Thursday, June 28, 2012

Evolution Professor: “The Tree is All Wrong”

When Charles Darwin proposed his theory of evolution in 1859 there were many scientific problems with the idea. Today, a century and a half later, we know of a great many more empirical challenges to the idea that the species arose spontaneously. The latest falsified expectation is that microRNAs, discovered only a few decades ago, when compared between different species do not align with the evolutionary tree. Evolutionist Kevin Peterson and colleagues are pursuing this research. “I've looked at thousands of microRNA genes,” explains Peterson, “and I can't find a single example that would support the traditional tree.”

While there remain questions about these new phylogenetic data, “What we know at this stage,” explains another evolutionist, “is that we do have a very serious incongruence.” In other words, different types of data report very different evolutionary trees. The conflict is much greater than normal statistical variations.

“There have to be,” adds another evolutionist, “other explanations.” One explanation is that microRNAs evolve in some unexpected way. Another is that the traditional evolutionary tree is all wrong. Or evolutionists may consider other explanations. But in any case, microRNAs are yet another example of evidence that does not fit evolutionary expectations. Once again, the theory will need to be modified in complex ways to fit the new findings.

It isn’t that any one particular finding falsifies evolution, but the consistent pattern of contradictory findings—from nature’s complexities to uncooperative patterns—show that evolution is not explanatory, but rather tautological.

h/t: bornagain77

62 comments:

  1. Once again, the theory will need to be modified in complex ways to fit the new findings.

    Absolutely. That's how science works.

    It isn’t that any one particular finding falsifies evolution, but the consistent pattern of contradictory findings—from nature’s complexities to uncooperative patterns—show that evolution is not explanatory, but rather tautological.

    oops.

    Well, I'll grant you one thing, Cornelius: the ill-defined notion you call "evolution", probably is tautological. But it has nothing to do with science.

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    1. Liddle:

      Absolutely. That's how science works.

      Not true. This is not how science works. Traditionally, an old theory that does not agree with new data is accepted as having been falsified and one or more new theories are formulated to take its place. For example, when Newtonian mechanics was found to be at odds with the data, two new theories took its place: the General and the Special Theories of Relativity. Newtonian Theory was relegated to non-relativistic situations.

      That's how it's done when scientists are honest.

      Delete
    2. Louis Savain: For example, when Newtonian mechanics was found to be at odds with the data, two new theories took its place: the General and the Special Theories of Relativity. Newtonian Theory was relegated to non-relativistic situations.

      That is not historically accurate. When anomalies were discovered, Newton's Theory of Gravity still remained the predominant theory. For instance, the anomalous precession of the perihelion of Mercury's orbit was discovered in 1859, yet General Relativity was still generations in the future. Rather, scientists continued to work with Newton's Theory of (almost) Universal Gravity for quite some time. Even today, Newton's Theory is taught as a useful and powerful theory.

      Keep in mind that scientific theories are models, and don't always perfectly represent all possible observations. Models are more or less useful, more or less accurate.

      Delete
    3. Not true. This is not how science works.

      Um, yes, it is.

      Traditionally, an old theory that does not agree with new data is accepted as having been falsified and one or more new theories are formulated to take its place.

      No, this is a misunderstanding. Occasionally an entire theory are found to be a hugely worse fit to the data than some alternative theory (geocentricity versus heliocentricity) and we say the model is "falsified". A better way of expressing it is as I just did: it has been completely superceded by a better-fitting model.

      But far more often, the model is continuously adjusted. A model never fits the data perfectly. That's why we use "goodness-of-fit" statistics to decide which of two competing models to retain.

      Also, be careful, when using "falsification" language. It is not so much theories that are tested (theories as in "explanatory narratives that might explain existing data) but hypotheses that are derived from them, and, in practice, the hypothesis we try to falsify is the null. And that only probabilistically (hence p values and confidence intervals).

      For example, when Newtonian mechanics was found to be at odds with the data, two new theories took its place: the General and the Special Theories of Relativity. Newtonian Theory was relegated to non-relativistic situations.

      Not really, as Pedant explains above. Newton's model is still a very good fit to data, within certain ranges. But we require a more complex set of equations if we are going to make good predictions outside those data ranges.

      That's how it's done when scientists are honest.

      It's not a question of honesty. It's a question of methodology.

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    4. Zachriel and Liddle,

      Haysoos Martinez! Why are you people so defensive? Will you gain eternal life is evolution is shown to be correct? What the heck are you defending that is so darn important? What are you afraid of? Be cool.

      The point I am making is that, unlike the theory of evolution, neither Ptolemaic epicycles nor Newtonian mechanics nor Einsteinian relativity theories have changed one iota since they were formulated. In science, it is customary and more honorable to formulate a new theory rather than to modify an existing one that is no longer adequate.

      Since the TOE changes so much due to repeated falsification of its predictions, it would have been better and more honest to number them: TOE1, TOE2, TOE3, etc.

      Delete
    5. Zachriel said

      "Keep in mind that scientific theories are models, and don't always perfectly represent all possible observations. Models are more or less useful, more or less accurate."

      So, It it would be perverse to withhold provisional assent to an imperfect model?

      Delete
    6. Louis: Since the TOE changes so much due to repeated falsification of its predictions, it would have been better and more honest to number them: TOE1, TOE2, TOE3, etc.

      Feel free to do so, Louis. As I keep asking, when anyone has a problem with "evolution": which bit do you have a problem with?


      Practically speaking, though, there aren't discrete formulations - it changes all the time, because it isn't a single theory, but rather an explanatory framework, which is subject to constant change in the details, but remarkably little change to the broad outline, which remains:

      Life probably started as a population of simple organisms which bifurcated and adapted over the eons into many highly specialised niches, with the vast majority of lineages going extinct on the way.

