Sunday, June 10, 2012

A Member of the National Academy of Sciences Repeated This Huge Evolution Blunder

The whole point of evolution—that the species arose all by themselves—is also the whole problem. Evolutionists wax eloquently about how there is no goal, plan or purpose to the world. Biology arose by chance events, such as random mutations, which did not have the species in mind. But how could the species possibly arise by chance? Such a proposition is highly unlikely, to put it kindly. How do evolutionists explain this probability dilemma? How do they explain away something that is astronomically unlikely? Simple. Evolutionists say the question has got it all wrong, for the evolution of the species is not, in fact, by chance at all. Yes, there are random events involved, such as mutations, but they must pass the test of natural selection which very much is not random. But this is yet another evolutionary blunder. Not only is it a misrepresentation of evolutionary theory, it fails to resolve the probability dilemma.

The University of California Museum of Paleontology’s website about evolution, funded by your tax dollars, claims that it is a misconception that evolution means that the species arose by chance. Here is how the website explains this supposed misconception:

Chance is certainly a factor in evolution, but there are also non-random evolutionary mechanisms. Random mutation is the ultimate source of genetic variation, however natural selection, the process by which some variants survive and others do not, is not random.

In other words, yes mutations are random, but natural selection is not. This blunder is elaborated by University of California professor and National Academy of Sciences member, John Avise. Avise repeats the argument that natural selection is not random, but he also argues that the biological variation, which is subject to selection, is also, ultimately, not random:

Advocates of Intelligent Design contend that complex biological features cannot arise by chance, the implication being that chance equates to natural evolutionary processes and anti-chance equates to sentient forces. From a scientific vantage, however, the driving force of adaptive evolution—natural selection—is itself the antithesis of chance. …

Natural selection can sift only among the genetic variants available for its scrutiny, and two of the three primary sources of genetic variability—de novo mutations and recombination—occur essentially at random with respect to forging adaptations. … In this important sense, the genetic fodder upon which natural selection acts can indeed be characterized as stochastic or chancy in origin.

The third source of population genetic variation entails a mixture of “chance and necessity.” Apart from de novo mutations and recombinant genotypes, the genetic variety available for natural selection in any generation is also a function of historical circumstance, that is, of idiosyncratic genealogical outcomes that have been affected by both stochastic and directive evolutionary processes across all prior generations. Evolution going forward can work only with the biological substrates provided by evolution foregone. These biological substrates—“ghosts of evolution past”—are not supernatural legacies, but instead they are real genetic lineages and real species that have been subjected for eons to the full panoply of evolutionary processes including natural selection (the directive agent of adaptive evolution) as well as idiosyncratic mutation, recombination, and genetic drift (stochastic forces in the sense described above). [Inside the Human Genome, Oxford, 2010, p. 27-8]

Avise’s mental gymnastics are painful to watch. This blunder is consistent amongst evolutionists, but no less astonishing. First let’s consider the claim that natural selection means the origin of species wasn’t by chance. Imagine a friend wins a one-in-a-million jackpot at roulette, but he claims it wasn’t by chance because he also had some losing bets. On his losing bets he collected nothing, but on his winning bets collected his winnings. Isn’t that the very antithesis of chance?

Of course not. This is a monumental blunder in thinking. Yes he doesn’t collect on his losing bets, and he does collect on his winning bets. But that does not change the fact that roulette is a game of chance. And it doesn’t change the fact that his beating the casino was unlikely.

According to evolution biological variation is random with respect to need or purpose. Natural selection doesn’t change this. It kills off the bad designs, but winning designs are nonetheless constructed by random variation—they are by chance. Every mutation and recombination event leading to whales, cherry trees and humans was, according to evolution, random. Likewise every losing design is also by chance.

In other words, some designs win and some designs lose. The process continues and the species evolve. But it is entirely by chance. The fact that some win and some lose doesn’t change this.

Avise’s second argument is that chance is also removed from the process because it is on-going, producing new species which become the basis for further evolution. This argument is equally fallacious.

A chance process that continues for awhile is still a chance process.

The evolutionary process is still by chance. If a frog evolved from an earlier amphibian—such that the evolution of frogs was limited in its possibilities—that doesn’t change the fact that the process was, from the beginning, by chance.

Every biological variation that occurs is random. Yes natural selection kills off the bad designs. And yes the process proceeds down certain pathways, producing certain species. But every species is produced by a series of random biological variations.

The origin of species by chance is unlikely. It would require a long, long series of random mutations that just happens to construct an incredible biological design. And this would have to occur repeatedly, for all of biology’s amazing designs. And in each of these long series of random mutations, there would need to be a great many—mostly undiscovered and unknown—intermediate designs. And these intermediate designs would have to be helpful to the organism.

From single proteins to cellular processes to whole organisms, the science gives little reason to think such a process is likely. Indeed the science repeatedly indicates such a process is likely to be very unlikely.

And the evolutionist’s appeal to natural selection changes none of this. Their claim that the killing off of bad designs means that the origin of species was not by chance, and that this resolves the probability dilemma, is not only false, it demonstrates an important failure in evolutionary thinking.

81 comments:

  1. Hunter:

    Such a proposition is highly unlikely

    Hunter, you must stop saying that. Every time you do, you will give the usual bozos an excuse to claim that IDers argue from incredulity. You must tell it like it really is:

    The probability of evolution is not minuscule. It is ZERO.

    Saying that dirt can organize itself into complex lifeforms due to chance interactions between molecules is like saying that the entire atmosphere of the earth can suddenly collect at a point above the north pole because the interactions between air molecules are random. Evolution is not just a religion. It's a religion of cretins for cretins. And pompous ones at that.

    The evolutionist's origin of life mantra: DIRTDIDIT!

    ReplyDelete
  2. The evolutionary process is still by chance. If a frog evolved from an earlier amphibian—such that the evolution of frogs was limited in its possibilities—that doesn’t change the fact that the process was, from the beginning, by chance.

    Every biological variation that occurs is random. Yes natural selection kills off the bad designs. And yes the process proceeds down certain pathways, producing certain species. But every species is produced by a series of random biological variations.


    What I see in this and the entire post is a complaint that evolutionary theory assumes an unguided (a-teleological) history of life on our planet.

    Hunter and his co-believers find that idea incredible and perverse. But all they do is complain about it.

    ReplyDelete
  3. Cornelius Hunter: The whole point of evolution—that the species arose all by themselves—is also the whole problem.

    You seem to confuse species with adaptation. Speciation can occur without adaptation, such as by chromosomal rearrangement, common in mice.

    Cornelius Hunter: Imagine a friend wins a one-in-a-million jackpot at roulette ...

    But evolution doesn't work by randomizing all the numbers. It changes what already works. In essence, it tinkers. Think of it as sending feelers out into the surrounding fitness landscape.

    New adaptations are not (usually) suddenly formed structures, but adaptations of existing structures. So the mammalian middle ear didn't spring into existence fully formed, but coopted bit-by-bit already working parts from the reptilian jaw. Each change was modest and seemingly inconsequential, but when you look at the endpoints, it is astounding.

