Technically, science only disproves things. The fact remains that, even given that we discover everything in the universe, we will not know if we have discovered everything in the universe. There can always be something else -- it's how science grows. We notice something, and attempt to come up with a reasonable explanation and description of that something. We test that description, and if everything matches up, declare that our description is good. The problem is, this is not always the case. It was probably a good description. Maybe there were some implicit assumptions in our description we didn't realize. Maybe we hadn't encountered a certain element just yet, due to our inability to detect a more subtle feature of the world, or due to that elements scarcity. So, while scientific inquiry deduces good explanations of the natural world, they are not the capital "T" Truth truths that we know, in an absolute sense, are true. They're just damn good approximations of Truth.

3) The limitation of truth in the natural world

So, what're we to do? Well, science is about it, when it comes to the natural world. Unless you're taking up the philosophical banner of absolute relativism, or have recently been convinced of Epicurus' physics, the natural world follows laws (again, rough). Our formulation of those laws may be off, but that doesn't change them existing. We, human beings, are not naturally in tune to these laws, can not deduce them from pure thought, and need to test the universe to understand them.

4) So, how do we find Truth?

Good question! It's one I think about myself. Supposedly, you could reach truth if you have a valid argument and all of the propositions in it are true. But there's no way of telling if your propositions are true. It's intuitive. It's subjective. And as Truth doesn't change (well, I guess that depends on who you ask), but we change all the time, we could know truth and not know that we knew it, and change again in pursuit of the elusive ends of our questioning. It's actually what Plato talks about in his "Symposium" -- it is the lot of the philosopher, the lover of wisdom (and therefore truth) to love and pursue wisdom, but he can never know it, only search.

So, in closing, while the scientific method shouldn't be applied to all areas of life -- that'd be mildly rediculous -- I think settling for approximations of truth ain't too bad a deal.

Just What is Chemistry Anyway?

2009-04-13T18:04:00.000-07:00

I realize maybe I got a little ahead of myself -- I should start simple, and actually, this is a question with an answer that bugs me.

My first day of freshman chemistry, chemistry was defined as "The study of change". It didn't make much sense to me at the time. I thought chemistry was about elements, beakers, drugs, and explosives. Not that I started studying chemistry for these reasons, that's just what came to mind. So, when defining chemistry, I expected "The study of the elements" or "The study of chemicals" -- but "The study of change"? Not at all.

Now I think I'm beginning to glimpse the reason for this definition. In the first semester, we dealt with chemical reactions like sodium hydroxide with water, which dissolves and heats the water -- a temperature change. We saw liquids combine to form solids -- a phase change. We observed as pink indicator disappeared in a beaker, indicating how acidic our solution was -- a color change. In essence, everything in chemistry can be related back to directly observing changes.

Still, isn't that what all science is about? A block changes position, but its physics. A group of flies change genes, but that's biology. We come up with explanations for change all the time -- so why does chemistry get labeled "The Study of Change"?

It bugs me. I don't think that the description really elucidates what students are about to study, and even after a fair amount of core material, I sit mildly perplexed. So why give a definition like this? I think I'd much prefer something along the lines of "Chemistry is the study of atoms". It's frank, direct, and while a bit boring, honest. While chemistry no longer claims to look at the fundamental pieces of the universe, that does not really matter. We study atoms. We study how they interact with one another, and while that is not the fundamental makings of our world, everything is still made of them, and understanding how they interact is understanding our universe. Just in a different way than, say, the general theory of relativity.

Still, boring definitions are not a great way to start off a class. You want to inspire wonder, awe, and excitement for the things to come, as well as engage minds to start thinking about the subject matter. Saying "Chemistry is the study of atoms" doesn't exactly teach very many people anything new. So, I offer an alternate definition:

Chemistry is the study of how a massive number of minuscule particles interact on the atomic level and what effect that has in our everyday world.

