Saturday, June 6, 2009

Studies of the Human Genome

Due to continual advances in DNA sequencing technologies, we have recently witnessed an explosion in the amount of DNA sequence data and the emergence of the field of genomics. The amount of sequence information continues to grow exponentially. Although sequencing the human genome for the first time was a monumental task, it is now much easier to obtain and compare the sequences of entire genomes.

In addition to humans, many other organisms have been sequenced, which allows comparisons with each other and with the human genome. Comparisons of the human and chimpanzee genomes have aroused special interest because it has been shown that the human and chimpanzee genomes share over 98% of their DNA sequences.

This high degree of similarity has troubling implications for those who believe that the Bible teaches that humans and chimpanzees are separate creations. Todd Wood is such a person who is trained in genomics and has examined this data closely. Wood’s paper can be seen here.
Although the paper is three years old, the story will not have changed substantially, except that the chimpanzee sequence is now more complete.

Wood treats the data honestly and candidly. Since he rejects a priori the possibility of common ancestry between chimpanzees and humans, he investigates possible ways of accounting for the high degree of similarity, none of which are well developed.

We invite you to read this paper carefully and comment on it.

If you need clarification on a point he makes, that's fine too.

How much are Wood’s suggestions for reconciling these data worth investigating?

If common ancestry is the best explanation of the data, what are the theological implications?

How would you fit Adam and Eve into such a scenario?


Dennis Venema said...

Thanks for posting this, Tony. I will provide my analysis in the next few days.

I am hoping, however, that others will be willing to interact over this paper, especially those who are uncomfortable with the idea of common ancestry.

There have been several individuals on this blog who have readily expressed doubts, concerns, etc about common ancestry. Digging through some of the blogs of these individuals, I note times when you have expressed doubts or theological concerns about "evolutionists" or evolutionary biology. Perhaps some of you do this from the pulpit from time to time, I wonder?

How is it then, given that this is obviously an area of concern for you, that you do not take the opportunity to grapple with the evidence - even if it is presented by someone who shares your presuppositions? Tony has even offered his expertise to help you understand Wood's paper, if need be.

So, my exhortation to you: you should at least attempt understand what you criticize, or cease criticizing those who have taken the time to grapple with the data.

Suppose Galileo could have offered Calvin a view of the phases of Venus through his telescope. Do you think he would have refused?

Jitse van der Meer said...

Comments by Jitse van der Meer on: Wood, T. C. 2006. “The Chimpanzee Genome and the Problem of Biological Similarity.” Occasional Papers of the BSG, No. 7: 1-18.

Overall, I found the review of comparative genomics very clear, professional and confidence-inspiring because Wood pointed out all the problems in creationist reasoning. Here is a rarity: a creationist author who is not biased. It has been a long time since I met one. The deeper reason for my appreciation is that here is a brother in Christ who is not an embarrassment for Christianity.

I do have comments mainly about the part that deals with an alternative creationist response, but that is fine. He makes an honest attempt and that is always to be appreciated.

p. 9, RE: “(2) biochemical similarity is functionally necessary in order for humans (and other organisms) to obtain food” and “The necessity for a common biochemistry for nutrient cycles does not explain why chimpanzees exist. They neither form a major source of dietary nutrients for most humans nor share a significant fraction of the diet of most humans.”
JITSE: here Wood evaluates an explanation for similarity offered by his scientific creationist colleagues. They suggest that genetic similarities have been created because humans and chimps must deal with similar functional requirements. I am puzzled by Wood’s assertions. True, this does not explain why chimps exist, but the problem being addressed is the similarity, not the existence of chimps. I am even more puzzled by his assertion that chimps are not food for humans. Am I missing something or is this as irrelevant as I think it is?

p. 11, left column, RE. flaws in Darwin’s reasoning.
“The first flaw is the theological assumption that the Creator’s will is unknowable.”
JITSE: this is a flaw only when taken as referring to God’s will regarding spiritual matters. But the context indicates Darwin was referring to God’s will with respect to the design of organisms. On that point Darwin was correct – God has not revealed his will.


Jitse van der Meer said...

