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New paper using the Avida “evolution” software shows …

File:Avida 2.6 screenshot.png

screenshot of 2.6

… it doesn’t evolve.

Remember when AVIDA proved Darwin right?

These results provide evidence that low-impact mutations can present a substantial barrier to progressive evolution by natural selection. Understanding mutation is of primary importance, as selection depends on the mutational production of new genotypes. Numerous changes that would be beneficial may nevertheless fail to occur because mutation cannot produce them in the time available.

Further, it is important for biologists to realistically appraise what selection can and cannot do under various circumstances. Selection may neither be necessary nor sufficient to explain numerous genomic or cellular features of complex organisms [2-4].

PDF and poster here:

Nelson CW, Sanford JC (2011) The effects of low-impact mutations in digital organisms. Theoretical Biology and Medical Modelling 8:9.

Nelson CW (2011) Selection threshold constrains adaptive evolution in computational evolution experiments. Great Lakes Bioinformatics Conference. F1000 Research 2:A13.

We feel this work uses Avida to demonstrate that the selection threshold and resultant genetic entropy, and also irreducible complexity, can be prohibitive to progressive evolution. Some highlights from the Conclusions:

“… there are several ways in which Avida’s default settings produce results which conflict with observations from biological experiments. Precursors necessary for the most complex logic operation in the program, EQU, are frequently produced by random mutation, yet confer very large fitness rewards. Fitness effects of beneficial mutations under Avida’s default settings range from 1.0 to 31.0, values that are extremely rare in the natural world. As a result, fitness increases by an average of 20 million in only 10,000 generations. This is roughly seven orders of magnitude greater than the changes observed in biological evolution experiments.

… most mutations in biological organisms are low-impact [29], and this class of mutations may dominate evolutionary change [1,2]. When Avida is used with more realistic mutational fitness effects, it demonstrates a clear selection threshold. Mutations that influence fitness by approximately 20% or less come to be dominated by random genetic drift. Mutations that affect fitness by 7.5 – 10.0% or less are entirely invisible to selection in this system. These results provide evidence that low-impact mutations can present a substantial barrier to progressive evolution by natural selection. Understanding mutation is of primary importance, as selection depends on the mutational production of new genotypes. Numerous changes that would be beneficial may nevertheless fail to occur because mutation cannot produce them in the time available.

Further, it is important for biologists to realistically appraise what selection can and cannot do under various circumstances. Selection may neither be necessary nor sufficient to explain numerous genomic or cellular features of complex organisms [2-4].

… The accumulation of slightly deleterious mutations may pose an important health risk for numerous species, including humans [74], and warrants further study using computational approaches… we recommend that future experiments with digital organisms employ more biologically relevant mutational fitness effects.”

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62 Responses to New paper using the Avida “evolution” software shows …

  1. This is good stuff. I’m a bit disappointed at the lack of mention of genetic entropy.

  2. Kairos is smiling ear to ear right now! :)

  3. Please take a look at this video – Rabbit born with no ears near Fukushima nuclear plant: http://www.youtube.com/watch?v=UqVY9azhH3U
    This demonstrates that mutations are always deleterious.

    I bet we will never see a rabbit with wings near Fukushima – mutations never add information. I would like someone at UD write about this case. Thanks!

  4. BA:

    You got that right!

    THAT POSTER JUST WENT INTO MY VAULT, WITH ITS OWN LINK AND THE LINK TO THE PAPER. (This is the first time I have seen 30 point text show up onscreen as tiny text! I guess I would need one of those scanning flatbed printers to give full size . . . )

    The point that the fitness function plainly has to be tuned and peaky to pass the good stuff on, is telling.

    Notice the co-author: Sanford of gene gun and genetic entropy fame.

    Bonus! (Nobel Prize holder, isn’t he?)

    GEM of TKI

  5. kairos, I bet this keeps you beaming for a while. LOL :) or at least until MathGrrl shows up with her obtuse indifference to the truth of the matter,, :)

  6. What is there here that’s new? We know that alleles with a small fitness advantage will mainly be affected by drift. And because of this, mildly deleterious alleles can also be fixed: this is the concept of genetic load. So what’s new?

  7. 7
    Elizabeth Liddle

    Not so fast, guys!

    It is certainly possible to set the parameters in a platform like AVIDA and see evolution fail.

    However, the authors imply that their parameters are more “realistic”.

    But the genome size of AVIDA organisms is orders of magnitude smaller than living organisms, as is the maximum population size (for most populations); in addition,the fitness landscape is not a function of the evolving population (or wasn’t the last time I looked), and the population reproduces asexually.

    And we know, from population genetics,that whether or not “genetic entropy” is a problem is highly depending on genome size, population size, and whether the population reproduces asexually. As the authors note, it is already well-known that when population size drops, especially in asexually producing species, build-up of deleterious mutations becomes a problem.

    However, we also know a lot about the mechanisms by which this “meltdown” is avoided in certain species, and we also know that when populations become very small, genetic health becomes a very real problem (which is why extinction is a very real threat even in populations in which there remain many hundreds of breeding pairs).

    Sanford’s thesis, as I recall from his book, is that lifeforms were created perfect approximately 10,000 years ago, and we are headed for mutational apocalypse.

    This claim is clearly infirmed by a great deal of data, not least being that species that reproduce much faster than others (e.g. mice and people) seem to be in very similar states of genetic health.

  8. Sanford’s thesis, as I recall from his book, is that lifeforms were created perfect approximately 10,000 years ago, and we are headed for mutational apocalypse.

    I’m going to go way out on a limb here and say that you haven’t actually read the book.

    I have no problem with analysis of asexual populations. If evolution doesn’t work there it doesn’t work period.

    But in light of the recent threads here at UD about being a critic of a book one hasn’t read, did you take nothing away from them?

  9. Mung – I’ve read Sanford’s book, and that’s a reasonable summary (although he mainly discusses humans).

  10. I’ve read Sanford’s book, and that’s a reasonable summary (although he mainly discusses humans).

    A summary, in order to be reasonable, should at the very least be factual.

    1. Where does Sanford claim that humans were created perfect?

    2. Where does Sanford claim that humans were created approx. 10,000 years ago?

    I’ve been glancing back through the book and I have yet to locate either claim. Perhaps I’ll try to quickly read it again if I can find the time.

  11. ok, so far I’ve re-read through Chapter 3.

    No mention of humans specifically, or even life generally, having been created approx 10,000 years ago, perfect or otherwise.

    But I did find this:

    Part of the Primary Axiom is that all genetic variation must come from random mutations, since no genetic variation by design is allowed. However, now that the era of genetic engineering has begun, this axiomatic assumption clearly is not true (because many living organisms now contain genetic variations design and engineered by man). Perhaps this simple fact can open our minds to the possibility of designed genetic variation which preceded man!