Maybe a bit cloggy, but still better than "We're gonna talk about atoms, which originated from the mind of Democritus, but Aristotle blahblahblah..." Alright, I'm hamming it up, but still: There has to be something that actually describes what we're going to talk about in terms that people can understand, while simultaneously not bringing it down to a level where people don't grow as students. That's the great challenge of teaching: We must become experts in a field, understand it, and then be able to to inspire how we constructed these ideas from the bottom up in a group of individuals with differing minds and perspectives. So, while I won't say my definition is the best, I will say it's gotta be better than "Change" and "Atoms".

Lego's, the building blocks of life

2009-04-10T17:28:00.001-07:00

Organic chemistry is the study of carbon chemistry. The term "Organic" is a hold over from way back in the 1800's when it was believed that the molecules of life could only come from life -- a sort of distinction between the matter of inanimate objects and the matter of living beings. This isn't too far off: In fact, Carbon behaves in ways that no other element does. So much different, in fact, that it and water are considered necessities when searching for life. The main reason Carbon is thought necessary for life is that it is the only element that can form exceptionally long chains -- up to millions of atoms in a single molecule! The molecule closest to it in chemical nature is Silicon, and the longest chain of silicon is roughly around 10 Silicon atoms long. However, the distinction is untrue. It was disproven when a chemist by the name of Wohler (that "o" is actually an omlaut) created a compound known as Urea from ammonium and cyanic acid. Urea was a well known compound in Wohler's time that originated from mammalian urine (hence urea), but both ammonium and cyanic acid were classified as inorganic compounds, essentially showing that organic matter can originate from inorganic.

When studying organic chemistry, there is an analogy I like to employ. That analogy is Legos. I played with Legos as a kid quite a bit. And it's funny, but Legos, made of Carbon, create a great analogy for Carbon and all of the elements involved in the chemistry of Carbon. When studying organic chemistry, we classify different combinations of elements into "functional groups". When certain elements are bonded to other elements in a certain pattern, they exhibit similar traits -- observable chemical traits. They interact with each other in certain ways, break off, form new bonds, and become new compounds. Essentially, each group is like a Lego: You have small, stout blocks that build the basis for many Lego structures -- the Carbon atoms of Legoland -- and you have long blocks, similar to long "R" carbon chains ("R" just denotes "Carbon chain"). You have specialized blocks that can only fit in certain places, like the cannons, or the flags and flag poles, or the little switches. These are similar to the other functional groups in organic chemistry: They all behave in a certain way (due to their chemical make up) and can only attach to other groups because of their behavior (Think of the castle gates: Feasibly, they can serve as gates, or grates on the ground, but they aren't very good rockets for your space Lego sets).

Carbon chemistry, in this sense, is just playing with Legos. Except, with chemistry, you can't use your hands to pick a block off and re-stick it somewhere. The building blocks are too small. You have to figure out ways to interact with the building blocks without picking them up and putting where you want them: And this is where reaction mechanisms come in. Mechanisms, as a whole, are a step-by-step diagram of what occurs on the chemical level during the process of a chemical reaction. You show where electrons move from and to, what charges various elements have (which can attract or repel electrons), and which elements attach to other elements. The electrons in carbon chemistry can be compared to the nubs on top of the blocks in Legoland -- they keep the blocks together. Armed with the knowledge of a given element or functional group's tendencies, you can pick apart carbon groups, reattach other functional groups, and end up with something entirely different. How that different thing behaves and how you get there depend on a lot of things -- more than I want to go into with this particular blog post -- but the basic analogy holds. You pick apart the blocks of life, and reattach those blocks to build a shape that, in Lego talk, may have started as a house, but is now an attack helicoptor.

Tropic Thunder and the Inevitability of Physics

2009-04-08T20:10:00.000-07:00

In the movie “Tropic Thunder”, the character played by Tom Cruise makes a statement: “Speedman is a dying star. A white dwarf headed for a black hole. That's physics. It's inevitable.” He then proceeds to dance while his goofy yes-man also dances in the background while shoving money in the face of Speedman’s agent to get him to stop worrying about Speedman’s plight. It’s funny as hell. I laughed a considerable amount. However, in the back of my mind, I kept thinking “You're misrepresenting physics!!!” Maybe I’m taking too much from a blockbuster absurdist comedy, but I couldn’t help but think, “Maybe this is how people perceive physics. Maybe they think it’s inevitable, certain, and complete -- movies are a decent representation of mass cultural attitudes” So... is physics inevitable?