Comments by Jitse van der Meer, continued.

p. 11, left column, RE. second flaw.
“The second flaw is the conclusion: If the scheme can be shown to be the same as resulting from common descent, it does not necessarily diminish the probability that God created it that way (since we don’t know why God created similarities). Instead, Darwin should have concluded that it becomes probable that common descent produced the scheme, assuming that no other explanation can be found - either natural or as determined from divine will.”
JITSE: there is a flaw in Wood’s argument, namely that Wood is accepts explanation in terms of divine action in science and blames Darwin for not holding the same position. That is exactly what Darwin explicitly did not want to do. Wood should have taken Darwin on his own terms and then there is no flaw in Darwin’s argument.

p. 12, RE: “Despite these shortcomings, it is possible that ReMine’s message theory could be modified to explain biological similarity.”
JITSE: According to Wood there must be an undeciphered grammar and syntax for the patterns of nucleotides in DNA. Once we unravel it we can read God’s message to us. This would be like decoding the Rossetta Stone. Speculative, but fascinating. Also desperate – according to information theory a sequence of thousands of the same nucleotide could not contain information. And there are lots of repeat sequences.

p. 12: RE: “Furthermore, a network pattern of similarity resulting from transposition could serve a non-naturalistic function since a network pattern is not expected from tree-like inheritance.”
JITSE: This is the first time he uses ‘transposition’ without explaining what he means. As a result, I do not understand how transposition could produce a network pattern of similarity that resists naturalistic explanation. If ‘transposition’ refers to the random exchange of chromosome segment throughout an individual’s genome, then there would be an explanation in terms of natural causes. Moreover, Wood seems to resort to a God-of-the-gaps approach: if a naturalistic explanation fails, divine action can explain it. I believe that even if there is a natural explanation, God is ‘doing’ it.

p. 12 right hand column.
JITSE: Although evolutionary biologists would see this argument as a throw-back to a static Aristotelian universe, I feel Wood has a substantial point. He sees organisms as wholistic entities and so do I. There is no convincing empirical evidence that wholes do emerge from parts such as in matter to life transition or life to mind.

p. 13, RE: Baraminology.
JITSE: The notion of a ‘baramin’ or creation kind originates from reading the biological species concept into the text of Genesis (created after its kind). I am disappointed that Wood is dropping is critical attitude here – it does not fit his previous style.

Jitse van der Meer

Tony Jelsma said...

Perhaps it will help to address some of the theological implications of common ancestry in turn. I personally feel that the best explanation of the data that Wood presents is common ancestry and would like some help from the theologians (amateur or professional) on the theology.
I can think of at several questions:
Firstly, how would the interpretation of passages like Genesis 1:27 and 2:7 be affected by common ancestry? Does a Reformed hermeneutic allow it?
Secondly, what are the theological implications of human death before the Fall, which common ancestry seems to require?
Thirdly, how do we interpret the Fall in such a scenario? Was it a real event, with a single person (or two)? How is our sinful nature transmitted, if we are all conceived and born in sin?
Fourthly, does common ancestry require or allow any kind of "divine intervention" in the process? I put the term in quotes because Reformed believers recognize that God is involved in every process, whether natural or supernatural, but you know what I mean.

Dennis Venema said...

First off, credit where credit is due: Todd has written a paper about human : chimpanzee homology that deals with the data honestly and forthrightly. Todd is another rara avis in the tradition of Kurt Wise. He is the only YEC geneticist of whom I am aware who deals with the data properly.

Todd is also a staunch believer that the YEC paradigm will ultimately carry the day: as such, he believes that in order to advance model-building from a YEC perspective, the movement needs to deal with the reality of current science. Todd’s approach stands in refreshing contrast to the anti-realism common to the YEC movement.

Todd’s discussion of the data, including his evaluation of common YEC arguments against common ancestry is worth the price of admission alone. This paper has stirred up trouble for Todd, I understand. For example, I know of no YEC ministry that links to, or even mentions this paper. As an example, a thorough search of the Answers in Genesis website (for whom Todd writes other material) turns up no evidence that this paper even exists. Likewise for the papers by Kurt Wise I have mentioned before. After I attended a recent YEC presentation on human evolution I emailed the speaker to ask if he was aware of Todd’s paper, and the fact that Todd rejected all of the arguments he had offered in his talk. After a little back-and-forth to provide him the link to the paper, I never heard from him again…


Dennis Venema said...

