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More Questions for Evolutionists

In this Nature Alert article, we find out that sponges, present as early as 635 million years ago in the fossil record, have 18,000 genes, among which are genes for apoptosis, that is, cell death. Now here is a creature that has “a simple body plan lacking organs, muscles and nerve cells.” Let’s remember that the number of human genes, prior to whole genome analysis, was thought to be at least 100,000. With early genomic results in, this number was revised downward. Today it stands at 25,000—and shrinking! (There are arguments for lowering it still) So the lowly sponge—no nerves, no muscles, simple as you can get—has around 65% the number of genes as humans.

Well, all of this presents problems for Darwinism.

First of all, we have 65% of the gene number of humans in little, old sponges—an organism that appears as far back as 635 million years ago, about as old as you can get [except for bacteria]. This kind of demolishes Darwin’s argument about what he called the pre-Silurian (pre-Cambrian). 635 mya predates both the Cambrian AND the Edicarian, which comes before the Cambrian (i.e., the pre-Cambrian) IOW, out of nowhere, 18,000 animal genes. Darwinian gradualism is dealt a death blow here (unless you’re a ‘true believer”!). Here’s a quote: “It means there was an elaborate machinery in place that already had some function. What I want to know now is what were all these genes doing prior to the advent of sponge.” (Charles Marshall, director of the University of California Museum of Paleontology in Berkeley.) I want to know, too!

Secondly, unexpectedly, this “multicellular creature” had an apparatus for ‘individual’ cell death—the cell had a way of bringing about it’s own death—prior to cells having the ability to attack harmful cells outside of themselves. So, somehow, before multicellularity cells decided they should kill themselves [Since apoptosis, i.e., cell death, 'evolved' as a defense mechanism, then why didn't the ability to destroy harmful cells exterior to the cell itself also 'evolve' at the same time? IOW, the cells forming the 'first' multicellular organism, brought this capacity with them]. Remember that Darwin states that if anything could be found present in an organism that was harmful to it, then this would be a disproof of his theory. Yet cells are capable of ‘suicide’ prior to there being a need for it. It can hardly be argued that a cell’s ability to kill itself is good for it. But I’ll bet there’s a few Darwinists who will want to convince us otherwise.

Finally, just as a FYI, here’s a PhysOrg item about ” . . .evidence [supporting] the hypothesis that human cells have the widespread ability to copy RNA as well as DNA.” This isn’t just copying of non-coding portions of DNA, but actual copying of RNA molecules within the cell. (What was that they were saying about the “Central Dogma of Molecular Biology”?) Taken together with the above observations, all of this points in the direction of cellular RNA being a communication system for various parts of non-coding DNA and cellular proteins (the coded portion of DNA), as well as the likely communication medium between DNA and the environment (we already know that environmental factors can result in RNA which then has inherited effects–briefly mentioned in the news item). It becomes increasingly clearer just how rather fundamental, and relatively insignifcant, proteins are in the big scheme of things.

Let the discussion begin!!

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56 Responses to More Questions for Evolutionists

  1. Heinrich: Yours was not the first post here. How is it that you now have top billing. Are you fiddling with the sytem?

    This is a non sequitur:

    Secondly, unexpectedly, this “multicellular creature” had an apparatus for ‘individual’ cell death—the cell had a way of bringing about it’s own death—prior to cells having the ability to attack harmful cells outside of themselves. So, somehow, before multicellularity cells decided they should kill themselves

    Sponges are multicellular, and presumably some of their ancestors were. So apoptosis could have evolved after multicellularity began, and the evolution of sponges.

    And theoretically, apoptosis can evolve in unicellular organisms if they reproduce clonally (actually you don’t need that, but clonality makes it a whole lot easier). It can happen if it helps clones survive. I guess slime moulds are an example of this.

  2. 2

    PaV,
    Thanks for this post. Dave Scott brought up the “front-loading” issue nearly 2 years ago here and I have been surprised that it has not gotten more attention at UD and other ID sites, seems like it deserves much more. Glad to see your post and David Tyler’s a few days ago.

  3. 3

    Just two quick comments:

    1) Already in the 80s people had estimated the number of genes in humans to be around 30,000. The higher estimates were published later.

    http://sandwalk.blogspot.com/2.....genes.html

    2) There are quite a few organisms that have more genes than humans.

    Namely the rice, discovered in 2002.

    Humans have fewer genes than rice
    Reporter Issue 120, 5 July 2002

    http://www.imperial.ac.uk/college.asp?P=3509

  4. PaV, this article is of interest to your article,

    Non-coding RNAs and eukaryotic evolution – a personal view – John Mattick – July 2010
    Excerpt: In fact almost every time you functionally test a non-coding RNA that looks interesting because it’s differentially expressed in one system or another, you get functionally indicative data coming out. But the compelling point is that regulatory RNAs provide an explanation as to why complexity doesn’t scale with the number of protein-coding genes. It was originally assumed that as complexity increased there would be more and more such genes – before the genome was sequenced there was speculation that humans might have a hundred thousand or more, and it was a huge shock that it’s much less, and doesn’t scale with complexity. But there are very large numbers of long non-coding RNAs, so this is where the real genetic scaling has occurred.
    http://www.ncbi.nlm.nih.gov/pm.....MC2905358/

    ,,,,,,But what will evolutionists do without their beloved “Junk DNA?” 8)

  5. Devil’s Advocate:

    1- The number of genes has been rendered moot due to alternative (gene) splicing which can the few and make many different products.

    2- Today’s sponges are just as derived as today’s humans- meaning the genomes of today’s sponges (spongi? lol) is not the same as the spongilos of eras long lost.

    3- Most of the genes we have don’t have anything to do with us being an animal- they are for basic cellular stuff

    My own advocate:

    4- Common design- using similar or identical components in totally different structures or applications

  6. semi off topic from Science Daily:

    Scientists Map All Mammalian Gene Interactions – August 2010
    Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome.
    http://www.sciencedaily.com/re.....142044.htm

    This is definitely a polyfunctional situation which further isolates the generation of functional information by random processes:

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

    K´necting The Dots: Modeling Functional Integration In Biological Systems
    Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream”,,,”those genes which govern major changes, the very stuff of macroevolution, apparently do not vary, or vary only to the detriment of the organism”
    http://www.uncommondescent.com.....l-systems/

    Insight into cells could lead to new approach to medicines
    Excerpt: Scientists expected to find simple links between individual proteins but were surprised to find that proteins were inter-connected in a complex web. Dr Victor Neduva, of the University of Edinburgh, who took part in the study, said: “Our studies have revealed an intricate network of proteins within cells that is much more complex than we previously thought.
    http://www.physorg.com/news196402353.html

  7. First, my apologies to Dr. Cornelius Hunter, since he’s already posted something on this sponge evidence.

    Second Opinion:

    The points you are making only point out what has been proposed by ID advocates a long time: namely, it’s not the genes that drive evolution or complexity; rather it is regulatory networks, networks which function in a way similar to computer programming. (And, of course, computer programming is a very evident form of design.)

