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Dawkins shows us transitionals, really.

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105 Responses to Dawkins shows us transitionals, really.

  1. Dr. David Berlinski: What Does It Take for Change? (Clip 5)
    http://www.youtube.com/watch?v=DRqdvhL3pgM

    Whales – Designed or Evolved? – Marc Surtees – video
    http://edinburghcreationgroup.org/whales.xml

    In A Whale of Trouble
    http://www.scienceagainstevolution.org/v3i11f.htm

    Whale Tale Two
    http://www.scienceagainstevolu.....2f.htm#new

  2. “The opportune appearance of mutations permitting animals and plants to meet their needs seems hard to believe. Yet the Darwinian theory is even more demanding: a single plant, a single animal would require thousands and thousands of lucky, appropriate events. Thus, miracles would become the rule: events with an infinitesimal probability could not fail to occur …. There is no law against day dreaming, but science must not indulge in it.” Pierre P. Grasse – past President of the French Academie des Sciences

    As well His claim for Genetic Similarity Confirmation is falsified:

    “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009)
    Excerpt: Even among higher organisms, “the problem was that different genes told contradictory evolutionary stories,”,,,“despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” ,,,,Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”,,,“We’ve just annihilated the (Darwin’s) tree of life.”
    http://www.evolutionnews.org/2......html#more

    This following article shows that the “same exact genes” have actually been shown to produce “completely different” adult structures:

    A Primer on the Tree of Life (Part 4)
    excerpt: “In sharks, for example, the gut develops from cells in the roof of the embryonic cavity. In lampreys, the gut develops from cells on the floor of the cavity. And in frogs, the gut develops from cells from both the roof and the floor of the embryonic cavity. This discovery—that homologous structures can be produced by different developmental pathways—contradicts what we would expect to find if all vertebrates share a common ancestor. – from the textbook Explore Evolution
    http://www.evolutionnews.org/2......html#more

    This following study reveals that genes can’t even be resolved to the hypothetical mammalian tree of life.

    A article in – Trends in Ecology and Evolution – concluded
    “the wealth of competing morphological, as well as molecular proposals of the prevailing phylogenies of the mammalian orders would reduce the mammalian tree to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.
    W. W. De Jong, “Molecules remodel the mammalian tree,” – Trends in Ecology and Evolution, Vol 13(7), pgs. 270-274 (July 7, 1998).

    i.e. research is finding there is zero meaningful linearity to be had between protein amino acid sequences and protein coding genetic sequences of different “kinds”….

  3. I remember listening to Dr. Geoffrey Simmons of the Discovery Institute destroy PZ Myers on the subject of whale evolution in a radio debate a year or two ago. I can’t find a link now, but believe me, it was one for the ages.

  4. This video smells a little off. It has got to be a set up. Such a weak presentation must be a faux sandbagging of Sir Richard. He must have better skeletons in his closet.

    What we have is 12 to 20 million years between each and the nostril thing has got to be a trap for the future. As soon as one points outs how ridiculous it is, someone will pull out a couple more that will be better.

    Who wants to take odds that this video is a trick to entice people to complain about its vacuousness and then they pull a couple rabbits out of the hat. Oh, I mean whales. But in the end it will still be weak but the attention will be on those who objected not the lack of evidence and the weak argument.

  5. “herb” (#3) wrote: “I remember listening to Dr. Geoffrey Simmons of the Discovery Institute destroy PZ Myers on the subject of whale evolution in a radio debate a year or two ago. I can’t find a link now, but believe me, it was one for the ages.

    Dr Myers apparently thought so too – see http://scienceblogs.com/pharyn.....r_what.php for his recollection of the “debate,” wherein Dr. Simmons showed a general lack of scholarship and professed ignorance of well-known intermediates in whale evolution.

  6. 7

    Well, Jerry, additional information on whale evolution is but a click away.

  7. Jerry, Dawkins and all of them predict point mutations by and large brought us from rocks to rock stars. So Dawkins is going to need to pull a million rabbits to be convincing. He knows this of course.

    Someone posted a great quote from Gould the other day, I can’t remember where.

    But basically, the breadth of our understanding of the picture that the fossil record has given us up till now;
    even if 90% of the fossil types are yet to be discovered, rules out any headway ever being made on missing links.

    IE. We already know that we’ll never get a neodarwin validation from the fossil record because so much has already been discovered from different strata and it amounts to no real linkage.
    I don’t know what to think of the fossil record myself.

  8. Paul Burnett,

    Well, I think we can excuse Simmons for not having the names of all those whale “ancestors” at his fingertips—he’s a doctor, not a paleontologist. Furthermore, no one is surprised that PZ posted an entirely self-serving account of the episode in his blog. What does he do when he gets creamed in a debate? He pretends it just didn’t happen.

  9. A few million years, a few million individuals, and a few million nucleotides being zapped by cosmic rays to produce errors in the genetic code, and voilà: a hippo turns into a whale.

    How could any rational person take this transparent fantasy seriously?

    Are guys like Dawkins completely out of contact with reality and modern science? Of course they are, or they wouldn’t make such preposterous, mathematically absurd, empirically-negated claims (as Behe elucidated in The Edge).

    This is not hard. Throwing trash into computer programs does not make them better, no matter how much time is allowed. Living systems are fundamentally based on information and information-processing machinery.

    The Darwnian mechanism is a quaint, 19th-century throwback to an era gone by, at a time when nothing substantial was known about living systems. Its defense is based not on science, logic, or evidence, but on an attempt to defend an archaic and nihilistic worldview.

  10. “Well, Jerry, additional information on whale evolution is but a click away.”

    You should write Sir Richard and help him out on this or write to the University of Nebraska and tell them how bad their video is and you have the information to make their analysis a little bit credible. As it is now, it looks like Dawkins is a mole for ID.

  11. “a hippo turns into a whale.”

    Gil, to be fair to them, they are not saying a hippo turned into a whale but some cloven forrest animal turned into both a hippo and a whale sort of like some type of unknown ape turned into both a chimp and a human.

    There must be a water gene somewhere in both the hippo and the whale.

  12. You know what I don’t see? Maybe I’m just not looking, but I’d like to see some math go into how many mutations are needed to go from the first step beyond abiogenesis to humans. And contrast this to the known time frame per the fossil record. Is not enough data known about mutations to do this? Seems like such an easy way to expose neodarwinism. Even if a lot of approximation is needed, it seems like something worthwhile.

    Just take out harmonious mutations being needed, entropy, and IC structures and focus on amount of mutations based on the overwhelmingly most common mutation we observe today, which is single nucleotide. Or whatever kind gives favors darwinian evolution best.

    I saw a youtube vid by an arab biology student one time which I’m having trouble finding, but he says that all the mutations on earth up till now don’t account for the amount needed for a single cell formation. I don’t know if he’s correct or not but he sure sounded smart.

  13. Nobel Laureate Christian de Duve has called for “a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.” DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life. Inanimate nature provides us with a variety of mixtures of small molecules, whose behavior is governed by scientific laws, rather than by human intervention.

    He also talks about a subject inextricably tied to theory of evolution if you’re a believer in the science of materialism – abiogenesis. You can not say abiogenesis “has nothing to do with theory of evolution” if you are a materialist, because they would both then be sub-branches of the science of materialism. (Which would be the science of the evolution of matter with the caveat that thought and/or information isn’t causative in the slightest way).

    “The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.”

  14. Well just whati was crtitcizing on the other post… transitionals.

    Ok first of all remember if Dawkin’s had a better example of transitionals he would be displaying it. This is their smoking gun but there are two big problems with the wale transitions.

    First this does nothign to support Darwin’s tree of life hypothsis. The tree of life shows how simple things starting off in the water turn into more complex things on the the land. Ironic that the one smoking gun for evolution would infact be in a sense a “devolution” from a large land dwelling creature- which lost functions like legss for walking and teeth- and transformed into a sea living creature. Reverse evolution- and although new adaptations have clearly been devolved or evolved here- the overall complexity has remained very much consistent in this example. There has been loss of function and new functions have arisen. But more interestingly overall the body plan has remained very much the same- thus the evolutionary changes are more minimal than Darwinists lead us to think.

  15. Dawkins should be in comedy.
    He’s good at telling fanciful stories but terrible at anything close to thinking clearly.

  16. Lamark,
    Here are a few quotes from Gould on the stasis of the fossil record that I think you were referring to:

    The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists –Gould

    The fossil record may, after all, be 99 percent imperfect, but if you can, nonetheless, sample a species at a large number of horizons well spread over several million years, and if these samples record no net change, with beginning and end points substantially the same, and with only mild and errant fluctuation among the numerous collections in between, then a conclusion of stasis rests on the *presence* of data, not on absence! — Gould

    http://www.blavatsky.net/newsl.....record.htm

    Whales Blowing Bubble Rings
    http://www.youtube.com/watch?v=eXqjMvGcrns

    Here is an old UD post on the subject from someone whose handle escapes me right now:

