Friday, 11 April 2014

Three possible ways to account for genetic similarity between apes and men

For those who have been following my blog as of recent, you would probably note I've been more concerned with the putative paleoanthropological evidences for human evolution (i.e. fossils and early human artifacts). While I think it's important to construct creation models to account for the paleoanthropological data, I recently realized the more potent challenge comes from genomics. Consider that we already have some models to account for the fossils (read the last post on this blog), all that's left to do is fill in the details and deal with potential defeaters. Substantial amount of work has been done in that region. On the other hand, the argument from genetic similarity is pervasive- regardless of which paleoanthropological model you choose, the problem of genomics would always be there. Also it is more impressive on the public psyche, because with molecules (as opposed to fossils) it's possible to speak with something of a mathematical precision (the all-too-popular 98% similarity idea) and there is lesser room for interpretation. So I thought I would dedicate one post to construct creation models to account for the genomic data. I should probably start off with a heads-up though: I haven't looked into the issue in any depth whatsoever. These are just preliminary meditations, and putting some proverbial flesh on them would require more study. As my study progresses, I will update this blog on the details of the three ways, possible defeaters and so on.

The problem

The argument from human-chimp genome similarity goes something like this: the vast amount of similarity between the genomes of the two species is better explained on common descent than on design. If the human species were created de novo without any evolutionary precursor, how would we expect our genome to look? Wouldn't it look markedly different from the precursors? Of course, some similarity is expected- like the all important housekeeping genes should be similar not only for humans and chimps but for all Eukaryotes. But the similarity is not confined to the essential housekeeping genes, they practically pervade the genome. What's more important is that a percentage of the human genome lacks function. For the parts that are functional, their function is not dependent on their sequence (i.e. they act as spacers between genes, form secondary structures for overall genome stability, act as buffers against mutations, and so on). The surprising phenomenon is that these regions too are similar between apes and humans. This is something that is clearly better explained on common descent.

The most popular creationist response here is common design- there is this much similarity because a common designer made both genomes. This is at best a partial solution to the problem. For the advocate of common descent, it is easy to say that the shared genes simply "picked up" these functions along their evolutionary journey. Think about an outdated car model- it may be completely useless for the function it was originally designed, but it may now have other applications (providing shelter in a rainy day for example). Similarly, a shared and seemingly non-functional sequence may have picked up a function along the way, but that doesn't make the similarity any less redundant. Another point is, the Designer could have made the human genome in a vast number of ways. For someone looking for a shelter, the designer could have given him an entire house- not an outdated car. This means the similarity between humans and apes are redundant. Even if these emanated from a design plan, they could have easily been different. But they're not. This is the fact that calls out for an explanation.

One of the key reasons why I think functionality of parts of the genome is thought to be a defeater to the chimp-human genome similarity argument is because this argument is confused with another, similar evolutionary argument- junk DNA. But it is crucial to understand the arguments are separate. The argument from junk DNA argues that the designer would not have filled the genome with useless matter. Simply pointing out the function of these putative junk sequences would suffice to silence this argument. But the argument from chimp-human genome similarity goes deeper- it appeals to the pattern in which humans and chimps have similar DNA, especially when it is reflected in the putative junk regions.

Notice the bottomline of this argument is not merely that the human and chimp genomes are similar, but that the similarity conforms to a certain pattern. It is this pattern of similarity that sits so well with common descent. For example- the similarity is not found only in functional but also in putative non-functional and/or non-essential regions of the genome, the similarity is more between the chimps and humans as compared to other lifeforms which underscores the trajectory of common descent, and so on. There are also specific instances of this similarity which sit quite well with evolutionary explanations, for example- the chimp chromosome 12 and 13 fusion, endogenous retroviral sequences found both in human and chimp genomes, and so on.

All of these problems are neatly summarized and talked about in creationist Todd Wood's brilliant 2006 paper "The Chimpanzee Genome and the Problem of Biological Similarity", available here.

The possible solutions

So, what are the possible ways to solve this dilemma? Here are three plausible ways.

1. Question the data. This is probably the most common approach among creationists today- argue that the chimp and human genomes are not "all that similar". The most intelligent defense of this line of reasoning comes from geneticist Jeffry Tomkins. You can access a number of his papers on the topic available here. Of course, this view isn't a complete solution of the problem, but it does take a substantial amount of wind out of the argument. An argument from common ancestry based on 99% genome similarity vs. one based on 70% genome similarity are markedly different.

Also check Tomkins' new book on the topic here.

2. Posit a different mode of de novo creation. When we say the first man was designed de novo, what do we mean by this? Do we mean that he was created completely out of the context of creation or the remainder of living systems? To me, this doesn't seem like the only choice. It could also be that the human beings are created in the matrix of the broader biodiversity brought about by evolution. Even though man was created de novo and all or most of biology's remainder was created through the instrumentality of evolution, it doesn't preclude that human design was based off of a broader "design plan". To see what I mean, consider this scenario. During the creation of the first man, instead of making his genome from scratch, the designer used the genome already available in the closest "relative" of man, and tweaked it just enough. As for the remainder of the genome which are either non-functional or non-essential, they were left as they are because, why not? Why would the designer want to create the rest of the genome from scratch when the one "cooked up" by the years of evolution works just as well? In this view, the human genome was created both through the instrumentality of nature as well as de novo. Much of the genome was "created" by means of guided evolution, while the remainder was "tweaked" by the hands-on Divine intervention to make us "human". In this view, the designer is both a "hands-off" creator when he acted through the instrumentality of evolution, and a genetic engineer when he intervened. In other words, much of the world is natural, while the creation of man is a miracle.

