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An Evangelical Geneticist’s Critique of Reasons to Believe’s Testable Creation Model, Pt. 2

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November 18, 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. 2

In part one of this series, Dr. Venema examined how Reasons to Believe (RTB) represents comparative human-chimpanzee genomics in its “Testable Creation Model.” In this section, he continues his evaluation of the RTB model by examining how it handles pseudogene evidence for human evolution. The full paper with complete footnotes can be found here.

The RTB Model and Pseudogenes

Pseudogenes (literally, “false genes”) are the remnants of once-functional genes that persist in genomes after they lose function. Pseudogenes are often shared among species in a nested pattern that strongly supports common ancestry. Additionally, the human genome harbors pseudogene remnants of genes devoted to non-mammalian ways of life. For those unfamiliar with this line of evidence for evolution, Darrel Falk and I have recently written about pseudogenes in the human genome for a lay audience. Since shared pseudogenes are such clear indicators of common ancestry, RTB has also expended significant effort on discussing pseudogene data in their major works. As such, pseudogene evidence is a second opportunity to test the scientific reliability of the RTB model.

Understanding the difference between two specific classes of pseudogenes is important for evaluating the RTB literature: specifically, processed versus unitary pseudogenes. Processed pseudogenes are the remains of RNA copies of genes that have inserted themselves into chromosomes, whereas unitary pseudogenes are the remains of genes that have been inactivated due to mutation. In the case of processed pseudogenes, the original gene remains intact and functional.

One of the most compelling features of pseudogene evidence for common ancestry is that pseudogenes (of all kinds) form nested hierarchies. Consider an example phylogeny (evolutionary history, or family tree) for four modern species (A, B, C and D) given in the figure below.

Phylogenies can be assembled using genome sequence similarity (grouping more closely related organisms together) as well as through other measures, such as anatomy. A phylogeny assembled through these criteria (which agree and reinforce one another) can be used to predict what the distribution of various pseudogenes will be in the four modern species. For example, pseudogenes from the very distant past (and thus present in the common ancestor of the whole group) will appear in all modern species, with the same mutations. Pseudogenes shared by species A and C (e.g. the pseudogene form of “gene X” in the diagram) are best explained as having been present in their common ancestor. Since the common ancestor of A and C is also the common ancestor of species B, observing a shared pesudogene between A and C makes a precise prediction: if the species do share common ancestry and we have the phylogeny correct, species B should have the same pseudogene with the same mutation. The pseudogenes should be present in a nested hierarchy. Note too that mutations may happen in a lineage after its last known speciation event (e.g. “Gene Z” in species C). In this case, this pseudogene should be unique to that species: we should not find it in the other species in the phylogeny.

One example of a nested, hierarchical pattern of unitary pseudogenes in primates is that of olfactory receptor pseudogenes. An analysis of these pseudogenes in humans, chimpanzees, gorillas and orangutans produces a nested hierarchy that independently groups these species into a phylogeny identical to the one assembled from sequence homology data: humans share the most pseudogenes in common with chimpanzees, less pseudogenes in common with gorillas, and so on (see below):

Most importantly, the nested hierarchical pattern is not violated: for example, all the pseudogenes present in both gorillas and humans (and thus in the common ancestor of these species) are present in chimpanzees (since the common ancestor of humans and gorillas is also the common ancestor of chimpanzees). Not one of these pseudogenes is out of place. A second, equally powerful line of pseudogene evidence for common ancestry is the presence of pseudogenes that show adaptation to manners of life that do not make sense for the organism in question. Whereas humans do need (at least some) olfactory receptors, the human genome contains pseudogene remnants of genes that mammals do not need. One example that I have discussed previously is the vitellogenin pseudogene found in the human genome. Vitellogenin is a protein component of egg yolk, and as such is a functional gene in amniotic (egg-laying) organisms. Humans are of course placental mammals, yet we have the vitellogenin gene present in our genomes as a unitary pseudogene. The two functional genes flanking the human vitellogenin pseudogene are the same two genes flanking the functional vitellogenin gene in chickens. These data make perfect sense if humans are descended from egg-laying ancestors and share common ancestry with chickens. It is very difficult to rationalize this data from an antievolutionary perspective. Since the common ancestor of humans and chickens was a reptile, this indicates that the vitellogenin pseudogene should be present in all non-egg-laying mammals. Studies so far have found this unitary pseudogene in wide variety of additional species ranging from dogs to wallabies. As expected, egg-laying mammals such as the platypus retain a functional version of this gene.

