t f p g+ YouTube icon

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

Bookmark and Share

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.

Next post in series >


View the archived discussion of this post

This article is now closed for new comments. The archived comments are shown below.

Loading...
Page 2 of 3   « 1 2 3 »
Fuz Rana - #39018

November 8th 2010

I thought it unusual that we (Reasons To Believe) never commented or responded to the chimpanzee whole genome comparison studies as asserted by Dennis Venema in this article. As I looked through our website, I discovered that indeed we had. The September 20, 2005 edition of our webcast, Creation Update was devoted to discussing several recent discoveries about the chimpanzee genome, human-chimp genetic comparisons, and the chimpanzee fossil record.

Creation Update #286
Chimp Genome Project
Air date: 09-20-05
Fuz Rana, Jeff Zweerink, and Krista Bontrager

Here is a link for convenience:
http://www.reasons.org/resources/radio-broadcasts-and-podcasts/cu-archives


Dennis Venema - #39020

November 8th 2010

Hi Fazale,

I haven’t said you haven’t commented on it - indeed, I point out that you mention it in that first edition of Connections in 2006. My point is that the RTB model, in its published form, continues to claim that that the most recent and extensive studies support an identity of at most 90%. The RTB books cite research prior to the 2005 paper for this point. The 2005 paper, however, does not support this at all.

Thanks for that link to the 2005 podcast.  I’ve listened to part of it, and you still claim that the best estimate for human - chimpanzee genomic identity is 90%. The fact that RTB discussed this paper in such detail in September 2005 only makes me wonder even more why it was omitted from CAS and MTT.

Based on listening to the podcast, I would like to see a detailed explanation of why you think the 2005 paper supports a value of 90% identity between the two species (if that is still your position).

You can reply here, or if you have articles on this I may have missed, please post a link.

Dennis


Clive - #39026

November 8th 2010

Fuz,

Thanks for commenting here. I would however be genuinely interested to know why you still appear to be advocating an explanation that young-earth creation biologists rejected over 4 years ago, namely ‘common design’ as an alternative for the data that supports common descent. Todd Wood published his (now rather famous) article in 2006 in the Papers of the BSG, specifically criticising common design as ad hoc and ultimately an inferior explanation. I’m curious as to why you still appear to have made considerably less progress in this area than YECs; at least they have admitted the problems they face and the inadequacy of their model.


unapologetic catholic - #39034

November 8th 2010

“There was nothing done to be deliberately deceptive regarding the failure to mention the work on the whole genome of the chimpanzee.”

OK.  Now that you do agree that the research shows a better than 98% similarity, do you agree that:

1.  A claim of < 90% similarity would now be “deliberately deceptive?”

2. Has RTB’s position on common ancestry changed as a result of the new findings?  If not, why not?


conrad - #39072

November 9th 2010

There may be SOME common ancestry but about 40 thousand years ago human evolution took a leap that was NOT the gradual effect of evolution.

He upgraded a chimp big time. SUDDENLY!

There are definitely similar parts BUT THERE WAS A BIG STEP IN THERE THAT DARWIN NEVER ENVISIONED..

What niche in the environment led to the development of chimps that could do calculus?

BUT GOD DID USE PARTS ALREADY AVAILABLE ON EARTH,... DNA LARGELY FROM CHIMPS.


NoNameMan - #39073

November 9th 2010

Great article by Dr. Venema.


Kevin - #39225

November 9th 2010

Nice work. Like others, I am interested to see the RTB response to this. I have looked around their site and found nothing so far. I did however find these Paradoxes Sunday School Class lectures by Hugh Ross, including this recent one from him on the recent Vibrant Dance conference, where he says that the theistic evolutionists he saw were “too specialiazed” and based their whole case on human genomics, to the extent of ignoring discoveries in other areas. He has some pretty brutal things to say about the threat that he thinks theistic evolution poses to the faith. It would be interesting to see more direct dialogue on this. Would RTB be allowed a response on here?


Liam - #39227

November 9th 2010

Wow, that Hugh Ross talk is orders of magnitude worse than much of the YEC folk science I’ve come across. He claims that mice, rats, and some birds are genetically closer to humans than chimps, and made some point about Neanderthals I didn’t get. Then he mocked the idea of human common ancestry with mice, and later pigs. He also talks about two other organisms that he says “aren’t related in any evolutionary paradigm.” Is he not aware that evolution posits UNIVERSAL common descent? I didn’t realise Reasons To Believe were so out of touch. I also find it odd that he doesn’t recognise most of the same attitudes and tactics in his own opposition to evolution that he so frequently encounters and decries in YECs’ opposition to other areas of science.


Jim - #39346

November 10th 2010

If BioLogos is attempting to build bridges with other evangelical organizations that have a high respect for science and scripture (e.g., RTB), this is absolutely the wrong way to do it.


R Hampton - #39348

November 10th 2010

A “high respect for science” would include acceptance of common descent and the associated empirical data like the great similarity between the genomes of Man and Chimp. Consequently, RTB’s theological objections betray such a notion.