  12. 12
    Elizabeth Liddle

    Mung, I have indeed read Sanford’s book, rather thoroughly in fact, although it was about a year ago now. Nonetheless still I have it beside me now, so I can check.

    I may have misremembered the 10,000 years ago (although I am fairly sure that Sanford self-identifies as a Young Earth Creationist – however I may be recalling that from some source other than the book). However, I will quote from his “Postlude” (page 157 in my copy):

    When I was young, I accepted the factthat I was going to die, and that all of the people I loved were going to die. I accepted it, but it robbed me of joy, to say the least! I was taught that there was still one hope: that the world was getting better….

    I now believe this was a false hope. I still believe we should diligently apply ourselves to making this a “better world”, and to be responsible stewards of the world we have been given. But I see our efforts as a holding action at best. While science can reasonably hope to prolong life, it cannot defeat death. Degeneration is certain. Our bodies, our species, and our world are all dying. It is simply not in our power to stop this very fundamental process. Isn’t this obvious when we look around us? So where is the hope? If the human genome is irreversibly degenerating, we must look beyond evolution in order to have a hope for the future.

    It took me a while to actually figure out his point at the beginning, because I assumed he was an IDist, and that his point was that if evolution was true, we would be degenerating, and therefore some Intelligent Designer/Repairman must be invoked to explain our obvious rude genomic health.

    But at about Chapter four I think, I realised that that wasn’t his thesis at all – his thesis was that we really were degenerating into extinction, from a previous pristine state, presumably as a result of the Fall.

  13. ‘that we really were (are) degenerating into extinction,’

    ,,,though the time scale is off, the principle is correct;

    ,,the evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”

    I went to the mutation database website cited by John Avise and found:

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.biobase-internation.....mddatabase

    I really question their use of the word ‘celebrating’.

    Human Evolution or Human Genetic Entropy? – Dr. John Sanford – video
    http://www.metacafe.com/w/4585582

    This following study confirmed the detrimental mutation rate for humans, of 100 to 300 per generation, estimated by John Sanford in his book ‘Genetic Entropy’ in 2005:

    Human mutation rate revealed: August 2009
    Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome. (Of note: this number is derived after “compensatory mutations”)
    http://www.nature.com/news/200.....9.864.html

    This ‘slightly detrimental’ mutation rate of 100 to 200 per generation is far greater than even what evolutionists agree is an acceptable mutation rate for an organism:

    Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction
    Excerpt: Shakhnovich’s group found that for most organisms, including viruses and bacteria, an organism’s rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.
    http://www.sciencedaily.com/re.....172753.htm

    All life eventually succumbs to the effects of Genetic Entropy over very long periods of time, but humans are especially vulnerable. As This following study reveals:

    Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally – September 2010
    Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).
    http://www.uncommondescent.com.....literally/

    As well, the slow accumulation of ‘slightly detrimental mutations’ in humans, that is ‘slightly
    detrimental mutations’ which are far below the power of natural selection to remove from our genomes, is revealed by this following fact:

    “When first cousins marry, their children have a reduction of life expectancy of nearly 10 years. Why is this? It is because inbreeding exposes the genetic mistakes within the genome (slightly detrimental recessive mutations) that have not yet had time to “come to the surface”. Inbreeding is like a sneak preview, or foreshadowing, of where we are going to be genetically as a whole as a species in the future. The reduced life expectancy of inbred children reflects the overall aging of the genome that has accumulated thus far, and reveals the hidden reservoir of genetic damage that have been accumulating in our genomes.”
    Sanford; Genetic Entropy; page 147

    further note;

    MUTATIONAL MELTDOWN IN LABORATORY YEAST POPULATIONS
    http://onlinelibrary.wiley.com.....x/abstract

    Here is a relevant paper on genetic entropy in other species:

    Muller’s Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution
    http://www.ncbi.nlm.nih.gov/pm.....MC2279117/

  14. 14
    Elizabeth Liddle

    Well, ba77, we seem to have found something we agree on!

    And actually, I think we can infer Sanford’s timeline from his figures for mutational buildup. Now that I come to think about it, I think that’s how I ballparked his 10,000 years. On page 113 in my copy, he estimates extinction for our species in 300 generations.

    Allowing 3 generations per century, that gives a max of 10,000 years from pristine state to extinction.

  15. Elizabeth,

    ‘we seem to have found something we agree on!’

    And who says miracles don’t happen???

    ,, as to time scale, the Mendel’s Accountant program developed by John Sanford and Walter Remine, does allow for ‘time-scale’ variation so as to accurately reflect reality,,,

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

    But for me, regardless of the time-scale issue, I find Genetic Entropy to hold for all biological adaptations that I can find, as well as was clearly elucidated by Dr. Behe in his recent paper;

    ================

    semi OT: Although Genetic Entropy surely spells the end for any delusions of grandeur that neo-Darwinists may have entertained for man, or anything else, evolving into higher and higher lifeforms, such as the delusion of grandeur mentioned at the 6:50 minute mark of this following video,,,:

    The Anthropic Principle – Fine Tuning Of The Universe – Michael Strauss PhD. – video
    http://www.metacafe.com/watch/4323661/

    ,,, the long, slow, irrepressible, slow march of decay is not really that much different from the fact, as clearly illustrated by Barry Arrington in his post, i.e. we all, 100% of us, die someday!!!,, But the blessed hope we have as Christians is the fact that Christ really did, with 100% certainty, defeat death on the cross so as to be propitiation for us that we may escape death and inherit eternal life. If will but humbly accept His healing hand into our life,,,

    Healing hand of God – Jeremy Camp
    http://www.youtube.com/watch?v=_-aE7zQTeEg

    ,,, etc.. etc.. etc..

  16. 16
    Elizabeth Liddle

    Just better say, ba77, in case I have inadvertently misled you – we do seem to agree on what Sanford is saying.

    However, we probably disagree on whether he is correct (I don’t think he is!)

    But it seems to me that is the clear thesis of his book.

    Mung, I think you owe me one :)

  17. Elizabeth, once again you are ignoring the evidence. This is science Elizabeth, this is not stating what you ‘feel’ is right. If you disagree with the conclusion you have to present evidence not just disagree. Moreover you have to specifically counter the studies I cited with studies of equal or greater weight!!!. For you to fail to grasp this simple point of the scientific method shows me that you either don’t know how to properly weigh evidence, or that you are operating under a philosophical bias. There is no other option. You may protest this, but it really matters not to me for my eye is staying on the evidence first and foremost, not your feelings of being upset that i call you of unfair weighing of the evidence!