      And that "adaptation" is the result of small variations in hereditary characteristics that confer differential reproductive success in the current environment. This last was Darwin's really great contribution, and has been actually observed, in the lab, field, and in computational applications.

      Delete
    7. Blas: So, It it would be perverse to withhold provisional assent to an imperfect model?

      You're still confusing fact and theory.

      Louis Savain: The point I am making is that, unlike the theory of evolution, neither Ptolemaic epicycles nor Newtonian mechanics nor Einsteinian relativity theories have changed one iota since they were formulated.

      Epicycles were a modification of previous cosmologies. And Einstein's theories have been modified, such as the cosmological constant.

      More specifically, you're confusing the various mechanisms of evolution with its history over time.

      Delete
  2. I wouldn't "harrumph!" too loudly just yet CH. These are tentative, unverified results. As explained by the article, there are certainly other plausible hypotheses for the mRNA data that are actively being investigated.

    Please note that this issue was raised by an evolutionist, with data/results presented for peer review to evolutionists, and being investigated further by evolutionists. Proper scientific process is being followed and additional evidence is being gathered that will shed more light on the phenomenon. As always, any modification to the theory if required will be driven by the data, not the other way around.

    Science CH. You should learn about how it works sometime.

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    1. Thorton:

      there are certainly other plausible hypotheses for the mRNA data that are actively being investigated.

      You mean more just-so stories that cannot be tested? I agree.

      Delete
    2. You seem under the impression that hypotheses about evolutionary processes cannot be tested.

      This is not true.

      Delete
    3. "You seem under the impression that hypotheses about evolutionary processes cannot be tested.

      This is not true."

      "Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way. - Doug Axe PhD.

      Nothing In Molecular Biology Is Gradual - Doug Axe PhD.
      http://www.metacafe.com/watch/5347797/

      Testing Evolution in the Lab With Biologic Institute's Ann Gauger - podcast with link to peer-reviewed paper
      Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger's paper, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,".
      http://intelligentdesign.podomatic.com/entry/2010-05-10T15_24_13-07_00

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

      “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010
      Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit')
      http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

      Michael Behe talks about the preceding paper on this podcast:

      Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010
      http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00

      Where's the substantiating evidence for neo-Darwinism?
      https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

      Delete
    4. Liddle:

      You seem under the impression that hypotheses about evolutionary processes cannot be tested.

      This is not true.


      You mean that you have a test that can falsify the hypothesis that all Earth species arose via Darwinian evolutionary processes? Would you run that test by me one more time? I must have missed it the first time around.

      Delete
    5. Louis Savain

      Liddle:

      You seem under the impression that hypotheses about evolutionary processes cannot be tested.

      This is not true.

      You mean that you have a test that can falsify the hypothesis that all Earth species arose via Darwinian evolutionary processes? Would you run that test by me one more time? I must have missed it the first time around.


      You miss a lot of things Louis.

      First, take the fossil record. Make an objective 'best fit' phylogenetic tree based on morphological similarities and estimated timelines.

      Second, take the genetic record. Make an objective 'best fit' phylogenetic tree based on DNA segment similarities and estimated divergence times.

      Compare the two independently created trees. If they disagree to any degree of statistical significance, evolution is falsified.

      Guess what Louis - the test has already been done. What do you think the results were?

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    6. Thorton do you mean this test:

      Nature Article Finds MicroRNAs are "Tearing Apart Traditional Ideas about the Animal Family Tree"
      Casey Luskin June 29, 2012
      Excerpt: When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn't cooperate. If the traditional tree was correct, then an unprecedented number of microRNA genes would have to have been lost, and Peterson considers that highly unlikely. "The microRNAs are totally unambiguous," he says, "but they give a totally different tree from what everyone else wants.",,, Maybe the reason that different genes yield different evolutionary trees is because there isn't a single unified tree of life to be found. In other words, perhaps universal common ancestry is simply wrong.
      http://www.evolutionnews.org/2012/06/nature_article061471.html

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    7. Stupid evolutionist:

      You miss a lot of things Louis.

      There is nothing to miss. See below.

      First, take the fossil record. Make an objective 'best fit' phylogenetic tree based on morphological similarities and estimated timelines.

      Second, take the genetic record. Make an objective 'best fit' phylogenetic tree based on DNA segment similarities and estimated divergence times.

      Compare the two independently created trees. If they disagree to any degree of statistical significance, evolution is falsified.

      Guess what Louis - the test has already been done. What do you think the results were?


      Only in the feverish imagination of a stupid evolutionist does this test prove that Darwinian processes are responsible for the origin of the species. This could have easily been the result of design evolution as well.

      Try again, stupid.

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    8. This comment has been removed by the author.

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    9. Louis: You mean that you have a test that can falsify the hypothesis that all Earth species arose via Darwinian evolutionary processes? Would you run that test by me one more time? I must have missed it the first time around.

      No, I don't. That's not a validly formulated hypothesis. In fact, it's a theory rather than a hypothesis. However, what we could do is derive a testable hypothesis from that theory - i.e. figure out what we would expect to see if the theory were true. It wouldn't, and couldn't, tell us whether there were any exceptions to the rule though. Notoriously, in science, you can't do that. At best we can say "we haven't found any".

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    10. Louis Savain

      Only in the feverish imagination of a stupid evolutionist does this test prove that Darwinian processes are responsible for the origin of the species. This could have easily been the result of design evolution as well.


      You didn't ask for a test that proves Darwinian processes are responsible for the origin of the species. You specifically asked for a test that could potentially falsify the idea, which the above test can do.