While a goal of physics is to predict what will happen in the physical world based upon observations of what the physical world has done so far, it is far from inevitable and complete. Physics, like all sciences, is based upon a unifying idea (or theory) supported by observations (empirical results). The results presented in classical physics have been confirmed time and again, but that does not mean that they are not subject to change.

Now, did Newton start with observation and then move to creating a system to explain those observations? I have no idea. In fact, it doesn’t matter. What does matter is that the theory is backed by observations.

Observations of what? Well, glad I could write in a format to force that question from you! Classical physics, and physics in general, is an exercise in constructing a system of understanding of the entire physical universe. Usually physics takes a “subtractive” approach – it tries to find a root cause for events. We could construct an understanding of the physical world by testing ideas that deal with, say, the chemical make-up of a substance. While that is important to physics, it’s not the end. Instead, it tries to see what all objects do (Though the cross-over between physics and chemistry is great, they’re still very different. More to come in future blog posts!).

So, to give a starting point, from general observations we can say that all objects seem to be subject to movement. They move from point A to point B. There isn’t a single object that doesn’t seem to do this. While it is possible that such an object exists, we have no reason to believe that it does, and if something doesn’t move, from our everyday experience, it’s usually because something is in its way, not because the object itself simply does not move by virtue of a characteristic internal to itself (something usually referred to as an “intrinsic” or “intensive property”).

So, all objects move, that’s terrific. But how? What causes an object to move? Well, this can be answered in several ways, but I think the simplest answer is “ a Force”. You may be familiar with the term from high school physics and Newton’s Second Law expressed mathematically: F = ma. But if not, the concept is fairly simple and associated with the normal definition: Force is something that pushes an object. You force a door open. You shove a box. You pull a rope. Gravity pulls you towards the ground. All of those are forces, and "Force" is just the general concept for anything such as that. You’ll notice that Force (the F) is defined here by two terms, m and a, defined as mass and acceleration respectively.

Well, no shit!, you say, of course objects move because of acceleration! Hold your horses, I ain't done. If we divide the equation by the “m” term, then we get

F = a
m

Now, to help with the explanation to come, I want to go over the classical physicist’s definition of mass:

Mass is the property internal to an object that resists changes in movement.

It's a different definition than what is normally used, namely because it's not as intuitive, nor does it really reference things we think about on a day to day basis. Normally, mass is explained simply as "Stuff", or "Matter". But there is a reason for this particular definition – because we’re dealing with movement of an object, we define mass in terms that includes only that object, instead of the “stuff” that an object might be made of. You’ll note, if we somehow had a way to quantify Force (and we do), that if we have a larger force then we’ll have a larger acceleration, because “Force“ is on top. Simultaneously, if we had a way to quantify mass (which we also do), then we’ll have a smaller acceleration. Intuitively speaking, this is because the object we’re dealing with is heavier. Think of shoving a basketball. Now think of shoving a bowling ball. Which seems harder to move? Which moves faster if you were to shove them both with the exact same amount of Force? Well, the basketball would accelerate more of course.

This brings us to another one of those stickler points that physics text-books get hung up on: “Acceleration”. In day-to-day speech, it’s actually a lot closer to the physics definition than its given credit, I think. But then, we usually don’t say “I wish that fucker in front of me would accelerate!”, it’s normally more like “Damnit, speed up!”, and that’s where the hang up occurs. Speed, in the jargon of the physicist, can be equated to velocity in some direction, and velocity is the measure of how much time it takes for an object to move from one place to another, or the measure of how far an object would go in a given amount of time if it were to continue going at the same speed in that direction (which is exactly what your speedometer measures). So, again back to the jargon, acceleration is a change in speed. In specific, it’s how much time it takes for you to change your speed from one velocity to another, which itself is just a measure of how fast it takes to get from point A to point B. Think of your speedometer, again. When you start to push the "Go" pedal, usually it only takes a few seconds to reach the "30 mph" mark, but it takes longer to go from "70 mph" to "80 mph" -- your acceleration is less than what it was, but your velocity is greater. This all relates back to the movement of objects -- in physics, we call this displacement -- And now we’re back to where we began: movement! Objects move. How? Force. A force changes an object’s acceleration, a measure of how fast an object changes its speed in some direction, which in turn is a measure of how fast an object goes from point A to point B. And now we have a simplistic sort of explanation that we can attempt to apply to all objects, because all objects move, and all objects have mass.

