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Respected Cornell geneticist rejects Darwinism in his recent book

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!)

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104 Responses to Respected Cornell geneticist rejects Darwinism in his recent book

  1. This book sounds very exciting. It makes me wonder though, why respected academics need to wait until they retire before “coming out” against the doctrine of the sufficiency of natural agency.

  2. What a coincidence. I was just talking about (or rather speculating about) how what random mutation & natural selection really does is accumulate small deleterious changes in the genome of a species until it eventually drives it into extinction. I take it Sanford would agree.

    This would be good material for the Cornell IDEA students to bring into MacNeill’s class. I’d love to hear his response to it. Thanks Sal and JohnnyB!

    And a note to JohnnyB – I gave you the ability to publish articles just now. Something I’ve been meaning to do for a while now. Go to the meta-link for admins on the sidebar and all should be clear. I look forward to seeing your first article here.

  3. Has John Sanford published his findings in a peer reviewed journal?

    Sanford has published a lot of work in genetics in peer reviewed journals. However, in this case we can rest assured they won’t even consider publishing it because it bucks the party line. Do you have any real criticisms of the book or is that the best you got? -ds

  4. In retrospect, I realize that I have wasted so much of my life arguing about things that don’t really matter.

    Exactly!!!

    The age of the Earth and common descent are parlor games. Entertaining and interesting but nothing to take so seriously that one should upon it base a system of values or replace another system of values.

  5. For the record, Sanford doesn’t accept an old earth or common descent. See http://www.talkorigins.org/faq.....html#p1803

    For the record, can you explain how this is relevant to Sanford’s knowledge of genetics or are you just playing the guilt by association card because you have nothing else? Do you have any actual criticism of the book? -ds

  6. DaveScot:

    thats exactly right. I read Sanford’s book. What he is saying is that the mutations aren’t a normal bell curve but heavily skewed toward deliterious mutations. BUT, they are not skewed toward really disasterous mutations, and most (over 98%) are actually slightly deliterious, and therefore would not get selected out. Therefore, they just hang around the genome building up until – Extinction! He also made the statement (and I can’t verify the truthfulness of it) that in all the years of plant genetics he has NEVER really seen any mutation that added information or improved the state of the organism. He mentioned that things like hairless dogs and other viruses actually reduced the information. He likened it to a broken car alarm – it makes people who hate the blarring noise happier, but it doesn’t make for a stronger car :-)

    I really hope this thread gets longer because I liked the book, but don’t have the background to verify if all the information was sound. I would learn alot from the discussion.

  7. Seems like a great read!

    Unfortunately, the cover of this book is almost indistinguishable from that of a “UFO: Expose the Truth” type book.

  8. Thanks Sal I’ve just ordered the book through Amazon. My impression is that our PT friends aren’t quite aware of the book nor of who JS is. Please read some “kind” stuff taken from:

    http://www.pandasthumb.org/arc.....e_clo.html

    K.


    Send in the clowns
    Nick Matzke posted Entry 939 on April 5, 2005 10:46 PM.
    Trackback URL: http://degas.fdisk.net/cgi-bin/mt/mt-tb.cgi/937

    In the I am not making this stuff up category, the ID crowd is planning on sending a battalion of pseudoscientists to Kansas this May for the upcoming ID Kangaroo Court. On the front page of the Intelligent Design Network’s “we’re not promoting ID” website, we find:
    …..
    John Sanford, PhD Geneticist, Associate Professor Cornell University Date of
    anticipated testimony: May 6

    Comment #23553

    Posted by RPM on April 6, 2005 01:30 PM (e)

    Here’s what I could find regarding the some of the witnesses to be brought in to testify. I limited my discussion to the “biologists” with PhD’s as people way out of their field and with less than “expert” qualifacations hardly warrant mentioning.

    John Sanford, PhD Geneticist, Associate Professor Cornell University Date of anticipated testimony: May 6

    I graduated with a Bachelors in Genetics from Cornell, so I was extremely interested to find out who John Sanford was. I thought, no way he was really in the Molecular Biology and Genetics department, and I didn’t remember him from my undergrad days. For those of you unfamiliar with the field, Cornell is a leader in evolutionary genetics. It turns out Sanford is at the agricultural research station in Geneva, NY (about an hours drive from the main campus in Ithaca). He’s in the Dept. of Horticultural Sciences, and he describes his research as “at the interface between molecular genetics and plant breeding, for the purpose of crop improvement.” I’m not sure what to make of him.

  9. Note “samantha” and Jack Krebs posts and the “any port in a storm” approach.

    Telling.

    http://en.wikipedia.org/wiki/I.....dishonesty

  10. 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.

    funny, I wrote the following sentence last week:

    Evolutionary science, as it is currently taught, is predicated on the axiom that life arose independently of the intervention of any intelligent entity, and it proceeds from there to attempt to explain the origin of observed biological effects as being a result of purely natural processes.

    Is this what you call “evolutionary convergence”?

  11. As for the UFO, I thought the same thing. Most of the graphics look like they came from a clip art collection :-) But, they really are there to illustrate his points. The UFO on the cover relates to his premise that if we have an instruction manual for an airplane, if over years we have slightly deliterious mis-spellings (that don’t cause the entire plane production facility to collapse into pieces), will those mis-spellings eventually transform the instruction manual from one that can produce a plane to producing a spaceship. Again, I don’t have the proper background to assess the soundness of the argument. So, I would really welcome some of the more intellectually honest anti-ID folks to provide a good critique of the book (I think great_ape has been fairly even handed on this blog).

    I liked the Cornell alum’s assessment that was posted earlier: I haven’t heard of JS, so thererfore he must not be important. Yeah, and the gene gun is nothing more than a water pistol :-)

  12. Jack Krebs hyperlinked to Sanford’s creationist beliefs, but he could have well hyper linked to Sanford’s account of his journey of faith in that very same testimony at Kansas.

    I– just one more comment in terms of my qualifications to discuss this, is most of my career I’ve been an atheistic evolutionist;, later in life I became a theistic evolutionist, and later I became a– a Biblical Christian.

    John Sanford

    It would be easy to think from Jack’s characterization that Sanford rejects Darwinism because of his religious views, actually, it seems the opposite: Sanford adopted a religious view because he rejected Darwinism.

    Regarding the book, this was the easiest read of population genetics I’ve come across. I have graduate level books on the topic (such as Hartl and Clark), but this book was able to communicate the same material with greater clarity.

    Let’s say we have a population of bacteria or insects in equilibrium and no new selection pressures like an antibiotic or pesticide are introduced. According to Darwinist ideas, a random mutation could come along any minute which spawns an overtake of the entire population with this new beneficial mutation. Well it doesn’t happen, and it especially doesn’t happen in mammal populations. That is the concept of “beneficial mutation”, it doesn’t happen to a sufficient degree for it to be detected by any of our researchers.

    The concept of “beneficial mutation” is often equivocated where the “beneficial mutation” being referred to is the kind that happens under intense selective pressure like a pesticide (for insects) or antibiotics (for bacteria). But this is hardly the kind of evolution that will be creative of serious amounts of integrated complexity. What would have been experimentally desirable is to see mutations spontaneously appear which add benefit in an stable environment, but it doesn’t happen. Spontaneous beneficial mutations I suppose will go the way of spontaneous generation!

    Sanford showed the graph of :

    1. Bell Curve idealization of mutations (equal numbers of beneficial and deleterious)

    2. Kimura’s distribution (no beneficial mutations, closer to the truth)

    3. Actual distribution (very very few beneficial mutations, and such selection pressure as to effectively be neutral)

    #3 really stood out. The left side was almost all deleterious and the right side had almost no beneficial mutations. Perhaps I’ll post the graph. This was in line with Kimura’s distribution (which can be inferred partly from Haldane’s work).