    Joseph:

    Nice to see you back here.

    In the first place, you have not addressed the rather severe challenges this poses to Darwinian thinking. This absence is telling.

    As to your particular points:

    1 – The number of genes has been rendered moot due to alternative (gene) splicing which can the few and make many different products.

    This fact further underscores the point that genes play a minor role in evolution given that we know that the splicing removes the non-coding sections called introns which seem to clearly be involved in regulation of the alternately spliced protein products.

    2- Today’s sponges are just as derived as today’s humans- meaning the genomes of today’s sponges (spongi? lol) is not the same as the spongilos of eras long lost.

    Well, you have one of two alternatives: either you can say that the genes needed for vertebrate evolution were present long before they were needed; or, you can say that the sponge, once evolved, continued to add genes to its genome despite their not having any function. I’d hate to have to choose between those two options.

    3- Most of the genes we have don’t have anything to do with us being an animal- they are for basic cellular stuff.

    Well said. I wholeheartedly agree–if that is indeed the case. But, again, how does Darwin explain the abrupt appearance of 18,000 genes analogous to vertebrates 635 mya? This destroys his theory. And this isn’t just hyperbole. As I have often said, Darwin would not be a Darwinist today.

    My own advocate:

    4- Common design- using similar or identical components in totally different structures or applications

    I’m not sure of your point here. It seems to sound like how I, and I suspect many others here at UD, envision the way things actually happen(ed).

  8. Bornagain,

    That polyconstrained complexity idea is cool. Thanks for sharing. I wonder if anyone has written a book that stacks the evidence against evolution into a comprehensive framework that estimates the probabilities involved as it goes along.

    For example, after the first chapter, entitled, “Fine tuning of the universe, except for solar system” the probability equals 1 x 10 ^ -100. Then chapter 2, “Fine tuning of solar system” chance of life 1 x 10 ^ 250 (or whatever). Chapter 3 Irreducible complexity … etc etc etc.

  9. Collin, you can thank Dr. John Sanford, in his book Genetic Entropy, for the polyfunctional equals polyconstrained idea.

    As far a sequential book of probabilities from universe to humans, I have gathered evidence in a somewhat sequential way as you suggested here:

    Intelligent Design – The Anthropic Hypothesis
    http://lettherebelight-77.blog.....is_19.html

    the sequence, from universe to humans, picks up about a fifth of the way down the page. In fact I try to answer these following questions:

    The following are some basic questions that need to be answered, to find if either the anthropic hypothesis or some materialistic hypothesis is correct.

    I. What evidence is found for the universe’s ability to support life?

    II. What evidence is found for the earths ability to support life?

    III. What evidence is found for the first life on earth?

    IV. What evidence is found for the appearance of all species of life on earth, and is man the last species to appear on earth?

    V. What evidence is found for God’s personal involvement with man?

    As you can see Collin, the ‘book’ could be consolidated greatly so as to focus strictly on probabilities as you suggested.

  10. Collin @ 7 “I wonder if anyone has written a book that stacks the evidence against evolution into a comprehensive framework that estimates the probabilities involved as it goes along.”

    These calculations, although overwhelmingly compelling to a rational thinker, never seem to make a dent in the true believers. They are apparently impervious to reason.

    So in an effort to attack their argument at the level of first principles, I propose the following arguments.

    If naturalism( including materialism/physicalism – N,M,P) was true, then the laws of physics could explain everything. (This is necessarily true as that is part of the definition of N,M,P. Thus the law of identity is used in the antecedent and consequent.)

    But the laws of physics cannot explain language (because physics has nothing to say about symbols and rules – only the interactions of sub-atomic particles in energy fields).

    Therefore, naturalism is false.

    This is a necessary conclusion. It cannot not be true if my premises are true. My premises are true. Therefore the N,M,P argument should be over.

    It can be taken one step further.

    If neo-darwinian evolutionary theory is true then ALL of life can be ultimately explained by the laws of physics.

    But the laws of physics cannot explain the genetic code/language or biological information. (nor any other language or information – see first argument)

    Therefore, neo-darwinian evolutionary theory is false.

    Not only that, it cannot possibly be true.

  11. tgpeeler, bornagain,

    Thanks for the interesting info/thoughts!

  12. tgpeeler:

    It’s interesting that you appeal to first principles when it comes to the true believers. Fr. Stanley Jaki took that very position and was rather dismissive of the ID approach.

    In terms of the fruitfulness of this approach—that is, will it prove more effective than the ID approach in changing minds/being persuasive—it has struck me lately that the tilma of Juan Diego is proof positive that some supernatural agency was operative in our world. The best of evidence supports this. So, if the true believers won’t be convinced by that, they won’t be convinced by anything.

    Yet, OTOH, you have theistic evolutionists like Ken Miller: what about them? There, I think, it is only probabilistic arguments that will work. I have the impression that most of the TE’s simply suspect that the Creator endowed his material creation with the ability to ‘find’—beyond all imaginable odds—correct combinations of nucleotide bases, lipid structures, etc., that ‘life’ needs. And, so, even probabilistic arguments won’t likely work.

    So, you see, I’m a pessimist.

    However, I think in the end science itself will answer these questions. The remarkable work now being done, extrapolated into the future, will, I feel, result in such an organized entirety of evidence pointing in the direction of design that is will simply not be reasonable to think otherwise.

    So, maybe I’m an optimist! :)

  13. PaV,

    I don’t think that TE’s will be convinced by anything. I think that they take their position because they are Christian but want to be aligned with the biggest bully on the block which is not ID.

    Their position is kind of like one that my friend took concerning free will. He said that God predestinates all of our choices AND we have free will. I didn’t understand it, but I didn’t mock him because I know that I have strange beliefs too.

    TE’s just seem to believe that God did it AND it happened in natural, undirected ways. How do you contradict that?

  14. 635 mya predates both the Cambrian AND the Edicarian, which comes before the Cambrian (i.e., the pre-Cambrian) IOW, out of nowhere, 18,000 animal genes. Darwinian gradualism is dealt a death blow here (unless you’re a ‘true believer”!).

    If life first appeared some 3.5 billion years ago, approximately 3 billion years before these sponges appear, how is that “out of nowhere”? I mean, presumably these genes could have arisen gradually over those many hundreds of millions of years.

  15. 15

    I have the impression that most of the TE’s simply suspect that the Creator endowed his material creation with the ability to ‘find’—beyond all imaginable odds—correct combinations of nucleotide bases, lipid structures, etc., that ‘life’ needs.

    This view does not preclude a design inference. TEs are design theorists when it comes right down to it, they just don’t want to admit it for political reasons. Fine-tuning is a design argument. In fact it’s a specified complexity design argument.

  16. PaV, there is nothing in the article you quote to support your claims.

    The best experts in the field were forecasting 20-30,000 genes human many years ago.