    The hypothetical example of the evolution of whales supposedly took place over approximately the last 50 million years. In about 50 million years a hippopotamus-like animal supposedly transformed into creatures incredibly well adapted to life in the sea such as dolphins and whales. The body systems of these creatures have marvelously engineered sonar systems, adaptations for deep diving, fast swimming, underwater birth, etc. etc. These systems would require scores of books to describe the engineering designs in the exhaustive detail required, and more scores of books to describe the growth development schemes for these systems. In the dolphin evolution example, the biological sonar system is just one of many different systems that had to be elaborated simultaneously by selection from random variation. These are just some of them, for just the sonar system: – Sound signal emitter to produce an optimal very short broadband pulse – Hearing mechanism, middle ear, cochlea, adaptations for aquatic life – Hearing perception acuity and frequency coverage matching echoes received from produced sounds – Computation of distance and direction from echo delay and phase characteristics – Neural pattern recognition and processing including ability to extract features and classify the extracted features from modulations and amplitude of returned echoes – Feedback processes to optimize the emitted signal and the return reception process for particular types of targets and distances. – Time variable receiver gain to greatly reduce hearing sensitivity during signal emission – Emitter power gain control to reduce power as range decreases – Emitted ‘click’ rate control to increase rate as range shortens – Accompanying behavioral modifications to accommodate this in hunting, reproduction, etc. At the same time the same sort of processes had to be going on in a coordinated way to develop the other amazing features like underwater birth, deep diving adaptations, food gathering structures and behavioral strategies, etc. etc. The genetic coding for just one of these organic machinelike systems must contain at least the sort of amount of information as a design manual for a Boeing 747. The real problem of the entire animal is orders of magnitude greater, where an analogy would be trying to convert and modify an M1 battle tank into a submarine. The multitude of separate coding elements required by the organism to build and operate each evolving organ system must have changed in a coordinated parallel fashion with the others, where the phenotypical reproductive advantage of any one genetic change is partly a function of vast numbers of other genetic coding elements that are themselves changing at different rates. Any single gene modification would often require another or multiple particular different genetic modifications to happen simultaneously for there to be an adaptive advantage in the right direction, or even to avoid death. To put it mildly, The numbers just don’t work for this as a Random Variation + Natural Selection process. Romans 1:20 For the invisible things of him since the creation of the world are clearly seen, being perceived through the things that are made, ‘even’ his everlasting power and divinity; that they may be without excuse:

  17. As well, This scenario of cloven hoofed animals evolving to whales clearly highlights the alchemical methodology Darwinists have always used in trying to make their case, for we have no evidence from foundational molecular biology or foundational physics that anything like this can happen in 50 million years, or can even happen in the entire age of the universe for that matter:

    The malaria parasite, due to its comparatively enormous population size, has in 1 year more mutation/duplication/selection events than all mammal lineages have had in the entire +100 million years they have been in the fossil record. Moreover, since single cell organisms and viruses replicate, and mutate/duplicate, far more quickly than multi-cellular life-forms can, scientists can do experiments on single celled organisms and viruses to see what we can actually expect to happen over millions of years for mammals with far smaller population sizes.

    Malaria and AIDS are among the largest real world tests that can be performed to see if evolutionary presumptions are true.

    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.” Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    http://www.evolutionnews.org/2....._edge.html

    A review of The Edge of Evolution: The Search for the Limits of Darwinism by Michael J. Behe
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    Thermodynamic Argument Against Evolution – Thomas Kindell – video
    Part 1 http://www.youtube.com/watch?v=nI1RiTOQ4do
    Part 2 http://www.youtube.com/watch?v=PgzWMccWOe8
    Part 3 http://www.youtube.com/watch?v=JQBjguaBueE

    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.

  18. Lamarck

    You wrote:

    Maybe I’m just not looking, but I’d like to see some math go into how many mutations are needed to go from the first step beyond abiogenesis to humans. And contrast this to the known time frame per the fossil record. Is not enough data known about mutations to do this?

    Let me state at the outset that I’m not a biologist or even a scientist, but I’ll have a go anyway. Here’s the formula I’ll use:

    Number of changes
    (i.e. “mutations” or other events)
    =
    Number of generations leading up to you
    x
    average number of events per nucleotide per generation
    x
    average number of nucleotides in the organisms that were your ancestor.

    (Yes, I’m aware that there are many kinds of changes in organisms – Professor Allen NacNeill has catalogued 47. I’m using the word “mutation” as a cover-all term.)

    Next, I’ll make the following simplifying assumptions:

    1. Life has been around for 4.5 billion years.

    2. For the first 4 billion years, the average generation time of the super-successful lineage leading up to you was equivalent to that of modern bacteria, during the exponential phase of their growth – i.e the phase during which bacterial cells grow most rapidly. According to Teresa Tiel, of the Department of Biology, University of Missouri, St. Louis, the fastest growing bacteria have generation times of 15-20 minutes under optimum growing conditions (see http://www.umsl.edu/~microbes/.....cteria.pdf ).

    3. For the last 500 million years, the average generation time was the same as that of fish or frogs (say, one year), but the mutation rate per generation was the same as for modern humans (I’m being generous here).

    4. Because your ancestors were such a smart, reproductively successful bunch compared with the other lineages, most of whom fell by the wayside, let’s say that during the first 4 billion years, their mutation rate was 1,000 times the normal rate.

    Now, according to Professor Lawrence Moran (Department of Biochemistry, University of Toronto), the average mutation rate for bacteria, worms, mice and humans alike is about 10^-10 per nucleotide per replication. E. coli bacteria have 4.2 × 10^6 base pairs. “Every time a bacterium divides this amount of DNA has to be replicated; that’s 8,400,000 nucleotides (8.4 × 10^6)”
    ( http://sandwalk.blogspot.com/2.....rates.html ). Let’s say 10^7 for round figures. If the mutation rate in your unicellular ancestors was 1,000 times the normal rate, then that’s 10^3 X 10^-10, or 10^-7 per nucleotide per generation. Thus we can expect one mutation per generation.

    Now, if one generation equals 15 minutes (one quarter of an hour), then the number of generations from the first organism up to 500 million years ago was (4 x 10^9) years x 365 days/year x 24 hours/day x 4 quarters/hour = approx. 1.4 x 10^14. Since there’s one mutation per generation on our optimistic assumptions, that’s 1.4 x 10^14 mutations up to the first fish, 500 million years ago, on a very, very generous estimate. Let’s be extremely generous and assume that all of these mutations were beneficial, and not neutral or deleterious. Then we have 1.4 x 10^14 beneficial mutations.

    Now for the mutation rate in the line leading from the first ancestral fish (500 million years ago) up to modern humans. Professor Larry Moran quotes Douglas Futuyma (2005) as saying that “Each of us was born with at least 350 new mutations that make our DNA different from that of our parents.” Let’s say 1,000 for the sake of generosity. Although the human generation time is about 25 years, let’s very generously assume the same number of mutations per generation in each generation leading from the ancestral fish 500 million years ago up to you, and let’s also assume a mean generation length of just one year, as fish reproduce faster than humans do. That’s 500 million x 1,000 mutations per generation, or 5 x 10^11, which is negligible when compared to 1.4 x 10^14, so the total number of steps could not be more than 1.4 x 10^14.

    More realistically, E. coli usually divide about once every 24 hours (100 times slower than the rate I postulated), and probably the mutation rate was 10, rather than 1,000 times higher than the general background rate for the lineage leading up to you. Also, let’s say that only 1% of mutations are beneficial. Then that brings us down by a factor of 10^2 x (10^3 / 10) x 100, or 10^6. Thus the number of beneficial changes up to the first fish might have been only 1.4 x 10^8.

    If only 1% of mutations are beneficial, then the number of beneficial mutations from ancestral fish to you could be no more than (5 x 10^11) / 10^2, or 5 * 10^9, which interestingly is higher than the more realistic figure of 1.4 x 10^8 for the number of mutations up to the first fish.

    The interesting result of all this is that we don’t know whether more mutations were required to get us from primordial cell to fish or from fish to human. But realistically, the number of transformations (or changes) from the first cell to you is likely to have been no more than about 5 billion.

    Is that enough for Darwin’s mechanisms to do their work? Personally, I doubt it.

  19. Mr vjtorley,

    Thank you for the quick calculation. I would make two points.

    1 – population size in general would have a great effect on the number of changes explored per time step

    2 – 5 billion beneficial mutations is larger than the size of the entire human genome, and certainly larger than the number of differences between our genome and E. coli’s genome. That says to me that ther are plenty of resources for the Darwinian mechanism to work.

    You could alternaively work backwards from the human genome of 3 billion bases, say a beneficial mutation was necessary to create every one of them (assuming there is no junk DNA) and ask at what rate must beneficial mutations occur. 4.5 billion years / 3 billion required beneficial mutations = 1.5 years per beneficial mutation. Can an ocean full of proto E. coli come up with one beneficial mutation every year and a half, dividing every hour or every day? I would take those odds!

    I realize all these calculations are crude, but this does show that Deep Time is Darwin’s friend.

  20. Mr Jerry,

    There must be a water gene somewhere in both the hippo and the whale.

    Their ancestor was a Picses! ;)

  21. Nakashima-san:

    The big problem is that his would require a continental pattern of functionality, i.e spanning the configuration space with a rather implausible fitness landscape. Think about noise and the rather precise statements in programs, thus what would happen by overwhelming probability if random bits in programs were to cumulatively vary.]

    GEM of TKI

  22. “Their ancestor was a Picses!”

    That explains why we take showers.

  23. KF:

    Why do you assume that a fitness landscape that makes evolution along certain trajectories possible must be implausible?

    Applying ‘noise’ to a computer program is very different than allowing a genome to vary. You need to demonstrate why your argument from analogy is valid in this context. Does the analogy still work when discussing languages like Lisp?

    what would happen by overwhelming probability if random bits in programs were to cumulatively vary.

    Without any selection the program would stop doing what it was written to do and end up doing something else. With selection, well if the noise were applied within a framework like GP, then the program would also change but now that change would be, on average, positive with respect to some measure of function.

  24. KF-san,

    Yes, but that was Mr vjtorley’s assumption, that you could string together 5 billion beneficial mutations cumulatively. Nilsson and Pelger make the same assumption in their work.

    I think that common descent – the fossil and genetic evidence – does argue for what you have termed continental patterns of functionality.

  25. Do genomes have the plasticity needed? NO!

    there are many ancient bacterium recovered and “revived” from salt crystals and amber crystals which have been compared to their living descendants of today. Some bacterium spores, in salt crystals, dating back as far as 250 million years have been revived, had their DNA sequenced, and compared to their offspring of today (Vreeland RH, 2000 Nature). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence.