    He then went on to discuss signal-to-noise ratios. We all know that noise can destroy the transfer of information (like trying to whisper to someone from a distance in a noisy room). He showed that natural selection acting on the phenome (which contains phenotypes) is precluded by “noise” from selecting a sufficient number of nucleotides in the genome. So even if there are beneficial mutations, they are drowned out for the most part by noise! Thus selection has the power to reach only a limited number of nucleotides in the genome.

    He also pointed out important developments in information storage in biology, that there are layers of information in DNA. We have looked at DNA as storing information sequentially as we read the nucleotides sequentially, but there may indeed be information in the 3-D structure!

    Do you all remember the 56K modems where you could actually listen in on the modem signal. Did the modem sound like noise or specified information? Statistically it sounds like white noise (that is by design actually), but it is actually rich in specified complexity.

    Suppose an Mp3 music file was being transmitted by this modem. If you listened to the modem signal, you might think it’s noise, but by demodulating the signal (changing perspective) what sounds like noise is revealed to be actually be music! That is what is beginning ot happen to our understanding of the information content of biological systems, we are changing our perspective to view biology as information rich rather being full of junk (typical Darwinist viewpoint). Sanford highligted developments in how our perspective is changing about the information richness in biology. He gave examples of ingenious data compression schemes where loads of information are now being discovered.

    Sanford shows that this rich repository of information has been steadily getting eroded and will continue to erode even if a maximal amount of eugenic selection is applied. Because of the intense data compression, there is no way random mutation could create such compressed structures (try making an Mp3 music file with a noise generator and see what happens!).

    The erosion of the genome of the is also an empirically falsifiable claim, so Sanford is making a testable hypothesis. Futhermore, the graphs in his book (inspired by Kimura) are also subject to experimental falsification and validation (in fact it seems to me, the hypothesis has been vindicated repeatedly in the lab).

    This is SO much better than that article about Genetic ID. Keep running with this one! -ds

  13. When a PhD-type agrees with NDE then the PT crowd trumpets his credentials and labels him a “real scientist”. When they don’t agree with NDE then they are labeled as “pseudo scientists” or worse.

    The No True Scotsman rides again!

  14. Kairos,

    Thank you for visiting our weblog. All of my reading of population genetics (even grad level books) does not seem to contradict anything in Sanford’s book. Sanford wrote to a popular audience, nothing he said about the important basics struck me as really deviating from accepted knowledge.

    I especially appreciated his references to information theory as that is my background. Please report back if you have any reservations about something he wrote, and please report the parts you agree with.

    Thanks.

    Salvador

  15. Lurker: “The No True Scotsman rides again!”

    I was unaware of this expression, but discovered that it is by Anthony Flew!

    http://en.wikipedia.org/wiki/No_true_Scotsman

  16. This book is now on my reading list.

    The Primary Axiom is transparently false on the face of it. Take even a trivial computer program composed of a few lines of source code and do the math. The combinatorics generated by random tinkering with the source quickly swamp any conceivable probabilistic resources. Random modification of the code will produce gibberish until the universe undergoes heat death.

    Life runs on a computer program of such vast sophistication, complexity, and functional integration that the Primary Axiom is a laughable proposition. As DaveScot pointed out in another thread, it might have seemed reasonable in 19th-century Victorian times when it was thought that the universe was infinitely old and that the cell was no more complicated than a blob of Jell-O, and that it could easily arise by spontaneous generation in nature.

    But that was then and this is now. The Primary Axiom is dead, but not yet buried, at least in academia. They have propped up the cadaver in a rocking chair, just like Norman Bates’ mom. But take a look at her face and you’ll see that she’s a rotting corpse. The taxidermy is wearing off.

  17. #16 I completely agree, but unfortunately it is as easy to realize that ND is deadly wrong (not by darwinists, obviously…) as it is extremely difficult to give it the KO punch. If you consider that the trivial work by Lenski, Pennock etc. has been trumpeted as a final proof that M+S is able to generate complex information … !

    #14 Sal, I will read carefully the book as soon as I will receive it (package dispatching to Europe is quite slow).

    K.

  18. Wow, this is the fastest growing thread I’ve seen on this site!

    I personally was most intrigued with the following statement:

    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.

    I had a major discussion with my brother just last summer about signal to noise ratio. Dispite he being an electrical engineer, I was not able to communicate the signal to noise equation to him. This equation is very valid. I think I need this book, and need to give my brother a copy of it.

    I am a bit concerned at the suggestion that John Stanford is a young earther. Trying to climb this mountain too is a lot. Its like trying to fight a war on two fronts, especially when one of those fronts is surely a loosing cause. The evidence for an old earth is not the “house of cards” that NDE is. I actually believe that NDE went along for the ride as the old earth and common descent became established.

  19. >I had a major discussion with my brother just last summer about signal to
    > noise ratio. Dispite he being an electrical engineer, I was not able to
    > communicate the signal to noise equation to him. This equation is very
    > valid. I think I need this book, and need to give my brother a copy of it.

    > What do you mean exactly by “signal to noise equation”?
    > I am a bit concerned at the suggestion that John Stanford is a young
    > earther. Trying to climb this mountain too is a lot. Its like trying to
    > fight a war on two fronts, especially when one of those fronts is surely a loosing cause. The evidence for an old earth is not the “house
    > of cards” that NDE is.

    What’s the problem? As a catholic I’ve no problem with old earth and I maintain that it’s right. But the real front is against NDE

    K.

  20. “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

    I would very much like to read this book, but I fear the electronic evidence of its purchase would place me on the top secret government “people to not let in the bunker when the asteroid strikes” list. So I generally refrain from making such purchases. I once bought an “edible wild plants” book once from Amazon and have since received advertisements that would suggest I’ve been placed on the “probable right-wing militia member” list. Then again, I’m posting here, so perhaps it’s too late for me already. In any case, I would like to examine the work in detail b/c I would very much be interested to know how Sanford deals mathematically with 1) the ability of recombination to alleviate some of the “deleterious burden” of these mutations over time and 2) epigenetic interactions among these “slightly deleterious”, supposedly un-purifiable negative mutations.. W. Rice’s lab has shown empirically [see, for example, Science. 2001 Oct 19;294(5542):533-4.], and others theoretically, that recombination in sexual organisms alleviates some of the burden by “freeing” quality genomic segments from being dragged down to extinction along with deleterious alleles. The question here, of course is: “Is it enough in a given situation?” The devil, as they say, is in the details. And the details here are so complex that I’d like to know how he deals with them because, last our checked, theorists were still struggling to work out the full ramifications of recombination on popgen. Maybe, out of moral compulsion, he’ll ultimately publish the whole thing freely onine for the enlightenment of all. Then again, maybe I could just buy it with cash from a bookstore so it couldn’t be traced.

    Must do some $work now, but here’s something for folks to ponder. Although any given slightly deleterious mutation may have too small an effect to be purified, any given individual whose genome–essentially a chimera of what’s available from in the population–collectively had many fewer such mutations would overall fair better reproductively. *Particularly* if those deleterious mutations acted epistatically. Repetition of such reproductive success would ultimately– depending on the *specific* numbers involved (recombination frequency and distances, population size, mutation rate, distribution of mutation effects,etc.)–reduce the frequencies of these slightly deleterious mutations (un-purifiable on their own) and could serve to hold off genetic doomsday. Details, details, details, and some of these details we’ve little chance of knowing. Population genetics, when applied to real flesh and blood organisms, is terribly difficult. We do, however, have a masterful knowledge of how multi-colored beans behave in jars.

    C’mon apeman. Here I’m trying to say to Darwin got something right and you question it! :roll:

    It is most difficult always to remember that the increase of every living being is constantly being checked by unperceived injurious agencies; and that these same unperceived agencies are amply sufficient to cause rarity, and finally extinction.