  18. Mung, I think you owe me one

    I’m sorry. For what?

    You claimed:

    Sanford’s thesis, as I recall from his book, is that lifeforms were created perfect approximately 10,000 years ago, and we are headed for mutational apocalypse.

    You’re standing by that?

    Or are you saying I owe you one for thinking you had not read the book? That’s one I’ll grant you.

    But you failed to answer either of my two questions.

    1. Where does Sanford claim that humans were created perfect?

    2. Where does Sanford claim that humans were created approx. 10,000 years ago?

    It took me a while to actually figure out his point at the beginning, because I assumed he was an IDist, and that his point was that if evolution was true, we would be degenerating, and therefore some Intelligent Designer/Repairman must be invoked to explain our obvious rude genomic health.

    You mean because he writes:

    For the purpose of further discussion and, and for the rest of this book I will be happy to give the theorists their model of life as “pools of genes” and the idea of selection on the level of single nucleotides.
    (3rd ed. p.55)

    But at about Chapter four I think, I realised that that wasn’t his thesis at all – his thesis was that we really were degenerating into extinction, from a previous pristine state, presumably as a result of the Fall.

    In spite of what he says about showing why the “Primary Axiom” has to be false?

    My reading is that he is saying, if we take the assumptions of the Darwinists, this is where it leads. So their assumptions are false.

    And actually, I think we can infer Sanford’s timeline from his figures for mutational buildup. Now that I come to think about it, I think that’s how I ballparked his 10,000 years. On page 113 in my copy, he estimates extinction for our species in 300 generations.

    Allowing 3 generations per century, that gives a max of 10,000 years from pristine state to extinction.

    So you’re putting words in his mouth and calling it the thesis of his book based on some calculations that you did and an assumption that you made?

    Are you talking about Fig. 10b labelled “Crow’s fitness decline”?

    You miss the part where he says “assuming Crow’s model of truncation selection”?

    And the part where he says “assuming an additive model”?

    And on the previous page where he says “none of these assumptions are remotely reasonable”?

    And what gave you the idea to extrapolate the graph into the past? Sanford does not do so. He doesn’t include any sort of timeline other than number of generations. He doesn’t say where he thinks we are on the timeline.

    You’ve given me no reasaon to think you’ve accurately identified the thesis of his book.

  19. 19
    Elizabeth Liddle

    Mung:

    For thinking I had not read the book :) Nay, for assuming had not read the book and waggling your eyebrows at me for not heeding the warnings about what happens to people who presume to critique books they have not read :)

    But that’s OK :)

    If I’ve got his thesis wrong, I’d be interested to hear what it actually is it, but I have actually read it extremely carefully (several times, in fact), and I also located and read quite a number of his references.

    As I said, I had read elsewhere that he was a Young Earth Creationist (I’m afraid I can’t give you a direct citation, as it was in several sources, including, IIRC, an interview with Sanford himself), but I had also put an upper limit on his creation date by actually reading his book. I don’t think he would disagree with that upper limit (but you could check with him).

    I don’t have it with me right now, but, yes, I did read the part where he assumes Crow’s truncation model (I also read the Crow paper in question). I think you will find that he regards the upper limits as generous. Indeed he regards, Crow, Kimura and (IIRC) Kondrashov as all supporting his thesis of inevitable terminal “genetic entropy”.

    I’m not “putting words in his mouth” apart from the ones I actually copy-typed from the book. I am paraphrasing, and I believe I am paraphrasing correctly.

    You say:

    My reading is that he is saying, if we take the assumptions of the Darwinists, this is where it leads. So their assumptions are false.

    Yes, that was my initial reading too, as I began the book. But it doesn’t seem to be the correct reading. Read the postlude (from which I took that quotation). He appears to believe that the human genome is in a steady decline from an initial state of perfection (although I’m not sure that he explicitly states that there were no deleterious alleles when humans were first created) to inevitable and painful extinction.

    And what gave you the idea to extrapolate the graph into the past? Sanford does not do so. He doesn’t include any sort of timeline other than number of generations. He doesn’t say where he thinks we are on the timeline.

    Sanford extropolates into the future, and “number of generations” doesn’t allow for very wide confidence intervals (not orders of magnitude anyway, even if we allow for biblical lifespans). So that puts a ne plus ultra on his date for the origin of people.

    Unfortunately for Sanford, it doesn’t explain why faster-breeding species are not already extinct.

    It’s a very odd book.

  20. From Wikipedia, for what it’s worth (there are citations for the quotes):

    Formerly an atheist since the mid-1980s, Sanford has looked into Theistic Evolution (1985–late 1990s), Old Earth Creation (late 1990s), and Young Earth Creation (2000–present). According to his own words, he did not fully reject Darwinian evolution until the year 2000. An advocate of intelligent design, in 2005 Sanford testified in the Kansas evolution hearings on behalf of intelligent design, during which he denied the principle of common descent and “humbly offered … that we were created by a special creation, by God.” He also stated that he believed the age of the Earth was “Between 5,000 and 100,000″ years. An analogy Sanford uses to illustrate alleged evidence of design is that of a car versus a junkyard: “A car is complex, but so is a junkyard. However, a car is complex in a way that is very specific — which is why it works. It requires a host of very intelligent engineers to specify its complexity, so it is a functional whole.” Intelligent design proponent William Dembski touts the accomplishments of Sanford as evidence of the scientific status of intelligent design and has endorsed Sanford’s book, Genetic Entropy & the Mystery of the Genome.

  21. Elizabeth states;

    ‘It’s a very odd book.’

    ,,,and oddly you cannot show a single violation of the principle of Genetic Entropy!

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    ,,Speaking of a very odd book, It turns out that Darwin’s “Origin of Species” is a theological book, not a science book! Now I find that to be EXTREMELY ODD!!!

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species
    Excerpt: His analysis, “Charles Darwin’s use of theology in the Origin of Species,” BJHS 2011, argues that Darwin used theology throughout his 1859 masterwork to argue for the truth of his theory of descent with modification by natural causes. Darwin’s theology was not merely negative, entertaining the assumptions of his creationist opponents as hypotheses simply to contradict those assumptions with evidence.

    Rather, Dilley argues, Darwin employed theology in a positive fashion, as support for his own position. “In the Origin,” Dilley writes, “Darwin used a specific theological view of God’s relationship to natural laws in order to argue for evolution and against special creation.” The Origin supplies abundant evidence of theology in action; as Dilley observes:

    I have argued that, in the first edition of the Origin, Darwin drew upon at least the following positiva theological claims in his case for descent with modification (and against special creation):

    1. Human begins are not justfied in believing that God creates in ways analogous to the intellectual powers of the human mind.