    Cornelius Hunter: ... but he claims it wasn’t by chance because he also had some losing bets. On his losing bets he collected nothing, but on his winning bets collected his winnings. Isn’t that the very antithesis of chance?

    Even in this case, it depends. If he buys every available number, then he can guarantee his success. The biological equivalent is mutational saturation, where over time, every possible mutation occurs. One of those mutations can be beneficial, depending on the environment. Nor is it necessary to buy every number as it is quite possible to hedge your bet. While evolution certainly will not hit on every possible adaptation, we can directly observe the process of mutation and adaptation, a.k.a. the fact of evolution.

    Cornelius Hunter: A chance process that continues for awhile is still a chance process.

    Roll enough times in Craps, and eventually you will make the point or seven-out. It's inevitable. Please note that we are making a firm prediction of a random process.

    You seem to have a misunderstanding and an inordinate fear of randomness. Consider a woman wanting to attract the attention of her lover. She puts the tiniest drop of perfume behind her ear. Random forces waft those molecules across the room into her lover's nostrils. Completely random forces predictably distribute the scent. The procreation of her line may depend on it.

    ReplyDelete
    Replies
    1. But what about a case where an adaptation requires a number of random mutations before there is any benefit. The numberrs begin to work against it. Or take a case where one mutations by itself is actually harmful, like proteins that lose stability when they acquire a new ability. You need more mutations to compensate. There comes a point where it becomes highly improbable.

      Delete
    2. That's right. Evolution is not a guarantee that all living things will adapt and survive.

      Take the extreme case of something like a catastrophic Earth impact event. The environmental changes will be far too sudden and violent for any adaptive response and the fossil record shows vast numbers of species simply disappearing, presumably wiped out by such events in the far distant past.

      Even in much quieter periods an appropriate adaptive response might not be available in time - or available at all - so the unfortunate species still succumbs to environmental change.

      Looking at the fossil and geological records you could argue thet we are very lucky to be here at all, that it took a lot of other species going extinct to make way for us. Nor is there any guarantee that we won't go the same way in time. The odds are against us. We're very vulnerable. Another super-volcano eruption or direct hit from a big enough chunk of space debris and we could go the way of the dinosaurs - maybe leaving the cats to try their luck in a few million years time.

      Delete
    3. Zachriel:

      Even in this case, it depends. If he buys every available number, then he can guarantee his success. The biological equivalent is mutational saturation, where over time, every possible mutation occurs. … Roll enough times in Craps, and eventually you will make the point or seven-out. It's inevitable. Please note that we are making a firm prediction of a random process.

      But this is nothing more than evolutionary mythology. Even for a single protein you need far more evolutionary experiments than are physically possible (even according to evolutionists numbers!).

      Delete
    4. Except we're back to square one, as this assumes evolution is merely random. It also assumes you know all the possible outcomes, which would be necessary to perform any sort statistical calculation in practice.

      Assuming a designer pre-selected any specific protein isn't neutral as it would represent an explanatory framework by which you extrapolate observations.

      Delete
    5. Cornelius Hunter: But this is nothing more than evolutionary mythology. Even for a single protein you need far more evolutionary experiments than are physically possible (even according to evolutionists numbers!).

      What Scott said. Back to square one.

      Evolution doesn't work by random assembly, but with what already exists. It if far more likely to find another useful protein by mutating a working protein, or by recombining parts from working proteins, than from random assembly.

      For instance, how could luciferase, a 500-residue bioluminescent enzyme, evolve? Turns out that a single substitution in a related acetyl-CoA synthetase results in a substantial increase in bioluminescence function.

      Prado et al., Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site, Photochemical & Photobiological Sciences 2010

      Delete
  4. In other words, this is yet another reiteration of the Argument from Incredulity. Darwin's basic proposal, that the diversity of life can be explained by a process of small, incremental changes taking place over enormaous spans of time, is felt to be too improbable to accept.

    Yet we have no reason to think that what we believe has any direct bearing on how the world is, quantum phenomena notwithstanding, BA77.

    I need hardly point out that for thousands of years people were convinced that the Sun orbited the Earth because that is how it appeared. We know that it isn't true now, it could not have been true then and all that believing didn't make it true. Besides, when the vast majority of all that evolution was taking place there were no people around to believe or observe anything.

    For a long time people accepted the various creationist myths because there seemed to be no reasonable alternative, although, in a sense, the answer had been staring them in the face for quite a while. Plant and animal breeders had known long before Darwin that the forms of living things were not fixed, that they could be changed by selective breeding over time. Darwin just took the next step of asking why couldn't environmental pressures do the same thing.

    What Darwin's theory lacked, as he was perfectly well aware, was a mechanism which could account for how the changes could happen and be passed on to subsequent generations. Mendel's research neatly filled that gap.

    Of course, as Dr Hunter never tires of pointing out, things have got a lot more complicated since then. Natural selection of random mutations is no longer seen as the only or even the primary engine of evolution.

    What has not changed, however - what is as undeniable a part of the natural order off things as gravity - is that living things change over time and those changes can be influenced by external pressures, whether artificial or natural.

    If the world was created by some unimaginably powerful 'Originator' then that being created living things that could evolve over time. If, as I believe, there is no compelling reason to believe such a being exists then the whole thing must have come about through some other process. Either way, life changes over time.

    ReplyDelete
  5. CH, I know I'm not suppose to laugh at other's post, but you're making it darn near impossible. Your latest misrepresentation of actual evolutionary theory is just so ridiculous that it's all I can do to not spray coffee on the monitor. It's like you've decided to write these articles for people with the education level of third graders. I guess you know your Creationist target audience, but still...

    Roulette is a horrible model for evolutionary processes because the game does not carry forward heritable traits that increase the chance of winning. Also, when scientists say selection is non-random they merely mean selection doesn't have a uniform probability distribution. Variations give some individuals a better chance to survive and reproduce than their neighbors, so they tend to reproduce more and have those beneficial variations increase in the population.

    You know that, and we know you know that, so why do you keep lowering yourself with deliberately false representations of the real process?

    Tell you what. If you honestly think that it's "all chance" and that the accumulation of heritable beneficial traits doesn't matter, let's play poker one night. You have to play each hand with the original 5 cards you're dealt. I get to discard and redraw up to 3 times for each hand. Since we're both just relying on chance, that means it's a fair and equal game, right? What stakes do you want to play for?

    ReplyDelete
    Replies
    1. Thorton you state: "I get to discard and redraw up to 3 times for each hand."

      Thorton please tell me exactly where the 'discard pile' is in the fossil record for all the failed evolutionary experiments. Evolution seems to have a uncanny ability to hit upon the right design first time every time without ever having to 'discard'. The game certainly looks to rigged!

      For instance, where is the discard pile of failed fossils for the winning hand of the trilobite eye?

      Trilobites suddenly appeared in the Cambrian (lowest fossil-bearing) stratum with no record of ancestry. The trilobite eye is made of optically transparent calcium carbonate (calcite, the same mineral of its shell) with a precisely aligned optical axis that eliminates double images and two lenses affixed together to eliminate spherical aberrations [McC98, Gal00].