    The unperceived agency is random mutation. Which of course is no longer unperceived. Darwin got something right! I’ve been saying for a long time Darwin was also probably right about Lamarckian inheritance of acquired characters being the primary source of adaptive change. That shoe is dropping as we speak. The next shoe to drop should be the notion that the amount of change that can be produced in any given species is bounded internally and is generally constrained to scale and cosmetics. To quickly know what kind of limits I mean by scale and cosmetics look at the range of variation in dogs. There’s no difference between a dachshund, a chihuahua, and a wolfhound that isn’t simply a matter of relative feature size and cosmetics. Those are the limits of allelomorphism. Now you might ask what is then responsible for the big creative changes that include novel cell types, tissue types, organs, and body plans. Those were all front loaded and their expression is under developmental control – the phylogenetic stem cell! Nothing in macroevolution makes sense except in the light of phylogenetic stem cells. -ds

  21. In comment 4, tribune 7 wrote,

    “[Sanford wrote,] ‘In retrospect, I realize that I have wasted so much of my life arguing about things that don’t really matter.’[/Sanford quote]

    Exactly!!!

    The age of the Earth and common descent are parlor games. Entertaining and interesting but nothing to take so seriously that one should upon it base a system of values or replace another system of values.

    So I wrote, “For the record, Sanford doesn’t accept an old earth or common descent. See http://www.talkorigins.org/faq.....html#p1803,”

    and then DaveScot wrote, “For the record, can you explain how this is relevant to Sanford’s knowledge of genetics or are you just playing the guilt by association card because you have nothing else? Do you have any actual criticism of the book? -ds”

    Dave, I was responding to tribune7′s comment, and I started “for the record.” I wasn’t discussing, much less criticizing, the book – I was just responding to tribune7.

    I haven’t read the book, but I did listen to Sanford when he spoke at the Kansas BOE Science Hearings in May, 2005. 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.

    Note well that I am aware that one can criticize, as I gather Sanford has done, evolutionary theory as an issue separate from offering an alternative model, and I am not offering any comments here on Sanford’s work because I am only vaguely familiar with it based on his presentation in Kansas.

    But given that at some point criticizing a theory and offering an alternative have to intersect, the fact that Sanford is a young-earth special creationist might at that point be relevant.

    Your comment was in the moderation queue when I responded to it and since you didn’t specifically address tribune I had no way of knowing you were responding to him. Nonetheless, in this comment you confirm that I was right about you playing the guilt by association card. Sanford appears to be accounting for empirical evidence as far as I can tell. You’re Christian, Jack. Should I consider your opinions about everything else biased by you needing to justify your belief in some sort of immaterial immortal soul that gets a passkey into heaven by declaring your faith in a man that claimed to be the son of God? Maybe you should display the same courtesy for Sanford that I do for you and not try to discredit him by aspersions to belief in miracles and supernatural beings. Gil got you pegged alright. Any port in a storm. Shame on you. -ds

  22. 22
    LowenheimSkolem

    So we shouldn’t trust Sanford at all because he isn’t sure about the age of the earth?

    I’m no YEC, but that kind of reasoning leads to disasterous conseqeunces.

    Should we reject Godel’s results because he thought people were trying to poison his food and thus starved himself to death?

  23. Dave –

    First, thanks for letting me on the post list! I am very honored!

    Second, I agree wholeheartedly with your comments about natural limits of variation, but I wanted to add something else. I think that we are going to find that there is a lot _more_ non-morphological variation that goes on from generation-to-generation than morphological variation. Perhaps much of this is wrapped up in development, but I also think that some of it will be found to be passed on in genetics. That is, while we remain morphologically stable, perhaps our biochemistry adapts to changing conditions (obviously limitted by internal semantic constraints).

    In fact, I think that we will find something else in biological change — that the way in which different organisms change depends greatly on the need within the environment as a whole — that organisms are designed to create ecosystems. By sensing other plants and animals in the area, they have specific adaptations for different conditions, which attribute to the environment as a whole. You may even be able to go as far as using data on variation to hypothesize the purpose behind different organisms, though I think the reverse might be more fruitful for those who dared to go there:

    http://baraminology.blogspot.c.....e-and.html

    Shades of Lynn Margulis… Follow the Gaia links if you aren’t aware of it already. -ds

  24. ds,

    I wasn’t trying to be contrary so much as bring attention to some key forces at work which would oppose genetic deterioration and *possibly* avert extinction. When there are conflicting forces at play, the ultimate outcome is clearly dependent on the relative strength of each. While Darwin is commendable for understanding that imperceptible damage does occur, he had no idea the ultimate magnitude nor the ability of organisms/populations to counterbalance them via various means. For that matter, neither do we at this stage. So I think it’s a very important topic for us to be discussing, but ultimately a definitive answer can’t be drawn IMO b/c pertinent data and theory is still lacking (particularly in regards to the influence of recombination). It is incumbent upon evolutionists to make a strong case–preferably sooner rather than later– that under a robust range of conditions genetic doom is avoidable from a mutation/popgen perspective. This is another hole in the current evolutionary framework in my opinion and one of the most critical ones. Currently this hole shows a incompleteness in evolutionary theory, but it can *not* be considered an evidentiary contradiction to the theory until all the relevant forces and magnitudes are properly accounted for. If this should prove impossible, then it can never be presented as counterfactual argument against evolution/darwinism. At the same time, its unresolved status will remain a crucial structural weakness in the inductive case for evolution/darwinism.

    So how do you explain the extinction of 99.9% of all species that ever lived and the average lifespan of families being about 10 million years? I’m all ears. -ds

  25. For the record, can you explain how this is relevant to Sanford’s knowledge of genetics…

    Did anyone else read the cross-examination? How much of it questioned Sanford on any aspect of his scientific specialty? Too bad it wasn’t a court in which Sanford could claim the question to be outside his area of expertise and the examiner could be required to show relevance.

    But let me think some abobuth Sanford’s thesis that these mutations accumulate and cause extinction. What is his evidence for the conclusion that extinction is the effect of the accumulation of these mutations? Certainly, on a young-earth view, there has not been time enough. On a young-earth view, extinctions are the result of the flood. And on a young-earth view, evolution absolutely had to occur in order to account for present numbers of species! YEC is incoherent.

  26. 26

    John Sanford said, “When subjected only to natural forces, the human genome must irrevocably degenerate over time.”

    In the natural world, natural selection will eliminate the most harmful deleterious mutations. However, humans are often protected from the full consequences of some very harmful mutations, and people with some bad mutations often survive long enough to reproduce. But even among humans, there is a limit to how harmful a deleterious mutation can be and still allow the person to survive long enough to reproduce.

    Most random mutations are not deleterious enough to be under significant selection pressure. Google the “nearly neutral theory of evolution”. -ds

  27. bFast: “I am a bit concerned at the suggestion that John Stanford is a young earther.”

    Let me clarify my view on the effects of Sanford being a young earther. We are all entitled to a little error. In fact I very much dislike people who don’t respect their own ability to err. However, I have seen a lot of evidence that “young earth” is in error. If Sanford has a brilliant work, but muddies it with a significant error like young earth, then his brilliant work is likely to become the proverbial baby thrown out with the bath water.

  28. Dave, I don’t see at all where I have implied any guilt to Sanford, by association or otherwise. My point is that if one has doubts about evolutionary theory, and especially if one ever wants to offer alternative explanations to be considered, it surely makes a difference whether one thinks that the earth is old or young, and whether common descent is true or not. If one accepts an old earth, one has a long sequence of organisms to explain, (99.9% of which are extinct, as you point out), but if one accepts a young earth and the creation of all kind of organisms at the same time, then what one has to explain is different.

    This is not an accusatory statement, I don’t think, but rather more or less a statement of fact: whatever alternative to evolutionary theory one might have, the context of the age of the earth and the truth or not of common descent is essential background for ones ideas.