    It is not a problem for evolutionary theory if sponges have a similar number of genes to humans.

    The sophistication of sponges shows that they had ancestors we have not discovered yet. We may never discover them as records of early life are hard to find. What is the problem here? Surely you’re not claiming this as evidence that sponges came into being suddenly and fully formed, are you?

    Your statements about apoptosis are a misunderstanding of the article.

  17. Peepul I like this question you asked PaV:

    ‘Surely you’re not claiming this as evidence that sponges came into being suddenly and fully formed, are you?’

    But Peepul it is not solely Design Theorists that notice this discontinuity. In fact some prominent evolutionary materialist have noticed the ‘suddenness’ pattern as well:

    I like this following paper for though it is materialistic in its outlook at least Eugene Koonin, unlike many materialists, is brutally honest with the genetic evidence we now have.

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

    Biological Big Bangs – Origin Of Life and Cambrian – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4284466

    It should be noted that Dr. Koonin tries to account for the origination of the massive amounts of functional information, required for the Cambrian Explosion, and other ‘explosions’, by trying to access an ‘unelucidated and undirected’ mechanism of Quantum Mechanics called ‘Many Worlds’. Besides Koonin ignoring the fact that Quantum Events, on a whole, are strictly restricted to the transcendent universal laws/constants of the universe, including and especially the second law of thermodynamics, for as far back in time in the universe as we can ‘observe’ these ‘laws’ in action, it is also fair to note, in criticism to Koonin’s MWI scenario, that appealing to the undirected infinite probabilistic resource, of the quantum mechanics of the Many Worlds scenario, actually greatly increases the amount of totally chaotic information one would expect to see generated ‘randomly’ in the fossil record. In fact the Many Worlds scenario actually greatly increases the likelihood we would witness total chaos surrounding us,,, as the last five minutes of this following video points out:

    The Absurdity Of The Many Worlds Hypothesis – William Lane Craig – Last 5 minutes of this video
    http://www.metacafe.com/watch/4784630

    Though Koonin is correct to recognize that the infinite probabilistic resource of ‘Quantum Mechanics’ does not absolutely preclude the sudden appearance of massive amounts of functional information in the fossil record, he is very incorrect to disregard the ‘Logos’ of John 1:1 needed to correctly specify the ‘controlled mechanism of implementation’ for the massive amounts of complex functional and specified information witnessed abruptly and mysteriously appearing in the fossil record. i.e. He must sufficiently account for the ’cause’ for the ‘effect’ he wants to explain. And as Stephen Meyer clearly points out, the only known cause now in operation sufficient to explain the generation of massive amounts of functional information is intelligence:

    Stephen C. Meyer – The Scientific Basis For Intelligent Design – video
    http://www.metacafe.com/watch/4104651

    This following paper corroborates Koonin’s observation of irreconcilable differences being found in the genetic evidence with Darwinian evolution:

    Why Darwin was wrong about the (genetic) tree of life: – 21 January 2009
    Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts – also known as tunicates – are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says. .”We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”
    http://www.newscientist.com/ar.....-life.html

    As a point of interest, I would like to point out that this, ‘annihilation’ of Darwin’s genetic tree of life, article came out on the very day that Dr. Hillis, a self-proclaimed ‘world leading expert’ on the genetic tree of life, testified before the Texas State Board Of Education that the genetic tree of life overwhelmingly confirmed gradual Darwinian evolution. One could almost argue it was ‘Intelligently Designed’ for him to exposed as a fraud on that particular day of his testimony instead of just any other day of the year.

  18. Joseph,

    You said:

    2- Today’s sponges are just as derived as today’s humans- meaning the genomes of today’s sponges (spongi? lol) is not the same as the spongilos of eras long lost.

    This is an assumption on your part. You are assuming evolution in order to claim this is not a problem for evolution.

    Sponges claimed to be VERY OLD have been found that are very close to present day sponges. So, if they are really as old as claimed, this would be a problem for evolutionists because there doesn’t seem to be enough time to evolve all those genes.

    tj

  19. tjm:

    Three billion years is not enough time to evolve all those genes? The evidence suggests that life on Earth arose some 3.5 billion years ago and that sponges appeared over 600 million years ago. That leaves a very long time in between to evolve all those genes, as well as all that intricate cellular “machinery”.

    Three billion years is a very long time.

  20. Heinrich [1]:

    This is a non sequitur:

    Secondly, unexpectedly, this “multicellular creature” had an apparatus for ‘individual’ cell death—the cell had a way of bringing about it’s own death—prior to cells having the ability to attack harmful cells outside of themselves. So, somehow, before multicellularity cells decided they should kill themselves.

    Sponges are multicellular, and presumably some of their ancestors were. So apoptosis could have evolved after multicellularity began, and the evolution of sponges.

    And theoretically, apoptosis can evolve in unicellular organisms if they reproduce clonally (actually you don’t need that, but clonality makes it a whole lot easier). It can happen if it helps clones survive. I guess slime moulds are an example of this.

    Well, first of all, thank you for fulfilling my prediction. According to Darwinism, life comes from nowhere, and then develops the ability to kill itself. Wonderful! How logical! Somehow a ‘unicellular’ organism ‘knows’ that it should kill itself for the good of the clone. It must be filled with ‘unselfish’ genes.

    Secondly, if you wish to posit multicellularity as prior to sponges, then why didn’t the ability for cells to kill the cells adjacent to it develop? It seems like both of these abilities would aid multicellular critters. So why did one develop, and not the other? So we KNOW that the cell’s ability to kill its neighbor when needed DID NOT arise before the sponge simply because sponges don’t have this ability. Further, if a cell decides to kill another one because something is wrong with it, that makes Darwinians sense since it is simply protecting its life, which is not the case when a cell decides to commit hare kare. So, if the more logically Darwinian ability didn’t arise before, nor during, sponges, then why do you simply presume that an ability which is contrary to Darwinian hypothesizing arose prior to sponges? Is it just one of those things?
    And, here’s what you say: “Sponges are multicellular, and presumably some of their ancestors were. So apoptosis could have evolved after multicellularity began, and [before] the evolution of sponges.”

    So your argument rests on a presumption and a hypothetical. Wonderful!

    Here’s something similar: “If I had a million dollars, presumably I’d be on vacation instead of being in front of the computer.”

    And I wrote that note at the top of your post. Why is it in number one position? Are you playing with the software here. I hope the administrator is reading this. If you have, you should be bounced out of here.

  21. Peupel:

    PaV, there is nothing in the article you quote to support your claims.

    Really? So when Charles Marshall said, “What I want to know now is what were all these genes doing prior to the advent of sponge,” that doesn’t support my contention that the sponge, having such a simple body plan, and having arose first (in the article they talk about the sponge being the “first lineage” that broke off from our LCA), demolishes the Darwinian myth of ‘gradualism’? Really?

