Placing Consciousness in a Biological Context

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.

The Central Dogma

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.

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.


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

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.