Vera Berry - #39364

November 11th 2010

My expertise in science is not evolution but anatomy and physiology in humans. Specifically, I am a neonatal RN.  Over the years, I have dealt with premature infants more than any other situation in medicine. And if there is one thing that I know, it is that humans do not respond well to incremental changes in respiration as neonates. IOW, they die if someone does not intervene. For the naturalistic evolutionary model to work, neonates must be able to adapt to a whole new set of respiratory conditions without intervention. Not even a million years would accomplish such a feat. Blood pH only has a small margin to fit in. 7.35-7.45

RTB’s model, imvho, takes the breadcrumb trail that God left within the creation as shown in Scripture and shows how the testing of the natural world demonstrates His hand in creation in this faith-based universe.  RTB reconciles and demonstrates the harmony of the Bible and science.

The problem with not being specially created is that there is no special purpose for mankind. He is nothing more than a glorified animal and that is not who we are. There are people on a fast track to hell because they doubt the Bible. We have effectively shared this material to help them regain their faith in the Word.


Louise - #39392

November 11th 2010

Thank you to Professor Venema for this article, as a layperson it is difficult to interpret and comprehend (or maybe it is just me) the various genomic studies due to the scientific terminology and methodology. If the human and chimp genomes have a higher percent similarity than RTB material is saying then they should be correcting that and not misleading people.

I heard a recorded talk online somewhere that said the horse and zebra genomes were more dissimilar than the human and chimp genomes or something to that effect. I tried to google that and came up with recent scientific papers but I cannot tell if just certain sections of the genomes were compared or the whole genomes and what the percentages are.  I wonder about comparisons of African and Indian elephant genomes and brown bear and polar bear genomes etc. Is there a good resource that someone can point me to that discusses some of this new genomic information? I have read Shubin’s “Your Inner Fish” which was interesting but not quite what I am looking for.


R Hampton - #39421

November 11th 2010

The problem with not being specially created is that there is no special purpose for mankind.

The Catholic Church teaches us that only the soul is directly and divinely created, and of course, that only humans ensouled as such. Because God chose when, where, and to which of our ancestors to bestow eternal souls, Adam and Eve were the first human animals to become human beings. Thus evolution does not affect - one way or the other - our special purpose.


Rich - #39452

November 11th 2010

Comment removed because of straying from the topic in the Dr. Venema’s post


R Hampton - #39455

November 11th 2010

Comment removed because of straying from the topic of Dr. Venema’s post.


Moses Kostamo - #39570

November 12th 2010

Great article Dennis, and thank you Fuz for responding/contributing to the conversation.
I am a lay person, but my understanding the situation is…that RTB has acknowledged more recent studies, but continues to rely on the older ones as the newer studies undermine their position. Am I correct? It would be nice to hear some explanation from RTB why the newer/more complete material is not referenced, or if they feel it is flawed.  If they are aware of more recent data, but choose to ignore it…it does seem they are being deliberately deceptive.


Dennis Venema - #39606

November 13th 2010

Hi Moses (how’s life up in PG these days)?

My interest in how RTB handles the chimp / human comparison started more than a year ago when I listened to a recorded tape of Rana claiming that the identity value was 85% - 90%. Frankly, that floored me - it’s common knowledge among geneticists that the comparison value, even including indels, is around 95%. Even Answers in Genesis admits that! At first I thought that RTB just didn’t know about the key paper, but to my surprise they did - but they had never acknowledged it in their books.

Even more surprising was the podcast I reference above in the article where RTB claims that the Xenopus : human identity figure is 80% (as way to try to throw all genomic comparisons into doubt). I’d be VERY interested in seeing RTB justify that value in writing. You can’t take two wildly different measures (one significantly underestimating human/chimp, one grossly overestimating Xenopus/human) and attempt to disparage a whole field of study (comparative genomics) by inappropriately comparing them directly. (cont)


Dennis Venema - #39607

November 13th 2010

(Cont from 39606)

This sort of pattern, and reading through the RTB literature / listening to RTB podcasts to make sure it wasn’t an isolated case but really was a pattern, finally convinced me I needed to write this article. I did spend quite a bit of time praying it through first, though.

In the end I decided it needed to be said. RTB is an overtly Christian organization, and this pattern, whatever the cause behind it, hinders my Christian witness to my colleagues in the biological sciences. From their viewpoint, they see it as deliberate deception in order to support a religious view. I have been careful here not to accuse RTB of wrongdoing, but merely lay out the data and explain how it appears to outsiders. We also gave Fuz an advance copy before posting it here.

Perhaps in the coming days we will see a response from RTB that addresses these issues.


Kim - #39692

November 13th 2010

As an avid follower of RTB and Biologos, it would be nice to see the two of you working together more. In my honest opinion, Biologos stands on shaky theological ground while RTB may need to update their scienctific case. If you guys combined forces, I believe it would tremendously help those of us struggling with this debate altogether. Calling each other out on mistakes is only going to slow this process down.

God Bless!


Dennis Venema - #39700

November 13th 2010

Hi Kim,

Thanks for the comment. I can’t quite picture how RTB and Biologos working together would look. On the science side, RTB is an antievolutionary organization: they deny common ancestry; claim that pseudogenes are all functional/will be shown to have function; claim that whole-genome comparisons between humans and chimps have never been done; claim that the entire field of human population genetics is flawed in favor of their model, which is not scientifically rigorous, etc etc. The RTB approach is to create an “alternate biological science” that fits their model of scripture. The RTB model is not scientific, and it misrepresents large areas of biology.

The mission of Biologos, on the other hand, is to promote an understanding of mainstream science within the Christian community, and provide resources to help Christians see that genuine science is not a threat to faith (at that it can even be theologically invigorating).


Page 2 of 3   « 1 2 3 »