Monday, September 16, 2013

Genomic evidence for evolution

I'm going to quote and comment on this article:

Before commenting on the specifics, I'd like to make a general observation. Venema is a theistic evolutionist. Therefore, he permits God to be involved in the creative process at some stage.  However, that raises the specter of arbitrariness. He allows just enough divine involvement to kickstart theistic evolution, but disallows more extensive divine involvement, viz. progressive creationism, intelligent design, fiat creationism, or omphalism. However, it's unclear how he draws a principled line in the sand. There's a sense in which Lewontin was right: once God gets his foot in the door, how do you disinvite him from further participation? 

Now, that doesn't mean anything goes. The Biblical God is not a frivolous, capricious, irrational agent. He has a good reason for whatever he does. There's a middle ground between deism and occasionalism. 

The first line of evidence, and perhaps the one most widely discussed by Christian apologetics organizations, is that of gene sequence similarity. If, indeed, humans and chimpanzees are descended from a common ancestral species, then the individual gene sequences of these two species would be predicted to have a high degree of similarity due to inheritance from a common ancestor, or homology. Moreover, homology for individual genes should exist at two levels: the amino acid level (the functional sequence of a given gene’s protein product), and at the nucleotide code level (the underlying DNA code for the required amino acid sequence). Since the nucleotide code has numerous coding options for a given amino acid sequence (i.e., the nucleotide code is redundant), genes in related organisms are predicted not only to share amino acid sequences but also nucleotide sequences, despite a large number of possible coding options. Thus, related organisms should display homology at both levels of code.
A second, unrelated line of evidence is that of synteny. Synteny is a technical term for conservation of gene order along chromosomes between relatives. Put more simply, the hypothesis of common ancestry predicts that not only will related species have similar genes, but that they will also have these genes in a very similar spatial pattern.

But this overlooks an alternative explanation: the principle of plentitude, which includes continuity and gradation. Here's a summary:

The kernel of the principle is the idea that a world containing a rich variety of beings is more valuable than one containing only one sort of creature. The natural world is thus pictured as consisting of a great hierarchy of beings, beginning at the lowest end of the scale with inanimate objects (e.g., rocks, stars), then ascending to living things that lack sentience (e.g., trees, plants), and thence to living things that are sentient but not intelligent (e.g., animals), thence to living things that are both sentient and intelligent (e.g., humans), and finally to intelligent beings that are immortal (e.g., angels). At the summit of the hierarchy stands God. And it is usually added that God has chosen to create a world of this sort because it is intrinsically better that many kinds of beings exist, rather than just one kind of being or the best kind of beings. Given this value-judgement, it is no longer obvious that God is not morally justified in creating a world that displays the variety and complexity found in the actual world.

Here's a more detailed exposition:

Back to Venema:

A third line of evidence is that of pseudogenes. Pseudogenes (literally, “false genes”) are the mutated remains of gene sequences that persist in the genome after their inactivation. Common ancestry predicts that related species should share pseudogenes that were present in the genome of their common ancestor. Moreover, these pseudogenes should be in the same genomic location in both descendant species (i.e., they should exhibit shared synteny) and retain gene sequence similarity (i.e., continue to exhibit homology) in spite of their inactivation.

This raises two questions:

i) That's one of the more superficially impressive arguments for common descent is appeal to common chimp/human mutations. Inasmuch as these are (allegedly) transcriptional errors, they can't be chalked up to common design. 

One question I have is whether comparative genomics suffers from sample selection bias. Given the sheer number of plant and animals species, not to mention bacteria, viruses, &c., I assume that science has only mapped the tiniest fraction of extant species and stains–not to mention all of the extinct species and strains. The comparative data-base of genomics is in its infancy.

Scientists map the human genome, as well as things related to humans, or deemed to be relate to humans, viz., primates, human foodstuffs, human diseases. It maps things that have been a staple of research for decades, viz., fruit flies.

If, however, we were to actually map the genomes of all or even most species and strains, I wouldn't be surprised if that turned up many shared "accidental" sequences, which–however–would usually be discounted as anomalous or coincidental.

ii) Venema's way of framing the issue carries tacit assumptions. It assumes that these parallel chimp/human sequences are mutations. As such (so goes the argument), it must have happened in a common ancestor before chimps/humans diverged.

Now, I don't know the basis for assuming it's a mutation in the first place. Does that presume the parallel sequence is useless at best and maladaptive at worst? 

For if the parallel sequence is either neutral or beneficial, then, from a Christian theistic standpoint, there's no reason to presume that's a mutation or transcriptional error. That could be how chimps and humans were created.

Of course, if we allow for guided mutations, then mutations can also be beneficial.

A related issue is how we judge whether a mutation is nonfunctional, beneficial, or harmful. Seems to me that that's both spatially and temporally variable.

a) Temporally speaking, a mutation might be neutral or nonfunctional at the time it occurred, but prove beneficial down the line. And if we allow for guided mutation, God directed the process (i.e. resultant mutation) with that beneficial outcome in mind.

b) Spatially speaking, a mutation might be beneficial or harmful depending on where the organism resides. Take skin pigmentation or lactose tolerance. Depending on where you live, that can be adaptive or maladaptive. (I'm not saying skin pigmentation or lactose tolerance are necessarily mutations. I just use them to illustrate a principle.)

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