      Paleontologist Niles Eldredge observed, “These lenses--technically termed aspherical, aplanatic lenses--optimize both light collecting and image formation better than any lens ever conceived. We can be justifiably amazed that these trilobites, very early in the history of life on earth, hit upon the best possible lens that optical physics has ever been able to formulate” [Eld76]. Notice these lenses weren’t just good as, but were better than anything modern optical physicists have been able to conceive! ,,, “The design of the trilobite’s eye lens could well qualify for a patent disclosure” [Lev93p58].,,,

      The Optimal Trilobite Eye - per Dr. Don Johnson - Programming of Life page 68-66 and appendix F:
      Excerpt: The trilobite lens is particularly intriguing since the only other animal to use inorganic focusing material is man. The lens may be classified as a prosthetic device since it was non-biological, which also means the lens itself, with apparently no DNA inherent within, was not subject to Darwinian evolution.
      https://docs.google.com/document/pub?id=1TiZcs0eginyh6rijCGd3kwC3CeawjQV1AsC6Xvvnx44

      Evolution vs. The Trilobite Eye - Prof. Andy McIntosh - video
      http://www.metacafe.com/watch/4032589

      further notes:

      Here is a page of quotes by leading paleontologists on the true state of the fossil record:
      Excerpt: "In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms." Fossils and Evolution, TS Kemp - Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

      "Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual transitional sequences.”
      George Gaylord Simpson (evolutionist), The Major Features of Evolution, New York, Columbia University Press,
      https://docs.google.com/document/pub?id=15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg

      Whale Evolution vs. The Actual Evidence – video - fraudulent fossils exposed
      http://vimeo.com/30921402

      Fish & Dinosaur Evolution vs. The Actual Evidence - video and notes
      http://vimeo.com/30932397

      Bird Evolution vs. The Actual Evidence - video and notes
      http://vimeo.com/30926629

      Evolutionary Stasis (Of The Fossil Record) — Double-speak and Propaganda - video
      http://www.youtube.com/watch?feature=player_embedded&v=D09cehqHQ2o#!

      Delete
    2. bornagain77 June 10, 2012 6:49 AM

      Thorton please tell me exactly where the 'discard pile' is in the fossil record for all the failed evolutionary experiments.


      Extinct species pile?

      Evolution seems to have a uncanny ability to hit upon the right design first time every time without ever having to 'discard'. The game certainly looks to rigged!

      Texas sharpshooter fallacy.

      Delete
    3. While your at it Thorton, please tell me where the 'discard pile' is for the 'winning hand' of photosynthesis:

      The Sudden Appearance Of Photosynthetic Life On Earth - video
      http://www.metacafe.com/watch/4262918

      U-rich Archaean sea-floor sediments from Greenland - indications of +3700 Ma oxygenic photosynthesis (2003)
      http://adsabs.harvard.edu/abs/2004E&PSL.217..237R

      "There is no question about photosynthesis being Irreducibly Complex. But it’s worse than that from an evolutionary perspective. There are 17 enzymes alone involved in the synthesis of chlorophyll. Are we to believe that all intermediates had selective value? Not when some of them form triplet states that have the same effect as free radicals like O2. In addition if chlorophyll evolved before antenna proteins, whose function is to bind chlorophyll, then chlorophyll would be toxic to cells. Yet the binding function explains the selective value of antenna proteins. Why would such proteins evolve prior to chlorophyll? and if they did not, how would cells survive chlorophyll until they did?" Uncommon Descent Blogger

      In what I find to be a very fascinating discovery, it is found that photosynthetic life, which is an absolutely vital link that all higher life on earth is dependent on for food, uses ‘non-local’ quantum mechanical principles to accomplish photosynthesis. Moreover, this is very strong evidence that a non-local, beyond space-time, cause must ultimately be responsible for ‘feeding’ all life on earth,

      Non-Local Quantum Coherence In Photosynthesis - video with notes in description
      http://vimeo.com/30235178

      Unusual Quantum Effect Discovered in Earliest Stages of Photosynthesis - May 2012
      Excerpt: "The behavior we were able to see at these very fast time scales implies a much more sophisticated mixing of electronic states," Tiede said. "It shows us that high-level biological systems could be tapped into very fundamental physics in a way that didn't seem likely or even possible."
      The quantum effects observed in the course of the experiment hint that the natural light-harvesting processes involved in photosynthesis may be more efficient than previously indicated by classical biophysics, said chemist Gary Wiederrecht of Argonne's Center for Nanoscale Materials. "It leaves us wondering: how did Mother Nature create this incredibly elegant solution?" he said.
      http://www.sciencedaily.com/releases/2012/05/120524092932.htm

      Well, I certainly think 'mother nature' had a lot of help setting up a 'non-local' light harvesting apparatus:

      1 John 1:5
      This is the message we have heard from him and declare to you: God is light; in him there is no darkness at all.these.

      Toby Mac (In The Light) - music
      http://www.youtube.com/watch?v=5_MpGRQRrP0

      Delete
    4. Thorton I asked you where the discard pile for transitional fossils was, which leading paleontologists admit are indeed missing, and you point me instead to the fossils that went extinct after a long term stasis in the fossil record??? To use your card analogy, that does not reflect discarding cards to eventually get to a 'winning hand', but instead reflects the end of one hand and the deal of a entirely brand new hand.

      The Truth About Evolution - Transitional Fossils
      Excerpt: Major adaptive radiations provide a formidable challenge to biological evolution.,,, Major adaptive radiations of groups of vertebrates are:

      a) Placoderms in the early Devonian. Because they were heavily armored, jawed fish, intermediates and ancestral forms should have fossilized but none are found. No placoderms exist today.
      b) Chondrichtyes during the Devonian. They are the cartilaginous fish such as sharks and rays. Intermediates and ancestors are unknown.
      c) Agnatha Fish in the Silurian. These were jawless fish with bony skeletons. Intermediates and ancestors should have fossilized but none are found. Most types became extinct but hagfish and lampreys are living jawless fish.
      d)Tetrapods in the early Carboniferous. These were many, diverse forms of four-legged amphibians that are believed to have evolved from fish. But no fossilized links to fish have been found and specific interrelationships of the numerous lineages is unknown.
      e) Amniotes in the late Carboniferous. Amniotes are characterized by their complex reproductive system and include reptiles, birds and mammals. They are believed to have evolved from amphibians but their ancestry has not been determined from the fossil record.
      f) Archosaurs in the late Permian. They were reptiles with diverse sizes and shapes that became extinct in the Triassic. Some as long as six meters have been found.
      g ) Dinosaurs in the late Triassic. Dinosaurs include the largest terrestrial animals that have ever lived. Their diversity in size and shape was spectacular. Their ancestry is unknown and specific interrelationships of the numerous types is unknown.
      h) Teleosts in the late Cretaceous. These are bony fish approximately 20,000 living species in 35 orders and 409 families. Interrelationships of the higher groups are unknown.
      i) Therian mammals in the late Cretaceous and early Tertiary. These are placental and marsupial mammals. When they first appear in the fossil record, they are very diverse and interrelationships are unknown.
      j) Birds in the late Cretaceous and early Tertiary. There are estimates of 8900 living species in 166 families and about 27 orders. Fossil evidence is lacking for establishing the interrelationships of the orders of birds.