    Unless his work includes statements reflecting these things it’s irrelevant. Ideas are judged by their merits not by the people who hold them. You just couldn’t resist dragging Sanford’s religious beliefs into his book which as far as you or I know contains no religious concepts whatsoever and is entirely based upon good scientific method and empirical data. Just for the record, you’re a YEC bigot. -ds

  29. Jack Krebs said,
    “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.”

    Please elucidate for the simple minded(me) specifics. Why does it matter and please point to actual issues that would stop Dr. Sanford from creating sound scientific research.

    Once you’ve done this, we can review his accomplishments again in light of your observations.

    “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.”

    Again, please clarify specifics in regards to genetics or genetic modification, genetic research and how Dr. Sanford cannot or could not progress as well as any scientist by any other stripe. Maybe you do not fully understand young earth views in relation to genetic research. Maybe none of us do?

    I know I don’t fully understand them.

    I humbly cannot think of any practical application of your logic that would prohibit Dr. Sanford from excellent research.

    Maybe it would be good to make a list of facts why someone who is a young earth creationist cannot do genetic research as excellent as someone who is an old earth evolutionist.

    I’ll start the list…

    1) Most YECs believes rocks are younger than 7000 years(just making up an age boundary), therefore YECs would never discover magnesium or iron in the human body or blood cells.
    2) Most YECs believe humans have been on earth 6000 years, or in the case of Judaism, 5766, in that case, approximaly 3761 years BC, the earth was created. Therefore, YECs would never discover cellular apoptosis.
    3) YECs believe the earth was made in 6 days and the Creator, God rested on the 7th.

    Every old earth evolutionist knows ATP was created on the 8th day ;-) therefore young earthers would never find, understand, or research ATP, plus there’s no way God could create a giraffe, let alone an amoeba in 6 days.

  30. Jack as per posts 5 and 21 — I realize that I have wasted so much of my life arguing about things that don’t really matter.’[/Sanford quote] . . .“For the record, Sanford doesn’t accept an old earth or common descent.

    And I take his point as being they don’t really matter and aren’t worth arguing about unless they start being used in a metaphysical context.

  31. It’s true that slightly deleterious mutations can easily accumulate in populations, and even mildly deleterious mutations if the population size is small (Kimura: if Ns

  32. ds, 99% of my comment is missing.

    That’s the way I found it. -ds

  33. My last comment didn’t get through for the most part, but I was trying to say: Muller’s Ratchet says asexual species are doomed because of accumululation of bad mutations. Sex (recombination) can get rid of bad mutations (as great_ape said). In addition to recombination, sex allows sexual selection: females may prefer to mate with males that show evidence of not having too many bad mutations. This also lowers the genetic load of bad mutations. Whether all this is enough in practice, who knows? A big problem is that early life had no sex (well, so it is claimed anyway), so how did they avoid extinction? Possible answer: massive horizontal transfer of genetic information. Anyhow, to claim confidently that RM+NS automatically leads to degeneration is premature. Verbal arguments like that are just not very convincing when not backed up with mathematical models.

    Feel free to offer a better explanation for why 99.9% of all species that ever lived are extinct. -ds

  34. If one accepts an old earth, one has a long sequence of organisms to explain, (99.9% of which are extinct, as you point out), but if one accepts a young earth and the creation of all kind of organisms at the same time, then what one has to explain is different.

    Jack,

    Don’t mean to pile on. Feel free to ignore this and not respond if you so choose. I’ll understand. Are you saying that the number of extinct species one has to explain depends upon whether one holds to a YEC or old earth view? Why?

  35. “So how do you explain the extinction of 99.9% of all species that ever lived and the average lifespan of families being about 10 million years? I’m all ears.” -ds

    Of course I’ll have to give it the old college try… A *large* fraction of that >99% extinction rate is accounted for by a handful of cataclysmic global-level events a discrete timepoints. One in particular took out nearly everything alive up to that time. I can dig up the numbers and eras if you’d like. These are “environmental” (external) catastrophies and they account for a big chunk of extinctions. These events, like the infant mortality rate in humans, weigh significantly in calculating the average persistance of all families during across time. As for the remaining component of extinctions, populations can–in the rosiest of scenarios–max out at the population size supported by their niche. They can never “fix” like an allele can in an abstract population. At the other end of the scale there is N=0. Caput. Irreversible. Once you hit that absorbtion boundary, it’s over for a given lineage. Populations, from generation to generation, go on a more or less random walk contingent on environmental conditions, genetic conditions, etc. You can always fall from the top in terms of population size, but you can never recover from N=0. So yes, the playing field is skewed in favor of extinction. Part of the downward nudges do come from accumulated genetic mutations that haven’t been purified and consequently impact effective population size. It’s a nudge, and in some cases it may be the last nail in the coffin for a lineage, particularly since the effect grows worse in smaller populations. But the argument being put forth here, as I see it, is that it is an inevitable death-sentence and, as a consequence, is damning evidence against darwinian evolution. It is that last proposition I take issue with as it remains conjecture at this point. In my understanding of the scientific method you do not discard theories b/c conjectures (even plausible ones) are understood to be counterfactual. Something more rigorous is generally required.

  36. Lets extend Lurkers recognition of “The No True Scotsman rides again!” application while awaiting for significant rebuttal to genetic research being prohibited by young earth philosophy.

    No True Scientist is a Young Earther
    No True Scientist believes in a Creator
    No True Scientist believes in Design
    No True Scientist believes the world was created in 6 days
    No True Scientist believes a bladder can be created in 40 days
    No True Scientist believes an appendix is useful
    No True Scientist believes a diamond can be made in 5 days

    No True Scientist believes you can speed up a process

  37. Apeman A *large* fraction of that >99% extinction rate is accounted for by a handful of cataclysmic global-level events a discrete timepoints.

    Incorrect. Only a small fraction of extinctions are attributable to mass extinctions. The background rate of two to five taxonomic families every million years accounts for the vast majority of extinctions.

    There are estimated to have been between 5 and 50 billion species. At any one time an average of about 50 million are alive. There have been 5 major mass extinctions. If each took out 100% of the species they would only account for 250 million extinctions or 5% of the lowest estimate of 5 billion species or 0.5% of 50 billion species. Estimates go as high as 20 mass extinctions but as you can see even 20 extinctions of everything alive is still only 25% of the lowest estimate of total species and 2.5% of the high estimate. And of course mass extinctions don’t kill everything.

    Sorry, but I’m going to have to give you a failing grade on this one.

  38. “Do you have any real criticisms of the book or is that the best you got?”

    Aight! I put on my robe and wizard hat.

    The theory that the genome accumulates defects is nothing new. To say that this implies that variation and speciation cannot occur in the meantime is a non sequitur.

    This is analogous to the heat death of the universe. Sure, the universe is winding down, but there’s plenty that we can do before then.

    He implied that? I think you mistakenly inferred that. Perhaps you should admit up front that you didn’t read the book. Do you make a habit of criticizing things you’ve never seen or did you make an exception for Sanford’s book? -ds

  39. “Incorrect. Only a small fraction of extinctions are attributable to mass extinctions. The background rate of two to five taxonomic families every million years accounts for the vast majority of extinctions.” –ds

    Alright, so maybe I won’t be so quick to venture into paleontological speculations next time. Once I stopped to think for a moment, your numbers make much more sense. And once I then stubbornly looked up a review article on the matter–just to be certain, you know–your numbers are in the same ballpark. I had impressive figures like “95 percent of life eliminated at point X” stuck prominently in my brain from some distant lecture, but hadn’t properly considered the ongoing diversification/extinction rates over time. I stand corrected. I still contend that the latter part of my argument stands. (so let’s just pretend I placed most of the emphasis on this part.) External events (weather,etc.) factor heavily in the random walk of population sizes and distributions. Those sizes and geographic distributions affect extinction risk. Genetic deterioration certainly factors into the risk of extinction, but there is no compelling evidence to indicate it is an unavoidable death sentence.

