An Evangelical Geneticist’s Critique of Reasons to Believe’s Testable Creation Model, Pt. 1

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November 6, 2010 Tags: Genetics

Today's entry was written by Dennis Venema. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

An Evangelical Geneticist’s Critique of Reasons to Believe’s Testable Creation Model, Pt. 1

Today's post comes from a longer essay by Dr. Venema. Full footnotes can be found in the essay.

One serious critique of young-earth creationist attempts to explain the natural realm is that their explanations, typically rooted in religious dogma, have no flexibility to adapt and self-correct as knowledge increases.

-Hugh Ross
More Than a Theory, p. 20

Introduction

Reasons to Believe (RTB) is the most influential Old-Earth Creationist organization in North America. While RTB supports a mainstream scientific position on cosmology and the age of the earth, RTB rejects evolutionary biology. Specifically, RTB denies that humans share ancestry with other forms of life, such as Neandertals or chimpanzees. RTB also claims that all human are the descendents of a single, specially created couple who lived about 50,000 years ago. RTB has expounded a framework called the “Testable Creation Model” in three major books published in the last five years: Who Was Adam? was published in 2005; Creation as Science was published in 2006, and More Than a Theory was published in 2009. Furthermore, RTB claims that this model is scientifically robust.1 This same period however, has also seen the publication of much genetic data relevant to assessing human common ancestry. This paper will examine the interaction between RTB literature and several lines of genetics-based evidence for common ancestry. In so doing, I will address the scientific robustness and reliability of the RTB model. RTB welcomes such critique from qualified scholars in their works as a means of improving their model.2 This critique, while forthright, is offered without animosity and in good faith. It is my hope that RTB will find it useful for correcting several serious flaws in their approach to human origins.

A recent history of primate comparative genomics

When the human genome project (the endeavor to determine the complete DNA sequence of every human chromosome) was completed in 2003, the equivalent chimpanzee genome project was already underway. Just prior to the completion of the human project (from about 2002 on), detailed comparisons of large stretches of DNA between humans and chimpanzees became possible as both genome projects progressed. As the data came in, a range of estimates for the precise amount of identity between the two genomes was published in the mainstream scientific literature (Table 1).

Such estimates took two forms: measuring single-nucleotide differences in sequences found in both genomes while omitting inserted or deleted sequences (so-called “indel” mutations, because it may be difficult to determine if a difference is due to an insertion or deletion), or estimates combining both sources of variation. In the years preceding the completion of the chimpanzee genome in 2005, partial-genome comparisons repeatedly estimated the two genomes to be over 98% identical when omitting differences due to indels. Two pre-2005 studies took indels into consideration as well: Britten (2002) estimated the two genomes to be 95% identical, whereas Anzai et al. (2003) found only 87% identity. This paper examined a chromosomal region that contains immune system genes, and was not thought to be representative of the genome as a whole. This prediction was borne out in 2005 when the completed human and chimpanzee genomes were compared (2.9x109 DNA base pairs). The final tally was 98.77% identical when indels were omitted and 95% identical when indels were included. A second paper published in 2005 examined 1.85x107 DNA base pairs found in the portions of the chromosome that specify proteins, and found even higher identity (99.4%) in these sequences.

The RTB model and comparative primate homology: overview

A key tenet of the RTB model is that humans do not share ancestry with other forms of life. As such, RTB has invested considerable effort in reinterpreting human / chimpanzee genomic homology comparisons for their constituents. A notable feature of the RTB model is the claim that the whole-genome, human / chimpanzee homology value is in fact 85-90%, not 95-99%.3 As we have seen, comparisons between the human and chimpanzee genomes progressively improved in the early 2000s, culminating in the landmark whole-genome comparison of 2005. The fact that these data emerged over time allows us to investigate how RTB responded over the same time period, and as such examine the reliability of the RTB model as new data became available that were at odds with one of its non-negotiable claims.

The RTB model and primate genomics (2005): Who Was Adam?