    The best experts in the field were forecasting 20-30,000 genes human many years ago.

    Was that before they were predicting 100,000 human genes, or after?

    It is not a problem for evolutionary theory if sponges have a similar number of genes to humans.

    Nothing is a problem for people who want to deny, distort, and turn upside down, anything that conflicts with their hypothesis. Remember, it’s all what the meaning of ‘is’ is.

    The sophistication of sponges shows that they had ancestors we have not discovered yet. We may never discover them as records of early life are hard to find. What is the problem here?

    Ah, yes, the wonders of Darwinian logic. We may NEVER discover the sponges’ ancestors; but in the meantime, let’s just presume they were there. As you would say: “What is the problem here?”

    Surely you’re not claiming this as evidence that sponges came into being suddenly and fully formed, are you?

    Do you have any evidence that suggests it didn’t? You surely don’t have any evidence that it happened gradually.

    Your statements about apoptosis are a misunderstanding of the article.

    I don’t think so. Maybe it’s the author who has a misunderstanding, being blinded by Darwinism as he seems to be.

  22. NormO

    For you and the others that want to argue lifeforms prior to the sponge, here’s a couple of quotes:

    Telltale molecular fragments teased out of ancient sediment show that sponges existed some 635 million years ago — the oldest evidence for metazoans (multicellular animals) on Earth.

    As the earliest branching lineage from our last common ancestor, sponges can tell us a lot about what is needed to make an animal,” says geneticist Mansi Srivastava, the paper’s lead author, now a postdoc at the Massachusetts Institute of Technology in Cambridge.

    Bacteria existed prior to, or alongside, unicellular life. Unicellular organisms are protozoans. The first forms of multicellular life are the Metazoans. And sponges are the first.

    As is always the case with anything touching upon the Darwinian paradigm—there are NO intermediates. Alas.

  23. And I wrote that note at the top of your post. Why is it in number one position? Are you playing with the software here. I hope the administrator is reading this. If you have, you should be bounced out of here.

    Ouch. The reason my post was at no. 1 is that it was the first one submitted. But I’m in moderation, and it was held for a long time.

    IOW, you’re threatening to ban me for being in moderation!

  24. Somehow a ‘unicellular’ organism ‘knows’ that it should kill itself for the good of the clone. It must be filled with ‘unselfish’ genes.

    For slime molds we actually know quite a bit about that “somehow”.

    Secondly, if you wish to posit multicellularity as prior to sponges, then why didn’t the ability for cells to kill the cells adjacent to it develop? It seems like both of these abilities would aid multicellular critters. So why did one develop, and not the other?

    Because the cell death pathways sponges have were enough for it to control cancerous growth?

  25. Joseph,

    My own advocate:

    4- Common design- using similar or identical components in totally different structures or applications

    Isn’t that just saying that the designer used the same components over again? So what? Why is not nested hierarchies a more probable explanation? Unless we assume that the designer really is a god with unlimited magic powers, nothing about ID makes sense.

  26. @Pav:

    Heinrich isn’t playing the software – he is played by the moderation process: A comment which is approved after being moderated will be appear with the timestamp of its entering into the moderation process, not the completing of this – sometimes quite long – procedure.

    Most probably, Heinrich was the first to comment (there could be others, still held in moderation – or not approved).

    So, it wasn’t foul play at all, but just the effects of a cumbersome procedure some of us have to endure.

  27. Stephen Meyer has a new video up on ENV about ‘scientifically’ inferring to the best explanation for the origin of information:

    Stephen C. Meyer – What is the origin of the digital information found in DNA? – August 2010 – video
    http://www.evolutionnews.org/2.....37271.html

  28. Cabal:

    Kindly, think again.

    Lewontinian a priori materialism on the assumption that a Divine Foot in the door is chaotic has long since passed its sell-by date. In fact, it always was based on a caricature of theistic thought on miracles.

    Just to start with, as C S Lewis (at introductory level) was fond of remarking [and have you even read Miracles?] miracles are signs, and to stand out as pointers beyond the usual course of nature, they REQUIRE that there be a lawlike usual course of nature.

    As to best of alternative explanations of nested hierarchies of nature, you obviously are overlooking one little factual adequacy test: mosaic creatures like the good old platypus, with 18,527 protein-encoding genes which “contain alive-and-well representatives from mammals, birds and reptiles.”

    That is a good example of a code library with reuse adapted to particular needs. (And BTW, such mosaics put paid to arguments on alleged missing links and homologies in general, like archaeopterix and even tiktaalik.)

    Going further, you are sidestepping the key question: where do we on uniform observation empirically know that digitally coded functionally specific complex information and associated algorithms, and organised implementing machinery that makes otherwise passive information work, come from?

    So, on the Darwin-Lyell principle of explaining the unobservable deep past of origins on observed patterns in the present, which is superior: (i) intelligently directed contingency, or (ii) undirected chance and necessity that have never been observed successfully creating and implementing dFSCI?

    GEM of TKI

  29. BA: a good video catch. Added to the collection (and cf the linked page). G

  30. Joseph @ 5:

    The number of genes has been rendered moot due to alternative (gene) splicing which can the few and make many different products.

    Do you realise just how hard it is to do code interweaving and layering as a compression technology? [I never even TRIED to do it, thank God by the time I came along one didn't need to -- 500 - 1,000 bytes or so can do quite a fair piece of control! (Didn't the BASIC-powered, Z 80 processor TRS-80 originally come with a RAM of a few kbytes (wiki says 4)? [Wonder if the old unit in my old Dept is still around? Somebody did globular cluster simulations on it, early 80's!!!] But there are ace microcontroller designers who can and have done code interweaving. I would not want to see their headache pill bills.]

    Also, such interweaving where the different components are needed for cell activities makes for a kind of irreducible complexity.

    And, of course such interweaving of code is prima facie evidence of code libraries! (Just think about the proposed blind selection that has to produce the viable proteins, the interweaving and the regulatory code to pick which to frame! This does not compute . . . )

    GEM of TKI

  31. I just noticed this

    Bacteria existed prior to, or alongside, unicellular life. Unicellular organisms are protozoans. The first forms of multicellular life are the Metazoans. And sponges are the first.

    Bacteria are also unicellular, so they could not (by definition) live prior to unicellular life. And not all unicellular eukaryotes are protozoa: amoeboe and yeasts spring to mind.

    Aren’t stromatilites multicellular? I thought they pre-dated the metazoans by some time.

  32. In all seriousness, I must say I find this to be the single most compelling argument for ID. It’s a stumper (but I’m not really any kind of expert).

    I am curious if there is any literature specifically predicting this sort of thing — say, shortly after the discovery of DNA, some design advocate saying “We’ll probably find ‘too-soon’ DNA in some organisms.” Still, it is impressively strange stuff.

