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Respected Cornell geneticist rejects Darwinism in his recent book

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Genetic Entropy & the Mystery of the Genome
by John Sanford (October 2005)

Genetic Entropy

In retrospect, I realize that I have wasted so much of my life arguing about things that don’t really matter. It is my sincere hope that this book can actually address something that really does matter. The issue of who we are, where we came from, and where we are going seem to me to be of enormous importance. This is the real subject of this book.

Modern Darwinism is built on what I will be calling “The Primary Axiom”. The Primary Axiom is that man is merely the product of random mutations plus natural selection. Within our society’s academia, the Primary Axiom is universally taught, and almost universally accepted. It is the constantly mouthed mantra, repeated endlessly on every college campus. It is very difficult to find any professor on any college campus who would even consider (or should I say dare) to question the Primary Axiom.

Late in my career, I did something which for a Cornell professor would seem unthinkable. I began to question the Primary Axiom. I did this with great fear and trepidation. By doing this, I knew I would be at odds with the most “sacred cow” of modern academia. Among other things, it might even result in my expulsion from the academic world.

Although I had achieved considerable success and notoriety within my own particular specialty (applied genetics), it would mean I would have to be stepping out of the safety of my own little niche. I would have to begin to explore some very big things, including aspects of theoretical genetics which I had always accepted by faith alone. I felt compelled to do all this, but I must confess I fully expected to simply hit a brick wall. To my own amazement, I gradually realized that the seemingly “great and unassailable fortress” which has been built up around the primary axiom is really a house of cards. The Primary Axiom is actually an extremely vulnerable theory, in fact it is essentially indefensible. Its apparent invincibility derives mostly from bluster, smoke, and mirrors. A large part of what keeps the Axiom standing is an almost mystical faith, which the true-believers have in the omnipotence of natural selection. Furthermore, I began to see that this deep-seated faith in natural selection was typically coupled with a degree of ideological commitment which can only be described as religious. I started to realize (again with trepidation) that I might be offending a lot of people’s religion!

To question the Primary Axiom required me to re-examine virtually everything I thought I knew about genetics. This was probably the most difficult intellectual endeavor of my life. Deeply entrenched thought pattern only change very slowly (and I must add — painfully). What I eventually experienced was a complete overthrow of my previous understandings. Several years of personal struggle resulted in a new understanding, and a very strong conviction that the Primary Axiom was most definitely wrong. More importantly, I became convinced that the Axiom could be shown to be wrong to any reasonable and open-minded individual. This realization was exhilarating, but again frightening. I realized that I had a moral obligation to openly challenge this most sacred of cows. In doing this, I realized I would earn for myself the most intense disdain of most of my colleagues in academia not to mention very intense opposition and anger from other high places.

What should I do? It has become my conviction that the Primary Axiom is insidious on the highest level, having catastrophic impact on countless human lives. Furthermore, every form of objective analysis I have performed has convinced me that the Axiom is clearly false. So now, regardless of the consequences, I have to say it out loud: the Emperor has no clothes!

To the extent that the Primary Axiom can be shown to be false, it should have a major impact on your own life and on the world at large. For this reason, I have dared to write this humble little book which some will receive as blasphemous treason, and others revelation.

If the Primary Axiom is wrong, then there is a surprising and very practical consequence. When subjected only to natural forces, the human genome must irrevocably degenerate over time. Such a sober realization should have more than just intellectual or historical significance. It should rightfully cause us to personally reconsider where we should rationally be placing our hope for the future.

John Sanford

Sanford drew heavily from the work of Motoo Kimura, James Crow, and Walter ReMine. He featured a lot of data I had never seen, and he applied the concept of signal-to-noise ratios (from information theory) to show that the selection pressures are too weak for natural selection to transmit useful information into the genome. He made devastating critiques of naturalistic evolution using standard population genetics. It was a superb book, something one would expect from such a capable scientist. I’m surprised this book is relatively obscure, it ought to be required reading for serious IDers!

Sanford’s Bio: Cornell Professor of 25 years (being semi-retired since 1998). He received his Ph.D. from the University of Wisconsin in the area of plant breeding and genetics. He founded 2 successful biotech firms, Biolistics and Sanford Scientific. Most of the transgenic crops grown in the world today were genetically engineered using the gene gun technology developed by Sanford. He still holds a position of Courtesy Associate Professor at Cornell.

Here are some endorsements for the book:

In the Mystery of the Genome Cornell University researcher John Sanford lifts the rug to see what evolutionary theory has swept under it. He shows that, not only does Darwinism not have answers for how information got into the genome, it doesn’t even have answers for how it could remain there.

Michael Behe

I strongly recommend John Sanford’s Mystery of the Genome, which provides a lucid and bold account of how the human genome is deteriorating, due the accumulation of mutations. This situation has disturbing implications for mankind’s future, as well as surprising implications concerning mankind’s past.

Phillip Johnson

(thanks to johnnyb for alterting me to this book!)

Comments
Mung, No apologies necessary :) I agree with your assessment of naming--although there have been cases where people have named genuses from the discovery of individual species. This can only occur, however, once a thorough understanding of the contemporary and past diversity is already well established and that individual species is compared to that context. If you haven't already, see my posts touching on taxonomy/classification above. I was trying to find some common ground with bFast. To his credit, the fact that NDE-biologists were not, collectively, more deeply disturbed by the cambrian explosion-- given how they themselves understood the event it for quite a while--is testament to the fact that there is far more indoctrination in darwinian evolution than actual understanding. On this point I think many of us here are in agreement. Fortunately molecular genetics was ultimately was able to restore some amount of order in the universe so those of us who *were* legitimately disturbed could rest a little easier. A professor of mine once remarked that evolution is one of the most misunderstood theories in science: precisely because it has such a deceptive appearance of simplicity that it lends itself to a misplaced confidence in one's conception of it.great_ape
June 3, 2006
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DaveScot: I actually do think little spirits (called elementals) are the conscious co-creators in matter. Thanks for "outing" me. I believe the vast majority of humans who have ever lived believed this as well. This has no bearing on my credentials as a scientist, though, since I have none!