    If a species is weakened by accumulation of slightly deleterious mutations then doesn’t it make sense that it won’t be able to adapt and/or tolerate stresses like changing weather patterns, predation, etcetera as well it would otherwise? 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. I think Darwin got it right – there is an unperceived injurious agency constantly at work. The unperceived agency’s name is random mutation. Is creative evolution still happening today? How long ago did the last new genus appear? How long ago did the last new mammal species appear? -ds

  40. Raevmo wrote:

    Anyhow, to claim confidently that RM+NS automatically leads to degeneration is premature. Verbal arguments like that are just not very convincing when not backed up with mathematical models.

    You mis-represent the argument.

    Sanford claimed no such thing, he points out that known parameters about biology would not permit RM+NS to do the wonderful things it claims, he does not say it’s an automatic, but rather a consequence what constrains RM+NS in the real world.

    And before insinuating the argument was verbal rather than mathematical, you might do well to actually have the book in hand and be more specific in your criticisms.

    For example, do you have any objections to the variation of Kimura curve which Sanford offored on page 32? Or how about his claim on page 103 regarding the effective amount available withing the human population for selection is less than 1% based on the fact that noise overrides selection pressures?

    Salvador

  41. Some random quotes:

    If you want to receive a message on the radio, you need to limit the amount of “noise”, or static. If there is a strong interfering signal-the message is lost….Turning up the volume on your radio does not help overcome the static. We just wind up amplifying the static as much as the signal. To ensure minimal loss of information, there must be a favorable signal-to-noise ratio…

    In genetics, the signal-to-noise ratio is often expressed in terms of “heritability”. If a trait has high heritiability, this means that most of the variation observed for that trait is genetically heritable, and so this trait will be easy to select for. The essence of this concept of heritability is simply the ratio of heritable versus non-heritable variation. Non-heritable variation is largely due to variation within an organism’s individual environment, and is the source of “phynotypic noise”. So a genetic heritability value for a trait is essentially equivalent to a signal-to-noise ratio. For example, any observed difference in the intelligence of two people will be partly due to heritable genetic differences (genic differences which can be passed from parent ot child), and partly due to environment (i.e. nutrition, the quality of training, etc.)…This is equally true for height, speed, weight, etc….

    If Kimura’s estimate is correct that fitness typically has a heritability of only about .004, then only about 0.4% of phenotypic variation for fitness is selectable. This represents a signal to noise ratio of 1:250. One way of expressing this is that 99.6% of phenotypic selection for fitness will be entirely wasted. This explains why simple selection for total phenotypic fitness can result in almost no genetic gain.
    ….
    Another major source of noise–probability selection, not threshhold selection…
    ….
    There is a third level of genetic noise…which I’m going to call gametic sampling….
    …..
    There is abundant evidence that most DNA sequences are poly-functional, and therefore poly-constrained. This fact has been extensively demonstrated by Trifonov (1989)…

    Poly-constrained information, and poly-constrained DNA. DNA, like word puns, word palindromes, and word puzzles contains poly-functional letters, words, and phrases. Such sequences can only arise by very careful design….

    John Sanford

    And the book has so much more great stuff!

    Sal

  42. This sounds like a good book to get and read. Thanks for bringing this to our attention, Sal. For years the Darwinists response to anyone who questions how small scale adaptations can accumulate to large scale evolutionary changes is to ask “what’s the barrier to genetic change?” Implied in the question, of course, is that since no one can identify any such barrier to genetic change, then clearly none exists (forgetting thier own maxim that “absence of evidence isn’t evidence of absence!”). I wonder if Sanford’s book and the problems he discusses represent that just such a barrier exists and here it is!

    Any thoughts?

  43. When I was an evolutionist, I also was, at heart, a eugenecist….In light of a deteriorating human genome, should eugenics be re-examined. Unfortuately, this is already happening….

    John Sanford

    Greetings DonaldM,

    (I regret to say, I’ll be away for the weekend, so my visits to this thread will be limited. bummer.)

    That said, it would helpful to compare and contrast Sanford’s work to that of the other IDers.

    Behe outline broad barriers to Darwinian evolution and did some quantitative work on the improbability of protein evolution.

    Bill Dembski focused on design detection and mathematics that would be useful to researchers trying to assess if a physical object is designed.

    Paul Nelson and Stephen Meyers wrote extensively on difficulties facing morphological evolution as well as the problems in the paleontological record.

    Barrow, Tipler, Gonzalez, Richards, and others touched on cosmological-ID.

    Sanford and ReMine demonstrate mathematically from existing knowlege and that even under generous theoretical assumptions Darwinian evolution does not have the physical resources to fixate the vast number nucleotides in the genome. We know the limits of information transmission in modems and the speed of information infusion into hard disks. We also know whether a signal is sufficiently strong enough to overcome the noise in a given environment. Extending these valid concepts of information theory into the question of information in the genome is therefore natural. But what Sanford discovered is that Darwinian evolution is theoretically inadequate to solve the problem of information increase and maintenance. The numbers simply do not justify any acceptance of Darwinian evolution.

    Furthermore, Sanford’s claims have some verification in the lab, and is open to further empirical testing! Much like Kepler’s celestial mechanics supplanted epicycle theory in the prediction of planetary trajectories, I think Sanford’s model will be far more successful in predicting genomic trajectories. The ideas are testable in principle, and if biologist will be open-mindend with the data, they’ve been seeing confirmaiton of this all along.

    For example, if the degeration is as high as he claims, we won’t need to wait millions of years to measure it. Our resolution may be at the point we can actually test his ideas in the not too distant future. Furthermore, there are already some papers supportive of his thesis.

    From a practical standpoint, Sanford’s work has important medical implications.

    It’s amusing to think much of the food in our grocery stores may have been affected by his gene-gun technology, and now our outlook and treatment of the genome may also be affected because of his pioneering work.

    Much of his work simply makes inferences from well accepted sources of information. I think he was one of the few simply bold enough to come forward and say, “the emperor has no clothes”. The bulk of his claims were already in existing peer-reviewed literature which had been swept under the rug as a problem to be resolved in the future. As he pointed out, the deteriorating genome is already somewhat privately acknowledged by the eugenecists. Sanford simply re-visits the problems and argues scientifically why these unresolved problems with naturalistic evolution will never be solved.

    Sanford is one of the few individuals with such a stellar reputation and who is independently wealthy (because of his biotech firms) that he could withstand the backlash quite comfortably. I’m very grateful he came forward, and I hope the issues he put on the table will be discussed seriously in the scientific community.

    Salvador

  44. For what it’s worth, world class geneticist Brian Sykes gives the human race 100,000 years before male extinction. Though I’m skeptical of some of his reasons, geneticist Sykes (by no means an IDer), is at least in line with Sanford’s outlook. See: Adam’s Curse

    Adam's Curse

    Well-known Oxford geneticist Sykes (The Seven Daughters of Eve), in this lively and thought-provoking book, gives a genetic twist to the battle between the sexes.
    ….
    Sykes concludes by noting that, as evidenced by declining sperm counts and high percentages of abnormal sperm, among other variables, the Y chromosome is a genetic mess and is deteriorating so quickly that men could become extinct.

    At least Sykes gives a more interesting twist regarding the future: as males grow extinct, there will come a time there will be ten women for every man.

    Sal

  45. 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

    how could small changes moprphological or otherwise ever lead to anything at all ?

    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. Life on earth began from a seed which was programmed to diversify in a more or less fixed sequence just like a fertilized egg cell is programmed to diversify in a fixed sequence into all the different cell types, tissue types, and organs that make up the adult form. -ds

  46. Re #41: I wasn’t criticizing Sanford’s book, since I haven’t read it. I was criticizing the general tendency (predating Sanford’s book) to simply claim that RM+NS inevitably leads to deterioration and inevitable extinction without backing that up with a model. What Kimura curve are you talking about? I’m looking at my Crow and Kimura (1970) right now. Is it in there?