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”
    Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart, (thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

    a small calculation for the Chimp/Human scenario, using reasonable estimates for detrimental mutation rates, yields:

    Man has over 3 billion base pairs of DNA code. Even if it were true that body plans were encoded directly by the DNA code and that there was only 1% difference between the DNA of chimps and humans, that would still be 30 million base pairs of DNA difference. It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between monkeys and man, or monkeys and anything else for that matter. Since, it is now a clearly established fact at least 999,999 in 1,000,000 of any mutations to the DNA code will be slightly detrimental, harmful and/or fatal for the organism, then it is also an obvious fact there is at least a 999,999^30,000,000 to 1 chance that any monkey will fail to reach man by evolutionary processes. The monkey will hit a dead end of slightly detrimental, harmful and/or fatal mutations which will kill him, or slowly mutilate him before killing him. The poor monkey barely even gets out of the hypothetical evolutionary starting gate before he is crushed by blind chance. This would still be true even if the entire universe were populated with nothing but monkeys to begin with. This number (999,999^30,000,000 to 1), is fantastically impossible for any hypothetical beneficial mutation to ever overcome.
    Some materialists say symbiotic gene transfer, cross-breeding (yes, believe it or not, some materialists have even suggested cross-breeding with monkeys as a solution to the ‘information problem’), gene duplication and multiplication of chromosomes, alternative splicing etc .. etc .. are the reasons for the changes in DNA between humans and apes. Materialists postulate numerous unfounded hypothesis with the utmost confidence without ever a rigid basis in science to support them, and then many times, they will then relentlessly ridicule anyone as an ignoramus who dares question their unfounded mechanisms. Incredibly all this obfuscation and ridicule is done in spite of many solid evidences to the contrary for the consistent detrimental nature of mutations. Indeed, even if a truly beneficial random mutation/variation event to the DNA ever did occur it would be of absolutely no use for the mutation would be swallowed in the vast ocean of slightly detrimental mutations which are far below the culling power of natural selection to remove from a genome.

    Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Kondrashov A.S.
    http://www.ingentaconnect.com/.....4/art00167

    The Frailty of the Darwinian Hypothesis
    “The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,”
    http://www.evolutionnews.org/2......html#more

    High genomic deleterious mutation rates in hominids
    Excerpt: Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically (unusually) low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.
    http://www.nature.com/nature/j.....344a0.html

    etc…etc…etc…

  26. kairosfocus (22),

    “Think about noise and the rather precise statements in programs, thus what would happen by overwhelming probability if random bits in programs were to cumulatively vary.]”

    This is one of those areas where the software analogy breaks down. The genome isn’t precise, and we know that random mutations do crop up that don’t change the function of the organism at all. Try that with a single bit of a computer program and you’re likely to crash.

    The comparison of biology with engineering and/ or software is interesting as an analogy, but like all analogies it breaks down.

  27. Ah, BillB:

    I assume you have seen my response in the other thread. Pardon, again, my accidental use of the same abbreviation with two distinct meanings. [Us dyslexics tend to use abbreviations heavily . . . ]

    Now, on topic: it is rather convenient to dismiss a key characteristic of program-type digital strings ( = language-coded algorithms plus associated data structures) isn’t it: namely, as a rule they are quite vulnerable to perturbation i.e they come in islands of function in which some degree of error detection and correction can save function, but move much away and the function vanishes.

    Indeed, so much so, that no serious program is ever right the first time, as the programmers know all too well to their cost.

    That’s why there has been a migration from machine code [very efficient, if you can get it to work; which is hard as it is so counter-intuitive . . . as well I recall: FCBC 12FD . . . moving up to hex code (which is a simplification from bit code!) ] to assembly then higher level languages, only to see bugs following along. And, so, there is a whole field of praxis called debugging. Wiki, as just linked, begins:

    Debugging is a methodical process of finding and reducing the number of bugs, or defects, in a computer program or a piece of electronic hardware thus making it behave as expected. Debugging tends to be harder when various subsystems are tightly coupled, as changes in one may cause bugs to emerge in another.

    Tightly coupled?

    Well, that aptly describes the step by step processes not only in the cell but in the process of embryonic development. And in turn that means — starting from first life — we have to credibly get to the irreducibly complex networks of interacting systems that are deeply embedded at many levels in body plans.

    And so, islands of function are a very natural expectation and observation: how many genes gone bad does it take to get a fatal defect, starting with the very well founded fear of cancer due to radiation damage?

    GEM of TKI

    PS: This ARN page on an interview with Schutzemnberger on functional complexity — looks like this pushes my FSCI timeline back to Wistar 1966 — makes interesting related reading. Have fun.

  28. Mr Nakashima,

    Thank you for your post. I take your point about population size; however, in my example, I was simply counting the number of beneficial mutations that would have occurred along one particular lineage from a primordial proto-cell to a particular human being.

    It seems that our intuitions clash, regarding the possibility of getting from a proto-cell to a human being in 5 billion steps. You make a very good point when you remark that “5 billion beneficial mutations is larger than the size of the entire human genome, and certainly larger than the number of differences between our genome and E. coli’s genome” – although as kairosfocus astutely observed, you need to assume the existence of an improbably smooth fitness landscape, which allows the original bacterial proto-cell to transform itself into a human being in incremental steps.

    I suppose that an evolutionist might reply that although the fitness landscape is very nice from a human perspective, it is not so nice from the viewpoint of a hypothetical centaur, as there is no smooth series of incremental changes leading from proto-cells to centaurs. (If there were, presumably centaurs would have appeared at some time in the past.) An evolutionist might then argue that there are probably zillions of hypothetical intelligent life-forms which have never come into existence because they could never have evolved in a stepwise fashion from a primordial proto-cell – we humans being one of the very few intelligent life forms that were somehow able to do so. Still, to suppose that even one intelligent life-form could evolve in a step-wise fashion from a proto-cell is a very big “if” indeed. (Putting it another way: why isn’t Earth one of those unfortunate planets where evolution never got beyond the stromatolite stage?)

    Even if we grant your “if,” I would argue that 5 billion steps from “goo to you” will suffice only if we the universe we happen to live in is a very nice, “evolution-friendly” universe, where the laws of nature are rigged in humanity’s favor.

    Here’s why. From an engineering perspective, when you are transforming one kind of organism into another (say, a forest-dwelling four-footed animal into a whale), you have to make a large number of more or less parallel changes to the body’s internal organs and also to the systems needed to maintain life. (I use the term “more or less parallel” because I’m not trying to argue that all these changes would have to be perfectly synchronized. Still, they’d have to be fairly well-synchronized.) Not being a biologist, I have no idea how many system changes you’d need, and I wouldn’t even know where to look for information like that, but I’d guess that maybe 10^2 or 10^3 different kinds of more or less parallel structural and physiological changes would have needed to occur in the ancestor of the whale, for instance, judging from what Berlinski said in his video on whale evolution.

    At the anatomical, physiological and/or biochemical level, the notion that just a few billion changes should suffice to transform a bacterial proto-cell into Homo sapiens strikes me as unlikely. There are so many different structures and systems that would need to be created and made to work in harmony with other systems, that the number of transformations over 4.5 billion years would surely be orders of magnitude higher than 5 billion.

    Now, you might reply that evolution takes place at the level of the gene, not at the level of the anatomical organ or biochemical system. And you would be right. If you’re thinking purely in terms of base pair changes, a few billion alterations should certainly be enough to get us from a proto-cell to a human being.

    However, if the number of required anatomical, physiological and biochemical changes is several orders of magnitude higher (say, 10^6 times higher) than 5 billion, then we must suppose that on average, a single base pair change resulted in a very large number of different effects (say 10^6, or one million) at the anatomical, physiological and biochemical levels – instead of just one change or a few changes, as we might expect. Now, if that has been happening throughout the entire history of life, then the laws of nature which are responsible for our appearance of Earth must indeed be rigged in our favor. Evolution itself becomes a miracle; the universe must be “fine-tuned” for it to happen.

  29. In the second last sentence of my preceding post (#28), “our appearance of Earth” should read “our appearance on Earth.” Sorry.

  30. KF:
    1 – I’m dyslexic so I frown on it being used as an excuse for poor communication.

    2 – I’ve virtually completed a PhD in computer science so I know what debugging is.

    3 – My understanding of genetics is that whilst some genetic change can bring you close to catastrophic failure, others introduce changes in morphology, some subtle, some sudden. This (the evidence) suggests continental patterns of functionality. Genes and development are very robust to perturbation and very unlike some computer systems.

    4 – Your cut and paste does not aptly describe biological systems, it describes computational systems. At best it is weakly analogous to biological systems but not nearly strong enough to make the inferences that you like to make. You need to show that biology is as brittle as these other systems before you can make claims about the topology of function landscapes.

  31. Hi borne,

    Re: ancient bacteria being very similar to modern bacteria. A question to consider is this: if we can revive ancient bacteria, recovered from old salt deposits, then the process of erosion could also be continually releasing older bacterial strains onto the surface of the earth, could it not? What about the actions of man? Think how much mined salt is deposited on roads every winter. Both proceses could significantly (and continually) reintroduce ancient bacteria onto the surface. Both of these sources makes me wonder if we should expect modern bacteria to be as radically different from ancient bacteria as we might think.

  32. Dave,
    For whatever reason there is zero change in 250 million years,,,yet you have danced around this glaring deficit as if you have somehow defended the farce called evolutionary science. Yet there is much more evidence than just the ancient bacteria to give us good reason to believe Genomes have very limited plasticity:

    To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained to random mutations by poly-functionality, I will use a puzzle:

    If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome of say 500 interdependent genes, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their falsified genetic reductionism scenario I might add, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Which is translated ;
    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

    This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation.

    This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations.

