Debating Homo naledi on Premier Christian Radio

I took part in a debate on Premier Christian Radio last Thursday with Fuz Rana, of Reasons to Believe, on the new Homo naledi find and the respective cases for evolution and intelligent design.  It was quite fun and very cordial and respectful.  The host, Justin Brierley did a very good job of moderating and asking the right questions.  Let me know what you think.  Fuz spent some time talking about the book Who Was Adam? he co-wrote with Hugh Ross which, I am embarrassed to say, I have not read yet.  I need to do that post-haste. 

Todd Wood Responds on Excellence

Todd Wood has a follow-up post on the whole parallel cultures idea, in which he argues that having parallel cultures is not necessarily a bad thing. It is just that we, as Christians, can do better. He writes:

Yes, there are people out there who will look down on you for your background and your faith, but there are also folks who will not. If you do good work and keep at it, eventually people will take notice. Why should you let the bigots hold you back? Be excellent! Don't settle for a life and career of mediocrity.

That's the point. Christians don't have to settle for second best or leftovers. You can be excellent! You don't have to keep churning out sub-par dreck and whining about how the world is discriminating against your Christian values. You can be excellent with what you have. You don't have to settle.

I wish more Christians in the science arena thought this way. Given Fuz Rana's recent embarrassing post (one below this one), I am not hopeful.


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Fuz Rana on Human Evolution

Fuz Rana wants to know: “Will the Real Human Ancestor Please Stand Up.” He writes:

It is commonly reported that humans and chimps share 99 percent genetic similarity. For many people, this high degree of genetic similarity means humans must have evolved from an ape-like primate, sharing a common ancestor with chimpanzees. However, it should be noted that, when comparing the full genomes of humans and chimps, around one quarter of the two genomes don’t align and the similarity of those portions that do align is between 90 and 95 percent. (Go here and here for comparisons.)

According to the evolutionary model, humans and chimps share a common ancestor with gorillas. And humans, chimps, and gorillas share a common ancestor with orangutans. These presumed evolutionary relationships should be reflected in genetic comparisons between humans and the great apes, where scientists expect to find gorillas and orangutans displaying less similarity, respectively, to humans than to chimpanzees.

Yet, this is not always the case. Researchers have recently discovered that about one percent of the human genome displays a greater genetic similarity to orangutans than it does to chimpanzees. This result follows on the heels of an earlier study that found that 23 percent of random sequences sampled from the human genome point to a primate other than chimpanzees as our closest evolutionary relative.2 In other words, depending on the region of the genome that is selected, differing “evolutionary trees” result for humans and the great apes.

He argues that a key portion of evolutionary biology is violated because these genetic trees do not completely agree with each other and don't completely agree with the fossil record. In support of this idea, he cites three articles, the first of which is called “Incomplete Lineage Sorting Patterns among Human, Chimpanzee, and Orangutan Suggest Recent Orangutan Speciation and Widespread Selection.” (http://dx.doi.org/10.1101/gr.114751.110). Ironically, in a section of the article to which Rana does not refer, the authors of this paper write:

The exact amount of ILS [interlineage sorting] locally in the genome depends on the recombination rate and factors such as functional constraints (Figs. 4, 5). The observed ~1% of ILS is entirely consistent with the effective population size of 50,000 inferred for the human–chimpanzee ancestor and the speciation time difference of 8 Myr inferred between human–chimpanzee and human–chimpanzee–orangutan, assuming a generation time of 20 yr [emphasis mine].

How does this not fit an evolutionary model? These authors of this paper certainly think it does, an expected one, at that. No evolutionary biologist has ever said that there has to be 100% agreement between all different kinds of trees. It has never occurred to them that this would ever be a problem. That is a straw man argument that Rana has put up. In response to the argument of discordant trees, Dennis Venema has posted a great article on this concept of incomplete lineage sorting. He writes:

The fact that gene phylogenies/trees and species phylogenies/trees don’t always match is not something that surprises scientists, since it is a well-known phenomenon and the mechanisms underlying it are understood: species arise from genetically diverse populations and that diversity does not always sort completely down to every descendant species.

The second article that Rana cites is “Mapping Human Genetic Ancestry,” by Ebersberger et al. (http://dx.doi.org/10.1093/molbev/msm156). Once again, in a part of the article to which Rana does not refer, they write:

For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. This explains recurrent findings of very old human-specific morphological traits in the fossils record, which predate the recent emergence of the human species about 5-6 MYA. Furthermore, the sorting of such ancestral phenotypic polymorphisms in subsequent speciation events provides a parsimonious explanation why evolutionary derived characteristics are shared among species that are not each other's closest relatives [emphasis mine].

Funny, it doesn't look like the authors are proposing a non-evolutionary relationship here. Once again, it fits perfectly with what we think is going on with the fossil record, which indicates a human-chimp separation time at around 6 million years ago. In fact, this kind of scenario fits perfectly with the recent finding about the frame-shift mutation of the sugar molecule Neu5Gc, suggesting that sympatric speciation may have happened in the human fossil line (the G.G. Simpson in me just shuddered). It is, consequently, difficult to see how this article supports Rana’s conclusion.

