A Good Idea Gone Bad? Part II

After a long delay (I kinda forgot about it in the midst of a crunch in the lab), here is the much awaited sequel to my discussion on evolution from the old blog.

Part I: Introduction, and Why (Micro)Evolution is Good Science

Part II: What Molecular Biology Tells Us about Macroevolution, and How This is Compatible with Orthodox Christianity

It’s a rather big temptation to start writing about things I don’t know all that well in order to make a point, but I’m afraid I would not make much sense in the end. So, I’m going to leave any discussion of the fossil record, speciation, and other such things to the experts. An excellent book on the subject, by a professing Christian and Cambridge University professor of paleontology, is Life’s Solution by Simon Conway Morris. That said, I’m going to delve into something more comfortable: molecular biology.

Up to this point, I’ve argued that “microevolution”–that is, subtle changes within a species, especially in unicellular ones–occurs, and there is little controversy on that point. But, I deliberately left out “macroevolution,” or the evolution of different species from one another. It’s quite a bit harder to discuss scientifically, in my opinion, because it is limited to analysis of historical events. We can only, for the most part, examine things that have already taken place, presumably on a time scale that would exclude experimental science. The fossil record is one place to look, but I’d say that the genomic DNA sequence within each of our cells and those of all other living organisms on Earth tells a much more compelling tale.

Before getting into details about how this affects my view of evolution, it might be useful to get some terminology and basic assumptions out of the way first. Much of what I’ll be dealing with has to do with DNA and protein sequences. For those unfamiliar with molecular biology, DNA is the “code” contained within each of our cells that contains instructions for producing everything in the cell, made up of a linear combination of four different units (chemicals abbreviated as A, G, C, and T). It is read by specialized machinery into proteins, which are made up of a series of units called amino acids, each of which is coded for by a specific three-unit sequence of DNA (TGG produces the amino acid tryptophan (otherwise known as W), TTT produces phenylalanine, etc, etc). Proteins are the workhorses of our bodies, doing every function imaginable. Changes in DNA sequence will, obviously, cause changes in protein sequence, which may cause changes in the function of any given protein. There is redundancy in the “genetic code”–there are only 20 amino acids but 64 possible combinations of three DNA “letters”, so changes in DNA may not cause protein changes (and, in fact, the code is so well optimized that the more likely “errors” in DNA are less likely to cause protein changes). So, we have an elegant system in place to produce the machinery our body needs from a simple code, with a minimum of errors.

However, those errors do happen, on average three errors every time your genome is replicated by your cells (3 billion units of DNA per human genome, 1 error per billion units). Just the natural process of DNA replication is not 100% accurate, due to any number of different factors. Add in the damage that DNA takes from things like ultraviolet radiation and chemicals in our food, and there’s a very good chance that your cells are accumulating changes in their DNA. Of course, we have defense mechanisms against changes in DNA that are dangerous–these cells usually end up in a sort of programmed cellular suicide. But, even with all the defense mechanisms, changes in the DNA do happen. This can and does lead to cancer, but if it happens in the cells that will pass on genetic material to the next generation, it can also lead to inherited differences. Most of these changes will be completely insignificant, and of the rest, almost all will be damaging or deadly. But, there can be beneficial mutations in DNA. Antibiotic-resistant bacteria prove that to be the case, and there is no reason why we humans can’t have had beneficial mutations as well.

It is a basic assumption of evolutionary biology that if you compare DNA sequences between different organisms, the differences are a result of changes over a long time scale. Another fundamental assumption is that DNA sequences that are more similar are more closely related to each other. Now, I will readily grant that on the surface, the same data could be used to fit another model: one whereby God created each species one by one, and reused the same “parts” to varying degrees, depending on how similar each species was to each other. But, I think the other explanation–one using “Darwinian” assumptions–makes even more sense, and actually leaves us with an explanation even more affirming of God’s awesome power.

So, given this, let’s explore in a little more depth what DNA and protein sequences can reveal about “macroevolution.” If evolutionary assumptions are true, one prediction is that critically important proteins are most closely “conserved” over time, because any change within them would be deadly to the cell. One such function which is common to all “eukaryotes,” that is, organisms like us that have compartments called nuclei, is compacting several feet of DNA into a manageable size for protection, storage, and efficient use. Small proteins called histones perform this feat, and they are essentially unchanged from the smallest unicellular yeast to humans. But, if you look carefully at the genetic sequence, there are subtle variations. These variations are more pronounced from humans to yeast than from humans to, say, mice, and the differential variations can be used to calculate a “phylogenetic tree” of relationships between different organisms. But, histones are so similar that these differences are hard to see.

Other proteins that have multiple modules linked by regions that are just structural, not important for their actual function, can provide even more information. The proteins that I am most familiar with** have important parts on each end of their structure, but the middle of them is just a sort of scaffold holding the ends together. Common sense dictates that the scaffold could be made of any number of protein sequences as long as it remains the same size, shape, and rigidity, while the end regions that must interact with other specific proteins are much more restricted. That’s what I find if I look at these proteins in yeast, flies, mice, and humans. It’s immediately obvious that the central scaffold region is very different in these four, while the end regions are much more similar. A collaborator of mine actually made a single change in one protein based on looking at a region that was the same from yeast to humans, and found, exactly as he predicted, that it was critical for interacting with another protein. Regions nearby that were very different from organism to organism, when changed, had no effect. This only makes sense from a Darwinian perspective: over eons, genetic changes frequently accumulated in the regions of my proteins that aren’t all that important for their function, but because such changes were often damaging to the function of the critical regions, they weren’t preserved there nearly as often.

The material evidence in the case of protein and DNA sequence is utterly consistent with evolution. There are enough examples to fill hundreds of pages, but I hope two vague ones will suffice. Small proteins critical for “housekeeping functions” of all cells are nearly identical in all organisms, while bigger proteins that have multiple interactions and functions differ from species to species in fascinating ways. I find it a much simpler and more elegant explanation that God used evolutionary processes to create the myriad of living forms on the Earth, than that he made each of these proteins and organisms one by one. The minute details admit the former explanation much more readily than the latter.

But all this does not by any means rule out purpose. Just because a process appears “random,” like accumulation of genetic changes due to the mechanics of DNA replication and environmental insults, does not mean that there is not some order to it. First of all, changes to DNA are only maintained from generation to generation if they are not deleterious and happen in the cells that will pass genetic material to progeny. This is not random by any means. But that pales in comparison with the utterly different notion that God might have a higher order plan for Creation. Evolutionary mechanisms may appear directionless to us, but our knowledge is limited.

No, evolution just provides a material mechanism by which God created. The evidence is there, both on the experimental end for “microevolution” of bacteria and viruses, and for “macroevolution” from historical data, from DNA and protein sequences to the fossil record. This scientific explanation can say nothing about why we are here, and to conclude that we have no “why” because scientists can’t discern it is every bit as metaphysical a statement as to say that God created heaven and earth. Evolution is not a bad idea; it’s just a good scientific idea that can be used to do bad metaphysics. That’s not a scientific problem.

** I am happy to provide excruciating detail by email if anyone is interested (which I doubt 😉 ), but I prefer to remain vague because if one were to search the literature for these particular proteins, my name would pop up in the list of manuscripts and it’d be feasible to link my scientific career to my religious views…not good for my job prospects…


2 Responses to “A Good Idea Gone Bad? Part II”

  1. 1 Bekah December 29, 2006 at 10:57 pm

    Thanks! I’ve been waiting for this. 🙂

  1. 1 A blast from the past « Mors dei Trackback on December 4, 2009 at 2:33 am

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