    2. A God who is free to create as He wishes would create new biological limbs de novo rather than from a common pattern.

    3. A respectable deity would create biological structures in accord with a human conception of the ‘simplest mode’ to accomplish the functions of these structures.

    4. God would only create the minimum structure required for a given part’s function.

    5. God does not provide false empirical information about the origins of organisms.

    6. God impressed the laws of nature on matter.

    7. God directly created the first ‘primordial’ life.

    8. God did not perform miracles within organic history subsequent to the creation of the first life.

    9. A ‘distant’ God is not morally culpable for natural pain and suffering.

    10. The God of special creation, who allegedly performed miracles in organic history, is not plausible given the presence of natural pain and suffering.

    Nothing in Dilley’s article can be construed as challenging evolutionary theory, or supporting ID; his scholarly concerns lie elsewhere. As a student of the science-theology-philosophy triad, Dilley wants to understand how these areas of human understanding mutually inform each other. In that, his new article succeeds wonderfully, and will become a locus classicus for future analysis of the history and nature of evolutionary theory.

    The article will also be a category-buster to illuminate current discussions, where evolutionary biologists (such as Jerry Coyne or Richard Dawkins) continue to use theology to make their case for Darwinian evolution.
    http://www.evolutionnews.org/2.....46391.html

    On the Vastness of the Universe
    Excerpt: Darwin’s objection to design inferences were theological. And in addition, Darwin overlooked many theological considerations in order to focus on the one. His one consideration was his assumption about what a god would or wouldn’t do. The considerations he overlooked are too numerous to mention here, but here’s a few:,,,
    http://www.uncommondescent.com.....ent-362918

  22. It is also very interesting to note that right now on this very thread, that those who are trying to dismiss Genetic Entropy as a overriding principle of biological adaptations are presenting theological arguments against Sanford’s YEC views instead of focusing on the scientific evidence and presenting positive evidence that Genetic Entropy has been violated!!! i.e. If neo-Darwinism is so overwhelmingly true why is this???

  23. Speaking of evidence, This video is tells it like it is!

    Evolution Vs Genetic Entropy – video
    http://www.metacafe.com/watch/4028086/

  24. 24
    Elizabeth Liddle

    Oh, dear, we do seem to be in a muddle here!

    ba77, unless I am totally confused (which is perfectly possible) you and I are in agreement, and Mung is in disagreement, with the claim that Sanford is proposing that human beings (and indeed life in general) is on a inevitable downward trajectory towards “genetic entropy” which will end the extinction of all life, including our own – that we were once at (least near-) perfect, mutation-free beings, from which blessed state we have been declining due to unstoppable buildup of Very Slightly Deleterious Mutations (VSDMs).

    You and Mung, on the other hand, are in agreement, and I am in disagreement, with the thesis that “Darwinism” is a fatally flawed theory.

    Maybe we need to write to Sanford! Although actually, I think his position is perfectly clear from his book, although, like Mung, I assumed it was a “reductio ad absurdum” argument rather than a dire prediction until I got to about Chapter 4.

  25. Elizabeth; and yet the evidence:

    The current rate of extinction is from 100 to 10,000 species a year. This is between 100 and 1000 times faster than our best estimate of historical rates. (of note: it is thought that the “impact of man” is accelerating the extinction rate).
    http://www.sciencedaily.com/re.....073106.htm

    “Perhaps the most obvious challenge is to demonstrate evolution empirically. There are, arguably, some 2 to 10 million species on earth. The fossil record shows that most species survive somewhere between 3 and 5 million years. In that case, we ought to be seeing small but significant numbers of originations (new species) .. every decade.”
    Keith Stewart Thomson, Professor of Biology and Dean of the Graduate School, Yale University (Nov. -Dec. American Scientist, 1997 pg. 516)

    At one of her many public talks, she [Lynn Margulis] asks the molecular biologists in the audience to name a single unambiguous example of the formation of a new species by the accumulation of mutations. Her challenge goes unmet.
    Michael Behe – Darwin’s Black Box – Page 26

    Natural Selection and Evolution’s Smoking Gun, – American Scientist – 1997
    “A matter of unfinished business for biologists is the identification of evolution’s smoking gun,”… “the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.”
    Keith Stewart Thomson – evolutionary biologist

    “The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the position of some people at the meeting, the answer can be given as a clear, No.”
    Roger Lewin – Historic Chicago ‘Macroevolution’ conference of 1980

    “The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared.”
    from page 32 “Acquiring Genomes” Lynn Margulis.

    Selection and Speciation: Why Darwinism Is False – Jonathan Wells:
    Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another.”
    http://www.evolutionnews.org/2.....why_d.html

    Wired Science: One Long Bluff – Refuting a recent finch speciation claim – Jonathan Wells – Nov. 2009
    Excerpt: “Does the report in Wired Science mean that “biologists have witnessed that elusive moment when a single species (of Galapagos finch) splits in two?” Absolutely not.”
    http://www.evolutionnews.org/2.....bluff.html

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
    R. Milner, Encyclopedia of Evolution (1990)

    A general rule of thumb for the ‘Deterioration/Genetic Entropy’ of Dollo’s Law as it applies to the fossil record is found here:

    Dollo’s law and the death and resurrection of genes
    ABSTRACT: Dollo’s law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or “lost” developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints;
    http://www.pnas.org/content/91.....l.pdf+html

    Dollo’s Law was further verified to the molecular level here:

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe
    Excerpt: We predict that future investigations, like ours, will support a molecular version of Dollo’s law:,,, Dr. Behe comments on the finding of the study, “The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future.
    http://www.evolutionnews.org/2.....f_tim.html

    Evolutionary Adaptations Can Be Reversed, but Rarely – May 2011
    Excerpt: They found that a very small percentage of evolutionary adaptations in a drug-resistance gene can be reversed, but only if the adaptations involve fewer than four discrete genetic mutations. (If reverting to a previous function, which is advantageous, is so constrained, what does this say about gaining a completely novel function, which may be advantageous, which requires many more mutations?)
    http://www.sciencedaily.com/re.....162538.htm

    Some Further Research On Dollo’s Law – Wolf-Ekkehard Lonnig – November 2010
    http://www.globalsciencebooks......)1-21o.pdf

  26. 26
    Elizabeth Liddle

    Well, I just wanted to establish, ba77, that you agree that this is what Sanford is saying (or at least that if he isn’t he ought to be!)

    So I take it your position is that all living things are on a downward spiral into genetic meltdown from a once pristine (or near pristine) state?

  27. Well Elizabeth, and I just want to establish that you blatantly ignore evidence.

  28. 28
    Elizabeth Liddle

    Well, bornagain77, obviously I disagree :)

    But can you tell me: do you think that the human species is on an unstoppable path to genetic meltdown?

