Is It Possible To Resurrect Proteins From The Dead?

No, this isn’t Jesus resurrecting from the dead, that is a separate but factual issue however, in a recent publication we noticed some secular scientists making claims that ancient proteins (assumed to be four billion years old) can be brought back to life!

Live Science puts it this way…

Researchers have reconstructed the structure of 4-billion-year-old proteins.”

“The primeval proteins, described today (Aug. 8) in the journal Structure, could reveal new insights about the origin of life, said study co-author José Manuel Sanchez Ruíz, a physical chemist at the University of Granada in Spain.”

Exactly how life emerged on Earth more than 3 billion years ago is a mystery. Some scientists believe that lightning struck the primordial soup in ammonia-rich oceans, producing the complex molecules that formed the precursors to life. Others believe that chemical reactions at deep-sea hydrothermal vents gave rise to cell membranes and simple cellular pumps. And still others believe that space rocks brought the raw ingredients for life — or perhaps even life itself — to Earth.”

“But it’s difficult to recreate events that happened so far in the distant past.”

The BBC news put it this way…

“The resurrected protein is thought to have existed almost four billion years ago in single-celled organisms linked to the earliest ancestor of all life.”

Neo-Darwinism relies on gradualism which relies on nature being flexible in a step by step by a non-intelligent process. However, sooner or later nature always comes into conflict with Neo-Darwinism as the researchers found out…

“Prof Eric Gaucher of Georgia Tech, US, helped with the ancestral gene sequence reconstruction and commented: “A gene can become deactivated by as few as one or two mutations.”

Only one or two mutations (errors in the genetic code), talk about something very incompatible with the theory of evolution! Where is the flexibility that is supposed to be the law of nature? To answer such a question, they theorize there must have been a “discrete” jump where it wouldn’t be observable through gradual pathways because it went by so fast like it was traveling at the speed of light.

Another thing, shouldn’t this ancient fossil, assumed to be billions of years old, be much simpler rather than complex, possessing all these functions? Is that how evolution works from simple cells to more complex? The BBC really goes off the deep end by invoking science fiction that was popular long before man landed on the moon by claiming thioredoxin had emerge on Mars and was transported by meteorites because they believe in the early years of earth that Mars was more “flexible” for life than earth was. Even though no life on Mars has been found neither has elements to sustain life been ever found!

Before scientists speculate and tell us or debate what they believe about origins of life, they first must understand what life is first as pointed out by NASA’s magazine

“If we ever hope to identify life elsewhere in the universe, we need to understand what separates living creatures from non-living matter. A working definition lately used by NASA is that “life is a self-sustaining system capable of Darwinian evolution.” 

Evolutionists have never created life in a lab, let alone know how electricity from the sky causes life in a pond full of simple non-living chemicals. It is not science to make various claims because we observe very highly designed complex cells so they emerged somehow in an unseen ancestor. We have observed a functioning that cell requires to have all its parts working correctly at once to remain a functioning cell as evolutionist, Wilhelm Huck even points out! So was it a “discrete” miracle in evolution?

Science is supposed to be about observable, testable, and repeatable events rather than scientists telling us what they believe could have happened in a supposed billions of years time frame. And the cell wasn’t resurrected from the dead like the BBC claimed. I don’t blame them for wanting a “time machine” to observe the distant past, they would have learned a great deal on how the earth was intelligently designed.

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39 thoughts on “Is It Possible To Resurrect Proteins From The Dead?

  1. Michael, Michael! You — with a little help from the third-tier popular science press– have got your facts wrong again. This is where just a little actual background knowledge would save you from getting egg all over your face.
    Nobody has “resurrected” a dead protein and made it live again.

    Instead the researchers traced the evolutionary tree of various forms of a modern protein found in a number of animals, and come up with a DNA sequence that the common ancestor of that protein had at some point in history. Then they BUILT a protein –using recently developed biosynthesis tools— a replica of that protein from individual amino acid subunits in a solution.

