Tuesday, November 30, 2010


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.

Monday, November 29, 2010

Graduate School

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.

Thursday, November 25, 2010

Turkey-Day, 2010

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.

Sunday, November 21, 2010

Skepticon III

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

Wednesday, November 17, 2010

Points of Conflict in Evolution

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.


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.

Monday, November 15, 2010

Evolution, Science, and Politics

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.