      Try again, stupid.

      Says the guy who was too stupid to remember the question he asked.

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    11. Stupid evolutionist:

      Louis Savain

      Only in the feverish imagination of a stupid evolutionist does this test prove that Darwinian processes are responsible for the origin of the species. This could have easily been the result of design evolution as well.

      You didn't ask for a test that proves Darwinian processes are responsible for the origin of the species. You specifically asked for a test that could potentially falsify the idea, which the above test can do.


      Dummy. Did I ask for a test that falsifies both design evolution and Darwinian evolution? No, I didn't. I specifically asked for a test that falsifies Darwinian evolution. If the test you offered is what makes Darwinian evolution a science, then it follows that it also makes design evolution a science.

      Arguing with stupid evolutionists is like pulling teeth. I swear.

      Delete
    12. Louis Savain

      Dummy. Did I ask for a test that falsifies both design evolution and Darwinian evolution? No, I didn't. I specifically asked for a test that falsifies Darwinian evolution.


      And that's specifically what you got, bigger dummy.

      BTW, the test doesn't falsify Design because an omnipotent Designer has no constraints on how the design is done, either with or without matching phylogenetic trees.

      If the test you offered is what makes Darwinian evolution a science, then it follows that it also makes design evolution a science.

      The test doesn't make evolution a science, but being subject to falsification does make it a testable scientific hypothesis. That's something that ID does not have, which is why ID isn't scientific.

      Arguing with stupid evolutionists is like pulling teeth. I swear.

      Laughing at internet Creationist clowns OTOH is very enjoyable!

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    13. Stupid evolutionist:

      And that's specifically what you got

      Liar, liar, pants on fire. See my previous comment and feel like a fool.

      BTW, the test doesn't falsify Design because an omnipotent Designer has no constraints on how the design is done, either with or without matching phylogenetic trees.

      You pulled that one right out of your asteroid orifice, didn't you, dummy? ID does not postulate an omnipotent designer and never did. The only requirement is that the designer is intelligent. Were you raised by fundamentalist Christians? You sound like that other stupid evolutionist, PZ Myers who also got a fundamentalist chip on his shoulders.

      The test doesn't make evolution a science, but being subject to falsification does make it a testable scientific hypothesis.

      Wow. That sentence makes sense only to a stupid evolutionist. Being subject to falsification is the same as providing a falsification test, meat head.

      That's something that ID does not have, which is why ID isn't scientific.

      Intelligent design certainly predicts a non-nested hierarchy. I already explained the reason to you elsewhere but it went over your stupid evolutionist head. I won't make the same mistake again. You know: pearls, trampling swines and all that.

      Why is it that all evolutionists have room temperature IQ? It must be in the genes.

      Delete
  3. > Please note that this issue was raised by an evolutionist, with data/results presented for peer review to evolutionists, and being investigated further by evolutionists

    Yes, but that's where all the funding is. Had a creationist or ID advocate performed this study, it may not have been published, and we would have to wait for an evolutionist to repeat the experiment.

    Consider the case of Didier Raoult, called France's "most productive and influential microbiologist", he was temporarily banned from publishing in a dozen leading microbiology journals after releasing his book, Dépasser Darwin (Beyond Darwin), where he wrote that "de novo creation of entirely new species is possible" and "Darwin's branching tree of life should be replaced by a network of interconnected species."

    http://www.sciencemag.org/content/335/6072/1033.summary

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  4. I would like to know more about that "temporary ban".

    Do you have any other source?

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    1. I've searched, and all links lead back to that same Science Mag article.

      I'd like to see some independent corroboration.

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    2. http://scholar.google.co.uk/scholar?as_ylo=2006&as_yhi=2008&q=didier+raoult&hl=en&as_sdt=0%2C5

      Didier Raoult seems to have published as impressively and prolifically through 2006 to 2008 as throughout his impressive career.

      I smell a rat.

      Delete
    3. Ah, interesting. I just got hold of the full article. Catherine Mary writes:

      But some scientists grumble that manuscripts out of Raoult's lab often contain errors, for instance, as a result of unchecked genetic sequences.

      Indeed, problems in a paper about a mouse model for typhus got his lab in hot water in 2006. A reviewer for Infection and Immunity, a journal published by the American Society for Microbiology (ASM), discovered that four figures in a revised manuscript were identical to figures in the original manuscript, even though they were supposed to describe a different experiment.

      In letters to ASM, made available by Raoult, second author Christian Capo and last author Jean-Louis Mège, a group leader, accepted “full responsibility” for the problem, which they said involved only two figures. Capo, in his letter, wrote that he had made an innocent mistake; Mège wrote that Capo had subsequently failed to show the revised manuscript to other authors, who were on vacation, before resubmitting it. But after consulting its ethics panel, ASM banned all five authors, including Raoult, from publishing in its journals for a year. “We are not entirely comfortable with the explanation provided,” ASM officials wrote to Mège. “Misrepresentation of data … is an affront to the ethical conduct of scientific inquiry.”

      Capo and Mège accepted the decision, but Raoult wrote ASM that he wasn't at fault and that the “collective punishment” was “very unfair.” He appealed the ban, also on behalf of two other co-authors, but lost. Furious, he resigned from the editorial board of two other ASM journals, canceled his membership in the American Academy of Microbiology, ASM's honorific leadership group, and banned his lab from submitting to ASM journals, in which he had published more than 230 studies. His name has been on only two ASM journal papers since, both published in 2010. To clear his name, Raoult sent his ASM correspondence to French colleagues in 2007, along with a letter defending himself. “If I had been in the United States, I would have sued,” he wrote.