    The puzzle I listed is only poly-functional to 4 elements/25 letters of interdependent complexity, the minimum genome is poly-constrained to approximately 500 elements (genes) at minimum approximation of polyfunctionality. For Darwinist to continue to believe in random mutations to generate the staggering level of complexity we find in life is absurd in the highest order!

  33. born,

    if the bacterial population on the surface keeps getting continually infused by ancient bacteria, and has been for millions of years, what exactly are ‘modern’ bacteria? The logical answer is, there is no ‘modern’ bacteria that is a descendant of a long evolutionary lineage. And how different should we expect those on the surface now as compared to those found in the most ancient deposits? Considering that the ancient strains are continually infusing the surface, and have been doing so for millions of years, “not much”.

  34. Mr Vjtorley,

    Thank you for your response.

    With regard to the KF-san’s point about the landscape, it is not that it is smooth, just that it have a continuously positive slope. Even this is not strictly true in real life. For example, a gene that was only slightly deleterious might persist in a population long enough to meet up with another gene, and in that new combination it is no longer deleterious but beneficial.

    As you say, some changes must come quickly together to be useful. The devil is in the details of that kind of argument. Again details of population size, selection pressures and whether the population is sexual or asexual play a big role in whether these kind of changes are plausible or implausible. But even 1,000 changes in 100,000 years is quick on one scale, and a change every 100 years from another, more human, perspective.

    I certainly feel priveleged that humans are here and centaurs are not! ;) I think the natural progression of the fine tuning/priveleged planet position is that the universe is set up so that life is easy to form, and Earth is set up so that life can easily evolve – to humans, if you agree with Simon Conway Morris. In this view, evolution is as inevitable a consequence of the laws of physics and chemistry as nuclear fusion, and both have been used to create a place for humanity to figure out their relation to God. Along the way, a lot of neutrinos got formed, a lot of beetle species got formed, but it is all for our benefit.

    However, if the number of required anatomical, physiological and biochemical changes is several orders of magnitude higher (say, 10^6 times higher) than 5 billion, then we must suppose that on average, a single base pair change resulted in a very large number of different effects (say 10^6, or one million) at the anatomical, physiological and biochemical levels – instead of just one change or a few changes, as we might expect.

    Your previous post was pretty well grounded in numbers (round numbers, yes, I agree) most people would agree with, but here you’ve speculated beyond that. The genetic continuity between us and bacteria is strong. The common use of HOX genes and developmental regulators like FOXP2 across animals is the same argument at a different level of organization. We only have a few hundred cell types in our bodies. Your agrument would require genes that have thousands of simulataneous different effects to every cell type. I’ve never heard of even one such superpowerful gene being found, much less an argument that all genes are that powerful. I think you should retire this speculation as not supported by the facts.

    Thank you for such a rich and on-topic conversation!

  35. Mr Wisker,

    You’d also expect the bacteria that get trapped in salt deposits to be pertty specialised for living in high salt content water. That would be a niche that would punish change pretty harshly. I think a lot of extremophiles have strongly conserved genomes.

    (Alternatively, the environment could also enforce a convergence on a few solutions to the salinity problem.)

  36. Mr Jerry,

    As soon as one points outs how ridiculous it is, someone will pull out a couple more that will be better.

    I think a lot of the good sites for fossil whales are in the middle of a war zone right now in Pakistan. We might have to wait a while before they find more examples to fill out the sequence. :(

  37. Dave,
    Your conjecture is a lame excuse for stasis, not a concise explanation for why we have morphological and molecular stasis for as far back as we find bacteria in the fossil record as well as in salt mines.
    I laid out a brief outline of the “poly-constrained” reason for why we should expect extremely limited plasticity in a poly-functional genome, and this is ignored by you…Blind faith driving science once again! Far be it from me to argue with such a religious fanatic as yourself as you show yourself to be on this blog. Believe as you want I will waste my time no longer.

  38. BillB,

    The deal with the anology between computer software and biological specified complexity is simple. If you have undirected changes the “form”, as you put it, will change. The reality here is that the 2nd law of thermodynamics does not promote and upward climb in complexity and certainly not in specificity. This is why we don’t see great increases in useful specificity and complexity in software when it contracts a virus or develops errors. In fact we throw out the computer or take it to get fixed when this happens- and yes it requires an intelligence in the computer engineer to fix the damaged program. This raises the question of the origin of beneficial error protection functions within the cell- but hold on-

    The reason why software and genetics are a good analogy is because they are both beholden to unguided or non-purposive change, and they both exist in a physical dimension where the 2nd law rules.

    Most importantly though as Steve Meyer points out in his new book- the origin of the first life is even more perplexing here because you have no base system to appeal to- in other words you can no longer say that the genome is more receptive to unguided variants than a computer program because the genome does not yet exist. There is nothing to naturally select either- so all the functions with the cell must come from an undirected fitness landscape and material changes.

    Obviously when you are dealing with the origin of the genome itself- you run into the biggest gulf of improbability and unguided organization that needs to be bridged. Why should complexity increase? And more importantly what are the odds that it will in a specified and functional way? How this can be explained without intelligent guidance is the fundamental lacuna- and the same one we face when extrapolating the efficiency of the unguided Darwinian mechanism to all of the novel body plans presupposed in the tree of life and required for that model to preserve continuity and remain rational.

  39. I’m pretty sure most of the arguments made here can be summarized as “but look at all the gaps that remain in the story of all evolution ever”. When it comes to these whales, I believe there are only four arguments ID has left to choose from:

    1. None of the changes, even between two seemingly very similar fossils, could have come about as a result of genetic mutation. (For example, maybe genes actually don’t code for the size and shape of skulls.)

    2 (my personal favorite, I just think it’s cool to think about). None of these organisms could have survived in their environments at the time; naturalistic science is at an utter loss explaining what sort of niche they could find. Clearly, some sort of non-natural phenomenon was responsible for such creatures not drowning or otherwise suffering the consequences of being stuck between the worlds of land and sea. (Perhaps the same phenomenon provides for the survival of present-day cetaceans as well.)

    3. Whale evolution is not and never has been a problem for ID, which is only concerned with the irreducible complexity of “basic” but complex biological structures such as the BF, and the question of the origin of information in the first place.

    4. The fossils are simply hoaxes.

  40. bornagain,

    There is nothing to stop erosion from freeing bacterial spores on a continual basis. That, plus the rampant HGT that occurs between bacteria, tells us not to expect much difference betweeen surface bacterial strains and these ancient ones. Sanford’s current project sounds like it suffers from some flawed assumptions. Not a good start.

  41. 42

    I knew I recognized that room. Anyway, I used to go to that museum when I was a kid. In the basement they had several large sculpture displays of artist’s renditions of our primate ancestors. Yes, one of them was Nebraska Man. :D

    Needless to say, those displays are all gone now.

  42. Nebraska Man? The heart and soul of primate evolutionary theory, second only to Piltdown? I envy you, tragic mishap… :)

  43. tragic,
    I assume you went to this museum before nebraska man was debunked in 1927?

    http://www.sciencemag.org/cgi/.....6/1720/579

  44. BillB:

    As a computer scientist, you will appreciate the points — and the parallel drawn between computational systems and DNA-based biological ones — made by Mr Schutzenberger [inter alia late of the well-known Wistar consultation of 1966], on the reason functional complexity — his term — will appear in phase spaces as islands, here.

    An illustrative side-light on this on the bio side can be had from the overwhelmingly dominant pattern of the fossil record: sudden appearance, stasis of general body form, disappearance or continuation into the current world. that is, islands of function, on the principle that form follows function.

    GEM of TKI

    PS: Challenges come in degrees, as do circumstances. I pled guilty with X-plan’n, not for X-culp’n.

    PPS: We can now definitely trace the roots of that often derided descriptive term FSCI, to 1966.

  45. Ham. Do you see yonder cloud (skull) that ’s almost in shape of a camel (cetus)?
    Pol. By the mass, and ’t is like a camel (cetus), indeed.
    Ham. Methinks it is like a weasel.
    Pol. It is backed like a weasel.
    Ham. Or like a whale?
    Pol. Very like a whale.
    ATTRIBUTION: Hamlet. Act iii. Sc. 2.

    Willy was way ahead of Richard.

  46. Frost122585:
    I dont really see your point given that:
    1 – the 2nd Law of Thermodynamics does not prohibit increases in complexity or percieved functionality.

    2 – It doesn’t even prohibit the movement of heat from a cooler body to a warmer body, it just requires that work is done (and some heat dissapated) to achieve this.

    3 – Thermal entropy can go down as well as up, its about averages.

    4 – We have this thing called THE SUN!

    5 – You may want to look up ‘Maximum Entropy Production Principle’ – some interesting stuff.

  47. KF:

    I took a look at Mr Schutzenberger’s interview. The interview is from 1996 but even at this date he still seems to be rather behind the times in his understanding of biology and genetics.

    His thinking with regard to the whole idea of function is rather narrow and confused as well. No wonder he found the idea of a few thousand genes assembling an eye to be absurd – his notion of genes seems to centre on them specifying the structure of organs.

    It is my training as a computer scientist that makes me wary of naive comparisons like his.

  48. BillB,

    I have read some of the the material you pointed to. The point about thermodynamics is not whether it totally prohibits increases in complexity- nor whether heat can move and be compiled in one space or another. The question is the likelihood that that complexity will be moved in specific ways which increase functional* complexity. The specified complexity within the cell is so complex that we cant merely attribute it to the sun and the existence of a few proteins and or amino acids. The functional complexity is really quite astounding- and even if you have all the parts locally you still have the problem of assemblage. Thermodynamics 2nd law shows us that systems like these are not likely at all. So the gulf is the difference between the unlikelihood of functional specified complexity coming near and actual complexity of the cell itself.