Unitary pseudogenes present in nested hierarchies that independently group organisms into phylogenies assembled with other data are incredibly powerful evidence for common ancestry. Additionally, the fact that the genomes of multiple placental mammals (including humans) contain a unitary pseudogene clearly adapted for egg laying (in the precise genomic location predicted by common ancestry), is very challenging to explain from an antievolutionary perspective. Accordingly, any attempt to scientifically refute common ancestry must address these types of evidence in a convincing manner.

The most extensive discussion of pseudogene evidence for common ancestry in the RTB literature is found in WWA, where an entire chapter is devoted to the topic (pp. 226 – 243). While WWA does not specifically address the fact that pseudogenes are observed in nested hierarchies, it does at least mention that unitary pseudogenes with identical mutations are shared between primates, including humans and chimpanzees (pp. 228-230, 243). The more recent RTB books, however, make no mention of these data when discussing pseudogenes. The core of RTB’s attempt to refute pseudogene evidence in all three books is their claim that pseudogenes are functional sequences: “Non-coding DNA regions (including pseudogenes, LINEs, SINEs and endogenous retroviruses) aren’t really junk after all. These elements possess function.” (p. 235)

The evidence offered for this assertion are examples of pseudogenes and other “junk DNA” that have been shown to have function, specifically processed pseudogenes, SINEs and LINEs that have been implicated in gene regulation (pp. 235-243). This argument, however, is scientifically weak: rare examples of processed pseudogenes and repetitive DNA elements such as LINEs and SINEs that have retained or gained a function does not confer similar functionality on the many thousands of such sequences for which there is good evidence that they are not functional. Beyond this weakness is a more serious flaw: evidence for unitary pseudogene function is lacking. In WWA, RTB candidly admits that evidence for unitary pseudogene function is not to be found:

“What about the genetic material without a known function, such as the GLO unitary pseudogenes that humans and chimpanzees share? Currently the RTB model offers no explanation for this feature. The model does predict, however, that as with other classes of noncoding DNA, function will one day be discovered for these uniting pseudogenes.” (p. 243)

The later RTB books, however, do not distinguish between unitary pseudogenes and other pseudogene / repetitive DNA classes. The same examples of rare functional processed pseudogenes, LINEs, SINEs and endogenous retroviruses are given, but unitary pseudogenes are not mentioned at all in either CAS or MTT. Instead, the selected functional examples of non-unitary pseudogenes are used to imply that pseudogenes in general have been demonstrated to have function. This is misleading. Unitary pseudogenes remain highly problematic for RTB, and becoming vague on this point does not overcome the difficulty they pose for the RTB model.

In summary, discussions of pseudogene evidence in the RTB model are selective, misleading and simply ignore the strongest lines of evidence that pseudogenes provide for common ancestry. The RTB approach to pseudogenes also suggests that the differences between WWA and the two more recent books may be a pattern: RTB is able and willing to provide extensive detail when the data are inconclusive, but becomes vague and imprecise when data that challenge the model become available.

Conclusions

As we have seen, the RTB model of human origins with respect to common ancestry is seriously flawed. It misrepresents well-established science, fails to address the strongest relevant evidence against its position, and selectively presents data in an attempt to support a pre-determined position that humans and other apes do not share ancestry. As such this model is not a model that a believer can hold with scientific integrity. It may well be that RTB offers their model in good faith: if so, however, it demonstrates that they are not qualified to address these lines of evidence in a scientific manner.

While this series presents a careful analysis designed to substantiate my conclusions for a non-specialist audience, it should be noted that the scientific flaws in the RTB model are blatantly obvious to working scientists within the biological sciences. Moreover, scientists are likely to interpret these flaws as obfuscation or deliberate deception. As such, the packaging of such arguments with an overt Gospel message seriously compromises a Christian witness within this group and raises unnecessary barriers to faith. Within the community of believers, the extent to which one’s faith is supported by such arguments is also the extent to which one is rendered vulnerable to crisis should those arguments fail: “today’s reason to believe” sets one up for tomorrow’s “reason to disbelieve” should the evidence be examined.


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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Benoit Hébert - #40533

November 18th 2010

I am no geneticist, but I’m convinced by the evidence! As Old Earth creationnism is the most common view among French evangelical christians (I’m French), I thank Denis Venema for such an analysis. It will be very useful!


Terry - #40556

November 18th 2010

What does it say about RTB that they have been so publically shamed and yet have still made no response? Their organisation has been shown to be scientifically incompetent, and exposed for promoting falsehoods and fallacies, yet they appear to be ignoring this publication humiliation. Are there any supporters of theirs who are willing to stand up for them? Do any still exist? What does this behaviour mean for an organisation which claims to “promote harmony” between science and Christian faith?