      So it looks as though he and his lab were banned as a disciplinary measure from the journals of one publishing house, for scientific misconduct - nothing to do with Raoult's book.

      Odd that all I could find through google were links from anti-evolution sites, including this one, implying that Raoult was banned because he wrote an "anti-Darwin" book.

      Actually, his book sounds rather interesting. I wonder if it is out in English yet.

      And then there is his popular science book Dépasser Darwin (Beyond Darwin). “Darwin was a priest,” Raoult says, claiming that the image of the tree of life that Darwin proposed is inspired from the Bible. “It also is too simplistic.” Raoult questions several other tenets of modern evolutionary theory, including the importance of natural selection. He says recent discoveries in genetics show how frequently genes are exchanged not just between different microbial species but also between microbes and complex organisms, for instance, in the human gut. That means de novo creation of entirely new species is possible, Raoult argues, and Darwin's branching tree of life should be replaced by a network of interconnected species.

      Delete
    4. Interesting. Thanks for sharing this, since I don't have access to the full article.

      > four figures in a revised manuscript were identical to figures in the original manuscript, even though they were supposed to describe a different experiment

      This sounds more like an editing mistake than a deliberate falsification of data, although we can't know for sure. His lab has published hundreds of papers. Is it humanely possible to do that much research without having an error somewhere?

      I also wouldn't expect his critics to cite his views on Darwinism as their motive. But rereading the summary: http://www.sciencemag.org/content/335/6072/1033.summary , I now see that there's no causal relationship described between his views and the ban.

      Delete
    5. Actually, it looks like his book was released several years after his ban; didn't notice that the first time.

      Delete
  5. This reminds me of another half-baked study that purported to overthrow previously well-established science: faster-than-light neutrinos. The news received a lot of play on Uncommon Descent.

    Wait till this gets settled, Cornelius.

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  7. Some information of interest:

    -In this case, "the evolutionary tree" is specifically the tree of mammals, not the whole tree.

    -Peterson works under the unusual assumption that microRNA genes can be gained but almost never lost. This seems to be the case with many other animal clades, but it remains a controversial assumption (and something could be different in mammals). The article indicates a presence/absence analysis. I'd like to know what the sequences have to say as well. Peterson himself has incorporated other types of data in some of his previous work.

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  8. Liddle said:

    Well, I'll grant you one thing, Cornelius: the ill-defined notion you call "evolution", probably is tautological. But it has nothing to do with science.

    What exactly IS the definition of evolution Miss Liddle, because from everything I've read (on ALL sides) it can allegedly do anything evolutionists need it to do. When the evidence contradicts evolutionary predictions/expectations, well that just means there's more to learn about it. It's become an umbrella term meaning "whatever is found in biology"...how is that "science" when it's UNfalsifiable???

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    1. There isn't a single definition, National Velour, which is why, when "anti-evolutionists" attack "evolution", they need to make it clear exactly what they take issue with. They rarely do.

      You are not reporting what "evolutionists" say - you are reporting what "anti-evolutionists" say they say.

      What is called the "Theory of Evolution" encompasses the mechanism Darwin proposed, which has been observed to work in real time; the idea that extant species and those observed in the fossil record form a vast bifurcating family tree from simpler ancestral populations; that populations adapt to their environment over time by means of Darwin's proposed mechanism; that phenotypic characteristics (what organisms are like and the way they work) are inherited by means of molecular sequences in the DNA molecule; that phenotypic variance arises from variations in those sequences; that those variations arise from many different mechanisms involved in the replication of cells and the DNA they contain, as well as other mechanisms, including "horizontal" transmission mechanisms e.g. virus; that many gene sequences in DNA are involved in regulating the expression of other genes, so that a relatively slight variation in the regulatory gene network can have a substantial effect on the growing, and thus on the adult, organism...etc.

      So in a sense you are right, it is an "umbrella" term to refer to all we know about the way living things evolve over time, including the fact that they do (in the sense that populations over time consist of individuals who can differ quite markedly from earlier generations).

      So next time you read a criticism on "evolution" - ask the author what he s/he actually means - what is s/he he attacking.

      Because what "evolution" does NOT mean (except in the mouths of a few idiosyncratic and often hostile writers) is "life formed by chance and was not guided by a creator deity".

      That is a straw man, but one found frequently lurking.

      Delete
  9. Casey Luskin has a article up:

    Nature Article Finds MicroRNAs are "Tearing Apart Traditional Ideas about the Animal Family Tree"
    Casey Luskin June 29, 2012
    Excerpt: When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn't cooperate. If the traditional tree was correct, then an unprecedented number of microRNA genes would have to have been lost, and Peterson considers that highly unlikely. "The microRNAs are totally unambiguous," he says, "but they give a totally different tree from what everyone else wants.",,, Maybe the reason that different genes yield different evolutionary trees is because there isn't a single unified tree of life to be found. In other words, perhaps universal common ancestry is simply wrong.
    http://www.evolutionnews.org/2012/06/nature_article061471.html

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  10. Elizabeth, evidence that change is bound?

    Everything that we have observed in the history of science. Being an acknowledged pantheist you have great faith in the ability of nature to do things that have never been observed. For you it is not hard to extrapolate from a bird beak size increase of 1mm to evolving efficient flying, swimming, running, or mental abilities. You have great faith in nature. I simply don't buy such an extrapolation.

    Speciation. I have to say "actual" speciation to keep you from adding adjectives to muddle up the meaning of speciation. What I mean by speciation is speciation, not incipient speciation or what new adjectives that evolutionists want to add to evade their weak evidence.