    Then they tested it for activity in a modern animal, and fund that it did function,

    But there was no “resurrection: anywhere along the line. In other words, your headline is pure crap.

    Michael, you have to stop being so gullible..

  2. I don’t blame them for wanting a “time machine” to observe the distant past, they would have learned a great deal on how the earth was intelligently designed.

    Really? How would anyone learn about HOW life was intelligently designed from this ancient protein? What would intelligent design study about this protein to determine, say, what its original function was, or what its structure tells us about primitive life forms? ID has no purchase on these questions; they would not know where ti begin, or what questions to ask.

    The evolutionary purpose for reconstructing this protein, however, does yield a wealth of information. For example, the ancestor is extremely heat stable, much more than its modern descendants. This indicates that life may have begun in extreme environments, rather than in a “warm little pond.” The ancestor’s function was basic metabolism., so it would be preserved. It broke disulphide bonds, indicating that early life forms extracted energy from sulfur rather than other sources.

    Evolutionary science can glean a lot from this ancient protein. ID, on the other hand, is left with no less mystery than it started with,, slobbering in slack-jawed amazement at the unutterable complexity of the thing.</strong?

  3. It was the BBC that referred to the protein as “resurrected.” Michael states: “the cell wasn’t resurrected from the dead like the BBC claimed” so ad hominem (#1).

    … and come up with a DNA sequence that the common ancestor of that protein had at some point in history.

    Extrapolation beyond the evidence (#2), they extrapolated to what COULD have been the common form. In an evolutionary framework, the can’t accurately extrapolate as they don’t know the mutational pathway from the original to the present proteins.

    What would intelligent design study about this protein to determine, say, what its original function was, or what its structure tells us about primitive life forms?

    Straw-man [#3] (and in your case, argument from ignorance but I digress). That’s a claim that I am almost certain that you cannot prove. But since you are so passionate about it, what evidence do you have that backs up your contention?

    But you also performed a question begging fallacy (#4), can you identify where? If not, how can anyone trust your generalization of ID [#5] (another fallacy BTW)?

  4. The evolutionary purpose for reconstructing this protein, however, does yield a wealth of information.

    Misdirection (#6), is the information accurate? How can we test it? What multiple unquestioned and fallacious assumptions were made? List them.

    For example, the ancestor is extremely heat stable, much more than its modern descendants. This indicates that life may have begun in extreme environments, rather than in a “warm little pond.”

    Extrapolation fallacy on tenuous assumptions (#7).

    The ancestor’s function was basic metabolism., so it would be preserved. It broke disulphide bonds, indicating that early life forms extracted energy from sulfur rather than other sources.

    indicating that early life forms MAY have …. so exaggeration (#8) and extrapolation (#9) fallacies.

    Evolutionary science can glean a lot from this ancient protein.

    Oversimplification (#10). Any scientist could easily extract this information.

    ID, on the other hand, is left with no less mystery than it started with,, slobbering in slack-jawed amazement at the unutterable complexity of the thing.

    Repeated generalization (#11) and ad hominem (#12) fallacies.

    12 fallacies, metinks that’s a new record. Good job Olorin.

  5. Extrapolation beyond the evidence (#2), they extrapolated to what COULD have been the common form. In an evolutionary framework, the can’t accurately extrapolate as they don’t know the mutational pathway from the original to the present proteins.

    Pure denial. The evolutionary programs are the same ones that determine paternity in court, that track human migrations around the world. and that teased out the original wording of Chaucer’s Canterbury Tales from the thousands of imperfect copies available now.

    The point is that you do not have to know the step-by-step history of the changes. Upon what evidence do you base your claim that these programs do not work?

    In this case, the protein discovered by this method was tested and found to be perfectly functional Creationists claim that functional proteins are exceedingly rare in configuration space. This is one of the rare ones, and it’s functional. Furthermore, it has a suite of properties consistent with one general scenario of life’s beginning.

