Cornell Conference Genetics News Video

Gene gun inventor John Sanford on what Darwin got wrong

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Recently, we featured the now-published introduction to genetic theory at the Origin of Biological Information conference (Cornell 2011) by gene gun inventor and ID-friendly plant geneticist John Sanford (abstract and excerpt) . Here’s a vid of explaining “How Darwin Got It Wrong” in genetics:

Actually, Darwin didn’t know much about genetics, in the sense in which the term is used today. No one did in those days. And yes, Sanford is a creationist, but listen for yourself and judge.

A key difficulty with evolution theories based on Darwin (and make no mistake, that’s the majority*) is that such theories are based on an outdated view of how things work, but millions of people now make their living, in whole or in part, fronting such a view.

And we are not here talking about ridiculous stuff like the organized Darwin-in-the-schools lobby, legends in their own minds.

Just what we should do now is not for people who just can’t stand hearing a mob say bad things about them. If that is the worst you encounter, you will be doing well.

*See, for example, atheist philosopher Jerry Fodor on claims that “I’m not that kind of Darwinist any more.”

31 Replies to “Gene gun inventor John Sanford on what Darwin got wrong

  1. 1
    bornagain77 says:

    I really liked this interview on 100Huntley, with Dr. Sanford, as well,,

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video
    https://vimeo.com/35088933

  2. 2
    bornagain77 says:

    Of related note to what Darwin got wrong:

    What Your Science Teacher Got Wrong #1 – Chris Galanos/Dr. William Dembski – video
    http://www.youtube.com/watch?v=dX8M7YGM1l8

  3. 3
    Collin says:

    I am a fan of Sanford and his genetic entropy and other ideas.

    But Dr. Liddle said something that made me think: What about mice? In this presentation Sanford said that their computer simulation calculated that a species could live for only about 268 generations. Mice have surely had many more generations than that and have not yet gone extinct.

  4. 4
    scordova says:

    That’s if selection weeds out the mutations that create dysfunction, one runs out of population resources to keep the genome clean.

    The alternative is not to weed out the bad and let the population live, but the genome deteriorates.

    Example: the human population is growing, but we keep getting more and more diseases. We trade getting sicker instead of going extinct (which is what would happen if selection weeded out every functional defect).

    Remember, in the Darwinian world, sickness can be “beneficial” toward reproductive success. A mentally ill octomom (with 14 kids) is one of the most reproductively successful individuals on the planet!

  5. 5
    Collin says:

    Sal,

    I’m not totally sure I understand what you are saying. Is Sanford saying that if natural selection were more powerful, we’d be dead, but since it isn’t, we’re merely sick?

    I thought he must be saying that we are almost extinct because when I calculated the time for a generation (I assume 20 years) by 268, we get 5360. So I think this is why he is a YEC.

    But if I understand you correctly, we (or mice) could live much much longer because natural selection isn’t strong enough.

  6. 6
    JoeCoder says:

    @Collin #3

    Mice have shorter generation times and therefore likely fewer deleterious mutations. They also have a lot more offspring than humans allowing selection to work better–so while they should suffer from the mutational load problem. If you know the deleterious rate and the reproductive rate you can actually calculate whether selection can keep up:

    “It has been estimated that there are as many as 100 new mutations in the genome of each individual human. If even a small fraction of these mutations are deleterious and removed by selection, it is difficult to explain how human populations could have survived. If the effects of mutations act in a multiplicative manner, the proportion of individuals that become selectively eliminated from the population (proportion of `genetic deaths’) is 1-e^-U, where U is the deleterious mutation rate per diploid, so a high rate of deleterious mutation (U>>1) is paradoxical in a species with a low reproductive rate.” High genomic deleterious mutation rates in hominids, (Nature, 1999)

    So for humans, we get 60 to 160 mutations per generation, at least 10-20% of our genome is under functional constraint, and this gives us 6 to 32 deleterious mutations per child (most slight). Taking their Poisson probability distribution and using U=6, that means 1-e^-6 = 99.752% of the population will have to be selected away each generation for one lucky enough to have no deleterious mutations. For two to survive and maintain constant population size that would require on average 806 offspring per human female. Actually much more since natural selection is not omnisciently efficient.

    The mouse genome is about the same size as our own, although I’m having trouble finding their mutation rate. If you assume it’s half our own (taking a guess here), then they would only need to produce 2* e^3 = 40 offspring per generation (under artificial selection) to get by. So while I expect mice are also degenerating, they would at a significantly lower rate.

  7. 7
    JoeCoder says:

    That should read “40 offspring per mother”.