      Delete
    5. In Explaining the Cambrian Explosion, Has the TalkOrigins Archive Resolved Darwin's Dilemma? - JonathanM - May 2012
      Excerpt: it is the pattern of morphological disparity preceding diversity that is fundamentally at odds with the neo-Darwinian scenario of gradualism. All of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later. On the Darwinian view, one would expect to see all of the major differences in body plan appear only after numerous small-scale speciation events. But this is not what we observe.
      http://www.evolutionnews.org/2012/05/has_the_talk-or059171.html

      The Biological Big Bang model for the major transitions in evolution - Eugene V Koonin - Background:
      "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable;
      http://www.biology-direct.com/content/2/1/21

      Delete
    6. correction, the last post should have been addressed to Ian

      Delete
  6. Have some sympathy for batspit77. It must be terribly difficult to go through life without being able to form a single coherent thought.

    ReplyDelete
  7. Cornelius Hunter wrote: Imagine a friend wins a one-in-a-million jackpot at roulette, but he claims it wasn’t by chance because he also had some losing bets. On his losing bets he collected nothing, but on his winning bets collected his winnings. Isn’t that the very antithesis of chance?

    This is prima facie evidence that our creationist blog host does not understand natural selection. If you do not understand natural selection, how on Earth can you possibly claim to understand evolution, which is far more than simply natural selection.

    ReplyDelete
    Replies
    1. "If you do not understand natural selection"

      Perhaps you would care to write to these guys and tell them what they missed in their understanding of Natural Selection:

      Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010
      Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.
      http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies

      Or perhaps you would care to write Dr. John Sanford, inventor of the 'gene-gun', and explain to him what he missed in understanding Natural Selection:

      Natural Selection Falsified (Top Population Geneticists agree neo-Darwinism is not supported by the data) - Dr. John Sanford - video
      http://www.metacafe.com/watch/4587204/

      This following study highlights the 'princess and the pea' paradox mentioned by Dr. Sanford in the previous video:

      The GS (genetic selection) Principle - David L. Abel - 2009
      Excerpt: The GS (Genetic Selection) Principle states that biological selection must occur at the nucleotide-sequencing molecular-genetic level of 3'5' phosphodiester bond formation. After-the-fact differential survival and reproduction of already-living phenotypic organisms (ordinary natural selection) does not explain polynucleotide prescription and coding.
      http://www.bioscience.org/2009/v14/af/3426/fulltext.htm

      It is also extremely interesting to note, the principle of Genetic Entropy, which stands into direct opposition to the primary claim of neo-Darwinian evolution, lends itself quite well to mathematical analysis by computer simulation:

      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.cn/lecture/chinaproof.pdf
      MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
      http://mendelsaccount.sourceforge.net

      John C. Sanford - Bio
      Excerpt:
      * Co-developer of “Mendel’s Accountant” – today’s most advanced forward-time population genetics simulation program
      * Primary inventor of the biolistic (gene gun) process
      * Co-inventor of the Pathogen-derived Resistance (PDR) process
      * Co-inventor of the Genetic Vaccination process
      * Primary inventor of numerous conventionally-bred fruit varieties
      * Most of the world's transgenic crop acreage were transformed via my biolistic process
      http://www.nysaes.cornell.edu/hort/faculty/sanford/

      Delete
    2. So if someone produces more scientists who accept that natural selection ,combined with other materialistic means, produces the variety of life,you will be convinced?

      Delete
    3. You mean something like this?

      Perhaps I'm being overly pessimistic but I'd rate the chances of that happening at about the snowball-in-hell level.

      Delete
    4. No, I will be convinced by the evidence itself!

      Austin Hughes: Most Evolutionary Literature Showing Positive Selection in the Genome is "Worthless" - Casey Luskin - 2012
      Excerpt - When University of South Carolina evolutionary biologist Austin Hughes was asked about the problem with positive Darwinian selection, he says, "The problem is there really isn't all that much evidence that it actually happens to the extent to which it would be needed to explain all of the adaptive traits of organisms."
      http://www.evolutionnews.org/2012/01/austin_hughes_m055121.html

      Oxford University Admits Darwinism's Shaky Math Foundation - May 2011
      Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years.
      http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html

      Did Natural Selection Construct Metazoan Developmental Sequences? - Paul Nelson - July 2011
      The necessary and sufficient conditions of the process of natural selection (Endler, Natural Selection in the Wild, 1986) are (1) variation, (2) selection or fitness differences, and (3) inheritance. These conditions impose evidential demands on any investigator who wishes to employ natural selection in evolutionary (i.e., historical) explanation. Data from model systems (e.g., C. elegans, Drosophila, and Danio), as well as theoretical analyses, raise challenges for the use of natural selection as the causal process responsible for the origin of developmental sequences. In particular, the conditions of (2) selection differences and (3) inheritance have not been adequately described in current theories of the evolution of the Metazoa.
      http://www.evolutionnews.org/2011/07/paul_nelson_jonathan_wells_tak048301.html

      Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated)
      Casey Luskin April 12, 2011
      Excerpt: This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create....[N]eo-Darwinists say that new species emerge when mutations occur and modify and organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence.
      http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.html

      Darwinism’s Last Stand? - Jonathan Wells
      Excerpt: Despite the hype from Darwin’s followers, the evidence for his theory is underwhelming, at best. Natural selection - like artificial selection - can produce minor changes within existing species. But in the 150 years since the publication of Darwin’s Origin of Species by Means of Natural Selection, no one has ever observed the origin of a new species by natural selection - much less the origin of new organs and body plans.
      http://www.evolutionnews.org/2009/06/junk_dna_darwinisms_last_stand.html#more

      EXPELLED - Natural Selection And Genetic Mutations - video
      http://www.metacafe.com/watch/4036840

      "...but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have..."
      Maciej Marian Giertych - Population Geneticist - member of the European Parliament - EXPELLED

      Natural Selection Reduces Genetic Information - No Beneficial Mutations - Lee Spetner - Michael Denton - video
      http://www.metacafe.com/watch/4036816

      Delete
    5. Anaxyrus:

      This is prima facie evidence that our creationist blog host does not understand natural selection.

      No, the problem is not with the host. The problem is with evolutionists who, in this case, when confronted with the problem that “evolution is unlikely because it is a random, chance process” reply that there is no such problem because natural selection is not random and so saves the day. Killing off the bad designs doesn’t make random mutations hitting on complex designs any less random. Every mutation and recombination event leading to a cherry tree is still random, regardless of natural selection.

      Delete
    6. I see BA, it is only evidence if it is your evidence,

      Snowballs, mmmmmm, New Orleans style half raspberry ,half grape

      Delete
    7. As Bill says,

      " baby steps", after all where is the line exactly between simple and complex?

      Delete
    8. Cornelius Hunter

      Anaxyrus: "This is prima facie evidence that our creationist blog host does not understand natural selection."