    Then you claim that anyone —even a creationist— could suss out the properties of this ancient protein. That’s obviously false, because creationists did not discover it, so they would have nothing to analyze.

  6. Pure denial.

    Olorin, the researchers state the same thing. Is it that you cannot read?

    Upon what evidence do you base your claim that these programs do not work?

    I did not say that. [Note to self: Olorin cannot read].

    In this case, the protein discovered by this method was tested and found to be perfectly functional

    Perfectly functional? Is that designed protein God so that it is perfect? All hail!

    Furthermore, it has a suite of properties consistent with one general scenario of life’s beginning.

    Correlation does not always mean causation.

    Then you claim that anyone —even a creationist— could suss out the properties of this ancient protein. That’s obviously false, because creationists did not discover it, so they would have nothing to analyze.

    You actually answered your own assertion above as creationists wouldn’t be so simplistic to create an averaged protein in the first place. Unlike desperate chemical evolutionists, they would spot the extrapolation fallacy from miles away. Sadly, this still eludes your triple degree wannabe evolutionist brain.

    So I guess it is settled: Olorin’s fallacious logic stems from his desire to be an evolutionist even though he is a Lutheran Intelligent Design proponent.

  7. Olorin, the researchers state the same thing. Is it that you cannot read?

    Makes no sense. What are you talking about here?

    Perfectly functional? Is that designed protein God so that it is perfect? All hail!

    Ditto.

    Correlation does not always mean causation.

    Correlation has nothing to do with my statement..

    . . . creationists wouldn’t be so simplistic to create an averaged protein in the first place.

    You obviously have not the slightest understanding of how these programs work. “Averaged protein”!! BWAHAHAUJHAJAJAAAAAAAAAA

    The same reconstruction method was used by Craig Venter in sequencing the human genome. And it has proven itself in other applications as well, as indicated before.

    So I guess it is settled:. Chazing’s definition of evidence excludes everything that is contrary to his opinions.

  8. Sorry about the formatting hash. Vision is impaired at the moment.

    Olorin, the researchers state the same thing. Is it that you cannot read?

    Makes no sense. What are you talking about here?

    Perfectly functional? Is that designed protein God so that it is perfect? All hail!

    Ditto.

    Correlation does not always mean causation.

    Correlation has nothing to do with my statement..

    . . . creationists wouldn’t be so simplistic to create an averaged protein in the first place.

    You obviously have not the slightest understanding of how these programs work. “Averaged protein”!! BWAHAHAUJHAJAJAAAAAAAAAA

    The same reconstruction method was used by Craig Venter in sequencing the human genome. And it has proven itself in other applications as well, as indicated before.

    So I guess it is settled:. Chazing’s definition of evidence excludes everything that is contrary to his opinions.

  9. You obviously have not the slightest understanding of how these programs work. “Averaged protein”!! BWAHAHAUJHAJAJAAAAAAAAAA

    Yes, “averaged” is incorrect, “estimated” would be a better descriptor.

  10. By the same measure, Craig Venter only produced an “estimated” sequence of the human genome. MWAHAHAHAHAAAAAAA

  11. Fallacy alert: conflation.
    Venter: present day, directly testable
    This study: not present day, not directly testable
    I guess you can’t help yourself.

  12. The Venter-sequence3d genome has never been tested either, in a way you demand. Yet everyone, tout le monde, accepts this sequence. Demonstrates their confidence in the method. But an engineer on a small Caribbean island thinks it is merely and “estimate.:.

    So both are estimates, or neither is. Make your choice, and let the laughter begin.

  13. You are conflating again (I understand, you just can’t help yourself). I made no claims as to the accuracy of Venter’s method just that it was directly testable unlike this method. You’re quite a dim bulb.

    Your statement would seem to indicate that you believe that one needs to be on a large island in order to point out the obvious. Would that be your attempt at US continental styled ad hominem?