    I have to agree with great_ape that fluctuating population dynamics of finite populations almost guarantees that a species will go extinct sooner of later. That seems to be a sufficient explantion. Whether it is necessary, I don’t know. I could well imagine that many extinctions are caused by one species outcompeting the other (a form of NS). Species are usually well adapted to local conditions (including other species), but when new species arrive from far away, the invasive species can cause massive extinction. Look what happened in Lake Victoria when a new predator was introduced. Bye bye cichlids. There are many more examples. I have no idea how important this has been in the history of life, but it might have been quite significant. These two factors together (i.e. random population dynamics and competition) might well account for 99% of species having gone extinct.

    You admit you have no idea if your claims of extinction mechanisms are important in past extinctions or not but you’re still going to discount what’s at least an equally valid proposal for extinctions – deterioration of the genome through nearly neutral evolution. You appear to have an irrational bias in your thinking. Please explain. -ds

  47. 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

  48. 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.

  49. 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

  50. 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

  51. 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

  52. 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

    Salvador

  53. 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.

  54. 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

  55. 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.

  56. 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

  57. 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.

  58. 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. :P

  59. 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.

  60. 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.

  61. 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

  62. 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.

  63. “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.

  64. 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/gene.....ation.html
    http://www.nwcreation.net/arti.....eview.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.co.....ange1.html
    [currently down -- see Google's cache here -- http://72.14.203.104/search?q=.....ange1.html ]

    A good book on the YEC biology position is:

    http://www.amazon.com/exec/obi.....ative=9325

  65. 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.

  66. 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.

  67. 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.

  68. 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.

  69. 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

  70. 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.

  71. 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

  72. 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.

  73. 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.

  74. “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? –apeman

  75. 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

  76. 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.

  77. Raevmo,

    Thanks for the link to the abstract. I am familiar with some of Lynch’s work–he’s been quite prolific and tends to address interesting questions–but I had not seen this particular study. While I don’t think this will put to rest many of the questions raised here, particularly due to the timescales involved in laboratory experiments vs. the real world, it is at least something in the realm of empirical observation. It suggests that, at least in the laboratory setting in a competitive environment, lineages subject to measurable genetic deterioration via forced bottlenecks, when subsequently allowed to rebound in number, move in a *positive* trajectory in terms of genetic fitness. I find it quite interesting–and you all here should as well–that they describe this as a “surprising” result.

  78. ds, prior to my last two posts, I submitted a somewhat lengthy post responding to the circularity issue you raised above. Was it eaten on my end, or is it stuck in a filter somewhere? I hope I remembered to hit the submit button… It made mention of my beloved “philosophical pillow,” and hopefully it hasn’t been sent to oblivion.

    Tsk, tsk… you used a spam string p-i-l-l. -ds

  79. Great_ape, I didn’t know this work of the Lynch group either, until I stumbled upon it when checking out who had cited another interesting paper: Kondrashov’s “Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?” (1995, Journal of Theoretical Biology 175, 583-594).

    The surprising thing, according to the authors in the Discussion section, is that such a high fraction of deleterious mutations can be *compensated* (as opposed to back-mutated) by other new mutations and that there are potentially a large number of ways to ameliorate the negative effects of a given mutation.

    I took you off moderation because you’re bright and knowledgeable and not overly offensive. Don’t make me regret it. :-) -ds

  80. Mung: “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.”

    Ops, we seem to have bumped into an issue of semantics. It sounds that you are saying that a biologist would not find need to make an exhautic tree when there are only 50 to 100 creatures to classify.

    Lets try this again. If one found two organisms just after the cambrian explosion, two organisms which are now seen to be in two separate phila, would a biologist look at them at that point in time, and say, “hmmm these organisms are very much alike, but a little bit different” like say different like the Indian Elephand and African Elephant are, or would the biologist say, “hmmm, these organisms are very much different, thought they have some core similarities”, like say the difference between a lobster and a trout?

  81. Mung and bFast:

    Let me clarify the terminology. Darwinism states that diversity precedes disparity. That is, animals change a little at a time, this showing up first as just variation within species, then as new species, then only by a buildup of a lot of small changes over time do you actually get disparity — large-scale differences.

    The fossil record shows the opposite — the large changes happen first, and then you get diversity within the larger groups.

    Darwins prediction: diversity precedes disparity
    Actual condition of the fossil record: disparity precedes diversity

  82. Johnnyb, thanks.

  83. Jack, thanks for the time and lengthy response.

    “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).”

    This is where the confusion comes in. McEvo’s/Old Earthers apply a set of standards across the board based upon “historical science”. PZ Meyers called Dr. Skell a crackpot due to his YEC views and then utilizes this to promote the fact good science cannot be accomplished by people with YEC views or in the case of ID – same monotone rant. What I am earnestly attempting to do here is stop this categorization of scientist simply based upon historical science. Certainly, if one is arguing age of the earth, universe, etc., then each side will have to be equally and robustly analyzed. But as to daily scientific inquiry for research, creation of new medicines, etc., it has not one jot to do with current breakthru research.
    Please note that I am not arguing for teaching of creation science of even ID science. But I am arguing against the current label masters and also against discrimination of tenure or even staffing based upon such views. A YEC today entering into the Genetic research field, who is fully qualified, high marks, with a good Doctoral thesis should not have to worry about his career being squashed by the likes of a PZ. And we should all realize it will not stop science if a YEC enters into the field, or a university to do such research.

    “My short answer to this question is that I don’t think there is any area of genetic research that Dr. Sanford cannot do.

    Thanks, and this is important for all to understand. Because to much highly inflamatory rhetoric is tossed around(as Tina stated) on both sides. But the unfortunate truth is a label always put forth against YECs is they cannot do good science – simply again because of their view on historical age. This myth is a highly nuanced message propagated thru media on all levels and by scientist.

    But the most famous hype is It Will Destroy Science.

    “My disclaimer is that the phrase “based upon his YEC views” is out-of-place here.”

    That’s your opinion. It was to make a point and draw a clear line in the sand. It accomplished the task. Being a YEC does not destroy scientific standards and in fact we now see high standards in the case of Dr. Sanford. We should be able to seperate the “operational” as you say and the historical.

    “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.”

    Exactly and thank you for the response. Hopefully, parents with children who believe in YEC can encourage their children to seek scientific careers without fear of discrimination or retaliatory actions at the university level.

  84. The surprising thing, according to the authors in the Discussion section, is that such a high fraction of deleterious mutations can be *compensated* (as opposed to back-mutated) by other new mutations and that there are potentially a large number of ways to ameliorate the negative effects of a given mutation.

    I’m highly skeptical of these claims. Compesating errors by more errors?

    Healing happens at the organismal level, and there is reason to expect that it can happen at the population level as well based on discoveries with non-Mendalian inheritance. Such repair would be anything but random.

    I’m skeptical of Lynch’s characterization that it was a compensatory mutation in an undirected fashion. One might could just as easily invoke a healing mechanism! The thought that one can heal errors with more errors sounds a little implausible. It is more plausible that errors are compensated by pre-programed changes.

    I think the characterizations by these scientists are a little biased. I mean, after all, are the DNA mutations in the immune system to fight off threats purposeless and undirected and undesigned?

    PS
    An anecdote about Lynch: I quoted him last fall in a talk I gave at UVa at an IDEA meeting (mentioned here). Somehow, Lynch, 800 miles away was informed that I quoted him! He wrote me demanding I refrain from quoting him from his response to the article where I was featured in Nature (see Who has design’s on your student’s minds? and Lynch’s response ID or intellectual Laziness). Sheesh, does he have nothing better to do than police what is said at IDEA meetings (in Virginia) at schools 800 miles away from him (Indiana).