    So, apparently you don't have an example of animal speciation because of timeframe issues. It would be accurate then for me to say, that there does not exist one documented example of animal speciation (resist temptation in insert "incipient") in the history of science. Is that correct?

    The timeframe thing is a defense. You may feel its a legitimate defense, but it is nevertheless, a defense. It's not evidence.

    Fossil record. I do accept the fossil record, which is not one of gradualism, but of abrupt appearances of new life forms followed by stasis. Do you accept the fossil record?

    Where are all the intermediate species? Incomplete fossil data, soft tissues don't fossilize, etc. You have defensive arguments that you feel are legitimate, but its a defense, not evidence. Anyone can cherry pick from a field a mile deep and the size of the earth to force together a scenario that they prefer.

    You said, "But there is certainly plenty of evidence for new, or tuned, functions evolving from older functions, and, indeed, for new functions evolving from gene duplications.

    I'll try to dig some out though."

    I would be interested an example of an observed new function having evolved via mutation and natural selection that isn't the result of something breaking or epigenetics.

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    1. Ignorant Creationist

      The timeframe thing is a defense.


      It's not a "defense", it's an empirically observed fact. Complete speciation takes a lot longer that the "show it to me now!!" timeframe that ignorant Creationists demand.

      Where are all the intermediate species?

      They're in museums, and science journals, and listed all over the web. Same place they were the last time you asked fat man.

      List of transitional fossils

      All the places an ignorant Creationist avoids like the plague.

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    2. Ignorant Creationist

      I would be interested an example of an observed new function having evolved via mutation and natural selection that isn't the result of something breaking or epigenetics.


      Here you go again fat man. Another scientific paper that you'll completely ignore.

      Evolution of a new function in an esterase: simple amino acid substitutions enable the activity present in the larger paralog, BioH

      "Abstract: Gene duplication and divergence are essential processes for the evolution of new activities. Divergence may be gradual, involving simple amino acid residue substitutions, or drastic, such that larger structural elements are inserted, deleted or rearranged. Vast protein sequence comparisons, supported by some experimental evidence, argue that large structural modifications have been necessary for certain catalytic activities to evolve. However, it is not clear whether these activities could not have been attained by gradual changes. Interestingly, catalytic promiscuity could play a fundamental evolutionary role: a preexistent secondary activity could be increased by simple amino acid residue substitutions that do not affect the enzyme's primary activity. The promiscuous profile of the enzyme may be modified gradually by genetic drift, making a pool of potentially useful activities that can be selected before duplication. In this work, we used random mutagenesis and in vivo selection to evolve the Pseudomonas aeruginosa PAO1 carboxylesterase PA3859, a small protein, to attain the function of BioH, a much larger paralog involved in biotin biosynthesis. BioH was chosen as a target activity because it provides a highly sensitive selection for evolved enzymatic activities by auxotrophy complementation. After only two cycles of directed evolution, mutants with the ability to efficiently complement biotin auxotrophy were selected. The in vivo and in vitro characterization showed that the activity of one of our mutant proteins was similar to that of the wild-type BioH enzyme. Our results demonstrate that it is possible to evolve enzymatic activities present in larger proteins by discrete amino acid substitutions."

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    3. Thorton a new function was asked for and you provide:

      a preexistent secondary activity could be increased by simple amino acid residue substitutions:

      Does a 'preexistent secondary activity' being increased mean 'new function' to you Thorton?

      Is gene duplication a viable explanation for the origination of biological information and complexity? - December 2010 -
      Excerpt: The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case. Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. © 2010 Wiley Periodicals, Inc. Complexity, 2011
      http://onlinelibrary.wiley.com/doi/10.1002/cplx.20365/abstract

      Delete
    4. Thorton tries to literature bluff from wikipedia stating that transitional fossils are abundant, yet this is just plain fraudulent for him to claim as such. Here are a few examples of how neo-Darwinists tried to severally distort the fossil evidence to try to force it into their atheistic worldview:

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

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

      Further notes:

      "The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find' over and over again' not gradual evolution, but the sudden explosion of one group at the expense of another."
      Paleontologist, Derek V. Ager

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

      The Unknown Origin of Pterosaurs - video
      http://www.youtube.com/watch?v=XP6htc371fM

      Bat Evolution? - No Transitional Fossils! - video
      http://www.metacafe.com/watch/6003501/

      This suddenness witnessed in the fossil record extends to us, 'homo sapiens:

      When we consider the remote past, before the origin of the actual species Homo sapiens, we are faced with a fragmentary and disconnected fossil record. Despite the excited and optimistic claims that have been made by some paleontologists, no fossil hominid species can be established as our direct ancestor.
      Richard Lewontin - Harvard Zoologist
      http://www.discovery.org/a/9961

      Evolution of the Genus Homo - Annual Review of Earth and Planetary Sciences - Tattersall, Schwartz, May 2009
      Excerpt: "Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the 2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis."
      http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.earth.031208.100202

      Man is indeed as unique, as different from all other animals, as had been traditionally claimed by theologians and philosophers. Evolutionist Ernst Mayr
      http://www.y-origins.com/index.php?p=home_more4

      “Something extraordinary, if totally fortuitous, happened with the birth of our species….Homo sapiens is as distinctive an entity as exists on the face of the Earth, and should be dignified as such instead of being adulterated with every reasonably large-brained hominid fossil that happened to come along.”
      Anthropologist Ian Tattersall
      (curator at the American Museum of Natural History)

      “We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh (i.e. nonsense). Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates.”
      Henry Gee, editor of Nature (478, 6 October 2011, page 34, doi:10.1038/478034a),

      In Science and Human Origins, Casey Luskin Reveals the "Big Bang" of Human Evolution - June 2012
      http://www.evolutionnews.org/2012/06/in_science_and_061461.html

      Delete
  11. Elizabeth said, "which has been observed to work in real time; the idea that extant species and those observed in the fossil record form a vast bifurcating family tree from simpler ancestral populations;"

    "...has been observed to work in real time..."