  14. Although Venter’s method is theoretically capable of being tested, it has not been, nor will it ever be.

    You miss the point yet again. Everyone has enough confidence in the method that they accept it without question.

    Oh, wait—a few small parts of Venter’s sequence were found by the competing effort, before it was shut down. Those parts all agree with Venter’s method..

    And, once again for the hard of hearing, Venter’s method is also the one used to reconstruct the ancient protein. And, the protein has been tested in that it is functional, the odds against which are perhaps not astronomical, but exceedingly high And, in addition, its suite of characteristics are consistent with each other. The odds against this are also rather high. And this suite is consistent with a prominent hypothesis on OOL.

    But an engineer on a —well, OK, medium sized backwater of civilization— having no background whatever in paleontology or microbiology thinks it’s all a bunch of hooey. Well, pardon me, but the crocoduck again cries BWAHAHAHAHAAAAAAAAAAAAAAAAAA.

  15. That’s a whole lot of straw-man, conflation and ad hominem. You still don’t get it. It doesn’t matter if Venter’s method is being used, the main issue is that this is a guess of what the original protein would have been. So now you are conflating a method (Venter’s) with direct testability. Yup, BWAHAHAHAHAAAAAAAAAAAAAAAAAA is indeed what that would be.

  16. I see you have thoroughly convinced yourself you are correct.

    Now to convince someone else.

    You might start by asking Michael to explain the operation of the reconstruction algorithm, and why it works with the human genome but fails otherwise.

    Yo. Michael! You’re on.

  17. A news article last year[1] relates the story of Joe Thornton, a primary investigator in reconstructing ancient proteins. He sees his work as investigating how complexity arises during evolution.

    One of his discoveries is the evolutionary path of a gene for a function previously claimed to be irreducibly complex.

    The study flipped another finger to intelligent-design proponents—but “I’m sort of bored with them,” Thompson says

    His next project is to find the ancestor of the entire steroid hormone receptor family, which originally was sensitive only to estrogen, but evolved into forms sensitive to other hormones.

    ===========================

    [1] Pearson, “Raising the Dead,” Nature 483:390-393 (22 Mar 2012).

  18. That’s splendid Olorin. For the sake of your “gentle readers,”
    1. Please highlight where he actually dated the protein; and
    2. Please state explicitly how this is inconsistent with ID and/or creationism.

  19. 1. University of Oregon.
    2. Creationists are fond of using the metaphor of a tornado assembling i 747 in a junkyard. These reconstructions are like that. You take a r
    protein from hundreds of different present-day animals reconstruct common parts at several levels, eventually reaching one that fits all of them. Then you test the activity of the protein. As the IDers are fond of sating\, the odds that it will function are on the order of the 747-in-a-junkyard. So we have a lot of confidence in the result.

    Why is that inconsistent with common design? First, because it is such strong evidence that it was evolution that produced the modern proteins. Second, because none of the crown proteins are the same as, or similar to, or have the same function(s) as the ancestor. How can they be “common design” under those circumstances? They are all different “designs.” No creationist in the world could possibly find what are the common elements of the designs—Have they ever? No. Have they even tried? No.

  20. University of Oregon

    Good grief, where in his research (paper) did he date the proteins? What method? What values (and SD) did he find? Did they correlate with his initial assumed value(s)? What assumptions were made in the measurement method?

    First, because it is such strong evidence that it was evolution that produced the modern proteins.

    Assuming the conclusion [well at least this is a new fallacy, congrats on getting that far].

    How can they be “common design” under those circumstances?

    Were the proteins not ‘designed’ by Thornton and his staff?

    No creationist in the world could possibly find what are the common elements of the designs—Have they ever? No. Have they even tried? No.

    Contradiction. One cannot be expected to find that which one did not even try to find. Additionally, one would have to be God to make such a claim.

  21. Good grief, where in his research (paper) did he date the proteins? What method? What values (and SD) did he find? Did they correlate with his initial assumed value(s)? What assumptions were made in the measurement method?