    He gave the usual anti-ID diatriabe in his letter to me. I basically told him to go take a hike (engineers need not worry about reprisals from evolutionary biologists). I said that while we engineers are building space stations, evolutionary biologists are drawing phylogenetic trees that don’t even agree with each other, and these phylogenies may as well have been drawn up by kids with crayola crayons (I in effect suggested, “Evolutionary Biologists aren’t real sceintists”) . I then invited him to circulate my response to him to his Darwinist colleagues. :-)

  85. Scordova, I’m surprised that as a space station building engineer, you find it hard to imagine how the negative effect of one mutation could be compensated by another mutation. A mutation is not the same thing as an “error”. The “DNA is software” analogy only goes so far. I find it rather easy to imagine how, for example, the slowing down of one metabolic pathway can be compensated by the speeding up of another pathway by an appropriate mutation (say in a regulatory gene). Just like in space stations, there seem to be lots of redundancies in living organisms. I’m looking forward to the mutations being characterized so we know what we’re talking about here.

  86. Raevmo,

    that is a good observation. I have always wondered about the differences in transcription errors in say books (Sanford uses a technical manual as an illustration for simplicity), and living organisms that don’t just change, but respond to effects around them. Perhaps it is the same thing, perhaps not, as you indicate.

    hopefully Salvadore and provide more light on the subject. But, somewhat related to your question is what Sanford proposes as selection. We keep thinking about these billions of nucleotides that gets selected (say for instance I have 100 bad mutations, but 10 good ones – the best thing to do is select the 10 good ones, and throw away the bad). But, Sanford argues (and I think correctly) that you don’t get to select the 10 good ones, as mutation occurs at the point level, but selection occurs at the whole organism level. Therefore, natural selection doesn’t work on individual mutations, but has to select all 1 billion or so points. So, if I live and the guy next to me dies, you get my 10 good mutations and my 100 bad mutations, and so on, and so on.

    How do you think that effects your idea of compensation of good and bad mutations, if at all?

  87. ajl, you’re right that selection usually occurs at the whole organism level. But the reason why it’s often still OK to pretend as if selection occurs at the level of the mutation itself is because of sex and recombination. Every generation a reshuffling of the genes takes place, so that individual mutations will be “tested” against various genetic backgrounds. Only those mutations that do well *on average* against different backgrounds get selected in the long term. So your 10 good mutations will no longer be in the company of those 100 bad ones in the next generation, but will be together with other mutations, some bad some good. In a sense that is also a problem for compensating mutations, because if a bad mutation is rare and it happens to find itself in the company of a rare compensating mutation, then in the next generation they will probably no longer be together. Sex also breaks up good combinations. The reason why this couldn’t have been a problem in the Lynch experiment is that the bad mutations were fixed; everybody had the bad mutation. As a result, a compensating mutation would always be in the company of a bad mutation whose effects it could compensate.

  88. Raevmo,

    thanks for the clarification. I looked into the concept of recombination from Sander’s point of view (I am not a biologist, so this is just a fun learning environment for me). Below is his perspective as written in his book – perhaps you can provide a sanity check as to whether it makes sense since I haven’t a clue (and am not sure I’m even representing it correctly):

    “Firstly, when we examine the human genome, we consistently find the genome exists in large blocks (20,000 – 40,000 nucleotides) wherein no recombination has occurred – since the origin of man (some references put in…). This means that virtually no meaningful shuffling is occurring on the level of individual nucleotides. Only large gene-sized blocks of DNA are being shuffled. I repeat – no actual nucleotide shuffling is happening! “.

    From what you know of genomics, is this true? It seems that Sanders is saying that nearly neutral, deliterious point mutations can’t get selected out, because the selection happens at the whole organism, and there is no way for the entire organism to single out those mutations (as you acknowledged above). He is now saying that the same problem exists with recombination or shuffling since that occurs in larger blocks, so once again the larger blocks (of 20,000 nucleotides) have no way of selecting for the few point mutations in them. Therefore, it would appear that the 10 bad mutations we’ve been discussing get lost in the block of 20,000 and pass on through to the next generation. Remember, he is talking not about disasterous mutations, but deliterious, nearly neutral mutations which he surmises can’t get selected out. And it seems from Kimura’s curve, there is just more and more nearly neutral deliterious mutations that keep getting added in, even if there are a few good ones.

    Anyway, you seem pretty up on all this, so I wanted to find out from you if Sanders makes a valid point against recombination – heck, as of last week I never even knew shuffling occurred, let alone in blocks of 20,000 :-)

    BTW, this is one of the best threads on UD in a very long while – don’t you think?

  89. Scordova, I’m surprised that as a space station building engineer, you find it hard to imagine how the negative effect of one mutation could be compensated by another mutation.

    It can happen if it is by design. Any suggestion that compensatory mutations as a general mechanism without any pre-meditated design for those compensatory mutations is a stretch.

    That’s part of the whole problem here, a mutation happens and the Darwinists are quick to label it as an error! The more reasonable perspective regarding mutations:

    1. changes that are part of a designed capacity for change

    2. changes inconsistent with the original design, and would be labeled as undesirable

    Consider evidence for the immune system’s designed mutations by my friend Royal Truman:
    The Unsuitability of B-Cell Maturation as an Analogy for Neo-Darwinian Theory

    Proposed evolutionary processes which supposedly produced first bacteria and eventually humans are assumed to not have been driven by intelligent guidance. We must clearly distinguish between true randomness and a purposeful algorithm to cover a search space to converge on an intended goal.

    (A) Where fired shotgun pellets actually impact is only in an incomplete sense “random”. The gun barrel, triggering mechanism, explosive mixture, size and number of pellets, etc. are organized to solve a class of problem. Although the specific target need not be known in advance, the topology of desired outcome (in time and space) is part of the shotgun design. The design covers a constrained range of possibilities: it cannot kill bacteria nor whales (area), nor destroy satellites (distance) and needs a triggering mechanism (time). This permits a non-random outcome, such as killing a bird at a specific time and place with a high probability, with little risk of collateral damage.
    The designer of the apparatus need not specify the exact picometer each pellet will end up at. It suffices to ensure within a high probability that when used in the correct context and manner, the “random” behavior of the ensemble of pellets is within the intended tolerance.

    (B) Construction workers sometimes throw debris down a chute when repairing a building. One cannot predict the precise trajectories nor final location of every object thrown down. Nevertheless, the range of outcomes is constrained by the design which ensures bystanders aren’t killed.
    (C) In molecular modelling studies one wishes to identify an arrangement of atoms in three dimensions with an absolute energy minimum, which would represent the thermodynamic stablest configuration. Mathematical algorithms can guide the computer program down one of many (local) energy minima. How may one ensure there is not a better one? One trick is to store the best result so far, introduce “random” behavior to knock the settings away from the influence of the (local) minimum energy valley to permit other attempts to be made (yet deeper energy valleys).
    Superficially random search strategies are used commonly by intelligent agencies to explore a space of possibilities. There are many examples. The logic can be programmed into a robot to find its way around a room. Once foraging bees are in the vicinity where scout bees sent them (via a coded “waggle dance” message) to find food, they circle until the target is sighted. The bee uses its best guess as roughly a central point to initiate a “random” search strategy. Anyone not having a full picture of what is involved, and only concentrates on the bee’s flight behavior while homing in on the target, could be excused for seeing only “random” change.

    None of these examples are legimitate analogies for evolution, although superficially based on seemly “random” changes and selection of improved intermediate steps. As we shall see, B-cell hypermutation to home in on solutions within an acceptable tolerance, is another example of only superficially “random” behavior. All necessary equipment has been prepared in advance, and the “random” hypermutations begin only after a careful process of preparation to ensure suitable candidates have locked in on the goal, and they are then carefully guided towards the intended target.