      No, the problem is not with the host. The problem is with evolutionists who, in this case, when confronted with the problem that “evolution is unlikely because it is a random, chance process” reply that there is no such problem because natural selection is not random and so saves the day. Killing off the bad designs doesn’t make random mutations hitting on complex designs any less random.


      But evolution isn't just killing off bad designs. It's also saving the good designs and using them for the basis of the subsequent generations. Ignoring the heritability of beneficial traits part of the evolutionary process won't make the process go away CH, no matter how much disingenuous rhetoric you throw at it. Sorry, but in this case the problem really is with the host.

      Every mutation and recombination event leading to a cherry tree is still random, regardless of natural selection.

      The outcome of every spin of the roulette wheel is random chance, yet the casino still makes money on the game week after week, year after year. Why is that CH?

      Ready to play poker with me using my rules? According to you it's just chance so neither of us should have an advantage, right?

      Delete
    9. "It's also saving the good designs and using them for the basis of the subsequent generations."

      If it wasn't for the minor problems that no one has shown EVEN ONE functional protein arising by purely material, neo-Darwinian processes, and the fact that slightly detrimental mutations, which are far below the power of Natural Selection to eliminate from a genome before the slightly detrimental mutations spread throughout the entire population, then you would have a 'chance'. But as it sits now you have absolutely no firm empirical basis in science to make such sweeping claims as you are making, but only blind faith in your atheistic dream world! Moreover, even if you were to find empirical evidence for a functional protein being generated by purely material neo-Darwinian processes, you still would not have made even a dent in the primary question of, "where is the overriding Body-Plan information coming from?":

      Stephen Meyer - Functional Proteins And Information For Body Plans - video
      http://www.metacafe.com/watch/4050681

      Dr. Stephen Meyer comments at the end of the preceding video,,,

      ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009)

      ----

      Genetic Entropy - Dr. John Sanford - Evolution vs. Reality - video (Notes in description)
      http://vimeo.com/35088933

      Delete
    10. vel states: 'I see BA, it is only evidence if it is your evidence,'

      Actually vel, it is the evolutionists evidence to. In fact I consider the neo-Darwinian evidence stronger since it clearly illustrates the neo-Darwinists refusal to accept the overwhelming evidence against Darwinism even when it comes from their very own hands. With such refusal to acknowlege their own evidence, I couldn't more clearly illustrate the Dogmatic religious adherence of Darwinists even if I had hundred papers by ID scientists testifying to the same point.

      Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact - Cornelius Hunter - July 2011
      Excerpt: For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.
      http://darwins-god.blogspot.com/2011/07/response-to-comments-proteins-did-not.html

      Delete
    11. batspit77 never misses a chance to fire up his trusty "Blither-O-Matic" pointless C&Ping machine. Guy wears through three engines and a dozen set of tires on it each year.

      Delete
    12. Thorton, I mentioned to a lawyer friend of mine about Darwinists using ad-homimen attacks, such as you do, and his immediate response, before I even got to the particulars of how much you use it, was to say that Darwinists must have no real evidence to present since everyone in Law knows that ad-homimen attack is a underhanded tactic used by less than scrupulous Lawyers on the losing side of a case.

      4-Him - Can't Get Past The Evidence - music
      http://www.youtube.com/watch?v=WiRQxEOWdDw

      Delete
    13. Thorton:

      CH: No, the problem is not with the host. The problem is with evolutionists who, in this case, when confronted with the problem that “evolution is unlikely because it is a random, chance process” reply that there is no such problem because natural selection is not random and so saves the day. Killing off the bad designs doesn’t make random mutations hitting on complex designs any less random.

      Thorton: But evolution isn't just killing off bad designs. It's also saving the good designs and using them for the basis of the subsequent generations.


      Yup, you got it. And all the random changes that built the good designs, and all the future random changes that would build on those good designs, are still random. Natural selection doesn’t change that. As such natural selection doesn’t change the probabilities. There is a 27 order of magnitude shortfall between the number of evolutionary experiments needed to evolve a protein and the number of evolutionary experiments available to evolve a protein (according to evolutionists own numbers!). Natural selection doesn’t change that.

      Ignoring the heritability of beneficial traits part of the evolutionary process won't make the process go away

      You are laboring under a profound misconception. You have been strenuously arguing all this time for something you don’t understand. The heritability of beneficial traits doesn’t magically solve the problem. Evolution still means the species arose by chance. Of course the theory states that beneficial traits are heritable. But those traits had to have been hit upon by random change. The fact that each step along the way is heritable doesn’t make the mutations any less random.

      It would require a long series of random mutations that just happens to construct an incredible biological design. And this would have to occur repeatedly, for all of biology’s amazing designs. And in each of these long series of random mutations, there would need to be a great many—mostly undiscovered and unknown—intermediate designs. And these intermediate designs would have to be helpful to the organism.

      All of this must occur by random mutation and recombination events. Natural selection doesn’t change that. And just because halfway through the process you have intermediate designs built up, doesn’t make the process any less driven by chance.

      Delete
    14. Cornelius Hunter

      Yup, you got it. And all the random changes that built the good designs, and all the future random changes that would build on those good designs, are still random.


      So? The overall evolutionary process still isn't merely random.

      The heritability of beneficial traits doesn’t magically solve the problem.

      The only 'problem' is the silly strawman one you're trying to foist on everyone here. Sorry CH, your empty rhetoric doesn't work against the scientifically competent.

      Evolution still means the species arose by chance.

      Of course it doesn't, but that's the propaganda your Creationist groupies love to hear.

      The fact that each step along the way is heritable doesn’t make the mutations any less random.

      The fact that individual mutations are random doesn't make the entire process random either.

      Backgammon has a random component too - your roll the dice for every turn. That doesn't mean the backgammon world's champion is just a random person plucked from the millions who play the game.

      It would require a long series of random mutations that just happens to construct an incredible biological design.

      No it doesn't. It just takes a feedback process of random genetic variability filtered by selection and used for each subsequent iteration, the net effect of which is to accumulate the beneficial changes. Science knows of such a process, has known about it for over 150 years. Starts with an 'E'. You should read up on it sometime.

      And in each of these long series of random mutations, there would need to be a great many—mostly undiscovered and unknown—intermediate designs.

      There are.

      And these intermediate designs would have to be helpful to the organism.

      Wrong again. The changes can be beneficial, but they can also be effectively neutral WRT reproductive fitness. And wouldn't you know it, that's exactly what the fossil and genetic evidence shows happened.

      just because halfway through the process you have intermediate designs built up, doesn’t make the process any less driven by chance.

      "Driven by chance" doesn't mean the whole process is exclusively the result of chance.

      Sorry again CH. Sometimes your anti-science propaganda while still wrong is at least semi-plausible, but you really face planted on this one. Best to post lots more OPs and get this embarrassment to scroll off the page ASAP.

      Ready to play me poker by my rules yet? ;)

      Delete
    15. "Ready to play me poker by my rules yet?"