    Looking at the situation without rooting for my team, I notice a funny irony when it comes to this stuff in particular. IDists are suddenly in the position of arguing that these genes are mostly useless to their organism in the present (or are, in a sense,”junk”), because otherwise there’s less mystery to their occurring in an evolutionary context. Meanwhile, evolution-advocates must argue that these genes do/did present function with selective value, even if we don’t know it yet (just like IDists otherwise say about “junk”). LOL.

    Putting back on my team colors, I will say this: If we were bats, we would be astounded by how all the other mammals seem to have nearly-complete genes for wings, despite being unable to fly.

  33. PaV
    Yes, of course I would argue that sponges originated from earlier ancestors. For example:

    Large colonial organisms with coordinated growth in oxygenated environments 2.1?Gyr ago

    If that paper is blocked to you, here is the abstract:

    The evidence for macroscopic life during the Palaeoproterozoic era (2.5–1.6?Gyr ago) is controversial1, 2, 3, 4, 5. Except for the nearly 2-Gyr–old coil-shaped fossil Grypania spiralis6, 7, which may have been eukaryotic, evidence for morphological and taxonomic biodiversification of macroorganisms only occurs towards the beginning of the Mesoproterozoic era (1.6–1.0?Gyr)8. Here we report the discovery of centimetre-sized structures from the 2.1-Gyr-old black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, which we interpret as highly organized and spatially discrete populations of colonial organisms. The structures are up to 12?cm in size and have characteristic shapes, with a simple but distinct ground pattern of flexible sheets and, usually, a permeating radial fabric. Geochemical analyses suggest that the sediments were deposited under an oxygenated water column. Carbon and sulphur isotopic data indicate that the structures were distinct biogenic objects, fossilized by pyritization early in the formation of the rock. The growth patterns deduced from the fossil morphologies suggest that the organisms showed cell-to-cell signalling and coordinated responses, as is commonly associated with multicellular organization9. The Gabon fossils, occurring after the 2.45–2.32-Gyr increase in atmospheric oxygen concentration10, may be seen as ancient representatives of multicellular life, which expanded so rapidly 1.5?Gyr later, in the Cambrian explosion.

  34. “out of nowhere, 18,000 animal genes”

    –The only thing to come out of nowhere was that statement. There seem to be several odd assumptions in that one short phrase that I can only guess at.
    First, why is it 18,000 “animal genes”? What makes a gene an “animal gene”? We share thousands of genes with the alga Chlamydomonas reinhardtii; so are they “human genes” or “alga genes”? The assumption here seems to be that all of the genes of the first animal suddenly sprang into existence with that first animal. That would be like proposing that the ~25k or so genes that humans have popped into existence with the first humans.
    Another assumption appears to be that modern sponges have the same genome as sponges from 635 million years ago. I wouldn’t even necessarily assume that modern sponges are genetically much more similar (or perhaps no more similar at all) to sponges from 635 million years ago than humans are (for the same reason that humans are closer genetically to tuna than tuna are to lamprey.)

  35. goodusername,

    Since the morphology of the oldest sponges found in the fossil record demonstrates an extreme conservation of morphology to those found today,,,,;

    “Fossils of all of these types (of sponges) have been found in rocks dated from 580 to 523 million years ago.”
    http://en.wikipedia.org/wiki/Sponge

    and since functional proteins are known to be extremely rare in sequence space:

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723

    ,,,,and since the best evidence we have indicates that gene sequences DO NOT change over time,,,,:

    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

    ,,,,, Please tell me exactly why we should presuppose that the genes have drastically changed in the sponges over 635 million years while the morphology has not? Is there any good reason whatsoever for why we should presuppose this drastic disconnect from the other evidence other than the metaphysical position of neo-Darwinism requires it? Well I’m sorry goodusername that simply is not a good enough reason as far as science is concerned!!

  36. NormO,

    Are you sure you want to hang your hat on that ‘colony’ evidence?

    notes:

    Before the Ediacaran explosion 600 million years ago, the oldest fossils found appear to be ‘microbial colonial fossils’ that are 2.1 billion years old, and are separated by hundreds of millions of years from the Ediacaran biota. Moreover these ‘fossils’, that seemed to cause such excitement among evolutionists, are merely single celled organisms that lived in complex colonies that had no complex internal organs, nor complex body plans save for the interesting colonial pattern of the single type of cell. Here is the study and a following article putting the ‘fossils’ into correct perspective:

    Large colonial organisms with coordinated growth in oxygenated environments 2.1?Gyr (billion years) ago – July 2010
    http://www.nature.com/nature/j.....66.html#B1

    Do New Fossils Soften the Cambrian Explosion? – July 2010
    Excerpt: Second, these “fossils” are of dubious interpretation. They may be nothing more than fairy-ring colonies growing outward like bacteria in a Petri dish. Perhaps the matlike remains were flexible enough to fold on the inside in some cases. There is no indication of a coelum or tissue differentiation. They do not appear transitional to Ediacaran fossils, let alone to Cambrian animals.
    http://www.creationsafaris.com.....#20100705a

    It was amazing how quickly some evolutionists jumped on this very inconclusive evidence for ‘fossils’ of pre-Cambrian complex life hundreds of millions of years removed from the Cambrian explosion. I guess it just goes to show how desperate some evolutionists are for some evidence, any evidence, to counter the clear theistic implications that the Cambrian Explosion presents for life on earth:

    The suddenness of the Cambrian explosion has now been made even more dramatic since the scant ‘track’ evidence, that evolutionists had claimed were the tracks of worms in the pre-Cambrian strata, has now been brought into severe question:

    Discovery Of Giant Roaming Deep Sea Protist Provides New Perspective On Animal Evolution:
    Excerpt: This is the first time a single-celled organism has been shown to make such animal-like traces. The finding is significant, because similar fossil grooves and furrows found from the Precambrian era, as early as 1.8 billion years ago, have always been attributed to early evolving multicellular animals. “If our giant protists were alive 600 million years ago and the track was fossilized, a paleontologist unearthing it today would without a shade of doubt attribute it to a kind of large, multicellular, bilaterally symmetrical animal,” says Matz, an assistant professor of integrative biology. “We now have to rethink the fossil record.”
    http://www.sciencedaily.com/re.....130531.htm

    Even sponge embryos are found in the immediate pre-Cambrian strata:

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

    This following quote sums up the implications of these findings:

    “Without gradualism, we are back to a miracle.”
    Richard Dawkins

    As well, as is often overlooked, the Ediacaran biota themselves were soft bodied, but well preserved, fossils that add even more evidence testifying to the suddenness of the Cambrian Explosion. Because to state the obvious one more time, “if there were any transitional fossils leading up to the Cambrian Explosion then they certainly should have been found”:

    Macroscopic life in the Palaeoproterozoic – July 2010
    Excerpt: The Ediacaran fauna shows that soft-bodied animals were preserved in the Precambrian, even in coarse sandstone beds, suggesting that (the hypothetical transitional) fossils are not found because they were not there.
    http://www.arn.org/blogs/index.....proterozoi

  37. Bornagain77

    When it comes to genes, one can’t assume too much from morphology. Genes aren’t blueprints. As I already alluded to, we’re genetically closer to some fish, than those fish are to other fish.