I suddenly hear the theme music from the twighlight zone playing... -ds tinabrewer
June 3, 2006
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"That reasoning presumes that large taxonomic change is the result of a gradual process of growing genetic separation and that is a presumption without empirical basis because the process is so slow it can't actually be observed accomplishing what is claimed for it." --ds Circular reasoning? Personally, I like to think of it as "reciprocal illumination." In any case, I see what you mean, and even as I was writing my reply I suspected it would not be well received. But it is the best case I can come up with under the traditional framework. While positing a gradualism that is not explicitly observationally grounded (because it is, by my own admission, too slow to be observed) I can only hope to lay out a model of the biological world that I can subject to other tests (e.g. genetic queries, for instance) that *can* be observationally/empirically grounded. If my model holds up under such scrutiny, I would contend that the circularity you allude to is benign, and my justification for belief in the model is increased. This--and you philosophers out there excuse me if I butcher this one--is what I understand to be the "coherence theory" of epistemology, and it is the one I most closely identify with. In this theory, our understanding of the world is not built from the ground up, like a house of cards, but rather constructed like an interwoven fabric. Some threads are not supported directly by empirical evidence, but if they provide predictive and explanatory power for other peripheral threads that *are* supported by empirical data, then they are considered justified beliefs/threads. I won't even attempt to further justify any of this as it pertains to evolution just now, as my cell lines are in need of much tender love and care, but I just wanted to give you a sense of where I'm coming from philosophically. Ultimately, you're right ds, the empirical support for the gradualism premise is I draw heavily upon is, almost by definition, lacking--so I am once again forced to reflect on the philosphical assumptions underlying my argument. If I had access to a master dial that sped up or slowed evolution at my convenience, how fast would I need to crank up the speed before we could be empirically comfortably with the recent formulation of new higher-order taxa? (assuming such generation happens at all, of course) I don't know. I suspect fairly high. In either case, I think the issues I raised concerning the arbitrary nature of taxonomy would remain and would frustrate our efforts at most any tempo. Sigh. Still not a straight answer, I reluctantly admit. I can not say with certainty that creativity via evolution continues. Neither can I say it does not continue. If it has been creative in the past, I see no obvious reason for it to stop being so in recent history. I will, in this case, cling to my uniformitarianism pillow. Once again, I am forced to take refuge in philosophy. Like Hume, I can not even say with certainty that bread will continue to nourish me tomorrow. The pillow, however, lets me rest a little easier at night. Hmmm... Has anyone tried to market a "philosphical pillow" as a novelty gift? --apemangreat_ape
June 3, 2006
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I show below the abstract of a study by Suzanne Estes & Michael Lynch (2003), Evolution 57, 1022-1030. This study seems quite relevant for the discussion about whether or not mutation inevitably dooms populations. Enjoy. Abstract. Deleterious mutation accumulation has been implicated in many biological phenomena and as a potentially significant threat to human health and the persistence of small populations. The vast majority of mutations with effects on fitness are known to be deleterious in a given environment, and their accumulation results in mean population fitness decline. However, whether populations are capable of recovering from negative effects of prolonged genetic bottlenecks via beneficial or compensatory mutation accumulation has not previously been tested. To address this question, long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, previously propagated as single individuals each generation, were maintained in large population sizes under competitive conditions. Fitness assays of these lines and comparison to parallel mutation-accumulation lines and the ancestral control show that, while the process of fitness restoration was incomplete for some lines, full recovery of mean fitness was achieved in fewer than 80 generations. Several lines of evidence indicate that this fitness restoration was at least partially driven by compensatory mutation accumulation rather than a result of a generic form of laboratory adaptation. This surprising result has broad implications for the influence of the mutational process on many issues in evolutionary and conservation biology.Raevmo
June 3, 2006
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No biologist in his right mind, if transported back in time to just after the explosion, would say, “hmmm, we seem to have 50 to 100 separate species here”, or even 50 to 100 separate genuses.
bfast, You're wrong. Apologies to great_ape :). No organism is ever classified as anything other than a species. I've tried to point this out to you before but you just don't seem to comprehend the point. The biologist would classify the organisms into taxa. The starting point would be to classify them into species. No self-respecting biologists would look at one of those organisms and say, oh look, I have a phylum here. What they would have, would be a collection of species. Now, the question to be asked is, would they then be able to create a hierarchical classification from the species that they identified? The point is that they would still be classified as species, but the appearance of common ancestry would be significantly reduced due to the inability to place them into a hierarchical system of classification. Please try to understand this.Mung
June 3, 2006
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Michael, thanks for your thoughtful post. Let me try to answer some of your questions. In particular, I'd like to make some distinctions in order to clarify some issues.

First, Dr. Sanford has good academic credentials in his field. I looked at his CV and heard a bit about his work with the gene gun and genetically modified plants at the Kansas science hearings. He is a successful and accomplished scientist.

I don't think his YEC beliefs have much relationship to the work he has done in genetically modified organisms. In fact, he was not a YEC until eight or so years ago, I believe, although he also said at the Kansas hearings that he didn't use evolutionary theory in his work even when he was doing his gene gun research, even though he accepted evolutionary theory as a background framework at the time.

Right now his webpage at Cornell says "I am presently looking at the theoretical limits of mutation/selection." I know almost nothing about this research, which presumably is described in his book. At the Kansas hearings he referred to this research, but due to lack of time merely stated his some of his conclusions. At the hearings he also made the distinction between operational and historical science, saying that his work was operational science (being reproducible in the present), but evolutionary theory was historical science:

"Historical science becomes more and more uncertain and increasingly subject to error the further back you go and the more inferences that are made. And so very quickly, when you talk about very remote or very ancient events, you're talking speculation instead of science.