    I don’t think so, but if you do, then I’d be happy to discuss the evidence. If you don’t, then there’s something else on which we can agree :)

  29. Elizabeth, it is not me, per se, that you are disagreeing with, it is the evidence you are disagreeing with.

    post 13
    http://www.uncommondescent.com.....ent-382628

    To support your position that humans are not in the grip of Gentic Entropy, as is all life on earth, just show that this evidence in 13 is either false or that it is countermanded by other evidence. You ‘opinion’ matters not one iota, evidence has full authority!!!

  30. Elizabeth, it is interesting to note that John C. Avise, in alluding to the over 100,000 different disease causing mutations in humans, was trying to use a theological (God would not have done it that way) argument, as is overwhelmingly common type of argumentation with all neo-Darwinists, against ID. But the entire argument he is trying to make implodes, for in Avise pointing out the overwhelming detrimental mutation rate to humans, the point immediately arises that this is exactly NOT what Darwinism needs to make its case. Darwinism absolutely needs evidence that mutations are not overwhelmingly detrimental!!! But the Elizabeth, it gets far worse, for Sanford made his case when it was thought the detrimental to beneficial mutation rate was something like 1,000,000 to 1 against, but as Dr. Behe has recently pointed out, it turns out that even the precious few mutations we thought could be beneficial are in fact not beneficial!!!

    The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

  31. It’s a very odd book.

    Agreed! I didn’t much care for the book myself. I’ve fought against it’s use by people here at UD as an argument for ID.

    Too many unclear analogies.

    Too many references to “loss of information” without making it clear how we can tell when information is gained or lost.

    But I do think it unfair to ascribe to it as his thesis the ideas which you and Heinrich tried to do in this thread.

    If we take his argument and go back 10,000 years and apply your reasoning we should already be extinct. No?

    You can take certain things he writes, and you can extrapolate or infer from that certain things, but nowhere, so far as I have seen (I’m through Chapter 5 now), does he claim that humans were created perfect about 10,000 years ago.

    So to claim that’s the thesis of the book is without merit.

    Why didn’t you go for 6,000 years ago rather than 10,000? (See Figure 4 on page 65.)

  32. ,,,and oddly you cannot show a single violation of the principle of Genetic Entropy!

    Sigh. There is no “Principle of Genetic Entropy.” It’s a fiction.

  33. Lizzie @24:

    Oh, dear, we do seem to be in a muddle here!

    Indeed! LOL!

    BA77 and I do not agree about the book.

    He says it says what you think it says. I beg to differ.

    I think his position is perfectly clear from his book, although, like Mung, I assumed it was a “reductio ad absurdum” argument rather than a dire prediction until I got to about Chapter 4.

    That’s my stance. BA77 disagrees with me. So now, apparently, do you. He and I have already been down this road.

    You and Mung, on the other hand, are in agreement, and I am in disagreement, with the thesis that “Darwinism” is a fatally flawed theory.

    Probably for radically different reasons, though there may be areas of agreement.

  34. The current rate of extinction is from 100 to 10,000 species a year. This is between 100 and 1000 times faster than our best estimate of historical rates. (of note: it is thought that the “impact of man” is accelerating the extinction rate).

    And the evidence that this is due to “the principle of genetic entropy is? NIL!

    And since the fossil record is one of extinctions followed by new forms and radiation, this is explained on “the principle of genetic entropy.” HOW?

  35. 35
    Elizabeth Liddle

    Hey, Mung, glad we agree on something!

    As I said, I had misremembered where I got the 10,000 number, and it turns out it was a conflation between reading elsewhere that Sanford was a YEC (and considered that the book supported YEC) and the maximum-ish time length allowable under Sanford’s thesis between pristine and extinct. Yes, it’s an overestimate (but I was trying to be generous, as in another conversation about the book elsewhere on the internet, someone tried to argue that 4 generations per century was too many when you took into account the ages of the biblical patriarchs, and the assumption that in those glory days of a relatively pristine genome, people would have much longer fertile lives, and may even have bred much later.

    So I would still stand by my summary of Sanford’s thesis as: living things were created in a pristine state thousands (not millions or billions) of years ago, and are headed for extinction through genetic entropy.

    I may not have said it quite like that, but that seems to me to be his message. It’s certainly the message of his postlude – with the additional invitation not to give up hope, despite his pessimistic message but to look forward to new life in Jesus.

    Obviously I disagree with his insistence that we headed for genetic entropy. Not least of all he has made some pretty basic errors in population genetics (he cites Kondrashov’s work, yet completely ignores the fact that Kondrashov’s worst case scenario assumes small populations in relation to their genome size – if he followed Kondrashov’s thesis completely, the Ark bottleneck would have resulted in almost immediate genetic meltdown.)

    So we have a nice Venn diagram here – kind of Rock, Paper Scissors! You and I agree that genetic entropy is fiction (well irrelevant to human sized populations, anyway); you and ba77 agree that Darwinism is wrong; ba77 and I agree that Sanford is proposing that we are terminal genetic decline!

    Not sure if you call that common ground or a merry-go-round :)

    Cheers

    Lizzie

  36. If only DaveScot were still here, I’m sure he’d disagree with everyone.

    Obviously I disagree with his insistence that we headed for genetic entropy. Not least of all he has made some pretty basic errors in population genetics

    For me the funniest thing was to realise that he didn’t understand segregation variance. At one point his argument only made sense if offspring got their genes randomly from the whole gene pool, rather than just two parents. My thought was that I wished I’d been to the same parties as Sanford had.

    *sigh*

  37. To falsify the principle of Genetic Entropy is the same thing as falsifying ID,,, All you must show is that purely material processes are sufficient to produce a gain in functional information/complexity that is greater than the functional information/complexity that was already present in a parent species;

    notes:

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.metacafe.com/watch/3995236

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    Measuring the functional sequence complexity of proteins – Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors – 2007
    Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,,
    http://www.tbiomed.com/content/4/1/47

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).
    http://www.ncbi.nlm.nih.gov/pm.....MC1208958/

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8 ) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work

    For a broad outline of the ‘Fitness test’, required to be passed to show a violation of the principle of Genetic Entropy, please see the following video and articles:

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    i.e.,, the fitness test must be passed by the sub-species against the parent species. If the fitness test is shown to be passed then the new molecular function, which provides the more robust survivability for the sub-species, must be calculated to its additional Functional Information Bits (Fits) it has gained in the beneficial adaptation, and then be found to be greater than 140 Fits. 140 Fits is what has now been generously set by Kirk Durston as the maximum limit of Functional Information which can reasonably be expected to be generated by the natural processes of the universe over the entire age of the universe (The actual limit is most likely to be around 40 Fits)(Of note: I have not seen any evidence to suggest that purely material processes can exceed the much more constrained ’2 protein-protein binding site limit’, for functional information/complexity generation, found by Michael Behe in his book “The Edge Of Evolution”).

    further notes:

    Dr. Behe states in The Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.

    etc.. etc..