    This problem does not become easier once we have the cell either- in fact so long as the complexity increases into say higher taxa we have even greater improbable formation to account for.

    I think the fact that the sun is the way it is- also gets into the question of cosmological fine-tuning as well. Often Darwinists will say I am exploiting natural laws to prop up ID- but the existence of the “form” and specified position of the sun in relation to the Earth is not an issue of law but actually another question of directed or undirected design. Newton thought the design of our solar system to be utterly apparent.

    Some quotes that i think hit the point about the problem with a materialistic mechanical reductionist perspective…

    “Any living being possesses an enormous amount of ‘intelligence,’ very much more than is necessary to build the most magnificent of cathedrals. Today, this ‘intelligence’ is called ‘information,’ but it is still the same thing. It is not programmed as in a computer, but rather it is condensed on a molecular scale in the chromosomal DNA or in that of any other organelle in each cell. This ‘intelligence’ is the sine qua non of life. If absent, no living being is imaginable. Where does it come from? This is a problem which concerns both biologists and philosophers and, at present, science seems incapable of solving it.”

    Pierre Grasse,

    “In the face of the universal tendency for order to be lost, the complex organization of the living organism can be maintained only if work – involving the expenditure of energy – is performed to conserve the order. The organism is constantly adjusting, repairing, replacing, and this requires energy. But the preservation of the complex, improbable organization of the living creature needs more than energy for the work. It calls for information or instructions on how the energy should be expended to maintain the improbable organization. The idea of information necessary for the maintenance and, as we shall see, creation of living systems is of great utility in approaching the biological problems of reproduction.”

    George Gaylord Simpson

    Those quotes (pulled from http://www.evoinfo.org) get at the time point which is it is lovely to point to the sun or some other very improbably specified causes to account for how life can be purchased but you still never get away from the question of the origin of form, specificity, functionality and most important information. The bottom line is the theory of ID explains the fundamental cause of how these things came about which is intelligence. The idea of unguided evolution is therefore really not one that matches the evidence- and this has been known and realized for a long time- at least sense the discovery of DNA (which lead its co founder to accept panspermia ID). That is why self organizational theories were pursued for some time but have proven unfruitful. There really is no good reason why or how life could evolve without guidance.

    “The information content of amino acid sequences cannot increase until a genetic code with an adapter function has appeared. Nothing which even vaguely resembles a code exists in the physio-chemical world. One must conclude that no valid scientific explanation of the origin of life exists at present.”

    Hubert Yockey

    So how this conclusion applies to universal common ancestry- it is possible that the intelligent designer designed through and evolutionary process- but if intelligence is something that can manipulate matter on a cosmological level then that calls the entire theory of evolution into question. That is not only are the mechanisms inadequate but the tree of life itself is not required once we accept that intelligence acts on matter but does not reside within it’s boundaries. in other words an evolutionary tree of life is no longer required as matter can be manipulated at will by a cosmological intelligence. The only question then is what are the boundaries of the will of that intelligence?

    The 2nd law is the reality of our existence. The world shows no signs of materialistically necessary guidance. The laws of physics have even been shewn to break down at the subatomic level (uncertaintly principle). Thus, we don’t even know if materialistic necessity exists at all anymore. So why is science so hell bent on ruling out ID and demanding materialsitic and mechanically necessary causal explanations of life and information’s origin even when there are evidences agaist the sufficency of the DE mechanism and infavor of ID? It is abviously agenda driven- that is based on personal biases (some learned some innate). But in science both sides of the coin must be considered and I think the current evidence clearly points to a telelogical agent- especially in light of what we know about the 2nd law. Find me software randomly evolving into some brillaint functional program within it’s enviornment and we can consider macr oevolution- find me a Computer arising in nature from scratch with the loaded information already on it and we can consider origin of the first life via DE pathways.

  49. This Boston Globe article is a bit dated (2000) but it has some gems:

    Challenging Fossil of a Little Fish
    http://www.fredheeren.com/boston.htm

    Excerpts:
    CHENGJIANG, China — The fish-like creature was hardly more than an inch long, but its discovery in the rocks of southern China was a big deal. The 530-million-year-old fossil, dubbed Haikouella, had the barest beginning of a spinal cord, making it the oldest animal ever found whose body shape resembled modern vertebrates.

    In the Nature article announcing his latest findings, Jun-Yuan Chen and his colleagues reported dryly that the ancient fish “will add to the debate on the evolutionary transition from invertebrate to vertebrate.”

    But the new fossils have become nothing less than a challenge to the theory of evolution in the hands of Chen, a professor at the Nanjing Institute of Paleontology and Geology. Chen argues that the emergence of such a sophisticated creature at so early a date shows that modern life forms burst on the scene suddenly, rather than through any gradual process. According to Chen, the conventional forces of evolution can’t account for the speed, the breadth, and one-time nature of “the Cambrian explosion,” a geologic moment more than 500 million years ago when virtually all the major animal groups first appear in the fossil record

    And this beaut:

    The debate over Haikouella casts Western scientists in the unlikely role of defending themselves against charges of ideological blindness from scientists in communist China. Chinese officials argue that the theory of evolution is so politically charged in the West that researchers are reluctant to admit shortcomings for fear of giving comfort to those who believe in a biblical creation.

    “Evolution is facing an extremely harsh challenge,” declared the Communist Party’s Guang Ming Daily last December in describing the fossils in southern China. “In the beginning, Darwinian evolution was a scientific theory …. In fact, evolution eventually changed into a religion.”

    Catch that last line?

    Chen enjoys seeing his fossils get the attention. But to him, the big story is not that he has discovered our earliest traceable ancestor, but that the Cambrian explosion of new body plans is proving to be real, not an illusion produced by an incomplete fossil record.

  50. I just love this quote:

    “Evolution is facing an extremely harsh challenge,” declared the Communist Party’s Guang Ming Daily last December in describing the fossils in southern China. “In the beginning, Darwinian evolution was a scientific theory …. In fact, evolution eventually changed into a religion.”

    Life is strange,,,,LOL

  51. Excerpt from page two:

    What they had actually proved was that Chinese phosphate is fully capable of preserving whatever animals may have lived there in Precambrian times. Because they found sponges and sponge embryos in abundance, researchers are no longer so confident that Precambrian animals were too soft or too small to be preserved.

    “I think this is a major mystery in paleontology,” said Chen. “Before the Cambrian, we should see a number of steps: differentiation of cells, differentiation of tissue, of dorsal and ventral, right and left. But we don’t have strong evidence for any of these.”

    Taiwanese biologist Li was also direct: “No evolution theory can explain these kinds of phenomena.”

  52. Born,

    I like the last quote the best.

    Taiwanese biologist Li was also direct: “No evolution theory can explain these kinds of phenomena.”

    It is really funny to me how explicit it is.

  53. Vjtorley,
    Thanks very much for the calculation. That’s good to know it might be about five billion steps, of significant and harmonious mutations.

  54. Frost,, Yes It is VERY explicit ,,,as well this following quote is VERY explicit, and from the leading paleontologists in the world, and conforms exactly to what is predicted from a genetic entropy perspective:

    In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution.

    In the most published diagram in the history of evolutionary biology, Darwin illustrated what became the standard view of how new taxa, or animal categories, evolve. Beginning with small variations, evolving animals diverge farther from the original ancestor, eventually becoming new species, then new genera, new families, and the divergence continues until the highest taxa are reached, which are separated from one another by the greatest differences.

    But the fossil record shows that story is not true, according to Chen. The differences appear dramatically in the early days, instead of coming at the top.

  55. BA77, thanks, the second Gould quote is the one I was paraphrasing.

    I didn’t fully understand the polyconstrained genome argument. Is this for all genes or specifically regarding protein coding? What has a limit to it’s plasticity exactly. You say interdependent genes, I can’t tell if this is a subset of genes or all genes period.

    I don’t understand because we do see beneficial mutations albeit with info loss.

  56. Born,

    It is really interesting to see a scientist like Chen make such direct and explicit remarks. I have always said that i do not rule out the UCA picture of life but only remian skeptical- but in the case of Chen I would love to read some of his thoughts and work on this topic. Do you know of any resources I can read by him?

  57. bornagain77, lamarck, others: Can I interest you in one of my four doors (listed in my earlier comment), or any fifth door of your choosing?

    DG: That’s an interesting insinuation there, that the whale-fossil similarities are largely a product of our subconscious preconceptions. Huh.

  58. Lenoxus where have you been? None of the 4 doors you list do not seem to have anyhtign to do with ID (except for the possible connection to IC)- no offfense.

    First of all virtually any organism can evolve into any other organism via mutations and the like given enough imagination time and a well designed fitness landscape- but it is the improbability of those positive necessary mutations occurring that ID challenges. This is the question of did it happen by chance? That is, unguided, or was it the result of purposive design? SO no recourse to IC is needed.

    Secondly no one is calling them hoaxes and ID does not need to either.

    As for the idea of these creature not being able to live in their environment – I have no idea where that comes from and cant see how it relates to ID.

    Now as far as an objection to them possibly being transitional fossils that strongly support the universal common ancestry view of history there are two problems. First, these two species even though different are not that far apart. In other words the skulls remain very much alike and there is as much loss of function (teeth and legs) as there is gain in positive function (blow holes, swimming adaptions etc) – So the simple to complex claim of evolution is not clearly elucidated by this example.

    Now the second problem is that the tree of life is one where you start off in the oceans with water dwelling creatures and eventually more to the land to complex land dwelling creatures. The Whale example does not show this. This does not mean that there is not real evolution going on here but it does mean that this could be better case for “devolution”- which is an interesting problem here. I find it intriguing that the biggest example of UCA runs counter to the general trend of the tree of life. It just seems like another mysterious and improbable detail. And some will jump the gun and say it is not mysterious because the fossils of whales are so large that they just happen to be one of the ones we most easily find. Well that misses the point of “why should the largest fossils we find be of land dwelling creatures evolving/devolving into the oceans?”
    Either way it seems to run against the tree.