    One also can’t tell a whole lot about the morphology of a fossil from a soft (or mostly soft) organism.

    You mentioned that we’ve found fossils of the various “types” of sponges, but remember that we’re talking about an entire *phylum* here. The ‘types’ of sponges are enormous groups with a great deal of diversity: It is like talking about the ‘fish’ or ‘reptiles’ within the phylum Chordata.

    Keep in mind that this is merely the sequence of only ONE specie of sponge (the Amphimedon queenslandica). Another species may have a very different genome with drastically more or less genes. I predict that sponges will display a great deal of genetic diversity (not that that’s much of a prediction considering that, as I said, this is whole *phylum*).

  38. goodusername,

    Sorry but stating metaphysical presuppositions simply is not good enough. To back your claims for extremely plastic genomes, To counter the hard evidence I presented for presupposing the stability of sponge genomes, you have to empirically demonstrate drastic plasticity of genomes while morphology stays the same. Elsewise you are simply not even in the field of scientific endeavor!

  39. goodusername,

    try to look at this from my perspective. One the one hand evolutionists want to use genetic similarity evidence as evidence of common ancestry, even though body-plan morphogenesis is not even reducible to the genetic code,,,,

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    http://www.metacafe.com/watch/4187488

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer”Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

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

    ,,,,,,,etc..etc.. etc…

    ,,,,,,,, nor does genetic similarity even support the evolutionary framework if Genetic Reductionism were true,,,,

    Here is another article, written by an evolutionist mind you, that states the true pattern found for life, from comparative genetic evidence, is not the tree pattern Darwin had envisioned:

    A New Model for Evolution: A Rhizome – May 2010
    Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.
    http://darwins-god.blogspot.co.....izome.html

    ,,,,,yet despite the fact that neo-Darwinism is falsified for its foundational molecular framework in the first place, evolutionists still argue vehemently that common ancestry is shown to be true by genetic similarities,,, but here you come along and now you want completely divorce genetic sequences from morphology entirely. i.e. you are stating, despite much evidence to the contrary, that genetic sequences are not related to morphology at all since the morphology of sponges demonstrate extreme conservation!?!

    Do you see the extreme disconnect with claims here goodusername??? So which is it that you believe, 1) do you believe that genetic sequences are related to changing morphologies as is claimed by neo-Darwinists??? or 2) do you not believe that genetic sequences are related to changing morphologies as you are claiming in this instance???

  40. bornagain: After all these months, I really, really have to know: Why all the ,,,,,commas? :)

  41. Lenoxus I really don’t know, just kind of grown attached to them little fellows,,,, Here is a cool video for you that just came:

    Should Intelligent Design Be Taught as Science? Michael Behe debates Stephen Barr
    http://www.isi.org/lectures/fl.....4/lectures

    main page:
    http://www.isi.org/lectures/le.....40402af8e3

    ,,,,,,, it really was a pleasure to watch the debate,,,, Behe is really on top of his game in this debate!!

  42. Heinrich:

    Stromatilites (=stromatolites) are apparently rock formations thought to have been the result of some microorganism, and cyanobacteria in particular.

    Bacteria are protists. There is controversy over whether protists should be separated from protozoa. Either way, where are the intermediates prior to the sponges?

    Lenoxus:

    Glad to see the open-mindedness. Just one point, though, and it’s not a minor one.

    You say we IDers look at genes with no purpose as “junk DNA”, which, of course, we IDers generaly would oppose, while the Darwinists are arguing that the genes must have had/have a function—though it’s unknown. A seeming standoff. But remember this, the actual ID position has always been—and this comes from the design perspective—that the genes were only along for the ride, and that what really counted were the genetic programs that very likely existed in what the Darwinists referred to as “junk DNA”. This then would lead to the idea of “front-loading”, an idea long held by IDists since the 90′s, one long scorned by the Darwinists, but now, seemingly confirmed in our lowly little sponge.

    Food for thought.

  43. BornAgain:

    Bravo. Splendid reply.

    About the “soft-bodied” fossils in the Ediacaran: it always seemed to me that if you could find “fossil footprints”, then you could find anything. I haven’t made that argument before; but it seems more and more to be an inescapable conlusion.

  44. bornagain77,

    “One the one hand evolutionists want to use genetic similarity evidence as evidence of common ancestry, even though body-plan morphogenesis is not even reducible to the genetic code”

    –Even if one were to concede that body-plan morphology is not wholly reducible to the genetic code, what would that have to do with whether genetic similarity is evidence of common ancestry?

    “but here you come along and now you want completely divorce genetic sequences from morphology entirely. i.e. you are stating, despite much evidence to the contrary, that genetic sequences are not related to morphology at all since the morphology of sponges demonstrate extreme conservation!?”

    –What I said is that DNA is not a blueprint, i.e. one may be able to determine (for the most part) the morphology of a lifeform by studying the DNA, but the reverse is not true – one can’t determine the DNA of an organism by looking at its morphology (think of organisms with similar structures but with dissimilar DNA). Blueprints and a building are two ways of representing the same data – this is not the case with morphology and DNA.
    Also, DNA can change without much change in morphology – but the reverse is not true.

  45. Dave Scott brought up the “front-loading” issue nearly 2 years ago here and I have been surprised that it has not gotten more attention at UD and other ID sites, seems like it deserves much more.

    Has Dave Scot posting on a blog or forum somewhere? I have looked around for him since he left UD, but no success thus far.

  46. goodusername,

    Whatever your starting position as to the evidence that will be uncovered for genomes in sponges (Which are not controversial claims for me), I still hold that I have a very strong case for the stability of genomes over long periods of time with the work I’ve already cited on protein domains of Doug Axe, and also with the comparative work of Ancient to Modern Bacteria by Vreeland and company, as well as other work on ancient/modern bacteria by Cano and company. Whereas goodusername, if you are indeed holding to a neo-Darwinian position, you are merely asserting things that I already know. To try to make this clear for you, you have no mechanism for change, whatsoever, at the most foundational level of molecular biology (gene/protein) that we can test for, so as to make the assertions for extreme gene flexibility that I believe you are making for neo-Darwinism. To actually stay within the field of science you must counter the work of Doug Axe first and foremost, as well counter the work on ancient/modern bacteria, that show the same sequences, and then goodusername, if you really want to get to the nitty gritty of it all, scientifically, and prove that neo-Darwinism is not the dumbest idea ever taken seriously by science, you must falsify David Abel’s null hypothesis for the generation of information by material processes:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    ,,,,goodusername I know I’m not all that clear sometimes as to just how ridiculous evolution is, so thus I give you tgpeeler who puts it much more clearly than I can in this short video:

    Modus Tollens – It Is Impossible For Evolution To Be True – TG Peeler – short video
    http://www.metacafe.com/watch/5047482

  47. Bacteria are protists. There is controversy over whether protists should be separated from protozoa. Either way, where are the intermediates prior to the sponges?