      Thorton perhaps you can go to Vegas and try to talk those guys into 'playing by your Darwinian rules':

      Evolutionismist wins millions in casino! (Also quickly escorted to city limits)
      http://satirizingscientism.blogspot.com/2009/09/evolutionismist-wins-millions-in-casino.html

      Delete
    16. batspit77

      "Ready to play me poker by my rules yet?"

      Thorton perhaps you can go to Vegas and try to talk those guys into 'playing by your Darwinian rules'


      Vegas isn't the one offering the silly claim that since a process has a random component that the overall results must be completely random.

      Why don't you stop blithering for a second and explain why, if roulette is a game of pure random chance, why the house always wins an average of approx. 5% in the long run.

      Or better yet - explain why when a rock rolls down the side of a mountain, the bouncing path it takes may be random but the rock always wind up at the bottom.

      Delete
    17. Thorton, there is a vast difference between probable and plausible:

      Programming of Life - Probability - Defining Probable, Possible, Feasible etc.. - video
      http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/8/kckv0wVBYpA

      Signature in the Cell - Book Review - Ken Peterson
      Excerpt: "there are about 10 to the 80th elementary particles in our observable universe. Assuming a Big Bang about 13 billion years ago, there have been about 10 to the 16th seconds of time. Finally, if we take the time required for light to travel one Plank length we will have found “the shortest time in which any physical effect can occur.” This turns out to be 10 to the minus 43rd seconds. Or turning it around we can say that the most interactions possible in a second is 10 to the 43rd. Thus, the “probabilistic resources” of the universe would be to multiply the total number of seconds by the total number of interactions per second by the total number of particles theoretically interacting. The math turns out to be 10 to the 139th."
      http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell

      The Universal Plausibility Metric (UPM) & Principle (UPP) - Abel - Dec. 2009
      Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes.",,,

      cΩu = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108

      cΩg = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96

      cΩs = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85

      cΩe = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70

      http://www.tbiomed.com/content/6/1/27

      Delete
    18. Thorton:

      No it doesn't. It just takes a feedback process of random genetic variability filtered by selection and used for each subsequent iteration, the net effect of which is to accumulate the beneficial changes.

      […]

      Wrong again. The changes can be beneficial, but they can also be effectively neutral WRT reproductive fitness


      Got it. First it’s selection. Then when questioned evolutionists cut and run to drift. Meanwhile they’re 27 orders of magnitude short of reality.

      Delete
    19. Cornelius Hunter

      Got it. First it’s selection. Then when questioned evolutionists cut and run to drift. Meanwhile they’re 27 orders of magnitude short of reality.


      The only thing you're got is possibly the world's silliest strawman argument - that because part of a process is random that means the entire process must be random.

      I suppose that fits in well with your other equally goofy strawman argument - that because science doesn't know everything that means it can't know anything.

      Speaking of cutting and running, I notice you won't answer my roulette question, or my backgammon question. You also won't say if my rules for our poker game are fair. No sense actually answering a question for once and ending your long avoidance streak I suppose.

      If you need a second income CH, you may want to consider opening a shark-jumping school. You certainly have the experience. :)

      Delete
  8. This comment has been removed by the author.

    ReplyDelete
  9. Darwinian evolution endowed us with incredulity for a reason. We ignore it at our peril.

    ReplyDelete
  10. RkBall,

    Are you the Delphic Oracle?

    ReplyDelete
    Replies
    1. Darwinian evolution has endowed us with instincts as a means of ensuring our survival. Incredulity is one of them. Everyone on this site who dismisses darwinian evolution on grounds of incredulity provides yet more evidence that darwinian evolution is true. The more people doubt it, the more confidence we can have in it. If it ever reaches the point where no-one believes in it, it will have been conclusively demonstrated to be true. I await the day!

      Delete
  11. First, Cornelius is presenting false dilemma in regards to the unknowability of evolutionary theory. However, I'd suggest that Cornelius doesn't see it as a false dilemma as he doesn't recognize his pre-enlightenment, authoritative, justificationist conception of human knowledge as an idea that would be subject to criticism.

    Second, as I've pointed out before, creationism is misleadingly named, as it's a general purpose means of denying that creation actually took place. Specifically, when Cornelius claims evolutionary processes are "random" he's denying that they actually created the non-explanatory knowledge of how to build adaptations. As he puts it, it's a blunder to think this actually occurred.

    In other words, not only is his argument is highly parochial, as it doesn't take into account the different kinds of unknowability, but as a creationist he ultimately denies that creation took place at all.

    To elaborate further…

    The first kind of unknowability are scenarios where all the outcomes can actually be known. An example of this is Russian Roulette. Since we know all of the possible outcomes, we can use probability to make choices about it. For example, if for some horrible reason, one had to choose between different versions of Russian Roulette, with specific yet variable number of chambers, bullets and trigger pulls, one could use game theory to determine which variation would be most favorable.

    On the other hand, scenarios that depend on the creation of knowledge represent a different kind of unknowability, despite being deterministic. For example, people in 1900 didn't consider nuclear power or the internet unlikely. They simply didn't conceive of them at all. As such, it's unclear how they could have factored their impact into some sort of probability calculation about the future.

    So, In the face of the latter kind of unknowability, probability is invalid as a means of criticizing explanations, because the knowledge we'd need to calculate it doesn't exist yet.

    However, as a creationist, Cornelius denies that evolutionary process can actually create knowledge. Period. Therefore, the creation of knowledge couldn't be a barrier in calculating probabilities. Furthermore, he assumes that specific biological features we observe were pre-selected by a designer, which supposedly allows him to know all the possible outcomes, like Russian Roulette.

    As such, he assumes there is only one kind of unknowability.

    I'd also suggest it's this same assumption that is behind Cornelius's statements that "the science" or "the data" tells us evolutionary theory is unlikely. Again, since Cornelius cannot recognize is conception of human knowledge as an idea that would be subject to criticism, he doesn't recognize he's using an explanatory framework to reach this particular conclusion when extrapolating data.

    Of course, should Cornelius provide some alternative, better explanation for his claims, deny that he holds a pre-enlightenment, authoritative, justificationist conception of human knowledge, or illustrate how he genuinely recognizes such a conception as an idea that would be subject to criticism, I'm all ears.

    ReplyDelete
    Replies
    1. "he doesn't recognize he's using an explanatory framework to reach this particular conclusion when extrapolating data."

      coming from a guy whose explanatory framework results in this:

      'I tentatively accept the consequences of such a theory, including that I would also be a multiversal object, which includes at least 10^500 versions of myself' - Scott - Many Worlds proponent
      http://darwins-god.blogspot.com/2012/04/neuroscientist-most-seamless-illusions.html?showComment=1334583967799#c7217305678409346277

      Delete
  12. Cornelius, I'm mystified. You have a background in physics and biology, and yet you appear to have no understanding of evolutionary theory.

    And it now appears to me that this is willful.

    You are equivocating with the word "random" and should know better.

    Both variance-generation and natural selection are stochastic processes. Both are biased in favour of what produces a viable individual. However, variance-generation is not biased in favour of what makes a more viable individual than the parents, whereas "natural selection" is, by definition, a bias in the sampling of genetic variance in each generation in favour of what promotes successful reproduction.