I assume, then, that his current research about the limits of mutation and selection involves operational science - a lot of interesting work is being done in this area and I don't think Dr. Sanford's YEC views disqualify him in any way from doing research such as this.

However, following Dr. Sanford's lead, here I want to talk about the distinction between doing the type of research he has done (which he calls operational science) and drawing conclusions (inferences) about the past (which he distinguishes as historical science.) [Note: I don't particularly agree with this distinction, or at least with some of the implications that some make of it, but I am going to accept it for teh sake of this discussion.]

John Calvert, director of the Intelligent Design network, was the facilitator for the witnesses at the science hearings. At one point, Calvert asked Sanford to comment on "the proposed indicator [in the Minority proposals for the Kansas science standards that] would have students understand how to test an historical hypothesis about the cause of a remote past event by formulating competing hypotheses and then describing the kind of data that would support one and refute the other."

Sanford replied,

I think that what's proposed is excellent because developing alternative hypotheses and then defining experiments to discriminate between which hypotheses are stronger than others is critical to scientific method and critical to critical thinking.

Now in Sanford's new book, he reaches the conclusion that what he calls the Primary Axiom, "that man is merely the product of random mutations plus natural selection," is wrong - in fact, in Kansas he called it "categorically wrong."

This is clearly an inference about historical science and not merely a reproducible conclusion of operational science. Thus, as Calvert and Sanford both agree, one must compare "alternative hypothesis" and then define "experiments to discriminate between which hypotheses are stronger than others."

It is here that Sanford's YEC views come into play, and it is to this level of conclusion that I was referring when I wrote,

I do think that one's opinion about the age of the earth and common descent is going to be relevant to whatever ideas one has about the role of genetics in evolution. If one believes in a young earth and special creation, as Sanford does, then the phenomena one is trying to account for are very different than those addressed by the old earth common-descentist, even if the old earth common-descentist is an IDist, such as Behe or Dembski or DaveScot. ...

Sanford's alternative hypothesis involves a young-earth and special creation. Therefore, to reach his broad conclusion that the Primary Axiom is wrong, he needs to compare the two hypotheses - he must look at the complete range of data in order to see which hypothesis is more strongly supported. For instance, as someone mentioned above, a YEC must account for the rapid evolution of species within kinds, which is a different issue than those posed to an old-earther (irrespective of whether that person is an IDist, old-earth special creationist, or mainstream evolutionist.)

I am trying to be straightforward and scientific about the young-earth hypothesis and its relationship to genetics here. DaveScot said I was a young-earth bigot, and others have said that I brought up Sanford's young-earth beliefs merely to discredit him. While it is true that I don't think the earth is young (as is true for many in the ID world), I am trying to show here that the issue can be discussed based on its scientific merits.

However, I am also trying to show that if we do so, we need to apply the same standards, so the distinction that Sanford, Calvert and others make concerning operational and historical science need to apply to both hypotheses (young and old earth, common descent and special creation). What Sanford does in the laboratory is good science, as far as I can tell, but the conclusions he draws go beyond that; and thus should be held to the same level of skepticism, and the same standards of confirmation, as the other hypotheses.

So to answer some questions directly:

Michael says, "I await a specific example of genetic research Dr. Sanford cannot do based upon his YEC views."

My short answer to this question is that I don't think there is any area of genetic research that Dr. Sanford cannot do. My disclaimer is that the phrase "based upon his YEC views" is out-of-place here. From an operational science point of view his YEC views are not an issue, any more than his evolutionary views were involved when he invented the gene gun. He is working with how genes work now, in ways that are reproducible and testable by other researchers around the world, and the fact that he is a YEC makes no difference here.

But if he draws conclusions in the area of historical science, then his YEC views are an issue, because in the area of the historical sciences the mass of evidence that supports the competing hypotheses must be compared.

This is the distinction that I have been trying to make. I hope this is clearer.

Jack

he didn't use evolutionary theory in his work No one uses evolutionary theory to do anything useful, Jack. Evolution takes millions of years to do anything beyond changing the color of moth wings and the size of finch beaks. No practical applications worry about what's going to happen millions of years in the future. Duh. -ds Jack Krebs
June 3, 2006
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Hi all. I've appreciated the discussion, and I am working on an extended and hopefully thoughtful reply to the points being made in respect to my comments about Sanford - so please don't think I've bailed on the discussion. Thanks.Jack Krebs
June 3, 2006
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Michaels7: of course I agree with your point that Sanfords views on YEC do not prevent him from doing legitimate research elsewhere! I was only saying that to me, it sounds like Krebs was trying to point out, in my view correctly, that if you accept a young earth, you have a whole different perspective on things than if you accept an old earth. As commenter #64 has pointed out, YEC attempt to deal with this by positing "rapid evolution" and other things. I cannot speak for the science of YEC, as I am personally not interested in it, and feel fairly certain I can trust the old earth model. On the other hand, I don't utterly dismiss it either, simply because I'm not conversant enough to do so knowledgeably. Krebs may have been being naughty. Maybe not. But wouldn't you admit that his YEC views lead to unique problems in genetics, etc?