  59. Lenoxus, I’d like to answer it, maybe tomorrow I’m too tired for organized thought.

  60. 61

    In the basement they had several large sculpture displays of artist’s renditions of our primate ancestors. Yes, one of them was Nebraska Man.

    Maybe they were copies of the sculptures made by HF Osborn and McGregor (both members of the American Eugenics Society.) Pictures of those sculptures appear in countless old books and encyclopedia entries. They were pure fantasy, complete frauds based on absolutely nothing but imagination. Piltdown Man was among them.

    There is a plate photo of some of the Osborn-McGregor sculptures in the book The Direction of Human Evolution by AAAS president Edwin Conklin. Click here and scroll down to get the book.

  61. Frost,
    Here is a paper by Chen that just came out this year:

    2009: Chen Jun-Yuan
    The sudden appearance of diverse animal body plans during the Cambrian explosion.
    The International journal of developmental biology 2009;53(5-6):733-51.
    Abstract:
    Beautifully preserved organisms from the Lower Cambrian Maotianshan Shale in central Yunnan, southern China, document the sudden appearance of diverse metazoan body plans at phylum or subphylum levels, which were either short-lived or have continued to the present day. These 530 million year old fossil representatives of living animal groups provide us with unique insight into the foundations of living animal groups at their evolutionary roots. Among these diverse animal groups, many are conservative, changing very little since the Early Cambrian. Others, especially Panarthropoda (superphylum), however, evolved rapidly, with origination of novel body plans representing different evolutionary stages one after another in a very short geological period of Early Cambrian time. These nested body plans portray a novel big picture of pararthropod evolution as a progression of step-wise changes both in the head and the appendages. The evolution of the pararthropods displays how the head/trunk boundary progressively shifted to the posterior, and how the simple annulated soft uniramous appendages progressively changed into stalked eyes in the first head appendages, into whip-like sensorial and grasping organs in the second appendage, and into jointed and biramous bipartite limbs in the post-antennal appendages. Haikouella is one of most remarkable fossils representing the origin body plan of Cristozoa, or crest animals (procraniates+craniates). The anatomy of Early Cambrian crest animals, including Haikouella and Yunnanozoon, contributes to novel understanding and discussion for the origins of the vertebrate brain, neural crest cells, branchial system and vertebrae.
    http://www.biomedexperts.com/A....._explosion

  62. Frost,
    His notes of rapid diversity spanning within the Panarthropoda (superphylum) is consistent within the Genetic Entropy framework. As is clearly illustrated by the study of the arthropoda Trilobite by Mark Webster:

    The following article is important in that it shows the principle of Genetic Entropy being obeyed in the fossil record by Trilobites, over the 270 million year history of their life on earth (Note: Trilobites are one of the most prolific “kinds” found in the fossil record with an extensive worldwide distribution. They appeared abruptly at the base of the Cambrian explosion with no evidence of transmutation from the “simple” creatures that preceded them, nor is there any evidence they ever produced anything else besides other trilobites during the entire time they were in the fossil record).

    Excerpt from article:
    It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.”

    “From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” University of Chicago paleontologist Mark Webster; commenting on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

    Thus Chen findings are perfectly consistent with the Genetic Entropy framework,,,

  63. Also of note from the Boston Globe article

    “And, because his (Chen’s) years of examining rocks from before the Cambrian period has not turned up viable ancestors for the Cambrian animal groups, he concludes that their evolution must have happened quickly, within a mere two or three million years.”

    First off it should be noted that evolutionists have always tried to stretch the Cambrian to as many millions of years as they could get away with:

    Evolution’s Big Bang:
    “Yet, here is the real puzzle of the Cambrian Explosion for the theory of evolution. All the known phyla (large categories of biological classification), except one, first appear in the Cambrian period. There are no ancestors. There are no intermediates. Fossil experts used to think that the Cambrian lasted 75 million years…. Eventually the Cambrian was shortened to only 30 million years. If that wasn’t bad enough, the time frame of the real work of bringing all these different creatures into existence was shortened to the first five to ten million years of the Cambrian. This is extraordinarily fast! Harvard’s Stephen Jay Gould stated, “Fast is now a lot faster than we thought, and that is extraordinarily interesting.” What an understatement! “Extraordinarily impossible” might be a better phrase! …. The differences between the creatures that suddenly appear in the Cambrian are enormous. In fact these differences are so large many of these animals are one of a kind. Nothing like them existed before and nothing like them has ever appeared again.”
    Dr. Raymond G. Bohlin, University of Illinois (B.S., zoology), North Texas State University (M.S., population genetics), University of Texas at Dallas (M.S., Ph.D., molecular biology).

    Thus now evolutionists are stuck with a extremely short time frame of 2 to 3 million years, but does even this amount of time help them?

    NO!

    The “real work” of the beginning of the Cambrian explosion may in actuality be as short as a two to three million year time frame (Ross: Creation as Science 2006: Chen 2000) which is well within what is termed the “geologic resolution time” i.e. The time frame for the main part of the Cambrian Explosion apparently can’t be shortened any further due to limitations of our accurately dating this ancient time period more precisely.

    Origin of Biological Information and the Higher Taxonomic Categories By: Stephen C. Meyer; Proceedings of the Biological Society of Washington
    “To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies the absence of clear transitional intermediate forms connecting Cambrian animals with simpler pre-Cambrian forms. And, indeed, in almost all cases, the Cambrian animals have no clear morphological antecedents in earlier Vendian or Precambrian fauna (Miklos 1993, Erwin et al. 1997:132, Steiner & Reitner 2001, Conway Morris 2003b:510, Valentine et al. 2003:519-520). Further, several recent discoveries and analyses suggest that these morphological gaps may not be merely an artifact of incomplete sampling of the fossil record (Foote 1997, Foote et al. 1999, Benton & Ayala 2003, Meyer et al. 2003), suggesting that the fossil record is at least approximately reliable (Conway Morris 2003b:505).”
    http://www.discovery.org/a/2177

    Thus as Chen Stated:
    “the Cambrian explosion of new body plans is proving to be real, not an illusion produced by an incomplete fossil record.”

  64. Sorry, I don’t see the support for genetic entropy in that study at all. Where is the quick mutational meltdown? How is a family of thousands of species, lasting for 270 million years, evidence of rapid genetic failure?

    Webster himself offers two hypotheses, one of which is the exact opposite of genetic entropy.

    And just to be clear, the phrases “(Yet Suprisingly)”, and “surprising and unexplained” are your glosses. They don’t appear in the text.

  65. Nak,
    Please respect my wishes for you to refrain from any conversation I am in.

  66. Mr Nakashima,

    Both hypotheses are probably involved. Whenever we look at adaptive radiations (and the Cambrian explosion is certainly a spectacular example), the ecological conditions play an important role: no matter how variable a population is genetically, adaptive radiation will not occur without ecological opportunity. Rapid radiation requires both genetic variability and ample diverse niches. When it occurs, complex food webs develop that can be sensitive to subsequent changes in ecological conditions. Key changes in environment can produce spectacular collapses of these food webs– often resulting in extinctions of whole lineages which in turn contributes to a decrease in the overall species diversity.

    All of this is fairly basic ecology, and does not necessarily involve mutational meltdown to explain any of it.

  67. Dave Whisker’s main conjecture:

    “adaptive radiation will not occur without ecological opportunity.”

    And he is correct in that species will rapidly radiate when a proper environment presents itself, but he is incorrect to ignore that the propensity to radiate is always found to be much greater for “ancient” lineages and is also found to be severely limited for sub-species of the ancient lineage, which is exactly what genetic entropy predicts:

    African cichlid fish: a model system in adaptive radiation research:
    “The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory(of evolution).——-conclusion of the study?—— the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages”
    http://www.pubmedcentral.nih.g.....d=16846905

    Thus Dave has actually stolen from what is exactly predicted for the genetic entropy model to make it seem as if neo-darwinism is still viable as a theory, after what was a crushing blow delivered by the Cambrian Explosion i.e. he cannot extrapolate to adaptive radiation to explain how the species “arrived” in the first place. He needs to conclusively demonstrate how a novel species arises: Yet in
    “ALL” test for novel speciation we find severe limits:

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

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

    Selection and Speciation: Why Darwinism Is False – Jonathan Wells:
    Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.”
    http://www.evolutionnews.org/2.....why_d.html

    Dave then goes on to conjecture environmental/ecological constraints as a mechanism for why “consistent” loss of variability is found across the entire spectrum of trilobites. This is indeed far-fetched on Dave’s part for trilobites were prolific and had worldwide distribution for 270 million years… But to drive the point home as to how detached from reality Dave is in this matter, I will point out that the environment was not becoming more constricted for “evolutionary opportunity” as Dave imagines, but was instead being significantly enriched with a greater diversity of minerals, which clearly should have presented MORE opportunities for evolution to demonstrate its awesome powers of creating new species from the trilobites. (As well other species were doing well while the trilobites were slowly loosing diversity) Indeed trilobites with amazing new abilities should have been noted in the fossil record:

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization.
    http://www.reasons.org/The-Creation-of-Minerals

    Thus once again, when faced with what we find from the “real” world evidence, evolution falls apart with scarcely any rigid scrutiny at all.

    But all this goes to the heart of the matter for evolutionists NEVER address how natural process can generate information in the first place (they NEVER will) thus they have never even established their theory as viable with reality in the first place… That Dave would object to Genetic Entropy without ever addressing the main issue Genetic Entropy asserts from a foundation grounded in physics (Natural processes can only work to degrade the complex information found in life) is to highlight the slipshod method in which evolutionists practice science, They never connect with reality, with real science, and as such cannot rise above pseudo-scientific enterprise it has always been.