  8. 8
    scordova says:

    Collin,

    There is confusion on the matter on what Dr. Sanford means, and I’ve also conferred with Walter ReMine on the matter (ReMine’s work was the starting point of Sanford’s work).

    I probably expressed myself poorly so lets try again.

    Suppose we wanted to carry out an aggressive program of eugenics where we kill off every human that has a genetic defect:

    1. short sightedness (myopia)
    2. allergies of any sort
    3. obesity
    4. diabetes
    5. asthma
    6. propensity toward cancer
    7. tendencies to addiction
    8. attention deficit disorder
    9. obsessive compulsive disorder
    etc.

    The human race could go extinct real fast since the number of genetic defects keeps increasing with each generation. The alternative is to not kill off the bad and let the population continue even though it is sicker.

    In the simulations Walter told me there are at least two modes:

    1. keep population size constant
    2. let the population size decline by killing off defects

    If we adopt mode 2, the population goes extinct. If we use mode 1, the population persists but gets less functional. Either outcome is genetic entropy.

  9. 9
    Collin says:

    Thanks Joe, those are some interesting points.

    What do you mean by “functional constraint?”

  10. 10
    Collin says:

    thanks for explaining that Sal. Do you think that we will reach a tipping point and have a precipitous decline?

  11. 11
    scordova says:

    thanks for explaining that Sal. Do you think that we will reach a tipping point and have a precipitous decline?

    Yes, and even the evolutionary biologists in the know, acknowledge this. Examples:

    Sanford’s pro-ID thesis supported by PNAS paper

    And this book by Oxford geneticist Bryan Sykes:

    Adam’s Curse

    I think the Designer is letting us know we’re merely mortal, like the grass of the field, Pslam 90.

  12. 12
    JoeCoder says:

    By functional constraint, I mean a nucleotide “letter” that will have a negative impact on fitness (in most-to-all fitness landscapes) if it is changed. On my sourcse, the 10% comes from assuming common descent is true and mesuring the number of nucleotides shared among various mammal species. If anything mutated that spot it didn’t survive to tell about it. At best this produces a lower-bound estimate.

    The 20% is based on ENCODE’s count of protein-coding exons and bindings sites, which are only some of the types of sequences that have to be very specific to do their job.

  13. 13
    scordova says:

    JoeCoder,

    Do you understand FASTA files for human DNA? I’m trying to look at them, and I get multiple files for human chromosome 21, etc. Do I have to concatenate them or something. I’m trying to compare them to ChimpDNA. I think we can independently verify some of Tomkins results.

    I presume you’re a really good coder. 🙂

    Sal

  14. 14
    JoeCoder says:

    Unfortunately I don’t. I’m just a layman enthusiast who has been through Dr. Hasnain’s class on coursera, read a few ID books, and a lot of biology papers. My degree was in computer science and I program by trade, but I have yet to study bio-informatics.

  15. 15
    JoeCoder says:

    Strange that you ask though. I was just reading a few of Dr. Tompkin’s critics this morning. Unfortunately I don’t know enough about comparative genomics to make sense of it one way or another and don’t know who is right.

  16. 16
    JoeCoder says:

    Dr. Noor’s class on coursera. Lots of mistyping today!

  17. 17
    scordova says:

    don’t know enough about comparative genomics to make sense of it one way or another and don’t know who is right.

    Actually it appears evolutionary biologists don’t know much about comparative genomics either! I was aghast at some of the methodologies and Tomkins told me if he had been the reviewer of some of the papers (he’s been the reviewer of many secular papers since he ran the Genomics Institute in Clemson), he wouldn’t have passed a lot of the papers.

    The UNIX DIFF function is conceptually the most objective way to do comparisons. I’ll write a simple program maybe to explain where I’m headed. Dr. Tomkins wrote some software himself and showed the methodology. Some of it isn’t that hard if you have some pre-written code that can approximate DIFF. DIFF will essentially do the alignments for you if you have short enough snippets. 🙂

    How evolutionist said we’re close to the lungfish in DNA is with rather illegitimate methods (given the lungfish has a genome that is 130 giga bases and ours only 3-3.5 giga bases). DIFF would go ballistic if could be told that some effectively claim humans have 70-90% or better identity with lungfish.

    Can I contact you through e-mail? I think I have it through your UD profile.

    Sal

  18. 18
    wd400 says:

    A key difficulty with evolution theories based on Darwin (and make no mistake, that’s the majority*) is that such theories are based on an outdated view of how things work,

    No. Darwin described natural selection as an evolutionary force. Wright, Fisher, Haldane Dobzhansky and others updated it to account for the discovery of genetics, we continue to update our ideas in light of genomic data.