The third article that Rana has marshaled to his argument is by Morris Goodman, one of the dons of genetic analysis. The Goodman article appears in The Cambridge Encyclopedia of Human Evolution¹. He quotes Goodman as writing thus:

If the biblical account of creation were true, then independent features of morphology, proteins, and DNA sequences would not be expected to be congruent with each other. Chaotic patterns, with different proteins and different DNA sequences failing to indicate any consistent set of species relationships, would contradict the theory of evolution.

Rana is using this statement by Goodman to indict evolutionary theory, since, given what he thinks he has shown, that is exactly what the evidence of the first two papers is. The problem is that a bit further in the article, Goodman says:

Human serum proteins shown only small antigenic differences from orang-utans and gibbons, and tiny differences from gorillas and chimpanzees. Given the extensive morphological evolution involved, the extent of protein evolution between humans and other hominoids is surprisingly small. Alternatively, if the 'molecular clock' is applied to immunological distances and the divergence between hominoids and old world monkeys arbitrarily set at 30 million years ago, the human-African ape split occurs at 5 million years ago [emphasis mine].

Once again, perfectly in keeping with evolutionary theory and perfectly in keeping with the results by Ebersbrerger et al, who also (twenty years later!) see the evidence as pointing to a human/ape split between five and six million years ago.

It is difficult to find anything redeeming in Rana's post. It is further difficult to derive a conclusion that these articles don't support the evolutionary paradigm, since they all clearly do. Did he simply not read them? Did he hope that none of his readers would? For someone who is trained in molecular biology to employ such a standard creationist trick is astounding and deeply, deeply disappointing. It also lends more credence to what Todd Wood recently said about RTB:

I would recommend that no one accept any of RTB's arguments without fact-checking their claims first. I do not know whether these problems are due to lazy scholarship, ignorance, intentional deception, or ideological blinders. What I do know is that you cannot trust Reasons to Believe.

I can't add much to that.

¹Goodman, Morris (1992) “Reconstructing Human Evolution from Proteins,” in Steve Jones, Robert Martin, and David Pilbeam, eds., The Cambridge Encyclopedia of Human Evolution, New York: Cambridge University Press, pp. 307–13.

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Reasons to Believe and the Credibility Gap

Todd Wood has wrapped up his long series on the problems with Fuz Rana's interpretation of the human/chimp DNA differences and his responses to Dennis Venema's writings. He closes with some sobering thought:

To be honest, I do not believe that RTB will pay any attention whatsoever to this series of posts. Given Rana's insulting response to Venema's critique, I expect that they'll treat this as yet another "ad hominem attack." I've mostly written this series for third parties that might be confused about the Venema/Rana exchange. As far as I'm concerned, RTB's credibility is completely shot (read my analysis of their handling of the Neandertal genome for more evidence of errors and exaggerations on the part of Ross, Rana, and Samples: parts one, two, three). I would recommend that no one accept any of RTB's arguments without fact-checking their claims first. I do not know whether these problems are due to lazy scholarship, ignorance, intentional deception, or ideological blinders. What I do know is that you cannot trust Reasons to Believe.

This is very disappointing but, having read enough of Steve Matheson's writings, not entirely surprising. Once upon a time I had much respect for Hugh Ross and the work he did to try to convince the evangelical community that there could be a fulfilling theological construct that incorporated an old creation. He came to the University of Tennessee in the early 1990s and gave a series of compelling, cogent lectures on the astrophysical evidence. Even then, though, I had misgivings about what his (and his organization's) treatment of the biological data would be like. Now, it seems that my misgivings were well-founded and we have our answer.

Todd Wood Continues Taking Apart Fuz Rana

In the most gentle and Christlike fashion, Todd Wood is trashing Fuz Rana's interpretation of the ape and human genome similarities. Todd is up to part seven now, which can be found here. He writes:

In his latest post, Rana asserts the following about the argument for common ancestry from pseudogenes:

When evolutionary biologists present this argument, they make a number of assumptions, all of which appear to have questionable validity based on recent research results. For the pseudogene evidence to have potency: (1) pseudogenes must lack function; (2) their origin must be due to rare, random events; and (3) their juxtaposition to other genes must be arbitrary.

Everything he wrote there is utterly false. None of those conditions are required to argue for common ancestry from pseudogene similarity. Not one.

As Glenn Reynolds would say: OUCH! I would encourage you to read the whole debate. I am not qualified to comment at more than a superficially cogent level but I might try to say a few things. I haven't seen Steve Matheson wade in yet, but he may yet. If he does, expect fireworks. He has no love for RTB.

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Praise for Todd Wood

Larry Moran over at Sandwalk has been following the debate between Fuz Rana over at RTB and Dennis Venema, at BioLogos, about the human/chimpanzee genomic similarities. I have been meaning to comment on the debate but have gotten involved in my own posts and haven't had the time. Anyway, this came to the attention of Todd Wood, down at Bryan College, who has been running his own set of posts on the debate. Moran has this to say:

Fortunately for us, Todd Wood of the Center for Origins Research at Bryan College in Dayton, Tennessee, USA is on the case. Todd belongs to a young-Earth creation study group [BSG] but don't let that fool you. He's doing a pretty good job of sorting out the facts in the case.

This might seem somewhat backhanded but if you read what Wood has to say, he is obviously struggling with the lack of integrity on the part of RTB. It is nice to see a young earth creationist try to deal with the data honestly. Most of the time the lack of integrity exhibited by young earth creationists is maddening, distasteful and disheartening. Hats off to Todd Wood.