    “Physics is the only real science. The rest are just stamp collecting.” — Ernest Rutherford

  68. Mr BA^77,

    I’m sorry, but we have similar interests. I’m not stalking you, trolling you, or flaming you, just engaging a point you brought up. Please choose not to respond to any of my comments if you see fit. I won’t think less of you for it. If you want a private blog where Nakashima comments are not allowed, perhaps the mods here can help you.

  69. Mr Wisker,

    I agree that adaptive radiations usually have a strong basis in niche availability. However, the point of the Webster study was variation within species, not the success of trilobites at radiating into thousands of species that lived (cumulatively) for 270 million years. Certainly that is a point against using trilobites as an example of mutational meltdown as well.

  70. Nak,
    Why should I have to leave a conversation I am in the middle of and to which you have contributed nothing? Please respect my wishes for you to refrain from any conversation I am in.

  71. Mr BA^77,

    I’m not asking you to leave a conversation. Please, continue responding to Mr Wisker or anyone else as you see fit. You may ignore or respond to my comments as you please.

    I’m sorry you feel I’ve contributed nothing. I thought my comment on the relevance of genetic entropy to variable, long lived and diverse species was on topic. YMMV.

  72. Nak,
    If I felt you were willing to learn, I would not mind, but as you have repeatedly demonstrated, to myself and others, you will never concede ANY point when refuted, thus your supposed “contributions” are useless to any meaningful dialog I may be is since you have made it clear you are actually trying to impede any meaningful progress. If you continue to refuse to obey my request to you to refrain from conversations I am in, I will no longer contribute on UD.

  73. I would just like to say for the record that I believe Mr. Nakashima is acting well within his rights, in commenting on this thread. I would like to add that on those occasions when he and I have engaged in debate in the past, I have always found his comments to be polite and well-informed.

    In making the above statement, I do not wish my remarks to be construed as making any kind of criticism (implicit or explicit) of bornagain77, whose posts and links I appreciate.

  74. Mr BA^77,

    I don’t understand why you are continually raising the stakes for yourself. You can ignore me, I’m sure. But I think it is inappropriate to expect that any thread you have posted on is therefore offlimits for me to comment on also. That is hardly fair or within the moderation policy here on UD.

    Let’s get back to trilobites and genetic entropy.

  75. Mr Nakashima,

    I agree with you that trilobites are one of the last groups one would want to use as an example supporting the genetic entropy thesis (as well as ancient bacteria, as I have pointed out elsewhere).

    Here is an interesting tidbit regarding the ecospace and genome hypotheses:

    As an intriguing postscript, Valentine (1995) has recently concluded, through an analysis of the Hox/Hum homeobox genes, that the current understyanding of the molecular basis of development provides no support for the genome hypothesis, and that the ecospace hypothesis is more consistent as an explanation for the concentrated origin of phyla during the Cambrian explosion.

    That is, the more consistent hypothesis is that the ecospace of the Late Cambrian was full, and competetive exclusion precluded more innovation at the phylum level.
    But what about bornagain’s suggestion that ecological opportunity would be greater in the Late Cambrian? A little research on his part would have shown that there is evidence of a glacial period at that time. Basic paleoecology tells us that glacial periods result in significant amounts of seawater locked up as glacial ice on land. This results in lowered sea levels, which in turn reduce the area of continental shelves, where much of the marine life lives, creating increased competition and extinction levels. With a packed ecospace suffering restriction, food webs established earlier will collapse, resulting in mass extinctions

  76. Oops. The source of the quote is here:

    Bottjer, DJ JK Schubert, & ML Droser (1995). Comparative evolutionary paleoecology: assessing the changing ecology of the past. In Biotic Recovery From Mass Extinction Events, MB Hart, ed.

  77. Mr Wisker,

    Was there a polar continent during that era?

  78. BA77 ——-conclusion of the study?—— the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages”
    http:/

    Cherry-picking that doesn’t support your argument. From the same conclusions, not conclusion:

    The implication is that speciation itself (not just coexistence) is driven by ecological opportunity, inconsistent with predictions of speciation through drift and ecologically neutral sexual selection.

    Somewhat fishy fact-finding, I’d say.

  79. Mr Nakashima,

    Mr Wisker,

    Was there a polar continent during that era?

    No. That would happen later in the Ordovician, as Gondwanaland wandered over the pole, resulting in even more glaciation.

  80. I’m trying to grasp what, if anything, might be the specific relevance of genetic entropy to whale evolution. Is there some sense that, around halfway to their becoming “fully whale”, an evolving cetacean species should “run out” of information/variability/whatever, and thus would be “stuck” between two worlds until an intelligent force could contribute the needed genetic information?

    Earlier, Frost said something interesting:

    First of all virtually any organism can evolve into any other organism via mutations and the like given enough imagination time and a well designed fitness landscape- but it is the improbability of those positive necessary mutations occurring that ID challenges.

    This seems to be a somewhat related idea. The thing about probability is that, despite our intuition on the subject, nothing prohibits a long sequence of individually unlikely events from occurring — especially if earlier rare events tend to “stick” as they do with genetic heredity, while common events are usually filtered out by natural selection. (Given that, such sequences altogether expected.) It’s not like a Pakicetus would have to “re-invent” the aquatic lifestyle in passing genes to each of its babies. If every individual change is plausible despite being unlikely, what’s the problem with having a bunch of those changes occur?

    And how should we interpret the existence of the intermediary fossils, if in fact the fossils are genuine? (From much of the commenting here, I do get a subtext that they might not be genuine, that Dawkins is sort of pulling them out of his butt. For example, jerry earlier referred to “[pulling] a couple rabbits out of the hat. Oh, I mean whales”. Later, there was a mention of Nebraska Man. The title of this post is one I assume to sarcastically suggest that these are not “really” transitionals.)

    In that quote, Frost is also suggesting that the landscape might itself be “well designed” — a possibility often implied by people here at UD responding to computer simulations of evolution. Yet no ID theorist has specifically proposed that notion — why not?

    In any case, I personally don’t agree that “any organism can evolve into any other organism” — this is why evolutionists often bring up chimeras such as mermaids and flying horses, or, say, a species with the a long non-coding sequence shared by distant cousin species. (What if whales shared one with birds, but it was absent from all the intermediary species!) To this, IDers might respond by bringing up platypuses, and so the great conversation proceeds!

  81. 81
    Is there some sense that, around halfway to their becoming “fully whale”, an evolving cetacean species should “run out” of information/variability/whatever, and thus would be “stuck” between two worlds until an intelligent force could contribute the needed genetic information?

    First of all, assuming the present day whale is “fully whale” suggests that the species is no longer evolving, that today’s mammal is what was intended, what was in the design.

    Secondly, suggesting that a species would evolve in dissimilar environments with no adaptive variations, because it was intended to ‘end up’ as ‘fully whale, or fully hippopotamus, presupposes these species will be identical in another million years.

    How does the lack of a transitional fossil record indicate the evolution of this species was “stuck”?

  82. Mr. Nak,
    “Sorry, I don’t see the support for genetic entropy in that study at all. Where is the quick mutational meltdown? How is a family of thousands of species, lasting for 270 million years, evidence of rapid genetic failure?”

    There were over 50 phyla created in the cambrian explosion, and there’s 30 something now. Also since then there’s been no new phyla I believe. So these two points are part of Sanfords book. No new real variation allowed, and decrease in species.

    I’d like to know what evolution says about why reduced phyla, because from what I know of this is circumstantial evidence for entropy.

  83. I should also add that I don’t believe in Sanford’s 1000 generation meltdown, or however many it is. But I don’t know that he does either. It could be that he’s simply presenting the math based on what’s known. I don’t know I haven’t read his book myself.

    But too much emphasis is put on this part of the book. Sure, it IS called “genetic entropy”, but the other part of the title is “and the mystery of the genome”. Sanford is a top shelf geneticist, I’m sure he’s aware of trilobites.

  84. Lenoxus,
    “I’m trying to grasp what, if anything, might be the specific relevance of genetic entropy to whale evolution.”

    Part of genetic entropy is looking at the complex info in the genome and asking how it got there when all we see is loss of information when good mutations happen.

    If you look at the genome, and believe it codes for all the variation happening, then you’d think we’d see more complexity going into the genome concurrent with good mutations, but we don’t. Aside from a couple examples (nylonase is one) where morphological changes aren’t taking place, or large changes take place.
    Those couple examples are only small changes to existing structures.

    So GE asks, how are whales evolving?

  85. And a large change DOES to some degree have to happen all at once, or go vestigial.

  86. Mr Lamarck,

    That pattern of radiation and then dimunition in number is very common. You can see the same thing in car manufacturers or computer makers. In the early days a lot of tinkering is good enough, because really nobody is very good. Then one or a few start to distinguish themselves and starve out the competition.

    Another aspect of it is the random chance that lineages go extinct. Lets say there was a group of 10,000 ‘first humans’. Mitochondrial Eve isn’t one of them, she lived much later. What happened to that wonderful radiation of humanity? By random chance, their descendants haven’t survived. That’s not genetic entropy, that’s just actuarial statistics in action.

  87. Mr. Nak,
    But we’re looking at the net effect, taking in vast amounts of time and vast ecosystems and life variation. This is enough time to discern a pattern.

    Are you then postulating that no pattern would have emerged, and that we will in the future see again 53, then 2 then 500 then 40 phyla?

    Wouldn’t this fluctuation be seen in the fossil record and is it? I doubt I wouldn’t have heard about that. I’m talking about NO new phyla since cambrian and ALL phyla within a few million years, minus one aleady existing phyla. There’s no variation on that graph.

    “That pattern of radiation and then dimunition in number is very common.”

    In number of what? Species?