    It is for this reason only that variance generation is often described as "random" and natural selection as "non-random". But they are poor terms. Variants are not drawn from a flat distribution, but from an extremely peaked distribution in which all but very small differences from the viable parental genotype are very low probability. And "natural selection" is simply a bias in the sampling of those variants in favour of what promotes reproductive success.

    Which is pretty well how human design works, except that we also have some foresight. But we tend to choose the prototypes that perform best for further replication, and tweak them. Of those tweaked prototypes, we select those that perform best and tweak again.

    It is therefore not surprising that both systems result in efficient optimisation.

    ReplyDelete
  13. Hunter: It would require a long series of random mutations that just happens to construct an incredible biological design.

    I share Elizabeths amazement at how someone with a biophysics background can have this sort of basic misunderstanding. Are you equally amazed that genetic algorithms are able to find solutions to difficult problems even though they are likewise based on random mutations? Or that Monte Carlo algorithms can optimize pretty well? Such childish behavior would be excusable for a layman but not for someone with a PhD in biophysics from a respectable university.

    ReplyDelete
    Replies
    1. oleg:

      Hunter: It would require a long series of random mutations that just happens to construct an incredible biological design.

      oleg: I share Elizabeths amazement at how someone with a biophysics background can have this sort of basic misunderstanding.


      It is unclear where you have discovered the misunderstanding. Is the series not long, the biological variation not random, or the biological designs not complex?


      Are you equally amazed that genetic algorithms are able to find solutions to difficult problems even though they are likewise based on random mutations? Or that Monte Carlo algorithms can optimize pretty well?

      No I am not.


      Such childish behavior would be excusable for a layman but not for someone with a PhD in biophysics from a respectable university.

      You are the one equating GA’s and MC’s with the evolution of consciousness.

      Delete
  14. Oleg:

    Its is my understanding that genetic algorithms can only take you so far. They only improve on preexisting things. And they only work if each iteration produces some benefit. That might not be the case in real life. And they only work if they run on supercomputers. Regular computers aren't fast enough, Nature doesn't work nearly as fast as a supercomputer. Please correct me if I'm wrong.

    ReplyDelete
    Replies
    1. natschuster,

      I would have to correct essentially everything you have written. So why don't you take an opportunity to learn what a genetic algorithm is. The Wikipedia article is a great starting point. At a minimum, it should dispel some your misconceptions about GAs. For instance, not every iteration has to produce an improvement. And one does not need a supercomputer. But I will let you read the article first.

      Delete
  15. I read the wikipedia article as per your advise. It says that hey work by looking at every example in each iteration and picking the one that is most fit. That seems to me to mean that in each iteration there is one is an increase in fitness. How does this help when an adaptation requires a number of steps before there is a benefit? It also said that genetic algorithms tend to get stuck at local optima. This would seem to put a limit to how far it can go.

    ReplyDelete
    Replies
    1. There are lots of ways of writing GAs, and the best ones (in my experience) are ones that most closely mimic biological evolution.

      For example, when I write them, I usually use "sexual" reproduction - in other words, I let two "parents" "mate" to produce an offspring that inherits genetic material from both.

      And rather than "picking the most fit" to breed from (which is somewhat tautological), I let the fitness function loosely determine the probability of finding a mate.

      And often the offspring are less fit than the parents, but nonetheless go on to breed. It usually helps not to be too strict about which variants get to breed (as in biology) because often the really good solutions are achieved by means of steps that themselves do not confer increased (and may confer decreased) fitness. In other words, it helps if both variance generation and "selection" are strongly stochastic.

      This is one feature that prevents genetic algorithms from getting stuck at local optima; another is to have several dimensions of fitness (again, as in nature).

      In a high-dimensioned fitness landscape, local optima are rare, and when they occur, they are pretty optimal :)

      Delete
    2. oops, this reply was to natschuster's comment below.

      Delete
    3. oh, I did it right after all! I just realised that the comment below is a different comment!

      Delete
    4. That's not quite right, natschuster. Although sometimes people use such greedy selection schemes (only the fittest organism is selected), they are not the best performers as they tend to be stuck at local maxima. Typically the selection is less stringent as it allows the population to explore not only the direction of steepest ascent (and get stuck quickly) but also nearby directions.

      Delete
  16. The wikipedia article also says that genetic algorithms don't scale well. When you have to search a lot of things, (like a population of organisms) the numbers begin to work against you. That's why they don't work well when designing things like entire airplanes, or even entire airplane engines, but only things like propellor blades. (That's Wikipedia's example, not mine.) So it seems like GA's can only get you so far.

    ReplyDelete
    Replies
    1. This is true if you are looking for a specific solution to a specific problem - e.g. a fighter airplane.

      It is no problem at all if all that matters is that the population thrives in its environment.

      I think this is one of the big misunderstandings about evolution: IDists start with an amazing thing - a bacterial flagellum; a human genius - and then say: but it is hugely unlikely that this amazing thing would come about.

      And this true. If I wanted to design a human genius, I wouldn't use an evolutionary algorithm (at least not without a lot of Intelligent Tweaking). However, if I wanted to design, for example, a biosphere for a hitherto lifeless planet, I would certainly use one - indeed, I'd just seed it with self-replicating proto-cells, and let the process get on with itself. I would have no idea whether the result would be anything resembling any terrestrial life-form, but I would be confident that what did evolve would be extremely "well-designed" to thrive in that alien environment.

      Delete
  17. natschuster

    I read the wikipedia article as per your advise. It says that hey work by looking at every example in each iteration and picking the one that is most fit. That seems to me to mean that in each iteration there is one is an increase in fitness.


    Then your reading comprehension sucks. If we had all neutral mutations we'd still have one that is most fit. Theoretically we could have an iteration where every member of generation B had a decrease in fitness from the generation A that preceded it. But generation B would still have a member that was most fit relative to its neighbors.

    How does this help when an adaptation requires a number of steps before there is a benefit?

    It's called neutral drift. We can have neutral mutation A occur any time in the past and be fixed through drift, and neutral mutation B do the same. Then if a particular protein requires A B and C, you only have to have mutation C occur because A and B are already there.

    Behe completely ignored neutral drift in his EoE calculations, which is only one of the many reasons his idiocy was rejected.

    It also said that genetic algorithms tend to get stuck at local optima. This would seem to put a limit to how far it can go.

    'Tend to get stuck' doesn't mean 'always get stuck'. Either your reading comprehension is non-existent, or your honesty is.

    ReplyDelete
    Replies
    1. "It's called neutral drift. We can have neutral mutation A occur any time in the past and be fixed through drift,"


      May a darwinist of this forum explain why is used the word "drift" instead of chance?
      As I understand "drift" is used to explain that a given alele became predominant because it happen ramdomly in any binomial distribution.

      Delete
    2. Thanks Oleg, but that wasn`t my question. I would like to know why biologists uses the word "drift" instead "ramdom".

      Delete
    3. Thanks again Oleg. But now I am more confused as there was two concepts "steady drift" and "ramdom drift". So why "ramdom drift" became "drift" instead of "ramdom"?