  38. Hey, Mung, glad we agree on something!

    No doubt we agree on many things. But often times forums like this tend to emphasize disagreement over agreement.

    At times it can be useful to pause and discover common ground.

    I don’t find “genetic entropy” to be a useful concept.

    My experience has been that people who use it don’t understand it, just like thermodynamic entropy.

    Heck, I’m not convinced Sanford understands entropy.

    Author’s note: The term entropy has several uses. I am using the term entropy as it is most commonly used, i.e., the universal tendency for things to run down or degrade apart from intelligent intervention.

    I read things like that and facepalm.

    Please, please, please, people> If you care at all about the future of ID…

    Run! Away! From such Nonsense!

  39. So I would still stand by my summary of Sanford’s thesis as: living things were created in a pristine state thousands (not millions or billions) of years ago, and are headed for extinction through genetic entropy.

    Despite the lack of any statements by Sanford in the book to the effect that:

    1. Humans specifically, or living things generally, were created perfect.

    2. Humans specifically, or living things generally, were created approx 10,000 years ago.

    I am just stunned.

  40. BA77:

    To falsify the principle of Genetic Entropy is the same thing as falsifying ID

    NOPE.

    Sanford argues the exact opposite.

    Nothing beats going to the source material, imo.

    Yet even the best designed information systems, apart from intelligent maintenance and the continual intervention of intelligence, will always eventually breakdown.

    To falsify “the principle of genetic entropy” is to establish and confirm ID.

    See what I mean Lizzie, lol?

    People take Sanford’s book and make it say the exact opposite.

    I blame that on the author, frankly. He should have been more clear.

    My personal opinion is that he was indeed trying to ride the YEC fence. But it doesn’t follow that a YEC scenario was the thesis of his book. I trust you can understand the distinction, even if you don’t agree with it.

    Funny thing is, following the above quote we find:

    Computers are typically junk within 5 years.

    Due to entropy, lol? Is he serious?

  41. But is it his thesis?

    If the rate of loss was constant and at its current level for 300 generations (6,000 years) we would lose about 0.003% of our total information. This is huge (90,000 errors), yet it is conceivable given the extremely robust nature of the genome. However, if we continued to lose information at this same rate for 300,000 generations (6 million years) we would lose 3% of all our information! This would represent 90 million errors! This is inconceivable. p.153

    Put another way, 6 thousand years maybe, 6 million years, no way!

    But why would God create an “extremely robust genome” that could withstand 6,000 years of mutations without divine intervention but not a genome that could withstand 6 million years of mutations without divine intervention?

  42. Mung, you clearly are confusing things once again. Your very own quote here:

    ‘Yet even the best designed information systems, apart from intelligent maintenance and the continual intervention of intelligence, will always eventually breakdown.’

    Yet I clearly stated this:

    ‘All you must show is that purely material processes are sufficient to produce a gain in functional information/complexity that is greater than the functional information/complexity that was already present in a parent species;’

    Thus mung you clearly have misconstrued the clear meaning of what I meant by a violation of Genetic Entropy, for I most assuredly know that intelligence is THE ONLY thing in the known universe that has the capability to consistently violate Genetic Entropy. ,,,,

  43. Mung, though I should know better than to try,,,, the fairly ‘consistent’ background extinction rate plus the fairly ‘consistent’ Dollo’s law are two pieces of the puzzle that are pointing to something that is causing ‘loss’. For me Genetic Entropy is by far the leading contender as a plausible explanation. ,,,,

    notes:

    The first effect to be obviously noticed in the evidence, for the Genetic Entropy principle, is the loss of potential for morphological variability of individual sub-species of a kind. This loss of potential for morphological variability first takes place for the extended lineages of sub-species within a kind, and increases with time, and then gradually works in to the more ancient lineages of the kind, as the ‘mutational load’ of slightly detrimental mutations slowly builds up over time. This following paper, though of evolutionary bent, offers a classic example of the effects of Genetic Entropy over deep time of millions of years:

    A Cambrian Peak in Morphological Variation Within Trilobite Species; Webster
    Excerpt: The distribution of polymorphic traits in cladistic character-taxon matrices reveals that the frequency and extent of morphological variation in 982 trilobite species are greatest early in the evolution of the group: Stratigraphically old and/or phylogenetically basal taxa are significantly more variable than younger and/or more derived taxa.
    http://www.sciencemag.org/cgi/.....7/5837/499

    The final effect of Genetic Entropy is when the entire spectrum of the species of a kind slowly start to succumb to ‘Genetic Meltdown’, and to go extinct in the fossil record. The occurs because the mutational load, of the slowly accumulating ‘slightly detrimental mutations’ in the genomes, becomes too great for each individual species of the kind to bear. From repeated radiations from ancient lineages in the fossil record, and from current adaptive radiation studies which show strong favor for ancient lineages radiating, the ancient lineages of a kind appear to have the most ‘robust genomes’ and are thus most resistant to Genetic Meltdown. All this consistent evidence makes perfect sense from the Genetic Entropy standpoint, in that Genetic Entropy holds God created each parent kind with a optimal genome for all future sub-speciation events. My overwhelming intuition, from all the evidence I’ve seen so far, and from Theology, is this; Once God creates a parent kind, the parent kind is encoded with optimal information for the specific purpose to which God has created the kind to exist, and God has chosen, in His infinite wisdom, to strictly limit the extent to which He will act within nature to ‘evolve’ the sub-species of the parent kind to greater heights of functional complexity. Thus the Biblically compatible principle of Genetic Entropy is found to be in harmony with the second law of thermodynamics and with the strict limit found for material processes ever generating any meaningful amount of functional information on their own (LCI: Dembski – Marks)(Abel; Null Hypothesis).

    As a side light to this, it should be clearly pointed out that we know, for 100% certainty, that Intelligence can generate functional information i.e. irreducible complexity. We generate a large amount of functional information, which is well beyond the reach of the random processes of the universe, every time we write a single paragraph of a letter (+700 Fits average). The true question we should be asking is this, “Can totally natural processes ever generate functional information?”, especially since totally natural processes have never been observed generating any functional information whatsoever from scratch (Kirk Durston). This following short video lays out the completely legitimate scientific basis for inferring Intelligent Design from what we presently observe:

    Stephen Meyer: What is the origin of the digital information found in DNA? – short video
    http://www.evolutionnews.org/2.....37271.html

  44. Well, BA77, if you were willing to abstain from posting irrelevant quotes and links and actually engage in a conversation …

    But you’ve shown no willingness to do so, so …

    Your claim was that ID = Genetic Entropy.