    Good grief, indeed. There is no single “research (paper)..” Thornton has written extensively on this subject over the past decade.[1] He did not date the protein. The reconstruction algorithm dated it, using standard mutation rates. But the exact value of the date is not important. It is the structure that is important.

    There were no “assumed dates”. Your question is like asking for an assumed date of the next solar eclipse before an astronomical calculation finds that date. Ridiculous.

    The date measurement assumes known mutation rates. But again, the exact date is of no importance. The structure is important. No assumptions were made as to that question.

    First, because it is such strong evidence that it was evolution that produced the modern proteins.

    Assuming the conclusion [well at least this is a new fallacy, congrats on getting that far].

    This is how science proceeds—by assuming a theory and then testing it Thus reconstruction is such a test.

    The reconstruction algorithm assumes evolution, and its results confirm that the ancestor is functional, despite huge odds against it. This is evidence that evolution was operating here. If you assume special creation, then you must show some evidence as to how creation could explain this result. As I noted before, creation has no explanation—just as, for instance Ptolemaic astronomy had no explanation for phases of the moon and planets, but heliocentrism did. This reconstruction does that for evolution in that it found an evolutionary ancestor for an entire family of proteins. Creation on the other hand cannot explain why this reconstruction would work at all—in fact, it would say the odds are hugely against it.

    Were the proteins not ‘designed’ by Thornton and his staff?

    No. Not any more than the next eclipse date is “designed” by the astronomer who calculates it from an algorithm. Ridiculous.

    No creationist in the world could possibly find what are the common elements of the designs—Have they ever? No. Have they even tried? No.

    Contradiction. One cannot be expected to find that which one did not even try to find. Additionally, one would have to be God to make such a claim

    Tthat is obviously false A lot of things were found without looking for them. Teflon, aspirin, penicillin, warfarin, for a few examples. In fact, just yesterday I found my second set of car keys while tidying up the front hall table before some guests arrived. Contradiction? Were you sleeping through Remedial Logic 001 again?

    What claim are you referring to? That only God could find the common elements of a set of designs? Creationists attempt this all the time. Even engineers have been known to do it.

    =============================

    [1] Here are some papers on molecule reconstruction where Thornton is author or coauthor. Others have also written on this subject too, of course. The most recent one is online for your delectation: “Resurrecting Ancient Genes: Experimental Analysis of Extinct Molecules” (See here for supporting material, papers cited, etc.) “Two mutations triggered an evolutionary leap 500 million years ago,” U. Chicago, 24 June 2013 outlines the significant evolutionary changes and their significance to modern life.

    I’m not going to do all your work for you; if you challenge the theory that 99.9999% of life-science researchers accept, then the burden is on you. Creationists demined everything, but offer nothing.