    Um, no. Protists are eukaryotes.

    I don’t know where the intermediates are, but that’s because this isn’t my area. If you genuinely want to know, I suggest you do some research into sponge evolution, and see what the current theories are.

  48. Heinrich, neo-Darwinists don’t even have the simplest first steps of evolution down much less the next ‘step’ to sponges:

    Did DNA replication evolve twice independently? – Koonin
    Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus.
    http://nar.oxfordjournals.org/.....27/17/3389

    There simply is no smooth ‘gradual transition’ to be found between these most ancient of life forms, bacteria and archaea, as this following articles and video clearly point out:

    Was our oldest ancestor a proton-powered rock?
    Excerpt: In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,… Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria and the archaea).
    http://www.newscientist.com/ar.....tml?page=1

    Problems of the RNA World – Did DNA Evolve Twice? – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4564682

    Bacteria Too Complex To Be Primitive Eukaryote Ancestors – July 2010
    Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified…. There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote.
    http://www.creationsafaris.com.....#20100712b

  49. bornagain77,

    “if you are indeed holding to a neo-Darwinian position, you are merely asserting things that I already know.”

    –If you know what evolution/Darwinism claims, then good. The article I responded to, however, seemed to imply that evolution claims that somehow ALL the genes of a species originate with the origin of that species, and that one could supposedly study the genome of an ancient lifeform by studying the genome of a modern species that’s classified in the same taxonomic group (i.e. that we could study the ‘fish’ ancestor of vertebrates by studying the genome of a trout).

    From what I gleam from the Douglas Axe study, the results have nothing to do with the odds of a protein finding a role, or a role being filled by a protein, but rather the experiment had to with “how many variations of THIS particular protein can perform THIS particular job in THIS particular environment”. I would fully expect the results to show that the number of variations of a particular protein performing a particular role to be astonishingly small. Under such constraints, I’m not sure what relevance the study has.

    The Vreeland study was surprising, as there were fewer differences than expected between the ancient bacteria and the modern counterparts. Of course, it was also surprising to find 250 million year old bacteria (although the age is still controversial).
    Both surprises may have the same cause. If the bacteria are in fact that old, than the strain of bacteria must be able to basically turn off for long periods – perhaps millions of years. The calculation of how many differences there ‘should’ be in the dna of the ancient and modern bacteria are based on estimates of how many generations of bacteria separate the ancient and modern counterparts. If the bacteria has the ability to lengthen its generational time from days – to millions of years – than, obviously, calculations of how many differences there ‘should’ be between the two groups will be way off.

    With the Cano study, the differences between the ancient and modern bacteria were more in line with expectations:
    http://ijs.sgmjournals.org/cgi.....f_ipsecsha

  50. goodusername, I beg to differ on the Cano study ‘being more in line’ since I have in fact dug into this a bit:

    In fact here are my notes on the whole thing:

    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

    Evolutionists were so disbelieving at this stunning lack of change that they insisted the stunning similarity was due to modern contamination in Vreeland’s experiment. Yet the following study laid that objection to rest by verifying that Dr. Vreeland’s methodology for extracting ancient DNA was solid and was not introducing contamination because the DNA sequences this time around were completely unique:

    World’s Oldest Known DNA Discovered (419 million years old) – Dec. 2009
    Excerpt: But the DNA was so similar to that of modern microbes that many scientists believed the samples had been contaminated. Not so this time around. A team of researchers led by Jong Soo Park of Dalhousie University in Halifax, Canada, found six segments of identical DNA that have never been seen before by science. “We went back and collected DNA sequences from all known halophilic bacteria and compared them to what we had,” Russell Vreeland of West Chester University in Pennsylvania said. “These six pieces were unique”,,,
    http://news.discovery.com/eart.....vered.html

    These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland’s work:

    “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
    http://www.physicsforums.com/s.....p?t=281961

    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

    Dr. Cano’s work on ancient bacteria came in for intense scrutiny since it did not conform to Darwinian predictions, and since people found it hard to believe you could revive something that was millions of years old. Yet Dr. Cano has been vindicated:

    “After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber.”
    http://www.uncommondescent.com.....ent-357693

    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 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. Here is a revisit to the video of the ‘Fitness Test’ that evolutionary processes have NEVER passed as for a demonstration of the generation of functional complexity/information above what was already present in a parent species bacteria:

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

    According to prevailing evolutionary dogma, there ‘HAS’ to be ‘major genetic drift’ to the DNA of bacteria within 250 million years, even though the morphology (shape) of the bacteria can be expected to remain exactly the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. In fact recent research, with bacteria which are alive right now, has also severely weakened the ‘genetic drift’ argument of evolutionists:

    The consequences of genetic drift for bacterial genome complexity – Howard Ochman – 2009
    Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
    http://genome.cshlp.org/conten.....091785.109

  51. goodusername,

    As for your trivialization of the Axe study for rarity of proteins in sequence space. The study in fact overwhelmingly points out that neo-Darwinian evolution is NEVER EVER going to find ANY novel proteins in ANY random search. Thus what you so lightly dismiss as inconsequential, is in fact the very reason that we, from a purely unbiased scientific perspective, should confidently presuppose that genomes ARE NOT randomly drifting about searching for new function as neo-Darwinism requires. I might add that neo-Darwinism requires this ‘drift’ for purely metaphysical reasons with no empirical basis to appeal to to substantiate the presupposition. That you would be so impervious to this obvious fact doesn’t bode well for your predisposition in looking at this evidence. Nevertheless to give you a benefit of a doubt, that you really just don’t know any better, the thing that really nails down the fact that we should not expect extreme drift in genomes is this:

    Scientists Map All Mammalian Gene Interactions – August 2010
    Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome.
    http://www.sciencedaily.com/re.....142044.htm

    goodusername this is definitely a severely polyfunctional situation which completely isolates what we should a-priori expect for the generation of functional information by random processes. The reason why is due to the fact that it is now known to be in a severely polyconstrained limit for the amount of variation we can expect from such a overwhelmingly complex interwoven ‘polyfunctional’ situation. This following site gives a crystal clear example of the insurmountable difficulty this finding presents to neo-Darwinism:

    Poly-Functional Complexity equals Poly-Constrained Complexity
    https://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ

    this video gives explains a bit also:

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

    I could quote several recent studies indicating the severely polyconstrained nature of ‘protein networks’ as well goodusername!!!

    Insight into cells could lead to new approach to medicines
    Excerpt: Scientists expected to find simple links between individual proteins but were surprised to find that proteins were inter-connected in a complex web. Dr Victor Neduva, of the University of Edinburgh, who took part in the study, said: “Our studies have revealed an intricate network of proteins within cells that is much more complex than we previously thought.
    http://www.physorg.com/news196402353.html

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

    etc..etc..etc..