Like comparative primate genomics, the RTB creation model also hit a milestone in 2005 with the publication of Who Was Adam? (WWA) by RTB scholars Fazale Rana and Hugh Ross. This book narrowly predates the pivotal 2005 whole-genome comparison paper. Unlike two later RTB books (see below) this book discusses research-to-date on human-chimpanzee comparative genetics in extensive detail. (p. 212-215) WWA carefully distinguishes between estimates based on including or excluding indels, as well as chromosomal or mitochondrial DNA. However, WWA made a questionable claim when it states:

“The most comprehensive genetic comparisons indicate that humans and chimpanzees share genetic similarity closer to about 85 percent than to 99 percent. From an evolutionary perspective, if a 99 percent genetic similarity reflects a close evolutionary connection, then an 85% genetic similarity distances humans from chimpanzees.”(p. 223)

This assertion, however, was already at odds with the conclusions of the 2004 Chromosome 22 Consortium paper (Table 1), a paper that is cited in WWA as support for differences in human-chimpanzee gene expression. (p. 222) At the time WWA was published, RTB expected future genomic comparisons to widen the gap between humans and chimpanzees. (p. 223)

The RTB model and primate genomics (2006): Creation as Science

In early September 2005, a full comparison between the completed chimpanzee genome and the human genome was published in the prestigious journal Nature. This landmark paper used a sample size of 2.9x109 base pairs: it covered virtually the entire genomes of both species, dwarfing previous comparisons (Table 1). This comparison returned results consistent with previous studies: homology excluding indels was over 98%; including indels brought it down to 95%. As expected, the 2003 Anzai et al., paper (that found 87% homology including indels in one chromosomal region) was shown to be an inappropriate estimate for the genome as a whole. Beyond its wide impact in the biological sciences, this paper also received much attention from the mainstream media. This work, however, did not make any discernable difference to the RTB model. In 2006, another major RTB book, Creation as Science (CAS), appeared. In contrast to the lengthy, detailed discussion of human / chimpanzee comparative genomics in WWA, CAS has only a brief section as follows:

New research, however, indicates that the widely advertised 98 to 99 percent similarity between human and chimpanzee DNA is greatly exaggerated. Such claims are based on small segments of the human and chimpanzee genomes where common sense dictates that the similarities would be the greatest. While comparisons between the complete human genome and the complete chimpanzee genome have only recently begun, the most complete comparisons performed thus far indicate that the degree of similarity is more like 85 to 90 percent. (p. 156)

The above paragraph from CAS cites four research publications, each of which was previously cited in WWA: Anzai et al., 2003; Thomas et al, 2003; Arnason et al., 1996; and the Chromosome 22 Consortium paper of 2004 (Table 1). Surprisingly, CAS makes no mention of the actual whole-genome study published between WWA and CAS. On encountering this, I initially assumed that Ross and Rana were simply unaware at the time CAS went to press that the chimpanzee genome had been completed, or that perhaps they had mistaken the Anzai paper as a whole-genome analysis. Further investigation, however, failed to support these hypotheses. First, in an article published in 2004 in the RTB periodical Connections, Rana emphasizes that the Anzai paper is not a whole genome comparison and discusses its actual data set in detail:

Though these whole-genome comparisons are not yet possible, scientists are close, and preliminary results indicate that humans and chimpanzees are really not so genetically similar… another study found only 86.7% genetic similarity when segments of human and chimpanzee DNA (totaling 1,870,955 base pairs) were laid side by side.

Thus Rana correctly understands that the Anzai paper is not a whole-genome comparison. Secondly (and more significantly), Rana does mention the key 2005 whole-genome paper in the very first 2006 edition of Connections, and notes correctly that it is a whole-genome study:

Where were you on September 1, 2005? Perhaps you missed the announcement of a scientific breakthrough: the influential journal Nature published the completed sequence of the chimpanzee genome. This remarkable achievement received abundant publicity because it paved the way for biologists to conduct detailed genetic comparisons between humans and chimpanzees.

Rana uses this as an introduction to discuss another article from the same journal issue and does not discuss this key paper or its results, beyond a footnote referring readers to WWA. While this Connections article does not have a precise publication date, Rana cites accession of online material for this article as occurring on November 30, 2005. Other articles in this edition of Connections also cite access dates in late November 2005, suggesting that this volume was drafted in late 2005 for publication early in 2006. The chapter in CAS discussing human / chimpanzee genomics has references to online material cited as accessed in April 2006, indicating that this chapter was still in revision at this time. Taken together, these lines of evidence strongly suggest that RTB was aware of the key 2005 paper at the time the CAS chapter was in preparation, and that they correctly understood its significance as the first whole-genome comparison. The choice of language in CAS also supports this conclusion, since the chapter claims that “… comparisons between the complete human genome and the complete chimpanzee genome have only recently begun…” which makes sense only if both genomes were sequenced at the time of its writing. Despite this concession, CAS makes no mention of the key 2005 paper or its findings, and claims rather that “the most complete comparisons performed thus far” support homology values in the 85-90% range. In reality, only the Anzai paper, which covered a small chromosomal region expected to be disproportionately different between the two species, supports this value (Table 1).