Now, back to Tropic Thunder and the inevitability of physics: This is a basic explanation of the concepts held in Newton’s Second Law, but it’s not comprehensive. While I’ve made an argument for an explanation to explain all objects, we have to go out and test the ideas. To do a test, we can’t just say “Yeah, looks pretty good”, we have to have measurements. This is an attempt at being objective. People are biased, especially when they develop ideas of their own, so while pure objectivity is impossible, a strong attempt can still be made. Usually, as physicists, we rely upon math to create rules. This allows us to find numbers that, if our original thought is true, should correspond to measurements that we’ll make during the experiment. It also removes a lot of interpretation from data. Now, numbers can be manipulated in a number of ways (pun intended), so as a physicist, you usually try to stick to the raw measurements as much as possible to give support to a mathematical expression of an observation. If those observations don’t match up to what you thought you'd get -- for example, if you push both a bowling ball and a basketaball with "1 Force", and you measured their masses beforehand, you would be able to find what acceleration you should get, but then find that their accelerations are totally different from what you predicted -- then the experiment wins out. The theory (or law, or hypothesis, or whatever) is bunk. The end. Game over. Back to the drawing board. Try something new.

And that’s why the line in Tropic Thunder kind of bugs me – physics is one of the oldest sciences (at least as we currently understand the term "science"), and classical Newtonian Mechanics have a metric-fuck ton (This really should be an SI unit) of experimental support, but that still doesn’t mean “It’s Inevitable”. It means, up to this point, under the assumptions made by Newtonian physics (namely the three laws), our experiments have matched up to the theory. Simultaneously, this doesn’t mean you can just throw out all the experiments that have been collected and start from scratch – that would similarly be neglecting the experimental side of physics (as well as the idea that we usually build upon previous findings, rather than start over) – but it does mean that physics is confirmed by experiment, and is therefore subject to change if further experimentation reveals a flaw in the theory.

I think this point is missed mostly because in class it’s a lot easier to grade tests where there’s a numerical answer at the end. In addition, it’s easier to write tests that require you to apply theory. It’s also easier to teach to a test written in this manner rather than teaching about the thought that goes behind science. Plus, theory is important to understand and implement, so it's not bad to have these skills. But science is not that simple. And I find it rather sad that “Physics” is inevitable, but “Biology”, a science applying the same epistemic principles as physics, is held in contention for its fundamental theories. But, that is the subject of a blog for another day! This one’s already long winded enough.

PS: I say this is a simplistic explanation, because, well... it's simplified – some questions you may have asked during this explanation might include “Where does Force come from?”, “What happens when objects hit each other?”, and “How does that equation explain objects moving in more than one direction?” – and those are great questions to ask. Keep up the inquiry! Personally, I recommend taking a class because nothing can replace a teacher, but you can usually find a cheap physics text book, or check one out from your local library, or find other information on physics on the internet -- or, if you're feeling really daring, you could set up an experiment.

Experimental Error

2009-04-03T17:21:00.000-07:00

There is a phrase I come across in grading papers -- a phrase that is misunderstood and used incorrectly by undergraduates everywhere. I know this because I, too, misused this phrase to magically explain away all faults. That phrase is "Experimental Error". A faulty R squared value here, an unexpected color there, a strange vapor developing, an abysmal percent yield: All an encapsulated in a simple syllogism:

1. My experiment should do "X"
2. My experiment did not do "X"
3. Therefore, experimental error strikes again!

I don't know why we, as undergraduates, grasp onto this phrase. Perhaps it's because it seems simple -- after all, we're introduced to science handed down to us by the hands of Newton, et al., as an algorithm for answering multiple choice questions.