    Your claim was that if “the principle of Genetic Entropy” is false, so is ID.

    You left no room for, Genetic Entropy might be false (or meaningless) yet ID might still be true.

    So don’t blame me for where your stance takes you.

    ID is not dependent upon whether “the principle of genetic entropy” is true or false.

    Yet that, without doubt, is what you asserted to be the case. I quote:

    To falsify the principle of Genetic Entropy is the same thing as falsifying ID

    That was you, right? You wrote that?

    Was it false?

    I objected.

    I showed how not even Sanford himself adopts that stance.

    Don’t blame me.

    Thus mung you clearly have misconstrued the clear meaning of what I meant by a violation of Genetic Entropy, for I most assuredly know that intelligence is THE ONLY thing in the known universe that has the capability to consistently violate Genetic Entropy.

    So now you’ve embroiled yourself in a contradiction.

    Don’t shoot the messenger.

    To falsify “the principle of genetic entropy” is not to falsify ID (as you mistakenly claimed), but rather it affirms ID (as you now claim you were aware of all along).

    Go figure.

  45. Mung OK, if you think a violation of Genetic Entropy and falsifying ID are not directly related, then just show me a violation of Genetic Entropy without using any intelligence whatsoever!!!, In fact I laid out a basic outline for doing so here:

    http://www.uncommondescent.com.....ent-382770

    ,,,Complete with the exact test to be performed and calculations to be made!!! ,,,, But alas, much like the neo-Darwinists I challenge, I don’t think you will care to directly address the empircal challenge to substantiate what you claim!!! Just a guess, but I’ve been down this road once or twice and it all comes down to what you actually prove empirically,,, On a lighter note:

    Casting Crowns – “Glorious Day (Living He Loved Me)” – Live
    http://www.youtube.com/watch?v=KqrqPGt11bA

  46. Mung, This entropy issue is much deeper than you realize, but to try to make it simple, this ‘decay’ (entropy) is directly related to this:

    Evolution is a Fact, Just Like Gravity is a Fact! UhOh!
    Excerpt: The results of this paper suggest gravity arises as an entropic force, once space and time themselves have emerged.
    http://www.uncommondescent.com.....fact-uhoh/

    Entropy of the Universe – Hugh Ross – May 2010
    Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated.
    http://www.reasons.org/entropy-universe

    Roger Penrose – How Special Was The Big Bang?
    “But why was the big bang so precisely organized, whereas the big crunch (or the singularities in black holes) would be expected to be totally chaotic? It would appear that this question can be phrased in terms of the behaviour of the WEYL part of the space-time curvature at space-time singularities. What we appear to find is that there is a constraint WEYL = 0 (or something very like this) at initial space-time singularities-but not at final singularities-and this seems to be what confines the Creator’s choice to this very tiny region of phase space.” (which is 1 in 10^10^123)

    The Physics of the Small and Large: What is the Bridge Between Them? Roger Penrose
    Excerpt: “The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the “source” of the Second Law (Entropy).”
    http://www.pul.it/irafs/CD%20I.....enrose.pdf

    i.e. mung, entropy is actually fundamentally connected to the expansion of space-time itself!!!

    A ‘flat universe’, which is actually another very surprising finely-tuned ‘coincidence’ of the universe, means this universe, left to its own present course of accelerating expansion due to Dark Energy, will continue to expand forever, thus fulfilling the thermodynamic equilibrium of the second law to its fullest extent (entropic ‘Heat Death’ of the universe).

    The Future of the Universe
    Excerpt: After all the black holes have evaporated, (and after all the ordinary matter made of protons has disintegrated, if protons are unstable), the universe will be nearly empty. Photons, neutrinos, electrons and positrons will fly from place to place, hardly ever encountering each other. It will be cold, and dark, and there is no known process which will ever change things. — Not a happy ending.
    http://spiff.rit.edu/classes/p.....uture.html

    Romans 8:18-21
    I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. The creation waits in eager expectation for the sons of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the glorious freedom of the children of God.

    ====================

    Casting Crowns – If We’ve Ever Needed You (live)
    http://www.youtube.com/watch?v=2UBrwCPcoR0

  47. 47
    Elizabeth Liddle
    So I would still stand by my summary of Sanford’s thesis as: living things were created in a pristine state thousands (not millions or billions) of years ago, and are headed for extinction through genetic entropy.

    Despite the lack of any statements by Sanford in the book to the effect that:

    1. Humans specifically, or living things generally, were created perfect.

    2. Humans specifically, or living things generally, were created approx 10,000 years ago.

    I am just stunned.

    Well, you shouldn’t be. I pointed out the page in which Sanford cites Crow, and I also quoted from his postlude.

    I’m not the only person to have assumed that his thesis is I have summarized it. In fact you are the only person I’ve met who has disputed it.

    Tell me what you think his thesis is.

    I might actually write to him and ask :)

    Cheers

    Lizzie

  48. Well, since I don’t believe in “genetic entropy” (whatever that is) I don’t think I’ll be engaging in any “genetic entropy challenge.”

    Sorry. :)

  49. 49
    Elizabeth Liddle

    I’m not offering a “genetic entropy” challenge.

    But I retain the right to infer that when someone who does believe in “genetic entropy” posts a graph that shows that living things start clean and inevitably degenerate to extinction and appears to predict that that is happening to all living things that that same person thinks that we started off fairly recently near-perfect and that we are headed for genetic meltdown, especially when he actually says so.

    And he is also a well-known YEC.

    But YMMV.

  50. I’m not offering a “genetic entropy” challenge.

    Cross-posting. :)

    I was relying to BA77.

    But I retain the right to infer that when someone who does believe in “genetic entropy” posts a graph that shows that living things start clean and inevitably degenerate to extinction…

    Which chart/graph are you speaking of?

    I’m not aware of any that show:

    1. A perfect start.
    2. That ends in extinction.

  51. In fact you are the only person I’ve met who has disputed it.

    I am a rare bird :)

    But it seems to me that you and I both started out reading the book the same way, as saying the same thing, as having the same thesis.

    It’s just that you modified your opinion and I didn’t modify mine.

    Fair enough?

  52. 52
    Elizabeth Liddle

    Yes, fair enough. I certainly did a double take when it dawned on me what he must be saying.

    But are you still disputing that Sanford actually believes that his Genetic Entropy is actually happening? That we are currently bound for extinction? Have you read the Chapter entitled “Is the Downward Curve Real?”