Argon - #40559

November 18th 2010

The ‘pseudogenes have function’ counter is simply a red herring.

To Dennis’ commentary I would add that it is not just pseudogenes displaying nested heirarchy but other ‘macro-DNA’ structures as well. These examples include gene & sequence order, and relative chromosomal location. We see things that retain the hallmarks of having arisen and diverged as discrete units and we are familiar with the biochemical mechanisms that generate such rearrangements. Models based on ‘common design’ (as opposed to descent with modification) lack explanatory specificity to understand the gross chromosomal relationships we observe.


Darrel Falk - #40568

November 18th 2010

I would like to indicate that I’ve had communication with Dr. Rana about this matter.  Clearly, I wish he and others at RTB would have moved sooner to address the issues that Dr. Venema poses here.  Although I have no doubt that Dr. Rana and Dr. Ross are wrong about all of this, I want to emphasize that I remain absolutely convinced that they and others I have met at RTB are sincere people who I respect as brothers and sisters in the Lord.  They have expected a scientific answer to be forthcoming.  Although they are mistaken about the science, and they will eventually have to shift their position, I am praying that they might sense God’s Presence.  If you are a believer, I ask that you will join me in prayer about this matter.  If you’re not, please note how fellow Christians are called to work through differences.  We are called to much higher standards, and too often we fail.  But called we are, and we will do our best to honor our calling.

I am also very grateful to Dr. Venema for his very thorough and fair analysis.


Glen Davidson - #40572

November 18th 2010

Isn’t it wonderful how such duplication is miraculously created in organisms with separate origins?

OK, so much for the snark.  I just went for it because anti-evolutionists are practiced at coming up with excuses.

The difference between microevolution and macroevolution for so many is that the evidence that “proves” common ancestry in the former indicates no similar conclusion for the latter.

Glen Davidson


Argon - #40573

November 18th 2010

“Although they are mistaken about the science, and they will eventually have to shift their position, I am praying that they might sense God’s Presence.”

Darrel, I can appreciate your efforts but *why* will they have to shift their position? Is there anything new to bring to the table that wasn’t there several years ago? It’s hard to be: 1) a scientist, and particularly a biologist, 2) Interested in the area of work & 3) Not know about the plethora of data already out there. The core issue has little to do with science which only serves as a thin coat to justify a preferred scriptural interpretation. Data has little impact on such commitment.


Darrel Falk - #40576

November 18th 2010

Argon, 40573,

The data eventually wins the day.  If it doesn’t win over the people who run an organization, it certainly does for those who provide the financial resources.  I have too much respect for the sort of people that provide RTB with financial backing (engineers, medical doctors, successful business people, etc.)  to think that being so out of touch with scientific reality will be able to go on forever. 

I also think that people will come to recognize that their Concordist approach to reading Scripture (getting scientific data from the Psalms and from Job for example) causes one to miss the richness of what God wants to say in these magnificent God-inspired masterpieces.  Our God is too big for that and the people who provide the resources will come to see this.

Again, I ask that we, all of us, make this a matter of much prayer—not so much that one side will win, but that we might all be conscious of the love and Presence of God.


JWF - #40577

November 18th 2010

This post caused me to pause and consider the influence Reasons To Believe has had in my thinking. Like many conservative evangelical laymen, I’m on a journey from YEC to Evolutionary Creationism, and some of the first and most influential material I was exposed to was RTB’s.  I was at once impressed by the compassion expressed in Hugh Ross’ books, and was greatly relieved to find an organization that could make sense of modern cosmology and astronomy in light of biblical truths. Although I’ve moved on to embrace evolution rather than special creation, I’m still grateful to RTB for first revealing to me that mainstream science and faith are not necessarily incompatible.

It will be interesting to see what adjustments RTB makes to their creation model. Handled correctly, this could be an opportunity to greatly strengthen their ministry and widen their outreach. Conversely, there is an opportunity for disaster here as well.

Dr. Venema, thank you for sharing your expertise. Your efforts are greatly appreciated.


Cal - #40592

November 18th 2010

JWF:

I had the same experience as you! Strangely enough, playing too many ‘space-aged’ games got me thinking over the age of the universe and creation. I started to dig, not finding the 6k years and special materialization of life plausible as the evidence of almost every major science points away from it (and God is God of all truth and does not lie).