    Here is another article showing why we should a-priori expect polyconstraint on genomes:

    K´necting The Dots: Modeling Functional Integration In Biological Systems
    Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream”,,,”those genes which govern major changes, the very stuff of macroevolution, apparently do not vary, or vary only to the detriment of the organism”
    http://www.uncommondescent.com.....l-systems/

    goodusername and other than wishfulspeculation tell me exactly why we should ignore all this evidence and grant the neo-Darwinian presupposition of extreme drift for genomes??,,,.

    ,,,it turns out that all the evidence for evolution is actually nothing but hot air since they (neo-Darwinists) have in fact not passed the following simple test,,,,

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

  52. bornagain77,

    The Axe study, contrary to the abstract, wasn’t a “test for function”, it was a test for ONE particular function by mutating ONE particular protein. The “1 in 10^77” isn’t a calculation of how many sequences of possible proteins are functional – it’s a calculation of how many variants of “protein A” can perform “function B”. Whether the “functionless” variants may be able to perform functions “C”, “D” or “E”, who knows. Whether other unrelated proteins may be able to perform “function B”, who knows.

    The problem I see with the “polyconstrained” idea, is that there are often copies, multiple copies, of many genes in the genome.

  53. goodusername,
    speculation and excuses do not suffice to overturn the empirical evidence presented thus far (of which I could present much much more). If you want to follow the evidence where it leads that is all fine and well but I will not play endless games of hypotheticals with someone who is merely interested in hiding in whatever imaginary “could of, would of, should of” he can find to ease his inability to come to grips with the implications of a design conclusion.

  54. bornagain77,

    What speculation? It’s not speculation to point out that the Axe study was only testing for ONE function. The only speculation is saying that if it can’t do that ONE function that it can’t do any other function either! If your only test for function is “turning a screw” than hammers, chainsaws, and drills are “functionless”.

  55. goodusername, The proteins ALREADY ARE polyfunctional (more than ONE function). Polyfunctional in a way that puts severe polyconstraint on their ability to acquire any new novel functionality whatsoever! What the FACT is is that ANY search through sequence space to find a novel function that varies the codon/amino acid sequence WILL CONSISTENTLY destroy the multiple other functions that a protein is already performing in its duty! Yet neo-Darwinism has a metaphysical commitment, with no empirical support whatsoever, to the idea that proteins can vary in sequence space. This is more than a slight problem than can be overcome with your appeals to imaginary pathways. goodusername You MUST present countervailing empirical evidence that proteins can vary in sequence space! For you to merely state a belief that protein sequence variance can randomly happen is NOT even in the field of honest scientific endeavor!

    notes:

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    Human Genome “Infinitely More Complex” Than Expected – April 2010
    Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said, speaking of the gene regulation was a straightforward, linear process of gene coding for regulator protein that controls transcription. “Biology’s new glimpse at a universe of non-coding DNA – what used to be called ‘junk’ DNA – has been fascinating and befuddling.” If it’s junk, why would the human body decode 74% to 93& of it? The plethora of small RNAs produced by these non-coding regions, and how they interact with each other and with DNA, was completely unexpected when the project began.,,, In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the ‘virtual human’. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model.,,, The p53 network she spoke of is a good example of unexpected complexity. Discovered in 1979, the p53 protein was first thought to be a cancer promoter, then a cancer suppressor. “Few proteins have been studied more than p53,” she said. “…Yet the p53 story has turned out to be immensely more complex than it seemed at first.” She gave some details: “Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death and structure and DNA repair. It also binds to numerous other proteins, which can modify its activity, and these protein–protein interactions can be tuned by the addition of chemical modifiers, such as phosphates and methyl groups. Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development. In fact, it seems willfully ignorant to try to understand p53 on its own. Instead, biologists have shifted to studying the p53 network, as depicted in cartoons containing boxes, circles and arrows meant to symbolize its maze of interactions.
    Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.”
    http://www.creationsafaris.com.....#20100405a

    Here is part of the ‘network’ that p53 is interconnected with:

    ‘Linc-ing’ a noncoding RNA to a central cellular pathway – August 2010
    Excerpt: This current work demonstrates that several dozen lincRNAs are targeted directly by p53, and lincRNA-p21 in particular responds to p53 signaling by suppressing multiple genes across the genome to drive apoptosis. “We were surprised to find that lincRNA-p21 appears to be functioning as a global repressor, regulating hundreds of genes in the p53 pathway,” said Maite Huarte, PhD, first and co-corresponding author. “This lincRNA is playing defense for p53 to block other pathways in their efforts to interfere with p53′s critical job of tumor suppression by cell death.” lincRNA-p21 carries out this function by roping in other critical factors in the cell nucleus to assist in tamping down expression at specific genes. “In the same way that air traffic controllers organize planes in the air, lincRNAs organize key nuclear complexes in the cell,” said Rinn. “lincRNA-p21 specifically binds to a protein called hnRNP-K and then guides hnRNP-K to its final destination to shut down any genes that interfere with p53.” As exciting as these findings are for understanding multiple forms of cancer, they have far broader implications for understanding basic genome biology and multiple diseases.
    http://www.physorg.com/news199625236.html

    This following sight has a video and graph explaining the large scale regulatory role that has been found for RNA elements generated from ‘Junk DNA’ segments of the genome for p53:

    A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response – with Graph and Video
    http://www.cell.com/fulltext/S0092-8674(10)00730-0

    further notes:

    What makes matters much worse for the materialist is that he will try to assert that existing functional proteins of one structure can easily mutate into other functional proteins, of a completely different structure or function, by pure chance. Yet once again the empirical evidence betrays the materialist. The proteins that are found in life are shown to be highly constrained in their ability to evolve into other proteins:

    Dollo’s law, the symmetry of time, and the edge of evolution – Michael Behe – Oct 2009
    Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,,
    A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses.
    http://www.evolutionnews.org/2.....f_tim.html

    Severe Limits to Darwinian Evolution: – Michael Behe – Oct. 2009
    Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
    http://www.evolutionnews.org/2......html#more

    “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed – along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

    “A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble.”
    Problems in Protein Evolution:
    http://www.cs.unc.edu/~plaisted/ce/blocked.html

    Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors – Doug Axe
    Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular.
    http://nsmserver2.fullerton.ed.....lution.pdf

    etc.. etc..etc..

  56. of related note:

    The bad news for Darwinists just keeps coming:

    Remarkably, they find that the genomic locations of binding sites for two key regulatory proteins (OCT4 and NANOG) are poorly conserved across species, despite their functional importance in mammalian embryonic stem cell biology. […]

    Unexpectedly, only ~5% of binding sites for the two transcription factors OCT4 and NANOG were found in orthologous positions in human and mouse ES cells, suggesting major differences in genome-wide binding profiles between species.
    http://darwins-god.blogspot.co.....erved.html

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