      Delete
    4. It's a historical quirk, Blas. (An then there is the fact that random is an adjective, so random drift could not turn into random.)

      But be that as it may, Blas, you are asking the wrong question. To see what I mean, watch Richard Feynman's explanation on the difference between knowing the name of something and knowing something.

      Delete
    5. oleg said
      "It's a historical quirk, Blas."

      Behind any long lasting quirk there is a reason.

      "(An then there is the fact that random is an adjective, so random drift could not turn into random.)"

      But you can use ramdomly.

      "But be that as it may, Blas, you are asking the wrong question. To see what I mean, watch Richard Feynman's explanation on the difference between knowing the name of something and knowing something."


      I know the difference, but I do not underestimate the power of naming.

      Delete
  18. Elizabeth:

    I'm not sure what your point is. I'm saying that, to the best of my knowledge computer generated GA are not a very good way to design something like a motor, or a flagellum. Are you agreeing with.

    Thorton:

    I'm a little confused. Every iteration starts with everything being the same fitness. Then they mutate. The most fit is picked. If there isn't one that is the most fit, what gets picked? And, in real a mutations that decreases fitness tend to prove fatal.

    Does neutral drift work in computer generated GA's? And what about case where the mutations involved are actually harmful unless they happen all at once, e.g. a protein gaining a new ability but losing stability unless there is are compensating mutations.

    And I understood Wikipedia to be saying that GA's tend to get stuck at local optima so often that scientists have to figure out ways to get around it. In real life, that might mean that evolution happens very rarely.

    ReplyDelete
    Replies
    1. I'm not sure what your point is. I'm saying that, to the best of my knowledge computer generated GA are not a very good way to design something like a motor, or a flagellum. Are you agreeing with.

      I'm saying that if you want to design a specific complex piece of equipment, GAs may not scale up.

      That doesn't mean that evolutionary processes (or GAs) can't produce amazingly complex pieces of equipment, it just means that they may not produce the piece of equipment the GA writer happened to want.

      A very high-dimensioned GA might deliver a submarine when what you wanted was a washing machine.

      Or a squid when you wanted a tree.

      Delete
  19. natschuster: Does neutral drift work in computer generated GA's? And what about case where the mutations involved are actually harmful unless they happen all at once, e.g. a protein gaining a new ability but losing stability unless there is are compensating mutations.

    A while ago Elizabeth blogged about her experience with a numerical simulation of this sort. She can point you to the exact thread on her blog for details, but the bottom line was that a greedy algorithm had a hard time finding the best solutions as it tended to get stuck at local optima. A more relaxed selection preserved genomes that went down in the fitness landscape but eventually got to even higher fitness. So, yeah, neutral drift exists in GAs and is quite helpful in optimization.

    ReplyDelete
    Replies
    1. This is the thread: Creating CSI with NS.
      The relevant discussion starts about here: March 18, 2012 at 5:20 pm

      Delete
    2. And here is a happy ending: March 20, 2012 at 3:51 pm

      A genetic algorithm generates 500 bits of specified information.

      Delete
    3. Refutation Of Evolutionary Algorithms

      "Darwin or Design" with Dr. Tom Woodward with guest Dr. Robert J. Marks II - video
      http://www.youtube.com/watch?v=Yoj9xo0YsOQ

      Delete
  20. But does a real loose fitness criterion work in real life. Most organisms that aren't fit enough die. How relaxed can you get before it becomes meaningless.

    ReplyDelete
    Replies
    1. Technically speaking, all organisms (whether better fit or not) die—eventually. The important point is that better fit organisms leave behind more offspring. Sometimes the process is dominated by the nonrandom component (natural selection) and sometimes by the random one (neutral drift). Both limits have been studied in quantitative models and in a biological setting.

      Delete
    2. natschuster: But does a real loose fitness criterion work in real life. Most organisms that aren't fit enough die. How relaxed can you get before it becomes meaningless.

      Well, by definition, an organism that isn't fit enough to live, dies, or isn't fit enough to reproduce, dies without issue.

      The issue is what proportion of offspring are viable, and as offspring tend to be very like their parents (because inheritance is pretty faithful), and their parents are, by definition, viable, most offspring will be viable.

      The important thing is that there is plenty of variance, and the ranking isn't too severe (the competition too strong). If only the very fittest survive, the population variance will be reduced, and the population will run the risk of failing to have enough variance to adapt in the face of environmental change. This does, of course, happen, and most populations that have ever existed have gone extinct.

      However, as long as conditions are tolerable enough that a range of genotypes produce viable phenotypes, then the population stands a good chance of maintaining enough variance to be able to adapt to change.

      Delete
  21. So it's kind of like a Goldilocks thing. Fitness requirements not too tight, not too loose. How does that work in real life?

    ReplyDelete
    Replies
    1. natschuster: Fitness requirements not too tight, not too loose. How does that work in real life?

      The world is a big place. Organisms will spread out and diversify in order to reduce direct competition.

      Delete
    2. So it's kind of like a Goldilocks thing. Fitness requirements not too tight, not too loose.

      Well, it depends what outcome you are interested in, but in a sense, yes, at least if you are looking for complex and/or ingenious "solutions" to the problem of thriving in a challenging environment.

      A very harsh environment may limit adaptation because "solutions" along pathways that require deleterious intermediates may be unavailable. On the other hand a very forgiving environment may not do enough filtering to allow for interesting accumulations of advantageous genetic variants.

      How does that work in real life?

      Some very harsh environments only support a very limited range of lifeforms (extremophile bacteria, for instance); some populations go extinct when a benign environment is followed by a harsher one, because what was not deleterious in the benign environment becomes highly deleterious in the harsh environment; some populations are over-specialised and go extinct when their habitat is destroyed.

      Delete
  22. But its fitness that drives evolution. Unless there is too much fitness.

    ReplyDelete
  23. Too narrow fitness, change in environment,adios

    ReplyDelete
    Replies
    1. velikovskys

      "Too narrow fitness, change in environment,adios"

      There is no better way to put this, rubbish!
      Animals will often adapt to a change in environment. It's totally untrue that a change in environment leads inevitably to the demise of a species unless it possesses a mutation which would give it an advantage.

      Delete
    2. Tell that to all the mega fauna which occupied North America before the arrival of man. There is the same problem with crops bred for certain yields, a change in predator or conditions wipe out the entire crop The more diverse a population the larger chance some in the population will fit into the new conditions

      Delete
    3. velikovskys,

      "a change in predator or conditions wipe out the entire crop The more diverse a population the larger chance some in the population will fit into the new conditions"

      A change in conditions can wipe out a whole population in some cases, but as I said, it is not inevitable.

      Delete
  24. It's totally untrue that a change in environment leads inevitably to the demise of a species unless it possesses a mutation which would give it an advantage.

    Yes, of course it's untrue. Nobody has claimed that.

    But rapid enviromental change certainly puts populations at risk of extinction, as adaptation takes time.

    And does not depend on "a mutation", but on sampling of those genetic variants that tend to promote reproductive success in the changed environment.

    ReplyDelete