    Whatever happened to the timeframe issue? No examples of animal speciation (resist temptation to insert "incipient"), yet we have observed.

    Back to bird beaks and a fossil record interpretation that must be defended because it does not show a pattern of gradualism.

    You haven't given me a scientific reason to think that your conclusion that evolution is a fact is anywhere near valid.

    ReplyDelete
    Replies
    1. Ignorant Creationist

      Back to bird beaks and a fossil record interpretation that must be defended because it does not show a pattern of gradualism.


      Amazing that in this day and age with all the publicity about forensic analysis that we have a clueless boob who thinks unless you eyewitness an event the event can't have occurred.

      Even though we can measure plate tectonic movement with GPS and watch it cause the Himalayas to rise, no one observed the whole mountain form in real time so it never occurred. Right Pastor Ignorant?

      Even though we can watch a river eroding a canyon and measure the rate of down cutting, no one observed the entire Grand Canyon being carved by the Colorado river so it never happened. Right Pastor Ignorant?

      There's no cure for willful ignorance.

      Delete
    2. Tedford,

      Here are a bunch of scientific reasons that make evolution a fact:

      http://darwins-god.blogspot.com/2012/06/this-paper-will-be-cited-as-showing-how.html?showComment=1340972302962#c7149219287009648296

      Delete
  12. I think that it would be time well spent for all biologists and chemists to take at least one course in assembly language computer programming and a computer operation systems course. After all, so much of biology and living organisms is about information coding and storage.

    It will help them to get away from the "free lunch" mentality that seems to run rampant. When you're dealing with complex systems, anything that can go wrong, will go wrong and anything that you have not accounted for will not work. A simple coding mistake, a small omission in logic, a "free lunch" assumption can very well fail the entire program or system.

    ReplyDelete
    Replies
    1. What makes you think that assembly language and OS are good models for how organisms work?

      Have you studied any information theory? What books can you recommend?

      Delete
    2. Neal: When you're dealing with complex systems, anything that can go wrong, will go wrong and anything that you have not accounted for will not work. A simple coding mistake, a small omission in logic, a "free lunch" assumption can very well fail the entire program or system.

      Two comments here, both important, I think:

      First, "complex" and "robust" are not mutually exclusive. Human computer systems are notoriously brittle - a small coding error can cause the entire program to fail. That doesn't mean that complexity automatically necessitates brittleness - really good systems have lots of fail-safes. And we know that organisms are highly "robust" in that sense; every single child born (including identical twins even) has a unique genome - and the vast majority of children "work" - are viable organisms.

      Secondly, the actual mechanism proposed (darwinian evolution) as the source of this highly robust coding has robustness "built in". Unlike human coding processes which are "top-down", evolutionary coding processes are bottom-up. Robustness is a sine-qua non - if a proto-organisms can't replicate itself reasonably reliably, i.e. if slight deviations from perfect reproductive fidelity are catastrophic, then that organisms offspring aren't going to dominate the evolving populations.

      This is why, of course, that people are starting to use evolutionary algorithms to produce good code.

      Delete
    3. Elizabeth, the "fail-safes" in stable computer systems were put there because engineers have had years of experience in dealing with the many things that can go wrong. A great amount of IT resources are spent on test and quality systems because errors are anticipated as part of the development process. Complexity in computer systems certainly necessitates "brittleness" UNLESS intentional and proactive intervention is undertaken and tested before going into production. You can't just expect the "fail-safes" to magically pop into existence on their own, you need intense intelligent action to build them. My point was that a course in assembly language would be very instructional in seeing all the steps that go into coding a functional program... the high level coding languages do a lot of the steps behind the scenes. Do you know what it takes in machine code to type a "." and to get it on your screen, stored on disk, or printed? Everything must be accounted for and you really can't appreciate all the steps that must be designed into the system for you to type a "." unless you've done original low level coding before. That the vast majority of children "work", as you say, must likewise be appreciated. Even more so, because humans are in a completely different league of complexity than computer systems.

      Darwinian evolution is not bottom up. Prokaryotes are more complex than the space shuttle, and you have nothing but evolutionary speculation about any kind of organism or proto cell that supposedly proceeds them.

      You of all people in these discussions should know that there is no chemical mechanism for perfecting nonreplicating molecules via Darwinian processes. Your talk about proto-organisms can't do this and if that and then ... when you don't even know if proto-organisms ever existed! Is it possible to live with Darwinian assumptions so long that they become like reality?

      Delete
    4. Troy, the genetic code and biosystem logic are complex information communication systems. Likewise, computer systems are complex information communication systems.

      As far as study, any college level course on assembly language will probably do. The point is to adopt a mentality of detail thinking to escape the curse of the "free lunch" mentality. Evolutionists speak of their speculations as fact like Bernie Madoff speaking about investment opportunities.

      Delete
    5. Ignorant Creationist

      Troy, the genetic code and biosystem logic are complex information communication systems. Likewise, computer systems are complex information communication systems.


      "Rain clouds distribute moisture that waters the grass in my front yard. Lawn sprinklers distribute moisture that waters the grass in my front yard. Therefore if we want to understand rain cloud formation we should make all meteorologists study lawn sprinkler design."

      There's no cure for willful ignorance.