This is an entirely understandable stance.

Before studying science in college, scientists worked with equations, and said strange things. Incomprehensible to myself, I accepted that they knew what they were talking about, and I would have to be content with understanding the depth of life from the perspective of a book-ish layman. After all, while they understood what they were talking about, how could they possibly know how to live? They clam up inside of labs with white coats discussing BORING subjects, unlocking the secrets of super-technology and miracle drugs. Who wants to do that?

Well, now I dream of getting into research, but that's not what I'm trying to drive at. The point I'm trying to make is: This is not what science is. If Newton had applied the above syllogism to the problems of physics, he could have, essentially, concluded anything he wanted and explained that the dastardly villain "Experimental Error" had again interrupted the proper data from corresponding to his explanations!

So, briefly, I want to clarify: Experimental Error is not a human characteristic. Usually, when using experimental error to explain results, students will mention the weighing of reagents, or spilling liquids. This generates a great mental image for me: Students, rushing about full of frenzy, jittering with the excitement of discovery, they forget how to hold containers, how to read balances and spill chemicals (usually acids, or volatile organics) on counter tops, their notebooks, themselves!!! Someone forgot to mention they were using ether, they light a bunsen burner, and the entire class ignites into a conflageration of epistimic glory!

It's not this exciting in the lab, but the mental image picks me up in the middle of a the dry task of grading.

So, if not that, as witnessed by the sallow looks of entertainment deprived Freshmen, what? What is experimental error? Well, to try a simple definition: Experimental error is error we can not control due to the nature of experimentation. Now what the fuck does that mean? What can't we control? Well, it's not something I really grasped for a long time, and I think it's a difficult concept to grasp unto itself -- but suppose you're in the market for buying your first car. Not just a junker to get you by, but actually buying a car that you'll drive for awhile. It's a big purchase, and there are a lot of options out there. So, what do you do? You read what you can on types of cars, different brands, different models, different years. You look up the Kelly Blue Book value. You check the newspaper daily. You look at dealership prices. In general, you get a feel for what is already there from people who know what they're talking about, and then you take some cars for a spin. You get a feeling for what you like, you listen to the engine, and eventually, based upon what you've read about and what you've experienced, you make a purchase. The experimental error, in this situation, would be everything you didn't know about, everything you couldn't cover, due to your position as a fresh consumer -- maybe the car you bought has bad wiring, but nothing went wrong when test driving it. Maybe there was a better deal across town on the exact same car, but you didn't see it. That isn't exactly experimental error, but it's getting at it: It's something, because you are not all knowing and can't take every measurement ever conceived of everything, you just can't help. You eventually just make a jump: It's an educated jump, based upon current knowledge and experience, but a jump none-the-less, and then you find out, later on, if you made a good jump or not.

This isn't, in the strictest sense, what the scientific method is all about. There's a lot more to it, some of which I'm still trying to comprehend. But this, a common experience in most people's lives (eventually, anyways), is closer to the scientific method than the undergraduate rationalization of experimental error -- and we're supposed to be studying this stuff!

So why, exactly, do we formulate science this way? I could raise awareness of the inadequacies of our educational system, but that's about as vague and useless as fortune cookie advice. I don't have the answer to the question, it's a question for you, the reader! to think about. I know I will be.

Also, I want to introduce myself as a new blogger: I am a chemistry undergraduate minoring in physics at a small liberal arts college. I want to make particular emphasis about that -- the undergraduate status, not the liberal arts college -- because I am in no way an authority on the subjects I want to blog about. I am fresh, new, thinking, formulating, and quite possibly wrong in all instances. But I do put forth a good amount of effort into understanding what I'm talking about before I start talking about it, so everything I write will be in good faith, at least. I work as a TA at my college for the introductory chemistry labs, and I find that if I explain what I'm learning I feel I understand what I'm learning more. I will update weekly/bi-weekly, and the subjects will include: Science! Chemistry! Physics! Philosophy of Science! Science Education! Popular Science! So tune in next week!