if you accept a young earth, you have a whole different perspective on things than if you accept an old earth Well then, since you believe in a spiritual world that must give you a whole different perspective on things. Maybe little spirits animate everything, huh? -ds tinabrewer
June 3, 2006
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Tina, you're correct. Dr. Sanford does not need my pitiful post-secondary education of freshman and sophomore chemistry and biology classes to defend his record. But that was not my point - just to defend Dr. Sanford. If you notice, Jack stated he did not discredit Dr. Sanford's scientific abilities. This is precisely the issue. He cannot. But YECs just starting our are discredited from the getgo. I then pointed to the PZ Meyer descrimination of tenure for ID science. And then extrapolated the obvious reaction by PZ to YECs and by other academics in today's society. If you've ever read any of PZ's rants and screeds you know its not a giant leap of logic. If you think my tying it to Sternberg is inappropriate your welcome to that opinion. But then I pointed to Nature and Behe. This happens every day and its not at all related to science. Its related to worldviews and in my opinion unethical actions. Why else would nature allow arrogant comments by a letter, but not allow Behe to put forth his work? I then asked for a simple example of how Dr. Sanford cannot do genetic research. So far, Jack has offered none. I'm not defending Sanford here. I'm arguing against a strawman the size of our solar system. Here's another possible example. Chemist at MIT have for the first time been able to monitor NO in living, functioning cells; http://web.mit.edu/newsoffice/2006/sensor.html. Does YEC beliefs by a priori assumptions prevent them from similar discoveries or work? My point is no, not at all. I'm asking for a clear rebuttal, not unsubstantiated vague language in the form of "He or she's YEC views will affect their research in a negative direction" I'm trying to get beyond the noise and to directly verifiable research examples. Is it to much to ask for specific examples? If Jack's only point is the disagreement of age, then his point is moot and it serves no purpose just as Sanford related and Tribune7 pointed out albeit to Jack's consternation and disapproval on this blog. Sanford stated it makes no difference and all the time spent arguing was a waste of his valuable time. If Jack cannot demonstrate actual evidence of incompetence or the incapability to do genetic research due to specific worldviews - then Macro-Evolutionist have no leg to stand on. I do not need to defend Sanford. I hold him up to the light for all to see in a manner of speaking and that is precisely what Salvador did with this entry. It exposes lame arguments of McEvos against ID, YECs and tarring people as incompetent by use of religious bigotry based upon worldviews and not pure scienctific abilities. I'm not attacking Jack either. I just want specific example of research that Sanford cannot accomplish in genetic research.Michaels7
June 3, 2006
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great ape I couldn't seem to find a straight answer from you about whether evolution has stopped or not. Can you demonstrate that it is still happening today without using circular reasoning? The circular reasoning I'm talking about would be saying the evolution of higher taxonomic categories is a long gradual process of genetic change and since small genetic changes are still happening evolution is still proceeding. That reasoning presumes that large taxonomic change is the result of a gradual process of growing genetic separation and that is a presumption without empirical basis because the process is so slow it can't actually be observed accomplishing what is claimed for it. Are you beginning to see yet what a huge house of cards the modern synthesis is? It's all built upon a primary axiom that has not been observed and cannot be observed because it operates too slowly for observation. It's one giant extrapolation and the more data that is acquired the more trouble it has explaining things. The emperor has no clothes. The house of cards is about to collapse. But all is not lost. Darwin got at least one thing right. There's an unperceived injurious agency constantly at work driving species towards rarity and then extinction. The agency has a name today and that name is random mutation.DaveScot
June 3, 2006
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bfast, You're right; that's not what NDE would have expected. The cambrian explosion did present quite a conundrum for NDE for some time. Gould popularized several interesting aspects of the story in "Wonderful Life" some years back. What hasn't been nearly so popularized among the general public is that genetic data that came later indicated that these "instantaneous" phylums had much deeper histories than would appear in the fossil record. There was an explosion, to be sure, but it appears to be in the development of hard or otherwise better fossilized and discriminated parts. Prior to this time period most things appear to have been soft and wormy-shaped. This, to the best of my knowledge, is the currently favored explanation for the burst of forms in the fossil record. As I generally place more stock in genetic data than fossil data, I tend to believe this over other accounts.great_ape
June 2, 2006
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Great_ape:
So inevitably, when you look at the taxonomic data and ask “when was the last family generated?” you will very likely say “that sure was a long time ago.” This is because that's just how long it takes for lineages to diverge enough for our brains decide to categorize them as higher taxonomic groups.
Hope you don't mind that I beg to differ. Certainly the "drifting apart until a new category is called for" motif is exactly what you would expect when applying the NDE theory, it seems that something quite different has actually happened, especially in the higher taxonomical categories. It seems that the higer the category, the more instantaneous seems to be the transition. Consider, for instance, the cambrian explosion. In a period not exceeding ten million years, 50 to 100 phylums popped into existance. These primary body plans were fundimentally and startlingly different from each other from the get go. No biologist in his right mind, if transported back in time to just after the explosion, would say, "hmmm, we seem to have 50 to 100 separate species here", or even 50 to 100 separate genuses. From what I have read, which certainly isn't exhaustive, the phylums, classes and orders near-simultaneously popped into existance. First there was a phylum burst, then a class burst, then an order burst. This is not what NDE expects.bFast
June 2, 2006
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Mung -- I think the problem is that you are simply unfamiliar with the YEC position. YECs actually _do_ believe in a faster evolution, and this is one of the many reasons why Darwinism cannot have anything to do with evolution. They do not hide this aspect. The term for Creationists is Intrabaraminic Diversification. "What they need to be doing is producing models which allow for rapid evolution, lol." They do. I'll point you to some: http://www.grisda.org/origins/54005.pdf http://www.grisda.org/origins/52007.htm http://www.nwcreation.net/geneticrecombination.html http://www.nwcreation.net/articles/recombinationreview.html http://www.nwcreation.net/evolution_creation.html But the fact that the evolution is _rapid_ does NOT mean that it is unconstrained. In fact, it is precisely the fact that it is constrained which allows it to evolve so fast. See: http://www.issuesthatmatter.com/genomicchange1.html [currently down -- see Google's cache here -- http://72.14.203.104/search?q=cache:zG4Ly9B925cJ:www.issuesthatmatter.com/genomicchange1.html ] A good book on the YEC biology position is: http://www.amazon.com/exec/obidos/redirect?path=ASIN/0805427147&link_code=as2&camp=1789&tag=freeeducation-20&creative=9325johnnyb