      Delete
    6. Extreme Software Design In Cells - Stephen Meyer - video
      http://www.metacafe.com/watch/5495397/

      DNA Computer
      Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours.
      http://www.tech-faq.com/dna-computer.html

      On this episode of ID the Future, Casey Luskin interviews Dr. Donald E. Johnson about his 2010 book, Programming of Life, which compares the workings of biology to a computer.

      Programming of Life - February 2012 - podcast
      http://intelligentdesign.podomatic.com/entry/2012-02-17T13_29_15-08_00

      Here is the video that goes with the 'Programming Of Life' book:

      Programming of Life - video
      http://www.youtube.com/watch?v=k6iWX9nGocg&feature=list_related&playnext=1&list=SPAFDF33F11E2FB840

      * the genetic system is a pre-existing operating system;
      * the specific genetic program (genome) is an application;
      * the native language has codon-based encryption system;
      * the codes are read by enzyme computers with their own operating system;
      * each enzyme’s output is to another operating system in a ribosome;
      * codes are decrypted and output to tRNA computers;
      * each codon-specified amino acid is transported to a protein construction site; and
      * in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life.

      Cells Are Like Robust Computational Systems, - June 2009
      Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail."
      http://www.sciencedaily.com/releases/2009/06/090616103205.htm

      etc.. etc.. etc..

      Delete
    7. Neal: Elizabeth, the "fail-safes" in stable computer systems were put there because engineers have had years of experience in dealing with the many things that can go wrong. A great amount of IT resources are spent on test and quality systems because errors are anticipated as part of the development process. Complexity in computer systems certainly necessitates "brittleness" UNLESS intentional and proactive intervention is undertaken and tested before going into production. You can't just expect the "fail-safes" to magically pop into existence on their own, you need intense intelligent action to build them.
      Well, you do in human computer systems. But human computer systems aren’t, on the whole, built by evolutionary processes! There are real problems with his analogy.
      My point was that a course in assembly language would be very instructional in seeing all the steps that go into coding a functional program... the high level coding languages do a lot of the steps behind the scenes. Do you know what it takes in machine code to type a "." and to get it on your screen, stored on disk, or printed?
      Yes – but this is not how organisms work.
      Everything must be accounted for and you really can't appreciate all the steps that must be designed into the system for you to type a "." unless you've done original low level coding before. That the vast majority of children "work", as you say, must likewise be appreciated. Even more so, because humans are in a completely different league of complexity than computer systems.
      Yes indeed – but I meant “children” generically. Organisms reproduce. Computers don’t. The “programming” of organisms is a direct result of their capacity to reproduce, and directly affects their ability to reproduce. There is no analogy between the programming of a computer and what goes on in a reproducing cell.
      Darwinian evolution is not bottom up.
      Well, by “bottom up” I meant something that I consider true: all you need to kick-start Darwinian evolution is something that can reproduce itself with a little bit of variability. From that “bottom”, any variant that happens to increase reproductive efficiency will, by definition, become more prevalent.
      Prokaryotes are more complex than the space shuttle, and you have nothing but evolutionary speculation about any kind of organism or proto cell that supposedly proceeds them.
      We certainly have “speculation” but we also have theories and hypotheses and data. More importantly, we have a mechanism, and no good reason to suppose that that mechanism couldn’t work in the past just as we observe it working in the present.
      You of all people in these discussions should know that there is no chemical mechanism for perfecting nonreplicating molecules via Darwinian processes.
      Obviously without self-replication you can’t have Darwinian processes. I’m not sure of your point.
      Your talk about proto-organisms can't do this and if that and then ... when you don't even know if proto-organisms ever existed! Is it possible to live with Darwinian assumptions so long that they become like reality?
      I don’t really know what you are saying here.

      Delete
    8. Tedford, as usual, you didn't answer my questions at all. Obviously you don't know jack about information theory or evolutionary biology.

      I guess I shouldn't be surprised at this point, but I really am still amazed that an ignorant pastor has the hubris to pontificate on subjects he knows nothing about. That's all you do, isn't it, just lying and bluffing? How can you live with yourself?

      Delete
  13. Ignorant Creationist

    I think that it would be time well spent for all biologists and chemists to take at least one course in assembly language computer programming and a computer operation systems course.


    It would definitely be time well spent for the dirt ignorant Creationist pastor to take an evolutionary biology 101 course.

    It would help him get away from the rampant stupidity he displays every day, like "bird beaks are the only evidence for evolution", and "if we didn't see speciation occur in real time, then it never happened!"

    ReplyDelete
    Replies
    1. Yo, stupid evolutionist

      I haven't seen a single compelling evidence for Darwinian evolution. All I see is stupid just-so stories and stupid lies by stupid evolutionists like you, Thorton.

      Delete
  14. Louis Savain

    I haven't seen a single compelling evidence for Darwinian evolution.


    That's your problem Louis, not evolution's. Maybe if you looked someplace other than the inside of your own rectum.

    ReplyDelete
    Replies
    1. You're still a stupid evolutionist.

      Delete
    2. Possibly, but that doesn't affect one iota the fact that the theory of evolution is among the most strongly supported and empirically verified theories in all of science.

      Delete
    3. Only in the imagination of stupid evolutionists.

      Delete
  15. E. Liddle said:

    So in a sense you are right, it is an "umbrella" term to refer to all we know about the way living things evolve over time, including the fact that they do (in the sense that populations over time consist of individuals who can differ quite markedly from earlier generations).

    But that's my point Miss Liddle - What CAN'T be attributed to it? It has basically become (as Dr Hunter stated previously) "the blob."

    If falsified predictions/expectations are considered evidence FOR evolution, how is it a scientific theory when it can't be falsified??