Is this view ad hoc? Why would the designer want to create the entire chain of being through evolution, stop at the tail end of history, and then choose to intervene in the creation of man? Consider some factors. Muslims and Christians believe the birth of Christ was a miracle. Does this mean the birth process of Christ didn't mimic that of the birth process of other children? Or more to the point, is Christ in any way "unrelated" to the rest of humanity because of this unique mode of creation? I submit no. Similarly, the creation of the first man was unique and de novo, but the evidence does give the impression that he is "related" to the rest of biological systems. As for why the designer chose to intervene- I wrote the following on facebook a few days back which is relevant (please try to ignore the "Islamic" elements of the post and focus on the point):

I was listening to lectures on Prophet Muhammad's (peace be upon him) biography. In the part on the Prophet's heavenly journey, the lecturer said that one of the main reasons why prayer is so significant is that the Prophet was brought to the presence of God to receive this commandment.
Now someone with materialist inclinations may ask: what was the reason for this routine? After all, (being very blunt here) God could have done gotten the job done just as easily by sending an angel with the commandment of prayer. The answer Muslims would give is: this is not a question of efficiency in terms of getting the job done i.e. choosing the easiest of the options. Because the spiritual significance of prayer is so much, God's perfect wisdom necessitated that this information be communicated to the Prophet in person.
I think this consideration has bearing on the evolution question as well. The theistic evolutionist may argue: why bother making the first human being in the heavens de novo, when it would have been possible just as easily on earth, through the instrumentality of natural processes? One could reply that there is more on the line here than merely choosing the easiest of the options. Creating a vicegerent on earth and endowing him with consciousness and knowledge is something so spiritually momentous, that God's perfect Wisdom necessitated that it had to be done by special Divine action, with his direct involvement, no matter how materialistically efficient creation through evolution would have been.
This is relevant to the discussion I was having with another brother the other day. My point was, theistic evolutionists may say- it seems ad hoc to create the first man supernaturally just to endow consciousness on him, or make other relatively minor changes. This could be one response.
Quite frankly, I don't see any reason why this view would be ad hoc. If the earlier design works just as well, why bother making another design plan from scratch? Human creation should be seen in the context of the rest of the evolutionary drama happening on earth. When one looks at things that way, the putative evidence for common descent seem to fit just as easily on a creationist hypothesis.

That's the strength of this view- one could accept the data hook, line and sinker- but interpret it differently. The debate then would shift to whether this way of interpreting the data is ad hoc or not, I find reason to believe it is not. 

3. Hope for new explanations to show up. Finally, one can take refuge in the ever-changing nature of the scientific enterprise. The way genomics is progressing, it is very hard to predict when and how the science stands in a few years or so, and maybe we will find there are other ways of explaining the data than common descent.

An interesting example is a recent paper by Liu and Soper on the retroviral elements common in human and chimp genomes, available here. Rather than summarizing the contents, I would forward the readers to Todd Wood's fantastic review here, and get to the point: this is a really interesting and novel way of interpreting shared ERV sequences among humans and chimps, and it doesn't rely on common descent. I'm not saying the authors of the paper are completely successful in their endeavor, but just that it is a promising avenue to explore. Additionally, there have been efforts to explain other molecular evidences for common descent (for example, this paper by Tomkins talks about another way of approaching the "fusion site" argument).

What this argument states is that it is too soon to decide whether the genomic similarity only being explained by common descent is compelling. In light of some of the promising ways of explaining the data alternatively, perhaps they can be explained on hypotheses at home with special creation as well.


These are just the basic, skeletal forms of some of the different ways how the chimp-human genome similarity problem can be solved. These are not the only ways, however- Todd Wood's 2006 paper cited earlier outlines a few other ways.

Also, one should keep in mind that these arguments are not mutually exclusive. A cumulative view that takes all of the above into consideration should, I think, ought to convince one that the evidence is not all that strong, and perhaps could be accommodated on a special creation hypothesis as well.

I hope to keep this blog updated on all things genomics.

1 comment:

  1. Great post! I think by simply keeping all the options on the table, we can maintain that the evidence for human evolution by no means falsifies Islam. I would also include among these options the possibility of reconciling the Islamic texts with evolution, I guess by a parabolic interpretation of the hadith and/or matn criticism, just as another option on the table (despite the weaknesses of it).

    But of course, if it can be shown that none of the options explain the evidence, then it will be a different story.

    I think my scruple about solution 2 is this:

    On common descent, the similarities genetic sequences and patterns described above are certain.

    On solution 2, however, it seems less probable and less congruent for me to suggest that God would create Adam de novo, but create Adam's genes in the same exact sequence as the pre-existing hominids when He could have just as easily (being God) chosen any other of a vast variety of sequences for the gene which would have been functionally equivalent.

    Creating Adam with a different (but functionally equivalent) genetic sequence would be more consistent with the fact that He is creating Adam de novo (and it would illustrate total consistency of human creation with His Word, if creatio de novo is the proper interpretation of it), while the unnecessary similarity in genetic sequencing seems more consistent with the notion of common descent, in which this similarity is definitely expected. If God created Adam de novo however, we would have no reason to expect the same genetic sequencing as with prehominids when God could have chosen any of the many others. Do you get my point?