June 2, 2006
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"Something is certainly an unavoidable death sentence and 999 dead species of every 1000 that ever lived lie buried in mute testimony of that death sentence. We're just trying to figure out what it is." --ds We are basically in agreement here. I fully accept that genetic deterioration, particularly in smaller populations, has in all likelihood been a contributing factor to numerous extinctions. However, I see no reason at this time to maintain that it has been the *primary* cause in the majority of extinction events. As such, I don't see how it could be brandished as a knock-down argument against darwinian evolution and/or the modern synthetic view. Given our present state of knowledge, it is at most a nip at their heels. I still maintain that "existence itself" is effectively a death sentence for species (from a probabilistic standpoint) simply in virtue of the fact that a species can always drift downwards in total population size--on account of any number of factors--towards extinction. But such a population can never extract itself once it enters the black tarpit of annihilation. There is no equivalent resting point at the top of the heap so, given enough time, a given lineage is likely to dip a foot in the pit. Ultimately, the only thing that could potentially balance this rather bleak picture is the branching off of new species/lineages whose fates are no longer tied necessarily to the original. A diversified portfolio, if you will. The modern evolutionary view, as I understand it, holds that at least one--or at most a small number of such independent lineages of life--threads it wa back all the way to the origin(s) of life. If you were to accept this--let's ignore that nasty lateral genetic transfer for a moment--then at least one lineage (in the larger super-clade sense) has evaded death by genetic deterioration via both cladogenesis (branching) and anagenesis (morphing without branching). So far I have not encountered any evidence at the molecular level that would lead to rejecting this "tree of life" notion. ds, you would probably explain this longterm death evasion via phylogenetic stem cell theory. I can't really argue with that as I'm still hazy on some of the details. (Have you written up a more detailed account of PSCells somewhere?) Is the "creative period" of evolution over? If it is over, then the whole modern theory must clearly be tossed out and revamped. There is simply no reason for creativity to cease in the modern "algorithmic" conception of evolution--unless, perhaps, if the environment becomes supernaturally uniform and static. Even then sampling noise and mutation would still likely result in some amount of changes. (I wonder how genetic deterioration would play out in such an unaturally uniform environment..I'll have to think that one through some more.) Bonobos and common chimps split off roughly 0.8-1.2myrs-ago by most estimates. Pretty recent on an evolutionary timescale. They may still be able to interbreed--I can't recall if they have ever been demonstrated to do so--but in several dimensions these are different apes. As for when the most recent "genus" or higher-order taxonomic unit was produced, the tongue-in-cheek answer is "last time some phylogenist arbitrarily decided to separate one genus or family into two and wrote it up in paper that was--probably with a great deal of apathy--accepted by the community." The designation of the raw natural history data as taxonomic groups is essentially based on arbitrary human naming conventions, which are in turn based on how our brains like to categorize things. If you look at an actual phylogenetic tree, there are no natural punctuation marks that one could use to say "this is clearly a family/superfamily/genus/etc. There are branches and more branches. Some trees are more bushy than others, and their overall topology varies considerably. Consequently, people have drawn up taxonomic dividing lines where they are most convenient for pragmatic naming purposes. So the shorter yet more serious answer is that you can't really say when the most recent family/genus was generated. This is because, barring special creation, any relatively new family or genus would *necessarily be nested* within one of the existing taxonomic groups. It simply has no where else to come from given the modern theoretical framework. Only in hindsight, after much time, can you look back and say, "gee-wiz, this should be separated as its own family." Because of the arbitrary nature of taxonomic groupings, the amount of time required to "see" this distinction is rather lengthy. So inevitably, when you look at the taxonomic data and ask "when was the last family generated?" you will very likely say "that sure was a long time ago." This is because that's just how long it takes for lineages to diverge enough for our brains decide to categorize them as higher taxonomic groups. As an example of this somewhat arbitrary process, there are highly respected folks that argue that Homo (our genus) and Pan (chimps) should be merged into one. There are no compelling reasons for or against this IMO. The genetics tell us more about the actual relationships. The taxonomy tells us about our own psychology.great_ape
June 2, 2006
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There is a scientist who regularly chats on brainstorms at ISCID who finds about 1 million years to be maximim the amount of time that biology has been able to do its work. He clearly comes to this conclusion based upon the data that he sees, mutation rates, genomic degeneration, etc. I am coming of the mind that when biologists give up worship of the neo-Darwinian "god", they often seem to loose their belief in long timeframes as well. As I have seen a lot of evidence for an old earth outside of biology, it causes me to believe that these guys, Sanford and the ISCID fellow, somehow themselves have an incomplete understanding of nature. I guess that just shows that there is still a heck of a lot to learn about nature for us to learn about. Kinda refreshing in light of the NDE scientists' views that we pretty much have it pegged.bFast
June 2, 2006
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I am not sure all of this vigilant energy in defending the scientific honor of Sanford is really necessary. All Krebs did was point out that he is a YEC. I assume that if Sanford is a scientist of the calibre that everyone insists he is, then he would consider this to be mere information, and hardly a slanderous label. If he has looked at the science of it and finds a young earth to be a credible belief, then this also doesn't count as being a part of his religion: it is his scientific conclusion, and as such, he should accept the criticism that goes with holding such unorthodox views rather than need a bunch of ID knights defending his honor. On the other hand, if he holds to a young earth strictly because of his religious beliefs, and looks away from all of the contrary scientific evidence because his religious beliefs forbid him to look at it, then doesn't this constitute the same type of intellectual crime we spend so much time pointing out about Darwinists? Namely that their PRE-COMMITMENT to materialism causes them to "look away" from the clear evidence for design? I just don't see this as an ad hominem. While its at most a mildly dishonorable attempt to imply guilt by association, it certainly doesn't amount to Sternberging.