  88. Mr Lamarck,

    The “radiation, then dimunition” pattern won’t normally repeat, because the sophisticated descendants of the few remaining entities (phyla, car makers, etc) are still more sophisticated than any newcomer.

    In terms of the phyletic explsion of the Cambrian, there is one explanation that at that time the modules of body plan development fit together in a looser way than today. This allowed many different body plans to be developed rapidly which allows the exploratioin of more niches. If this hypothesis is correct, we won;t see any reradiation at the level of phyla because all phyla now have much more rigid developmental programs than their ancestors did 500 million years ago. So if you opened up a niche by (for example) wiping out all the spiders from the world, a descendant of termites or flies would rush in and grab the free lunch before any new phyla could form to exploit the free lunch. No new phyla, but maybe a new order of termite.

    Is that any clearer?

  89. Mr. Nak,
    What accounts for phyla reduction would then be:

    1. Things were more modular.

    I understand it insofar as it’s utter unfounded speculation.

    2. Niche filling on the food chain.

    This idea would always be an automatic stopper to phyla radiation, or species radiation for that matter. It wouldn’t matter if there were five phyla or fifty, it’s all one big food chain for any ecosystem.

    So that could be an answer for phyla reduction, except that the same idea never allows for there to be any radiation. So it can’t be true, unless the cambrian explosion was ID’d.

    Keep in mind that the niche/food idea would have to be always applicable in every case, because whatever mechanism is at work in phyla reduction, is working very absolutely, as I covered when I talked about the graph. So that’s why I can safely say that the niche/food argument isn’t true. Or it is true, but then automatically the cambrian explosion was ID’d.

    I liked your answer though it was interesting.

  90. lamarck:

    Aside from a couple examples (nylonase is one) where morphological changes aren’t taking place, or large changes take place.

    How do you know that nylonase do / don’t have less information available as a result of the mutations? How is the information content measured, since I assume you don’t mean the total amount of DNA?

    So GE asks, how are whales evolving?

    What is meant by “GE”?

    And a large change DOES to some degree have to happen all at once, or go vestigial.

    I guess that would be why modern-day whales breathe underwater. It’s hard to imagine what else they’d do — just sort of go to the surface for breaths? Some similar ad-hoc mechanism? That would just be weird. They clearly wouldn’t survive being stuck in the middle like that. :)

  91. Lenoxus,
    I’ll explain what I know, but let me know if something isn’t understood because I have a clear understanding of at least what I think I know.

    1. Nylonase made a whole new gene. This concept isn’t understood by many IDers. There’s an arbitrary cutoff point between a small change in a gene and a whole new gene and nylonase clearly fit the bill because it was a frameshift. All it’s base pairs switched partners. And miraculously this coded for something significant which this bug found advantageous, eating nylon. It was a bug in a pond next to a nylon factory.

    This is a whole other level than a gene duplication and resulting insertion or deletion in a codon. This too is an information gain technically. But this couldn’t account for the massive complexity of the genome built up over time. Because the change is likely near neutral and so doesn’t matter. This is the vast majority of beneficial mutations. Also we’re talking about large structures forming and a large amount of mutations coordinating is needed over a small amount of time.

    Unless of course your talking about this one in a million chance of a successful frameshift mutation which also codes for something very beneficial. If this happened all the time there would be no questions about whale evolution. So that’s what’s meant by a whole new gene. Everything changes, AND it codes for something significant which will last. AND this all happened in 20 years. We know this because nylon was invented this century. As an aside, this to me is further confirmation that the genome is preprogrammed to flexibly adapt in some way. Or that the organism’s intention matters in the equation. I just can’t believe this happened because of luck, there has to be something else going on.

    2. GE is genetic entopy

    3. Agreed on the whales.

  92. lamarck: So for you, nylonase is perhaps an example of ID, rather than an evolutionist refutation pulled from the dark corners of science? Excellent. I always get a tad annoyed when IDers refuse to see any ID happening in the world today, on the non-uniformitarian assumption that all of it is “done”. I think I would feel that way even if I were an IDer…

  93. Mr Lamarck,

    I would put is as phyla reduction was natural competiton/actuarial reality, while the lack of new phyla is less modularity/niches already being filled.

    I don’t think you can always assume that every niche is filled. Some mutations open up niches. The most obvious example is living on land. In the ocean there are niches for motile and sessile life, living on the surface, the floor, or free swimming, burrowing, etc.

    I agree that the modularity hypothesis is speculation at this point. We need to dissect the machinery of vo-devo to make it more than that, but at least that is a direction for a research program.

    I personally find the coincidence of multiple body plans appearing att the same time as body plans become reliably fossilisable to neat. i agree with the author of “In the Blink of An Eye” that a lot of body plan experimentation went on while bodies were still to small and soft to fossilize well. There could have been even more body plans tried and lost before we ever get a clue. It is frustrating that hundreds of millions of years of history is a blank slate. Or shale. Whatever. :)

  94. Mr. Nak,
    For some reason I didn’t see what you were getting at with #1 yesterday.

    So yes I agree that there’s a possibility that large bodies with more parts would have a harder time changing.

    Maybe one way to start studying this would be to look at # of base pairs between humans and chimps and compare that to number of pairs between two smaller and less complex related species. If more base pairs are needed between humans and chimps then maybe it’s true.

  95. Lenoxus, yes nylonase is that to me. One thing I’m unsure about is if a frameshift always means the whole gene shifts one letter over, or just part.

  96. In regards too nylonase- it is the result of an existent enzyme that occurs in certain bacteria- and can result or appear from a mutation – and so is therefore used as an example of mutations creating a positive or beneficial novel adaptation. Well the problem is that the enzyme that results in the ability to dissolve nylon is common in certain kinds of bacteria. SO it is more like saying someone developed the mutation for red hair when there are already people out there with red hair. Yes it can happen but it is more common than the kind of revolutionary novelty to explain the emergence of novel body structures and forms. Also there has not been much research into what is any negative effects that mutation may confer. The gene that protects against malaria also causes anemia – and the positive/negative trade off of mutation can become very grey sometimes in how it actually progresses a species. 99% of all species are dead and extinct- yet according to the theory of DE there was just enough luck to get us here. Nylonase hardly elucidates the question of emergence of specified complex novelty- and especially at the macro level.

    The question is always about guided vs unguided- and I personally dont think nylonase falls down in favor of either side.

  97. Frost,
    Good comment, but then the question becomes:

    What is the possibility of a frameshift mutation producing something more than chaos? It doesn’t matter if this enzyme is common to this bug. What matters is how long and complex the “digestive” pathway was and if this enzyme was in close proximity or some such thing, to enable a one mutation easy shift over to perform this new function.

    It’s not about the phenotype or what chemicals are in the body, but instead what’s happening in the genome.

    Keep in mind another bug used a different enzyme to eat nylon in a lab experiment. Reference wiki.

    A single point nucleotide mutation on an existing functional gene would seem a much more amenable and realistic solution to this change in eating habits, than making the gene into scrambled eggs and viola, the exact thing needed is produced.

    Disagree or any thoughts?

    Also anyone could jump in with a good challenge to what I’m saying if you knew how long the frameshift was, and so maybe not much existing FCSI damage if it’s very short.

    Turns out there’s 400 frameshifts providing FCSI

  98. Frost,
    Good comment, but then the question becomes:

    What is the possibility of a frameshift mutation producing something more than chaos? It doesn’t matter if this enzyme is common to this bug. What matters is how long and complex the “digestive” pathway was and if this enzyme was in close proximity or some such thing, to enable a one mutation easy shift over to perform this new function.

    It’s not about the phenotype or what chemicals are in the body, but instead what’s happening in the genome.

    Keep in mind another bug used a different enzyme to eat nylon in a lab experiment. Reference wiki.

    A single point nucleotide mutation on an existing functional gene would seem a much more amenable and realistic solution to this change in eating habits, than making the gene into scrambled eggs and viola, the exact thing needed is produced.

    Disagree or any thoughts?

    Also anyone could jump in with a good challenge to what I’m saying if you knew how long the frameshift was, and so maybe not much existing FCSI damage if it’s very short.

    Turns out there’s 400 frameshifts providing FCSI in humans. All the more evidence for my side I’d think.

  99. Huh, it seems like with the nylonase things the arguments go along the lines that there’s no way one mutation could provide such a complex, positive, and information-rich benefit. Yet if one accepts that it could, there’s not much more to say — nylonase was bound to happen sooner or later, no matter how many “casualties” occurred in the process.

    As for the question of negative results from the mutation, I imagine there probably were tradeoffs for the organism in terms of digesting other substances. (Pretty much all changes to an organism involve tradoffs, but that alone isn’t enough to stop evolution.)

  100. If the hippo was extinct and they found fossils of it along with evidence of it’s aquatic lifestyle, it would be heralded as an ancestor of the whale.

  101. 91
    Lenoxus

    I guess that would be why modern-day whales breathe underwater. It’s hard to imagine what else they’d do — just sort of go to the surface for breaths?

    They don’t breathe underwater, they need to come to the surface.

  102. Was that a joke?

  103. Lenoxus,
    “Yet if one accepts that it could, there’s not much more to say — nylonase was bound to happen sooner or later, no matter how many “casualties” occurred in the process.”

    Lenoxus, You’d have to accept that it could happen for sure. In the first reference Mario linked, Dembski’s saying there was a sufficient number of correctly placed stops to preserve FCSI and redundancy in the segment that got shifted that it seems it was possible, but that this is so rare that it doesn’t point to it being THE mechanism to evolve a whale. And also that this could be a sign of intelligent front loading or something, because it’s so freakishly convenient to have such a setup. That’s my interpretation, I don’t want to speak for him. So the thing to do would be to look at other frameshifts in nature.

    Regarding tradeoff’s not stopping evolution, the point is you need to get off the ground before you can fly with natural selection.

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