Todd’s paper is very odd from a YEC perspective: it has no apologetic value, it asks difficult questions, and it does not provide the simple, easy answers that YECs long for. Furthermore, the paper undermines many of the easy answers and apologetic approaches presented by the YEC movement. No wonder the movement, as a whole, wishes this paper didn’t exist.

Why then, did Todd write this paper? Because he’s first and foremost a scientist. He's also a true believer in the YEC approach. Ergo, he feels the need to try to advance a scientific model from a YEC perspective. (As an aside, I suspect most YECs have no real interest in the science, having rather only an interest in apologetics). Todd's paper is a clarion call for honesty in the YEC approach to origins – a call that, unfortunately, has gone unheeded.

What of Todd’s suggestion to revisit the work of ReMine? For those not familiar with ReMine’s work, he is an engineer (I believe) and ID advocate who has self-published a large (and, I have heard, rather difficult to understand) book called The Biotic Message. In it he discusses his “Message Theory” – two key points of which are as follows: all life is designed to demonstrate that there is only one Designer, and it is designed in such a way to resist all macroevolutionary explanations.


Dennis Venema said...

Todd is suggesting a modified form of ReMine’s thesis, I suspect, because he knows that ReMine’s second point above has utterly failed. Wood hopes to salvage the first point, however: that the biological similarity we see is the result of the Designer sending us a message that there is only one designer.

I don’t think there is much to be had from this line of argument (and, to be honest, I’m not sure if Todd does either). The amount of similarity we see between us and chimps goes way beyond what is needed to establish continuity of design, and extends into areas difficult to explain from a design perspective (such as shared errors like pseudogenes, etc). I suspect the appeal here is that Todd sees hope for salvaging this approach as an apologetic, not as a scientific approach. We will have to see if he fleshes out these ideas in the future.

I think this paper goes a long way to explain why there are so few individuals like Todd: once having seen the data and engaging it honestly, there are very few who are so tied to their YEC presuppositions that they will maintain the YEC approach knowing full well the quality and quantity of the data against their position. The vast majority fall rather into other responses: a refusal to honestly grapple with the data, or, once having seen the data for what it is, they move on from a YEC position.

Arnold Sikkema said...

One of our readers alerted us to an article on this topic found in the most recent on-line issue of Comment. Addressing the nature of the discussion, Lorna Dueck writes, “[W]hile I do not have much of a science background, I do have a job that demands of me that I encounter and engage fellow believers who are scientists…and their ideas.” I appreciate the patience of my biology colleagues as I overcome my own limitations in their field and attempt to take seriously what they have experienced in their discipline as we together seek to be faithful to Scripture and the Reformed confessions.

Tony Jelsma said...

Thanks Arnold, and our reader, for pointing out this article.
I do wish to draw attention to one paragraph in this article.

"Collins finds the Intelligent Design approach inadequate because, he says, it fails to qualify as a scientific theory. He argues that the Intelligent Design movement's arguments on the basis of irreducible complexity and similar "God in the gaps" explanations crumble in the face of scientific discovery. Instead, Collins believes in "Theistic Evolution," which means that he seeks to argue scientifically—in harmony with Christian faith—that the universe is 14 billion years old; that evolution, once begun, required no special supernatural intervention; and that the human race began with a colony numbering approximately 10,000, likely located in East Africa."

I have several comments to make about this paragraph.
Firstly, quite frankly, I'm getting tired of people saying what qualifies as a scientific theory and what doesn't.
Secondly, if Collins has read Behe's second book, he will see that irreducible complexity and other features of design do not crumble in the face of scientific enquiry. The origin of life is a particular case in point.
Thirdly, I'm wondering why no "special supernatural intervention" is permitted. That may well be the case but to prescribe how God may or may not create displays more hubris than I would dare.
Finally, the claim that humans started with a population of about 10,000 people in Africa has clear theological implications.
I have been waiting for over a week for our theologians to address my questions about common ancestry, to no avail. What does this mean for a literal Adam and Eve? The Fall?

Tony Jelsma said...

In case it wasn't clear from my last post (it probably wasn't), my criticisms are addressed to Francis Collins' comments, not the writer of the article, with whom I agree, particularly her last paragraph.

Dennis Venema said...