The RTB model and primate genomics (2009): More Than a Theory

The next major RTB publication dealing with human - chimpanzee genomic comparisons was More Than a Theory (MTT) published in 2009. The relevant passage in MTT is a lightly reworked version of what appears in CAS, with only one notable change: whereas CAS acknowledges that comparisons between the completed genomes are underway, MTT claims they have not yet been done (Figure 1).

Like CAS, MTT claims “the most complete analyses performed so far” indicate homology values in the 85-90% range, makes no mention of the key 2005 whole-genome comparison paper, and again cites exactly the same references as CAS, the most recent being the 2004 consortium paper (Table 1). Thus, four years after they were aware of the key 2005 paper, there is still no mention of it to be found in the RTB framework; moreover, MTT claims such an analysis has never been performed.

The RTB model and primate genomics – present day

The pattern we have seen in the major RTB books continues into the present. Rana, for example, continues to argue that the best estimate of whole-genome human chimpanzee homology is at best 90%. For example, during a recent podcast discussion of the completed western clawed frog genome (Xenopus tropicalis) Rana claims: “It’s common parlance that humans and chimps have a 99% genetic similarity. The actual data indicates probably it’s closer to 90% similarity as opposed to 99% similarity” before going on to imply that the higher value can only be supported through comparisons of specific genes. He then goes on to claim that sequenced frog genome shows 80% similarity to the human genome based on “the same reasoning.” The argument he makes is an attempt to cast doubt on the relevance of the human / chimpanzee comparison: if humans and chimps are 90% similar and humans and frogs are 80% similar, Rana claims these “are not meaningful comparisons in a biological sense.” Rana’s argument, however, is deeply flawed in that he is comparing two very different measures of similarity and claiming they are equivalent. The human / chimpanzee value, as we have seen, is 95% genome-wide identity (including indels) for the completed genomes of both species compared across approximately three billion DNA base pairs (Table 1). The 80% value Rana touts for the human / frog comparison, however, is merely a measure of the percentage of genes in the frog genome that have a similar gene in humans implicated in a human disease. It is not even a measure of the genetic similarity of those genes, but merely a fraction of the genes identified in frog that might be useful for studying human diseases. Rana, however, presents these two values as equivalent measures in an attempt to disparage human / chimpanzee genomic similarity. In reality, the genome-wide homology between Xenopus tropicalis and humans is slightly over 30%.

Taken together, these findings demonstrate the following: (a) RTB carefully followed the primary literature on human / chimpanzee comparative genomics up until and including a major paper published in 2004, even if it represented such studies selectively to their constituents; (b) RTB was aware of the key 2005 whole-genome study and correctly understood its implications at the time the first 2006 edition of Connections was drafted in late 2005; (c) RTB has made no mention of this paper (nor any paper in this field published since 2004) in two major works published after this paper was available; (d) RTB continues to claim, five years after this paper was published, that the most recent and most extensive evidence supports their preferred value of 85-90% homology (and that higher values can only be supported with small, biased samples), despite the fact that this conclusion is starkly at odds with the best and most extensive study available, and is itself derived from a comparatively small, biased sample; and (e) RTB has shifted from acknowledging (in 2006) that whole-genome comparisons have been done to denying (in 2009) that they ever have.

In the second part of this series, Dr. Venema will continue his evaluation of the RTB model by examining how it approaches a second powerful line of evidence for human evolution: pseudogenes.

A Response from Dr. Rana: “Creation as Science (2006) was initially published by NavPress and More Than a Theory (2009) was published by Baker as a reworking of Creation as Science. There was an urgency to get More than a Theory to the publisher so that it would be released to coincide with the Darwin Day Celebration. Hugh Ross intended both books to be an overview and summarized material from Who Was Adam? (2005) which was published before the whole genome work on the chimpanzee was published. This explains why the work on the whole chimpanzee genome was not mentioned in More than a Theory. There was nothing done to be deliberately deceptive regarding the failure to mention the work on the whole genome of the chimpanzee.”