    Whether Darwin knew what a gene was has nothing to do with wether evolutionary biology is right, or even if Darwinian models explain genetic data.

    As for Sanford – it is unlikely that anyone who can pull out the “you can make a phylogeny of anything” argument is worth listening to.

  19. 19
    wd400 says:

    How evolutionist said we’re close to the lungfish in DNA is with rather illegitimate methods (given the lungfish has a genome that is 130 giga bases and ours only 3-3.5 giga bases). DIFF would go ballistic if could be told that some effectively claim humans have 70-90% or better identity with lungfish.

    diff would go ballistic because it doesn’t deal with duplications or rearrangments. The lungfish genome will be fill of repetitive elements (that’s an evolutionary prediction, btw). Those elements can make a genome big, but if the thing that makes two genomes different is the accumulation of repetitive sequences then it takes relatively few events for a size difference to arise (there are also whole-genome duplications in many lineages).

    Comparative genomicists do know what they’re doing, it’s evident you do not.

  20. 20
    scordova says:

    Comparative genomicists do know what they’re doing, it’s evident you do not.

    So says the same guy who says some fish (like lungfish) are more closely related to humans than to tuna:

    http://www.uncommondescent.com.....e-to-tuna/

  21. 21
    Mung says:

    JoeCoder:

    Mice have shorter generation times and therefore likely fewer deleterious mutations. They also have a lot more offspring than humans allowing selection to work better–so while they should suffer from the mutational load problem.

    Can you perhaps explain why larger numbers of offspring do not make deleterious mutations more likely?

  22. 22
    Mung says:

    wd400:

    Comparative genomicists do know what they’re doing, it’s evident you do not.

    Watch out, Sal will ban you from his threads for personal attacks on him and for being a troll.

  23. 23
  24. 24
    Mung says:

    SAL: “The UNIX DIFF function is conceptually the most objective way to do comparisons. … DIFF will essentially do the alignments for you if you have short enough snippets.”

    wd400: “diff would go ballistic because it doesn’t deal with duplications or rearrangements.”

    SAL: “So says the same guy who says some fish (like lungfish) are more closely related to humans than to tuna”

    Why not thank him for pointing you away from making a fool of yourself trying to use diff rather than insulting him?

  25. 25
    Mung says:

    For Sal’s possible edification:

    “a single hyphen or dash can be used to represent a gap of indeterminate length”

    So yeah, good luck using diff.

    c.f.:

    http://www.genome.jp/tools/fasta/

  26. 26
    JoeCoder says:

    @Sal

    Yes, please do contact me by email. It would be great to chat.

    However I do agree with wd400 and Mung that diff isn’t a good tool for genome comparisons. To add to the rearrangements he also mentioned, DIFF would be completely blind to inversions–flip a 1MB sequence and it would count every nucleotide as a difference.

  27. 27
    JoeCoder says:

    @Mung at #21

    Can you perhaps explain why larger numbers of offspring do not make deleterious mutations more likely?

    A larger number of offpsring still each have the same average number of mutations, but there will be more outliers. So if the del rate is 3 per generation and there are 40 offspring, on average (according to the poisson distribution) there will be 2 that have no deleterious mutations. Wiki’s second paragraph on the poisson distribution is a great overview. And I see it come up frequently in the population genetics papers for modelling just this.

  28. 28
    scordova says:

    @Sal

    Yes, please do contact me by email. It would be great to chat.

    However I do agree with wd400 and Mung that diff isn’t a good tool for genome comparisons. To add to the rearrangements he also mentioned, DIFF would be completely blind to inversions–flip a 1MB sequence and it would count every nucleotide as a difference.

    I’m aware of the limitations, that’s why some variation of the DIFF algorithm is necessary. I have an associate in the BLAST and google community.

    I certainly wasn’t planning to use DIFF in a raw approach.

    I’ll contact you off list.

  29. 29
    wd400 says:

    So says the same guy who says some fish (like lungfish) are more closely related to humans than to tuna:

    I don’t think you realise that this is an entirely uncontroversial finding, and one that you have placed yourself on the wrong side of.

    I don’t you continue to highlight you preference for what you personally feel should be true over the evidence, but linking to that post is a pretty poor sort an insult.

  30. 30
    Joe says:

    wd400:

    Darwin described natural selection as an evolutionary force.

    And yet there still isn’t any evidence to support that claim.

  31. 31
    Mung says:

    Salvador:

    I certainly wasn’t planning to use DIFF in a raw approach.

    How else would you use it?

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