Hi Tony,
Are you speaking of Edge of Evolution? That book was the final nail in the coffin for me in terms of ID. Behe's arguments are fatally flawed. EoE is what you get when an antievolutionist biochemist tries to write a book on population genetics (no offense to any antievolutionists and/or biochemists present). This doesn't mean his ideas are "disproved," but EoE won't take you there. There’s a reason why Behe doesn’t submit his ideas for peer review.

I've been meaning to query you about ID. You seem to be ok with common descent of humans and chimps - are you a Behe-type IDer, then? If I may ask, what part(s) of modern evolutionary theory do you dispute, and why?

Tony Jelsma said...

Hi Dennis,
I'll respond more fully later but I first need some clarification on your position. Will you accept the possibility that living organisms can show evidence of design that can be scientifically detected?

Secondly, when surveying the views of theistic evolutionists, I find a surprising antipathy towards the idea that God might have somehow "intervened" in the creative process. Reformed believers hold that God in his providence upholds all things but I have had difficulty finding a theistic evolutionist who does not require some kind of "true randomness" which is random even to God. Darrell Falk might be one such person, what's your position?

Dennis Venema said...

Hi Tony,

You ask:

"Will you accept the possibility that living organisms can show evidence of design that can be scientifically detected?"

To answer that, I'll need to know what your definition of "design" is, as well as your definition of "scientifically." I have an ID colleague here at TWU in chemistry, and we go the rounds on these topics over lunch from time to time, and (like you) I find it helpful to have the definitions clear from the get-go.

As for your "truly random" comment - I'm not sure what you mean, to be honest. I don't think anything is "truly random, even to God" if by that you mean it is beyond God's control. Perhaps Arnold would like to comment on that from a physicist's perspective?

As for antipathy towards an "interventionist" idea of God: if evidence were present that such a "discontinuous" event had occurred, I would be happy to weigh it and consider it. It is certainly within God's purview to "intervene" (if one can really call God interacting with His creation 'intervening' in any meaningful way). Nothing in biology that I have seen thus far makes me reach for the "miracle" category as of yet. Nothing I have read in the ID literature makes me reach for that category either.

From a Reformed perspective, you rightly recognize that God ordains and sustains all things, and that this is no more or less "miraculous" than what we might call a "discontinuity" or "intervention." In that vein I very much enjoyed reading Arnold's take on an apple obeying the command of God as it falls.

To give you some more info on how I view ID, I see it as an argument from analogy: things in biology are analogous to things we know are designed (by people or animals); ergo, the biological entity is designed. Well, the strength of that argument depends on the strength of the analogy - I have yet to see a case where, in my view, the analogy holds up. The other line of argumentation I see in ID (Dembski's Explanatory Filter, for example) seems to me to be an argument from ignorance. You can't use Dembski's filter unless you have perfect knowledge of all "natural" mechanisms. I have also never seen Dembski actually use his filter and publish the results. Have you?

Another problem I have with the ID movement is that as it focuses on narrow examples (the flagellum, for example) it seems to dividing biology into "the miraculous bits God did" over against "the natural bits God wasn't involved in because 'Darwinism' can explain those." Well, I prefer to see God as the authour and sustainer of the whole deal. In their zeal to "prove" a Designer, I think they're ignoring a big part of His design.

Or so it seems to me. Your thoughts are welcomed.

Anonymous said...

Randomness is another concept (like Reality) that people use freely without bothering to define. I'll give my own definition: An event is random if it is not predictable knowing the preconditions. Thus, "random to God" is just an oxymoron. God knows all time and can "predict" or know any point of time.

I agree with Dennis. I find ID problematic in that it is interventionist, making a false distinction between regular and miraculous providence to explain existing scientific data.

--rick baartman

Tony Jelsma said...

Rick Baartman defines randomness as "An event is random if it is not predictable knowing the preconditions. Thus, "random to God" is just an oxymoron. God knows all time and can "predict" or know any point of time."
I agree entirely, but most TE's don't stop there but add that the randomness also applies to God. Why?

Rick further says, "I find ID problematic in that it is interventionist, making a false distinction between regular and miraculous providence to explain existing scientific data."
I would counter that (a Christian) ID would hold that God's actions in creation are not limited to the nonmiraculous but might include events that contravene the "laws of nature" or more precisely God's usual mode of action in providence. Our job is to try and find out what really happened.

The evolution of the first living cell isn't going to happen any other way, based on what we know about the origin of biomolecules, their combining into polymers and their being enclosed by cellular membranes.