Notes

1. For a review of these lines of evidence, see Venema, D.R. (2010). Genesis and the genome: genomics evidence for human – ape common ancestry and ancestral hominid population sizes. Perspectives on Science and Christian Faith 62 (3), 166-178.
2. Ross, Hugh. More Than a Theory: Revealing a Testable Model for Creation. Grand Rapids: Baker Books, 2009, p. 21.
3. Rana, Fazale and Ross, Hugh. Who Was Adam? A Creation Model Approach to the Origin of Man. Colorado Springs: NavPress, 2005, p. 223; Ross, Hugh. Creation as Science: A Testable Model Approach to End the Creation / Evolution Wars. Colorado Springs: NavPress, 2006, p. 156; and More Than a Theory, p. 187-188.


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Glen Davidson - #38802

November 6th 2010

There are two common ways to deny the evolutionary predictions of the hierarchical relationships among organisms that we see.  One is to continually obfuscate the nature of the evidence that does indeed show that such falsifiable predictions of evolution stand this test.  The other is incompatible with the first, which is to deny that such evolutionary predictions are meaningful, and to claim that patterns that they accept as evidence for “microevolution” are not evidence for “macroevolution” at all, but for “design.”

Oddly enough, nearly all creationists utilize both means of denial, without seeming to notice that the these methods are at cross-purposes with each other.  Obviously they are troubled by the patterns entailed by evolution being found, no matter how many times they insist that the patterns of common descent really reflect “design.”

Glen Davidson


Clive - #38803

November 6th 2010

Excellent article, very thorough, and without even bringing up further discussion of the RTB claim that there is scientific support for their view that “humanity traces back to a single woman and a single man.”  I’m wondering what RTB’s response will be? They are definitely well behind the times in their reporting of science in the genomic age. The explanation of the various pseudogenes is particularly powerful, but then so are other lines of evidence such as “transposable elements.” Todd Wood posted a response to an article from ICR a while back, but his points would be just a relevant to the RTB attempt to explain away data they don’t like;

“It is misleading to say that transposable elements are “functional” or “essential.” The vast majority of transposable elements in the human genome are nonfunctional copies that have been damaged(?) by point mutations. To my knowledge, there is no evidence of essential function for most of these transposable elements. Indeed, some eukaryotes (like baker’s yeast) that have comparatively few transposable elements.”


Clive - #38805

November 6th 2010

“The argument for the common ancestry of chimps and humans depends in no way whatsoever on the functionality of transposable elements. The argument is more compelling if the sequences are purely parasitic, but the overwhelming similarity still implies that chimps and humans could have shared a common ancestor, even if transposable elements had an essential cellular function. In my chimp genome paper, I challenged myself and my fellow creationists to account for biological similarity in a creationist context. To date, the challenge has not been met.”

RTB discussions of the fossil record also typically leave a lot to be desired, and people have exposed this on their show (any wonder that they stopped taking calls?). I’m wondering if any paleontologists would consider assessing their fossil record claims in more detail.


Papalinton - #38822

November 6th 2010

I followed to the site provided by Clive above and was completely disheartened by what went for discussion.  RTB has got it wrong, plain and simple, as indeed has Behe, Meyers, Chien to name a few.  This episode captured the inanity of RTB’s position and reflects, for me, many of the discussions even here on BioLogos, discussions such as a real A&E, old earth creationists and many others.  One commenter on that site referred by Clive pretty much captures the role of theism to science and many other areas of human investigation [through anthropology, neuroscience, psychology, sociology, history,  archeology etc]  :

“This is just pathetic.
We’re going to dump everything our religion has ever said. Yeah, -those- people were incorrect. Since you’ve disproven everything that has been said about life and existence according to Genesis, we’ll take our god and apply it to these new facts you’ve discovered.
That way we can still have our god and not look like imbeciles.”

The base for christian theology is somewhat shown to be on shifting sand and the shifting has been in only one direction since the advent of modern methodological investigation and research.


Ashe - #38824

November 6th 2010

Papalinton:

The base for christian theology is somewhat shown to be on shifting sand and the shifting has been in only one direction since the advent of modern methodological investigation and research.