I found RTB and from there onto BioLogos and beyond! God bless Hugh Ross and the staff on RTB along with those at BioLogos, with His Infinite Wisdom may we all be guided to gain a better understanding and marvel at the beauty of the work of His hands.


conrad - #40601

November 18th 2010

Well I like RTB.
So I am sure this post will be deleted.


DWD - #40617

November 18th 2010

“While this series presents a careful analysis designed to substantiate my conclusions for a non-specialist audience, it should be noted that the scientific flaws in the RTB model are blatantly obvious to working scientists within the biological sciences. Moreover, scientists are likely to interpret these flaws as obfuscation or deliberate deception. As such, the packaging of such arguments with an overt Gospel message seriously compromises a Christian witness within this group and raises unnecessary barriers to faith.”
This says so well what has motivated me to speak out on these issues in my conservative part of the country. It is NOT OK to to just go along with the prevailing fundamentalist interpretations of the Bible when you believe otherwise yourself. If you are a sincere Christian and not just someone enjoying “head exercises” over all this, integrity requires you to try to show others the failures of Creationist, ID, or RTB pseudo-science in order to witness to God’s truthful character. The hard thing is to present your views humbly and constructively, and to avoid knocking the foundation out from under someone else’s faith. I am still struggling with how to do this…


Karl A - #40647

November 19th 2010

That quote of Dennis’ also jumped out at me, Diane (40617).  May God help us to be truthful and loving as we seek to raise the bar of accountability in the origins debates.

Darrel’s call for prayer for the RTB principals is good too - imagine the heavy temptation they must confront (financial, face-saving, etc.) to NOT face the situation squarely.


John VanZwieten - #40698

November 19th 2010

Question for JWF and Cal,

Do you think you could have jumped to BioLogos directly, without moving through RTB first?


conrad - #40711

November 19th 2010

RTB should probably give up on this one.
But they have done a lot of good work making people look at science.

Genomics has developed so rapidly that everyone is probably outdated in their understanding.

My opinion is that if God made us on the Chimp chassis we are STILL AN UPGRADED MODEL OF BIPED.

THE BIBLE SAYS WE ARE MADE FROM THE “DUST OF THE EARTH”,.. I.E . EXISTING GENOMIC MATERIAL.

Apparently the writer of Genesis hoped to defuse just such an issue as has been raised,.. by preparing us with that statement..

RTB loses on this one but they are still a fine group.

But I agree with DWD,..... thinking independently is good too.


Cal - #40712

November 19th 2010

John:

It’s possible, both have a candor about them that they know science, as is done in the university, is “thinking God’s thoughts after him” and not some boogeyman shadow organization trying to destroy Christ (as if it were possible).**

Though I think RTB is not correct when it comes to their take on Evolution (Not necessarily Darwinism), they are not duplicitous, they are honest truth seekers and that power really gave me a look into the heart of a Christian scientist, something that made me elated.


**While a good chunk of scientists subscribe to atheistic materialism, this doesn’t invalidate all their work. It is only a minority that is being loudmouther, trying to promote their philosophy and take on the world and saying Christ is not compatible.


JWF - #40713

November 19th 2010

John (40698),

“Do you think you could have jumped to BioLogos directly, without moving through RTB first?”

I think the answer for me is no, given my particular background, I wouldn’t have made the jump straight to BioLogos on my own. I needed stepping stones, and RTB, among many other resources, helped me along the path. The word “evolution” still carries caries a lot of negative connotations among evangelicals, hence my original attraction to the term “progressive creation”. I also had to work through a lot of issues concerning the age of the earth and the proper handling of scripture before I was ready to tackle biological evolution head-on.

However, had one of my Christian brothers or a conservative Christian leader suggested or recommended BioLogos, I’m fairly certain I would have given this site a good, hard look. A trusted mentor can often help us find our way far more quickly than if we have to discover it on our own. Like DWD in 40617, I’m struggling to find ways to be that mentor.


conrad - #40715

November 19th 2010

This site has lots of shortcomings too.

It is probably not a good idea to worship ANY website.


Cal - #40752

November 19th 2010

Conrad:

Agreed


Justin Topp - #40841

November 20th 2010

Dennis,

These critiques and your PSCF paper have been outstanding.  Not sure if you saw the recent PLoS Genetics paper on endogenous viral elements but it was blogged about today by Ed Yong (http://bit.ly/9TCO5q) and Carl Zimmer (http://bit.ly/9x8Ijd).  Another tool to add to your toolkit…


James Blair - #40908

November 20th 2010

I would be glad to stand up for RTB if I was promised that my posts would not be deleted or removed.

I am not going to post lengthy posst that refute your positions only to have them eliminated.

So…do I have your moderators promise?


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