    > Bridgham JT, Eick G, Larroux C, Deshpande K, Harms MJ, Gauthier MEA, Ortlund EA, Degnan BM, Thornton JW (2010). Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. PLoS Biol 8(10): e1000497.
    > Harms MJ, Thornton JW (2010). Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion in Structural Biology 20:360-366.
    > Hanson-Smith V, Thornton JW (2010). Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution, 27(9): 1988-1999.
    > Bridgham JT, Ortlund EA, Thornton JW (2009). An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519.
    > Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW (2007). Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548.
    > Dean AM, Thornton JW (2007). Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics 8:675-688.
    > Bridgham JB, Carroll SM. Thornton JW (2006). Evolution of hormone-receptor complexity by Molecular Exploitation. Science 312:87-101, 2006.
    > Kolaczkowski B, Thornton JW (2004). Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
    > Thornton JW (2004). Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews Genetics 5:366-375.
    > Thornton JW, Need E, Crews D (2003). Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301:1714-1717, 2003.
    Harms MJ, Thornton JW (2013). Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nature Reviews Genetics, in press 2013.
    > Harms MJ, Eick GN, Goswami D, Colucci JK, Griffin PR, Ortlund EA, Thornton JW.(2013) Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors. Proceedings of the National Academy of Sciences USA. published online Jun 24, 2013.
    > Eick GN, Colucci JK, Harms MJ, Orlund EA, Thornton JW (2012). Evolution of minimal specificity and promiscuity in steroid hormone receptors. PLOS Genetics 8(11): e1003072. doi:10.1371/journal.pgen.1003072.
    > Finnigan G, Hanson-Smith V, Stevens TH, Thornton JW (2012). Mechanisms for the evolution of increased complexity in a molecular machine. Nature 481:360-4, 2012.
    > Carroll SM, Ortlund EA, Thornton JW (2011). Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor. PLoS Genet 7(6): e1002117.
    > Carroll SM, Thornton JW (2011). Lamprey endocrinology is not ancestral. Proceedings of the National Academy of Sciences USA 108(2):e5.
    > Eick GN, Thornton JW (2011). Evolution of steroid receptors from an estrogen-sensitive ancestral receptor. Molecular and Cellular Endocrinology 334(1-2):31-37.
    > Bridgham JT, Eick G, Larroux C, Deshpande K, Harms MJ, Gauthier MEA, Ortlund EA, Degnan BM, Thornton JW (2010). Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. PLoS Biol 8(10): e1000497.
    > Bridgham JT, Ortlund EA, Thornton JW. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519, 2009.
    > Keay J, Thornton JW. Hormone-activated estrogen receptors in annelid invertebrates: implications for evolution and endocrine disruption. Endocrinology 150:1731-1738, 2009.
    > Kolaczkowski B, Thornton JW. Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics. PLoS ONE 4(12): e7891,2009.
    > Carroll SM, Bridgham JT, Thornton JW. Evolution of hormone signaling in elasmobranchs by exploitation of promiscuous receptors. Molecular Biology and Evolution 5(12):2643-52, 2008.
    > Bridgham JT, Brown JE, Rodriguez-Mari A, Catchen JM, Thornton JW. Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLOS Genetics 4(9): e1000191, 2008.
    > Kolcazkowski B, Thornton JW. A mixed model of heterotachy improves phylogenetic accuracy. Molecular Biology and Evolution 25:1054-1066, 2008.
    > Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548, 2007.
    > Dean AM, Thornton JW. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics 8:675-688, 2007.
    > Kolaczkowski B, Thornton, JW. Effect of branch length uncertainty on posterior probabilities for phylogenetic hypotheses. Molecular Biology and Evolution 24:2108-2118, 2007.
    > Fox JE, Bridgham JT, Bovee TFH, Thornton JW. An evolvable oestrogen receptor activity sensor: development of a modular system for integrating multiple genes into the yeast genome. Yeast 24:379-390, 2007.
    > Thornton JW, Bridgham JT. Using ancestral gene resurrection to understand the evolution of protein function. In: Liberles DA, ed. Ancestral Gene Reconstruction. Oxford University Press, in press, 2006.
    > Bridgham JB, Carroll SM. Thornton JW. Evolution of hormone-receptor complexity by Molecular Exploitation. Science 312:87-101, 2006. Supplementary info.
    > Thornton JW. Evolution of gene families. In: Evolutionary Genetics: Concepts and Case Studies, ed. C. Fox and J. Wolf. Oxford University Press, 2006.
    > Thornton JW. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews Genetics 5:366-375, 2004.
    > Sarkar IN*, Thornton JW*, Planet PJ, Figurski D, Schierwater B, DeSalle R. An automated phylogenetic key for classifying homeoboxes. Molecular Phylogenetics and Evolution 24: 388-399, 2002 (* equal contributors).
    > Thornton JW, DeSalle R. Gene family phylogenetics: tracing protein evolution on trees. Experientia Supplementum (EXS) 92:191-207, 2002.
    > Thornton JW. Gene family phylogenetics: tracing protein evolution on trees. In: Techniques in Molecular Systematics, eds. DeSalle R, Giribet G, Wheeler W. Birkauser-Verlag, 2002.
    > Thornton JW. Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions. Proceedings of the National Academy of Sciences USA 98 (10), 5671-5676, 2001.
    > Thornton JW, DeSalle R. A new test to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily. Systematic Biology, 49:183-201, 2000.
    > Thornton JW, Kelley DB. Evolution of the androgen receptor: structure-function implications. BioEssays 20:820-829, 1998.