    In it he explicitly references Genesis, and cites the long lifespans of the patriarchs as evidence that the human genome was much healthier then. He even calculates a “line of best fit” through the “Biblical data” (Figure 14), and his caption reads:

    “The curve is very consistent with the concept of genomic deterioration caused by mutation accumulation. The curve is also very similar to the theoretical curves reflecting genomic degeneration shown in Figures 4(p65) and 10b (113).”

    The second of those is the figure I mentioned earlier, derived from Crow, and the first is very similar.

    So if he’s not saying that the evidence supports the hypothesis that we were created perfect, in the Garden of Eden, a few thousand years ago, and have been degenerating ever since due to Genetic Entropy, and will ultimately die out through genetic disease – what DO you think he is saying?

  53. 53
    Elizabeth Liddle

    PS: I’d actually forgotten that chapter, with the line of best fit through the patriarchs.

    He even states the equation to five significant figures!

  54. But are you still disputing that Sanford actually believes that his Genetic Entropy is actually happening? That we are currently bound for extinction?

    I am.

    It is clear that his arguments are based on current models which he plainly states he thinks are false.

    He also clearly leaves room for the intervention of intelligence as the explanation for why we are not extinct.

    Is the Downward Curve Real?

    Yes, I read it. I cheated and skipped ahead, lol. The title caught my eye. I thought I even quoted from it. Let me go back to it. I’ll get back to you.

  55. 55
    Elizabeth Liddle

    Cool.

  56. notes on mutation rate:

    Human Genome Project Supports Adam, Not Darwin – February 2011
    Excerpt: What is on the top tier? Increasingly, the answer appears to be mutations that are ‘deleterious’ by biochemical or standard evolutionary criteria. These mutations, as has long been appreciated, overwhelmingly make up the most abundant form of nonneutral variation in all genomes.
    http://www.creationsafaris.com.....#20110221a

    This following study confirmed the “detrimental” mutation rate for humans, of 100 to 300, estimated by John Sanford in his book “Genetic Entropy” in 2005:

    Human mutation rate revealed: August 2009
    Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome. (Of note: this number is derived after “compensatory mutations”)
    http://www.nature.com/news/200.....9.864.html

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57
    By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”
    http://books.google.com/books?.....38;f=false

    I went to the mutation database website and found:

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.biobase-internation.....mddatabase

    I really question their use of the word celebrating;

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

    Whether you like the conclusions or not, the evidence itself points overwhelmingly to Genetic Deterioration!!!

  57. Is the Downward Curve Real?

    Indeed, I already quoted from this chapter.

    Sanford paints a grim picture.

    “When Crow’s model is corrected to be more realistic, allowing for differences between individual mutations, I do not believe the downward trend will ever level off.”

    “the genome must degenerate”

    “the genome must degenerate”

    “man must be degenerating”

    “man must be degenerating”

    “man must be degenerating”

    “we are degenerating”

    YES, he really is repeating himself.

    “This makes eventual extinction of such genomes inevitable. I have termed this fundamental problem Genetic Entropy. Genetic Entropy is not a starting axiomatic position, rather it is a logical conclusion derived from careful analysis of how selection really operates.

    If the genome must degenerate, then the Primary Axiom is wrong.”

    “at some time in the past there must have been a time when there was less genetic damage in the genome.”

    “In conclusion, we can see that even using Crow’s most optimistic model, the downward curve for fitness is real, and in fact closely matches the downward curve for life spans recorded in the book of Genesis. The bad news is that our species, like we ourselves, is dying. The Primary Axiom is wrong. Information decays. Genomes decay. Life is not going up, up, up. It is going down, down, down. Selection does not create information, and at best it can only slow its decay.”

  58. Whether you like the conclusions or not, the evidence itself points overwhelmingly to Genetic Deterioration!!!

    I left my GDM (Genetic Detorioration Meter) at home. What does the current measurement indicate?

  59. 59
    Elizabeth Liddle

    Well, I may profoundly disagree with John Sanford, but I have the greatest respect for him as a human being. He has kindly given me permission to post the contents of our email exchange. I wrote:

    Dear Dr Sanford

    I am having a slightly odd argument over at Uncommon Descent about your book, Genetic Entropy. I have read it several times, and understood your thesis to be that humankind (and all living things) were created with perfect genomes a few thousand years ago, but have been deteriorating ever since, and will ultimately go extinct due to accumulation of VSDMs.

    Another poster seems to have read you differently, and takes your meaning to be that if Darwinism was true, this would be the case, but as it obviously not true, Darwinism must be false.

    The thread is here:

    http://www.uncommondescent.com.....are-shows/

    And the argument is between myself and “Mung”.

    Would you like to put at least one of us right?

    With very best wishes

    Elizabeth Liddle.

    He replied:

    Dear Elizabeth – I think you are both right. Given our current understanding of the mutation/selection process, there must clearly be a net loss of information over time in all genomes (with the possible exception of extremely small viral DNA genomes, which might escape this problem). This disproves the basic neo-Darwinian paradigm. What do we do with this fact? The most obvious conclusion would be a Biblical view of history, however the alternative would be to hypothesize that there are other forces (natural or supernatural), which help out mutation/selection. I personally hold the first view, but for those who find this too hard to believe, they are forced to choose the second view.

    Best wishes – John

    I then wrote:

    Thank you very much for your reply!

    Would you be happy for me to post it on the thread at Uncommon Descent?

    I should make it clear that I remain unconvinced by the ID argument (I guess you would call me a “neo-Darwinist) but your view will be shared by most of the posters at UD (in other words, it’s a friendly crowd!)

    With best wishes

    Elizabeth

    And he responded with his permission.

    Thank you Dr Sanford!

  60. Elizabeth, for someone who is given to the view that all life on earth is derived from the ‘change’ of the simple to complex, you certainly seem mysteriously resistant to any ‘change’ whatsoever to this supposed ‘truth of change’ that you hold, despite all contrary evidence. ,,, In fact, this ‘ironic’ characteristic of yours, of holding onto a inflexible truth, has actually been developed as a argument against your neo-Darwinist position;

    Can atheists trust their own minds? – William Lane Craig on Plantinga’s evolutionary argument against naturalism (inconsistent identity leads to failure of truth claim) – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” Creation-Evolution Headlines
    http://creationsafaris.com/cre.....#20110227a

  61. of related interest:

    Genetic Entropy vs. Evolution – The Stark Reality – video with references
    http://vimeo.com/24870022

  62. Elizabeth, of related note, it is also interesting to point out that this ‘inconsistent identity’, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to account for objective morality in that they cannot maintain a consistent identity towards a cause for objective morality;

    The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

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