It's ad hominem. His religion has as much to do with his scientific expertise as your gender does. Some things ought to be off limits. -ds tinabrewer
June 2, 2006
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Jack, thanks for responding to my third post... Maybe we'll get somewhere now. "Michael7 writes, “Frankly, this is worse than Krebs attack on Dr. Sanford's scientific abilities being limited by his religious views.”" "I don't believe I wrote any such thing." OK, you did not say anything about his scientific abilities and I was overly harsh in comparison to a politician, my apologies. It seems that politics is all there is these days in academia. Jack, humbly and with all due respect. Your initial response to Tribune7 was the equivalent of labeling a bank teller with past history of bank robbery. You know YEC labels in today's scientific hallways are sabotage laid down by many secular humanist and atheist. You're not blind to the mocking and scoffing, the levels of ridicule and persecution thrown at scientist with YEC views. People look past science and at the label. In your post to Dave, you expanded your response. But I asked you for specific substance. You did not respond. You elected to point out a label of young earth "for the record" and to a court record listed under "kangaroo" link on a site that sponsors Panda(now, didn't I just apply guilt by association?). Salvador rightly pointed out Dr. Sanford's opinions changed as he reviewed evidence. This flys in the face of a priori 'biblical' criticism of creationist by McEvo's. Evolutionist cannot say he is forcing his worldview onto science because in fact his worldview changed as a result of genetic research. You are not an unwitting player in this arena and neither are you blind to the dubious use of labels. The truth is there are good scientific creationist. But to be labeled a YEC is worse than dumb blonde jokes at the office watercooler. Stereotypes are good fodder for jokes and people laugh, but they're not truly representative of all people within a group. A YEC label is no joke, its a death knell in mainstream science, especially academia and you fully understand the repercussions to one's career. Maybe I'm wrong and you support hiring Young Earth Creationist in Genetic Labs based upon their skill sets and not their religious labels? You support Young Earth Creationist ability to publish in scientific journals based upon merit and peer-review? You were against the despicable treatment of Dr. Sternberg at Smithsonian? I'm asking seriously because I do not know your opinion. "That's all I've said in this thread. I have said nothing about Dr. Sanford's scientific abilities." You're right. You did not criticize his scientific abilities precisely because you cannot. You could however label him with the YEC monicker as if this would alter his ability to objectively look at data. But you have yet to provide real substance - only loose references. Looking at Dr. Sanford's remarkable career - can we all agree just how close-minded "some" are in their labels and zealous persecution of those in disagreement with neo-darwinism and McEvo? Can we recognize the absurd claims that good science cannnot be done by people with such beliefs? Since you said "nothing about Dr. Sanford's scientific abilities", are you willing to admit they are of highest academic quality? 25 patents, publishings, sterling academics, two biotech companies... This is a creative mind. I ask again as in my first post to you. Give specifics where Dr. Sanford cannot do legitimate research in genetics based upon YEC beliefs. Here's a simple example... 1) Dr. Sanford cannot research genetic causes of Mad Cow disease because of young earth/common descent beliefs. We all know this is not true, but I welcome a specific example by you that is true, or from anyone here. I'm not a scientist Jack. I have a computer background so I do not pretend to know all the answers. Everyone here knows I'm learning on the moleculor/genetic side. So, maybe I'm missing something in this ongoing debate and the persecution by McEvos of those who do not kneel to the altar of Darwin. If we cannot point to specific examples however in this scenario, then Judge Jones, NCSE, ACLU, and academia have explaining to do imo. I await a specific example of genetic research Dr. Sanford cannot do based upon his YEC views.Michaels7
June 2, 2006
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scordova:
Poly-functionality is a new twist on irreducible complexity! Darwinist's appeal to a variant of poly-funcitonality and re-label it as co-option, but little do they realize “co-option” (or I more properly say poly-functionality) is a double-edged sword! Poly-functionality offers serious resistance to evolutionary change, not to mention, it raises the question of how poly-functionality came about in the first place!
Actually, I think that co-option is a proposed mechanism whereby poly-functionality comes about. However, my understanding of poly-functionality is that it exists in a variety of forms. Co-option would be one protein being used for two separate tasks. However, proteins do a task, then divide up so that each sub-protein can do another. A DNA segment produces multiple different kinds of proteins based upon the enzymes (or something) present when the protein is being generated. A portion of DNA, say segment 104843 to 105678 will code for one protein, and an overlapping segment, say 105128 to 106399 will code for another. (This I, a non-biologist, have gleaned from my reading. My best knowledge is from Denton's "Evolution a Theory in Crisis.") Of all of these mechanisms, the one that remains the most evolvable is the simple co-option. There is a good chance with the co-opted gene that the second task looks similar to the first, so a mutation would work similarly well in both cases. (Consider for instance, the simple fastener, a nut and bolt, the fastener can be used in multiple situations. If it mutated slightly, got a little fatter, it may well work in all of those situations.) To give credit, other poly-functioning DNA situations are conceivably adaptable as well. If a DNA segment is used for two tasks, one critical, the other not critical, then the critical task can be the judge of an acceptable mutations. Consider, for instance, a DNA segment that is involved in, say, ligament develoment, and eye color. It is likely to make little difference to the organism whether its eyes have a different color, but the quality of the ligaments are a big deal. Remains, greater poly-functionality = greater challenge for NDE. The more research is done, the more poly-functionality is discovered. From what I have read, this is now a HUGE problem.bFast
June 2, 2006
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bFast: "Until today, I had not recognized nurture as a source of noise. If two animals grow up, one in a food-rich environement, one in a starved environment, the food-rich animal will be larger, stronger etc, despite his genes. If the weak one has the 'slightly beneficial mutation,' this fact will be lost when he competes with the well-nurtured animal." Good point. That's what I urged with a biologist friend a few weeks ago. I told him nature is a highly noisy environment. There is a degree of variation in all parameters that build a fitness function for a particular organism. Not all lions can run exactly at same speed, not all rabbits have enemies with equal strengths and intelligence and not all giraffes feed from trees of exactly same height. A beneficial mutation that slightly enhances only one parameter at a time (say speed) is likely to be lost and not selected among generations because there are many other various critical parameters that shows variations among memebers of that species. You can't assume that a slightly faster cheetah is likely to have more offsprings than slower members of its species. Access to food and water rescourses, geographical and climatic conditions, luck, intelligence and many other environmental parameters play an important role to determine the reproductive output of an animal. The only alternative remains for NDE to work is to have (highly improbable) large beneficial mutations that appear in only one step. For example a fully functional wing that evolves in one step out of thin air. :PFarshad
June 2, 2006
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I should note many creationists accept that a great deal of front-loaded evolution happened.
What is the implication of bottlenecks for front-loaded evolution?
For the creationist view of partial front loading, biologist Chris Ashraft has an essay on homologous recombination; Evolution: God's Greatest Creation. After reading that article, one Darwinist biologist at ARN quipped creationists are become more evolutionary than Darwinists!
I have been arguing this for quite some time. It cannot be otherwise. After the flood, something has to have led to the diversity we see today. Post-flood creationism? Creationists are hyper-evolutionists! When they argue against evolution, their argument becomes incoherent. What they need to be doing is producing models which allow for rapid evolution, lol.Mung
June 2, 2006
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Michael7 writes, "Frankly, this is worse than Krebs attack on Dr. Sanford's scientific abilities being limited by his religious views."