    Even if we assume common ancestry is true (contrary to the evidence) how do you know it's not guided by an intelligent being/agent?

    You see, you and I both have FAITH. Mine is in God as the creator and sustainer of life, as the first cause of "the natural/nature" etc and your faith is in blind random chance. Since neither of us were around to see how life started on this planet, how can you say it's purely naturalistic when all the evidence shows life the signs of design? Even Francis Crick stated he had to remind biology students that what they were seeing was not designed, but (allegedly) evolved.


    Let me ask you: If you didn't know the history behind the faces on Mt Rushmore, would you believe they were made solely by the elements?

    So why would you believe something much more complex (life/ biological traits) were? We need to have the same rational, logical mindset when studying biology that we do in regards to other things that show specified complexity.

    ReplyDelete
  16. But that's my point Miss Liddle - What CAN'T be attributed to it? It has basically become (as Dr Hunter stated previously) "the blob."

    No, it hasn't. Just because we use an umbrella term, that doesn't mean that there is no structure beneath the umbrella! Evolutionary theory covers a great many very specific postulated mechanisms, each testable, some falsified and some supported.

    If falsified predictions/expectations are considered evidence FOR evolution, how is it a scientific theory when it can't be falsified??

    Well, first of all, it is important to understand what we mean by "falsification". Firstly, "falsification" is always probabilistic, in science, not absolute; second we only falsify null hypotheses. So to "falsify" an evolutionary hypothesis, you have to treat it as the null - i.e. have an alternative hypothesis to test against it.

    Evolutionary hypotheses can certainly be falsified, in principle, but only by proposing an alternative hypothesis. The way it would work would be to figure out what we'd expect to see under the null hypothesis of some postulated evolutionary process, and then compare that to what is predicted under some alternative hypothesis.

    In contrast, ID is unfalsfiable until someone postulates what they'd expect to see under the null of an ID. But as long as the ID remains totally unspecified, there is are no constraints as to what we would expect under that null, and therefore no way of testing it against any other hypothesis.

    But it's also worth saying, I think, that, in general, what we call "theories" aren't cast in falsifiable form. Indeed falsification isn't even how science generally proceeds. What we do test are hypotheses, and generally we test them against some null, or against an alternative hypothesis.

    In other words, we fit models to data, and we choose the model that gives the best fit to the data. But all models are "false" in the sense that no model is a perfect fit.

    ReplyDelete
  17. National Velour Let me ask you: If you didn't know the history behind the faces on Mt Rushmore, would you believe they were made solely by the elements?

    Not if I knew what human beings looked like and could do. I would consider that fabrication by human beings was a much more likely explanation.

    So why would you believe something much more complex (life/ biological traits) were? We need to have the same rational, logical mindset when studying biology that we do in regards to other things that show specified complexity.

    Because there is a HUGE difference between biological organisms and [most] man-made artefacts, which is that biological organisms reproduce.

    There are two processes which we know can result entities with complex functionality: design and manufacturer by an intelligent self-replicating organism; and self-replication itself.

    So faced with a non-self-replicating object that looked as though it performed some function, I would infer that it was probably made by a self-replicating organism. Face with a self-replicating organism with sub-components that promoted the well-being of the organism, I would infer that it probably evolved.

    Conceivably, it could be both - it could be a self-replicating organism that was designed by means of an evolutionary process set up by another self-replicating organism.

    ReplyDelete
  18. E. Liddle said:

    Evolutionary hypotheses can certainly be falsified, in principle, but only by proposing an alternative hypothesis.

    How can it be falsified when it's the ONLY theory allowed? Everything is looked at through "evolution" glasses. What could falsify it?? If evidence that is completely OPPOSITE to what evolutionists' expected to find, is declared as evidence FOR evolution, what can't be called "evolution'???

    How is that science?


    I.D proposes life/biological traits shows indications of being intelligently designed, and the evidence supports that theory. As for I.D being falsifiable, I give you Uncommon Descent:

    ID is not proposing “God” to paper over a gap in current scientific explanation. Instead ID theorists start from empirically observed, reliable, known facts and generally accepted principles of scientific reasoning:

    (a) Intelligent designers exist and act in the world.

    (b) When they do so, as a rule, they leave reliable signs of such intelligent action behind.

    (c) Indeed, for many of the signs in question such as CSI and IC, intelligent agents are the only observed cause of such effects, and chance + necessity (the alternative) is not a plausible source, because the islands of function are far too sparse in the space of possible relevant configurations.

    (d) On the general principle of science, that “like causes like,” we are therefore entitled to infer from sign to the signified: intelligent action.

    (e) This conclusion is, of course, subject to falsification if it can be shown that undirected chance + mechanical forces do give rise to CSI or IC. Thus, ID is falsifiable in principle but well supported in fact.

    In sum, ID is indeed a legitimate scientific endeavor: the science that studies signs of intelligence.


    ]Because there is a HUGE difference between biological organisms and [most] man-made artefacts, which is that biological organisms reproduce.

    But you believe a living cell came from non-living matter, right? Where did the instructions to tell it to replicate come from? Despite everything Pasteur showed, you still believe that it CAN happen right? So, why do you reject complexity as having a creator/designer when it suits you?

    What about DNA repair? That just happened to come about as well? Would you believe Spellcheck just happened to come about because someone left a computer program running and after many glitches and power surges, etc it produced an intelligent correction system? Even if it COULD reproduce itself, the program would still have needed someone to write the code to tell it to replicate, correct?

    Why do you abandon logic and reason in exchange for blind, random chance when it comes to the darwinian myth?

    ReplyDelete