    It is not hard to postulate what happens at the organismal level (single organism) is extensible to the population level (evolution of populations). But recall, even in an organism with self-healing mechanism (such as human bodies), there is still eventual genetic entropy (copy errors in somatic cells begin to propagate!). If we extend the limits of self-healing from the organismal to the population level (evolution), we get a good perspective on Sanford’s thesis of genetic entropy.

  90. ajl, sure there are blocks in which no recombination has occurred since the origin of man. Given the size of the genome and the number of recombination events that could have taken place since then, there must be blocks without recombination. And it is known that recombination hotspots exists. But this doesn’t *at all* prevent selection from eliminting blocks that contain (slightly) deleterious (point) mutations. In sufficiently large populations there appears to be little risk of extinction through genetic erosion.

  91. Raevmo,

    Although we disagree, I find your post substantive, and I appreciate your efforts to make thoughtful contributions along with data citations.

    By chance do you have Sanford’s book?

    Thank you for participating.

    Salvador

  92. My pleasure Salvador, it was a nice thread. And no, I don’t have Sanford’s book. Isn’t there a free pdf floating around somewhere?

  93. Raemo,

    I’m not aware of any free pdf’s of his book. I welcome criticism of specific sections of his work as I’m recommending it to the IDEA chapters in Virgnia and New York.

    I value finding of any error in otherwise fine works of scholarship as well of affirmation of sections that are spot on.

    After reading graduate level population genetics books and then Sanford’s book, I think he makes a very solid case from a very basic, matter-of-fact, standpoint. It is evidenent his versant in population genetics (he’s an applied geneticist after all) and highlighted important nuances.

    Whether one agrees with him or not, I don’t think his ideas should be ignored.

    Salvador

  94. “eliminting blocks that contain (slightly) deleterious (point) mutations. In sufficiently large populations there appears to be little risk of extinction through genetic erosion. ”

    sure, but how does it select against it? If there are 20,000 nucleotides with some slightly deleterious ones, how is it able to pick up which ones to remove? It seems to me (and again, I’m no expert in this) that this is just a smaller version of the selection at the whole organism level. But, it still would appear to be too large of a block to identify a few slightly deliterious mutations mixed in with 20,000. Since they are nearly neutral, there really wouldn’t be anything to identify to select out, right? Also, there is no way to separate out the good and bad mutations within the block, at least I think.

    Sanford says “mutational hot spots will give us the mutant we want sooner in that location, but while we then wait for the complementary mutations within teh “cold spots”, the hotspots will proceed to back-mutate again. We are forced to keep re-selecting our good mutations within the hot spots, while we wait for even the first good mutation to occur within the cold spots”

    As to your statement of “sufficiently large populations”, Sanford says:

    “If a population is essentially infinite in size and is perfectly homogeneous, and if “noise” is both constant and uniform, and there is unlimited time – than all noise effects will eventually be averaged out, and thus even near-neutrals might be subjected to selection.” However, he goes on further to point out:

    - population size is never infinite
    - noise is never uniform

    So, I have always wondered about the whale to horse scenario. Whales do not reproduce like rabbits – or even gnats, so you have very long gestation periods, and very few offspring in the life of a single whale. It would appear to overcome the effect of noise and mutation, you need to approach infinite offspring, something higher mammals would never do.

    I know thats alot I’ve written, sorry about that. But I do have one question that I hope you will answer: we keep talking about beneficial mutations that can add information. However, Sanders indicates that he is just giving the benefit of the doubt on this, and that there really aren’t any beneficial mutations that add information out there that we have found. Is this true? (keep in mind, Sanders indicates that a hairless dog does have a “beneficial mutation”, but at the cost of actually losing information in the genome to accomplish it. That is, they are loss of function mutations that reduce net information within the genome. So, in terms of information content, they are still deleterious mutations. Thanks for all your great responses. I hope this thread is still of interest to you.

  95. Ajl, of course there is now way to remove individual nucleotides, but by removing a block containing the “bad” nucleotides (because the block as a whole is a bad gene) the “bad” nucleotides are removed anyway. The “badness” of a block depends on the number of bad nucleotides within it, and this determines the probability the block will be removed by selection. A population doesn’t have to be really infinitely large to be “effectively” infinitely large. What it takes is roughly that effective population size N>>1/s, where s is the selective disadvantage of the deleterious mutation. For smaller population sizes N, noise is important and bad mutations can more easily become established. That’s one of the reasons why conservationists are worried about natural populations becoming too small. Genetic erosion might drive the population to extinction.

    I have no idea what you mean by the “whale to horse” scenario. Did horses evolve from whales? Not to my knowledge.

    Beneficial mutations (that add information if you like) have been identified many times. Take bacterial resistance genes against antibiotics for example.

  96. Someone questioned how “epigenetics” might affect Dr. Sanford’s conclusions regarding genomic degradation. That is something I have been wondering also, since finishing Dr. Sanford’s book today, and just yesterday reading an article about epigenetics in the November, 2006 issue of “Discover”, with the cover heading: “The New Genetics – DNA Is Not Your Identity”.

  97. Raevmo,

    I am resisting the temptation to respond to your post with searing sarcasm. I want to maintain the decorum of UD but you are making it very very hard … arrrgh …. must resist … temptation to be sarcastic …. too late … can’t resist … already sarcastic … doh!

  98. [...] Cornell geneticist John Sanford pointed out many problems confronting the theory of Darwinian evolution, particularly human evolution. (See: Genetic Entropy ) Many of his arguments were subtle. Among them was his discussion of a somewhat obscure paper: Estimate of the Mutation Rate per Nucleotide in Humans by Nachman. Nachman writes: [...]

  99. [...] The human genome project took 3 billion dollars and 13 years to complete. By comparison, Solexa might be able to do a comparable job for a few thousand dollars per person (ideally even less) and in a much shorter time frame. (See the UD sidebar on Solexa Genomics.) Solexa might be viewed as an unwitting research partner of the ID movement. The fine work of two important ID proponents, Cornell geneticist John Sanford and independent researcher Walter ReMine, might finally get slam dunk empirical confirmation if Solexa succeeds in its grand quest. For example, a fundamental consequence of Sanford’s Genetic Entropy thesis is that there will be an unabated rise in Single Nucleotide Polymorphisms (SNPs) per generation per individual. If confirmed, this data will be more nails in Darwin’s coffin, and then Darwin Day might have to be renamed Darwin Bashing Day (or something else, how about Abe Lincoln Day? Solexa, Inc. is developing and commercializing the Solexa Genome Analysis System, which is being used to perform a range of analyses including whole genome resequencing, gene expression analysis and small RNA analysis. Solexa expects its first-generation instrument, the 1G Genome Analyzer, to generate over a billion bases of DNA sequence per run and to enable human genome resequencing below $100,000 per sample, making it the first platform to reach this important milestone. Solexa’s longer-term goal is to reduce the cost of human re-sequencing to a few thousand dollars for use in a wide range of applications from basic research through clinical diagnostics. For further information, please visit http://www.solexa.com. [...]

  100. [...] by John C. Sanford is available at Amazon. I wrote a little bit about Sanford 2 years ago here: Respected Cornell geneticist rejects Darwinism. These icons link to social bookmarking sites where readers can share and discover new web [...]

  101. [...] by Edward Willet Not by Chance – Shattering the Modern Theory of Evolution by Dr. Lee Spetner Genetic Entropy & The Mystery of the Genome by Dr. J.C. [...]

  102. [...] I have mentioned Dr. Sanford previously at UD. See: Respected Cornell Geneticist Rejects Darwinism. [...]

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  104. [...] of the months you can produce. Many scientists support his work and they know more than you. Uncommon Descent | Respected Cornell geneticist rejects Darwinism in his recent book Indeed this research below states that most clades showed a bias towards DECREASING complexity [...]

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