I don't believe I wrote any such thing. What I said - why is this so hard to understand - is that if one wants to propose an alternative model (front-loading being one that has been mentioned in this thread quite a bit), than whether one is an old-earther or a young-earther, or whether one accepts common descent (guided by frontloading or otherwise) or not (i.e., believes in special creation at some points) will make a large difference in the phenomena one needs to explain.

That's all I've said in this thread. I have said nothing about Dr. Sanford's scientific abilities.

I suggest you apologize for bringing up Sanford's religious beliefs and not stoop to ad hominem in the future. No is buying your protests of innocence. -ds Jack Krebs
June 2, 2006
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Salvador, not at all, thought it was a scrambled signal ;-) and thanks for pointing out the book. It is illuminating to see certain forces opposed to Dr. Sanford on artificial pretext. I look forward to reading it and have enjoyed the discussion.Michaels7
June 2, 2006
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bfast wrote,

Until today, I had not recognized nurture as a source of noise. If two animals grow up, one in a food-rich environement, one in a starved environment, the food-rich animal will be larger, stronger etc, despite his genes. If the weak one has the 'slightly beneficial mutation,' this fact will be lost when he competes with the well-nurtured anima'.

I believe that the signal to noise ratio issue is an NDE killer.

Well said.

However, there is another NDE killer pointed out here (as well as by Denton and others):
“There is abundant evidence that most DNA sequences are poly-functional”

Poly-functionality increases mutational resistance - both deleterious and beneficial.

Right on. Poly-functionality is a new twist on irreducible complexity! Darwinist's appeal to a variant of poly-funcitonality and re-label it as co-option, but little do they realize "co-option" (or I more properly say poly-functionality) is a double-edged sword! Poly-functionality offers serious resistance to evolutionary change, not to mention, it raises the question of how poly-functionality came about in the first place!

Oh well, time for me to be gone for a few days. I wish I could stay, but maybe next week I can join in on the fun.

regards to all,
Salvador

scordova
June 2, 2006
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Until today, I had not recognized nurture as a source of noise. If two animals grow up, one in a food-rich environement, one in a starved environment, the food-rich animal will be larger, stronger etc, despite his genes. If the weak one has the 'slightly beneficial mutation,' this fact will be lost when he competes with the well-nurtured anima'. I believe that the signal to noise ratio issue is an NDE killer. However, there is another NDE killer pointed out here (as well as by Denton and others): "There is abundant evidence that most DNA sequences are poly-functional" Poly-functionality increases mutational resistance - both deleterious and beneficial. If a protein is doing two farely separate tasks, a change in that protein which would prove beneficial for one of the tasks, will prove deleterious for the other. It is my understanding that this effect, poly-functionality, is the reason that the hystone H4 gene is all but identical between the bovine (cow) and the pea. Gould, I understand, suggested that rampant poly-functionality would be an NDE killer. Alas, poly-functionality is a "deleteriousness amplifier", the amount of deleterious effect caused by a mutation is amplified by the multiple uses placed on that portion of DNA. As such, poly-functionality should allow natural selection to more easily see the deleterious mutations above the noise, and remove them.bFast
June 2, 2006
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Raevmo: Scordova: what's with the Kimura distribution?
No beneficial mutations. Of course if the context is changes, one can make a defect "beneficial" like the mutation which causes sickle-cell anemia or defects in bacteria that create anti-biotic resistance. I do recall Ken Miller pointed out that there was the evolution of nylonase (the one case of a mutation that might be deemed beneficial). So Sanford was at least fair in modifying Kimura's graph to have a few paltry beneficial mutations. Kimura however was very successful in pointing out mathematically that selection of beneficial mutations could not drive evolution because of population cost issues (you'd have to kill off, or shall I say, "hack to death", too many of the inferior creatures at a rate unsustainable by the population's ability to reproduce), thus there simply could not be that many selectively beneficial mutations theoretically! Walter ReMine did work on highlighting the cost problems. Haldane's Dilemma and peer-review Salvadorscordova
June 2, 2006
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Salvador, you're bringing politics into this? The statement by an ex KKK? Maybe I do not understand your purpose? But Bird is hardly trustworthy to make such a statement without first looking in the mirror at his own naked body. His "noise" is to leave 50 million oppressed people to tyrants and darkness. Frankly, this is worse than Krebs attack on Dr. Sanford's scientific abilities being limited by his religious views.

