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New paper using the Avida “evolution” software shows …

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File:Avida 2.6 screenshot.png
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… 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.”

Comments
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_cReEbornagain77
June 9, 2011
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of related interest: Genetic Entropy vs. Evolution - The Stark Reality - video with references http://vimeo.com/24870022bornagain77
June 9, 2011
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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/crev201102.htm#20110227abornagain77
June 9, 2011
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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: https://uncommondescent.com/evolution/new-paper-using-the-avida-evolution-software-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!Elizabeth Liddle
June 9, 2011
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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?Mung
June 4, 2011
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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."Mung
June 4, 2011
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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/crev201102.htm#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/2009/090827/full/news.2009.864.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?id=M1PRvkPBKfQC&pg=PA57&lpg=PA57&dq=human+75,000+different+disease-causing+mutations&source=bl&ots=gkjosjq030&sig=gAU5AfzMehArJYinSxb2EMaDL94&hl=en&ei=kbDqS_SQLYS8lQfLpJ2cBA&sa=X&oi=book_result&ct=result&resnum=6&ved=0CCMQ6AEwBQ#v=onepage&q=human%2075%2C000%20different%20disease-causing%20mutations&f=false I went to the mutation database website and found: HGMD®: Now celebrating our 100,000 mutation milestone! http://www.biobase-international.com/pages/index.php?id=hgmddatabase 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/2010-11-unexpectedly-small-effects-mutations-bacteria.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.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic Whether you like the conclusions or not, the evidence itself points overwhelmingly to Genetic Deterioration!!!bornagain77
June 4, 2011
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Cool.Elizabeth Liddle
June 4, 2011
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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.Mung
June 4, 2011
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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!Elizabeth Liddle
June 4, 2011
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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?Elizabeth Liddle
June 4, 2011
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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?Mung
June 4, 2011
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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.Mung
June 4, 2011
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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.Elizabeth Liddle
June 2, 2011
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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. :)Mung
June 2, 2011
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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 LizzieElizabeth Liddle
June 2, 2011
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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. https://uncommondescent.com/intelligent-design/evolution-is-a-fact-just-like-gravity-is-a-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%20IRAFS%2702/texts/Penrose.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/phys240/lectures/future/future.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=2UBrwCPcoR0bornagain77
June 1, 2011
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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: https://uncommondescent.com/evolution/new-paper-using-the-avida-evolution-software-shows/#comment-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=KqrqPGt11bAbornagain77
June 1, 2011
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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.Mung
June 1, 2011
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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/content/abstract/317/5837/499 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/2010/08/stephen_meyer_on_intelligent_d037271.htmlbornagain77
June 1, 2011
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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. ,,,,bornagain77
June 1, 2011
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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?Mung
June 1, 2011
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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?Mung
June 1, 2011
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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.Mung
June 1, 2011
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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!Mung
June 1, 2011
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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.edu/szostakweb/publications/Szostak_pdfs/Hazen_etal_PNAS_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/pmc/articles/PMC1208958/ 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/2009/10/richard_dawkins_the_greatest_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/2009/10/nature_paper_finally_reaches_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/2011/04/16/when-theory-and-experiment-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..bornagain77
June 1, 2011
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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*Heinrich
June 1, 2011
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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 LizzieElizabeth Liddle
June 1, 2011
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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?Mung
June 1, 2011
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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.Mung
June 1, 2011
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