Of course not, you can have a solid Christian theology and accept all of mainstream science.


Gregory - #38830

November 6th 2010

“a pre-determined position that humans and other apes do not share ancestry” - D. Venema

Just to clarify, in terms of classification, do you consider ‘humans’ as ‘other apes,’ Dennis?


unapologetic catholic - #38831

November 6th 2010

“Just to clarify, in terms of classification, do you consider ‘humans’ as ‘other apes,’ Dennis?”

All are primates, sure.  You think differently?


Clive - #38840

November 6th 2010

In response to Gregory’s question, I’d suggest those interested watch this.


conrad - #38841

November 6th 2010

God made man from “the dust of the earth”.
How else would you describe DNA in ANE vocabulary?

Chimps and man are different.
God put in the differences.

AND THERE ARE HUGE DIFFERENCES!

Chinmps and men are NOT the same.

The upper paleolithic revolution signals some kind of abrupt change..
It all fits with the timeline.


conrad - #38842

November 6th 2010

Why are humans on such a narrow genetic base when chimps are not?

That is the important statistic,.... not the matching genes.

If chimps and humans are 95% similar genetically ,... the 5% makes a huge difference.
Only God could so deftly change the functioning of the model with minimal reengineering.

What evolutionary forces would induce that?

Did the chimps who could do math survive better?
I doubt it.

Why is there an ancestral Eve in the mitochondreal DNA of humans and no such single ancestor in chimps?


Papalinton - #38844

November 6th 2010

Hi Clive

@Clive - #38840
From your suggestion, even I was somewhat misinformed.  A good video.

Cheers


Papalinton - #38845

November 6th 2010

Hi unapologetic catholic

“Just to clarify, in terms of classification, do you consider ‘humans’ as ‘other apes,’ Dennis?”

All are primates, sure.  You think differently?”

All are primates, sure, and I certainly think differently from you.

Cheers


Unapologetic catholic - #38851

November 7th 2010

“Why is there an ancestral Eve in the mitochondreal DNA of humans and no such single ancestor in chimps?”

What makes you say that?  Of course there is.


beaglelady - #38911

November 7th 2010

Remember that it was Linnaeus who classified humans as primates, along with chimps, etc.


Bilbo - #38935

November 7th 2010

Papalinton - #38822:  “RTB has got it wrong, plain and simple, as indeed has Behe, Meyers, Chien to name a few.

Behe argues for common ancestry of chimps and humans in The Edge of Evolution.


Nick Matzke - #38936

November 7th 2010

This is a great post—one correction, though—it is better to say “percent similarity” or “percent identity” rather than “percent homology”.  Two sequences that are alignable can be 100% homologous—i.e. they share a common ancestor—even if they are only, say, 90% identical.  Differences in percent homology should be reserved for e.g. domain fusions where half of a protein descends from one ancestor protein, and the other half descends from another ancestor…


Dennis Venema - #38939

November 7th 2010

Thanks for the comment, Nick. You’re right - when I have a moment I’ll rework the paper to make those changes.

I’ve been musing on Rana’s reply (above) - and even if one accepts it at face value it should be obvious that it doesn’t address all the issues I raise in this article. For example, Rana was claiming a max 90% identity between humans and chimps as recently as May, 2010 (the date of the podcast I cite in the article). There’s hardly a publication deadline to meet for that. MTT is also a lot more than a lightly-reworked version of CAS. For one thing, in MTT Ross “scores” the RTB model based on several predictions made in CAS. Since RTB knew about the key whole-genome paper in 2005, there was a four-year period where they could have addressed it before MTT came out.

I think RTB owes a more thorough explanation to their adherents, frankly. If I was one I know I would want to hear it.


Darrel Falk - #38946

November 7th 2010

Just want to emphasize that I’m hoping we can stay on topic here and have deleted a few comments that could easily take us astray from the important points that Dr. Venema has raised.

Thanks,

Darrel


Bilbo - #38949

November 8th 2010

Sounds like we need a further response from RTB.


John - #38959

November 8th 2010

I think that given the public’s confusion on this issue, in that the average Joe can’t distinguish between humans and chimps “sharing 99% of their genes” (they share 100%, at least to 3 significant digits) and human and chimp coding cDNA sequences being 99% identical, it’ll be easy for RTB to obfuscate on this.


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