None are free until all are free. Isaiah 61. A true signal.

Sorry! Bad link! I fixed it, i re-linked "emperor has no clothes" to the wikipedia article rather that Senator Bird's essay. Bird's essay was the first that popped up in google, and I presumed it was only about Hans Christian Anderson's story. Thanks for pointing out my error! --Sal

Michaels7
June 2, 2006
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Hi Guys,
Here comes a question from Ignorance:
I always assumed that the signal to noise ratio had been shown to be in favour of demonstrating that deleterious mutations were not so frequent that information was lost more than gained-if information was lost more than gained -how could small changes moprphological or otherwise ever lead to anything at all ?
Sorry if this question leaves you slack jawed weak kneed and doubly incontinent but I had to ask .
cheers,
Wormherder

That is a good question, and the answer is that the problem of deleterious mutations has been mostly swept under the rug. But it's like a dead rat being swept under the rug, one could smell the rat even in existing peer-reviewed literature. I recall Crow commenting upon reading the data by Eyre-Walker and Keightley, Why aren't we extinct?. Crow tried to offer a solution through a model proposed in 1997, and Sanford devotes an entire chapter to Crow's supposed solution.

Regarding the signal-to-noise ratio, Sanford is one of the few to even point out it's significance in population genetic models!!!!!! I have several grad level books on population genetics, and they hardly address this important issue. So in answer to your assumption, the signal-to-noise ratio was not the reason deleterious mutions have been ignored because the signal-to-noise ratios were mostly ignored as well.

What is amusing about all of this is that the signal-to-noise ratio has been making it difficult to make real measurements of what is going on right now and it makes me wonder how much of literature out there is making inferences based on measuring random noise! I mean, we might be seeing populations of various creatures being overtaken by genetically inferior mutants that only got there by luck. We might well use Dave Raup's title: Bad Genes or Bad Luck? as the question of what drives the survival of species!

Regarding Raevmo comments, one does not need extraordinarly detailed mathematical models to recognize that information is being destroyed en-masse, or that spontaneous formation of complex specified information can happen via the propagation of copying errors constrained by selection.

That said, Dembski's displacement theorem does an excellent job of showing that formally. So if details is what one wants, details are available.

The mathematical models have been out for decades, what was needed was for someone willing to come forward and say, The Emperor has No Clothes!

Finally, as far as natural selection being able to "repair" a population by weeding out bad mutations, Sanford pointed it's like trying to use a hammer to repair a computer chip! There are some bad mutations that are so weak in selective effect that big bad natural selection can not see, much less fix! For example, Haldane's models point out how nasty it is to weed out mutations in recessive genes. I mean NASTY! Noise makes it hard for natural selection to fix problems. Blindwatchmakers do a poor job of computer repair.

Salvador

scordova
June 2, 2006
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Is there a suggestion that marine organisms have higher extinction rates than non-marine organisms? Perhaps they fossilize easier (exoskeletons in particular). The marine environment is perhaps not that stable. Right now we're seeing coral reefs dying on a global scale due to small temperature increases (or so they say), and there have been strong temperature fluctuations in the past.

Scordova: what's with the Kimura distribution?

It's true that the ocean environment does change but it is undeniably far more stable than land. It takes a very long time for the ocean to change while the air can change almost instantly. There's no difference in extinction rates land vs. ocean as far as I know but if changing environment were a factor it seems reasonable that we'd see a higher rate of background extinction on land. -ds Raevmo
June 2, 2006
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DaveScott: That's the whole point. They didn't. Something else did. The only answer that makes any sense to me is a front-loaded evolution.
Sanford alludes to front loaded evolution by passingly mentioning "designed mutations". But Sanford is not an all-out front loader (in the sense of Davison, Bill Dembski, Mike Gene, or Michael Behe, etc.) However, I should note many creationists accept that a great deal of front-loaded evolution happened, so in that respect the two major competing camps withing ID (those who postulate special creation versus those who postulate front loading) actually have some degree of commonality in their acceptance of front loading. The question is the degree, not whether or not front loading happened. For the creationist view of partial front loading, biologist Chris Ashraft has an essay on homologous recombination: Evolution: God's Greatest Creation. After reading that article, one Darwinist biologist at ARN quipped creationists are become more evolutionary than Darwinists! I would presume Sanford's front-loading is more in line with Ashcraft.scordova
June 2, 2006
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No, I'm not discounting the possible role of nearly neutral evolution. I just haven't seen a convincing model that shows it could be important. Some people here seem to suggest that Sanford has done this, but I haven't seen any details of his arguments/models.
It might be nice to make a model including both the random effects of fluctuating population sizes (due to environmental and demographic stochasticity) AND the accumulation of (slightly) deleterious mutations, and then see which process (if any) dominates the extinction probabilities. One would also like to have two versions: with and without sex. It is known (Muller's Ratchet) that asexual populations might actually go extinct due to accumulation of mutations. Models support this logic and there is some experimental and observational evidence as well I think. Since sex (or horizontal transfer) is so common, I believe this should be taken into account in the argument.

A great number of past extinctions were marine organisms. The marine environment is quite stable. That tends to rule out the weather as a cause. Muller's Ratchet is questionable due to horizontal gene transfer but it might indeed be why asexually reproducing organisms tend to have limited genome sizes and high fecundity, each of which mediates the speed by which nearly neutral mutations can accumulate. One should also keep in mind that high fecundity and small genome size pretty much guarantees a large number of perfect genomic copies in the next generation. In any case, I don't believe these are included in the number of species that ever existed as organisms with obligatory asexual reproduction don't tend to fossilize and the background extinction rate is established from the fossil record. -ds Raevmo
June 2, 2006
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