  22. (Now we stand back and wait for Chazing to complain, “You’re just trying to swamp me with a mountain of references.” That was the idea, yes. Dozens of references written by qualified biologists and peer-reviewed by dozens of other biologists, against Chazing’s electrical engineering background with no knowledge of biology and no exposure to experimental research of any kind. Or at least none that he is willing to share with us.)

  23. He did not date the protein.

    Shocker.

    This is how science proceeds—by assuming a theory and then testing it Thus reconstruction is such a test.

    Yes, but the conclusion does not necessarily follow. Thus, you have to explain why this invalidates both the creo and ID frameworks. What you have done is give your interpretation (like Thornton) but have not explained the creo/ID views and then systematically show how they are invalid. You are the one with “research experience” are you not?

    The reconstruction algorithm assumes evolution, and its results confirm that the ancestor is functional, despite huge odds against it.

    Oh? What were the odds?

    If you assume special creation, then you must show some evidence as to how creation could explain this result.

    Both creationist and ID sites have stated their views long ago.

    Creation on the other hand cannot explain why this reconstruction would work at all—in fact, it would say the odds are hugely against it.

    Since you are versed on the creationist/ID views, explain why exactly. And did you yourself not state that the odds were huge? So how would a creationist/IDer agreeing with you invalidate their view but not yours?

  24. No. Not any more than the next eclipse date is “designed” by the astronomer who calculates it from an algorithm. Ridiculous.

    False analogy. An eclipse is an occurrence, it has no primary biological functionality which can be tested.

    Tthat (sic) is obviously false A lot of things were found without looking for them.

    Apparently, you failed english 101. Hint: see the word “expected.”

    What claim are you referring to?

    The claim to know what creationists can or cannot ever do.

    …if you challenge the theory that 99.9999% of life-science researchers accept…

    Would you be kind enough to list the peer-reviewed global survey from which this 99.9999% claim is derived?

    A long publication listing, like your 99.9999% claim, is still an appeal to the fallacies of popularity and authority. Tsk, tsk, if only you could pass logic 101.

  25. He did not date the protein.

    Shocker.

    Why so?

    Thus, you have to explain why this invalidates both the creo and ID frameworks. What you have done is give your interpretation (like Thornton) but have not explained the creo/ID views and then systematically show how they are invalid.

    You have a peculiar view of scientific theories. Next you’ll ask me to invalidate the morpological-field theoy, and the the Pastafarian theory and the pink-flamingo theory and … well, you get the idea.

    What “interpretation” have I (or Thornton) given? The structure is not an interpretation, it’s the result of a calculation. Like the plans for an aircraft from a wing-design program. You don’t interpret they, you build them and determine whether or not tey work. There is some disconnect here where you don’t understand how this was done, or what it means.

    Oh? What were the odds?

    At least many millions to one. Your creationist buddies claim that finding a functional protein sequence would require more time than the age of the universe (our age, not your claimed age).

    If you assume special creation, then you must show some evidence as to how creation could explain this result.

    Both creationist and ID sites have stated their views long ago.

    Views, yes. They think reconstruction could never produce a functional result.. Too bad, you lose.

    Since you are versed on the creationist/ID views, explain why exactly.

    See above. re odds. The Creationists, after all, claim that evolution could not produce any new protein, because of the odds. Thornton’e result is the same but backward—it shows a functional protein despite those same odds.

  26. You have a peculiar view of scientific theories. Next you’ll ask me to invalidate the morpological-field theoy, and the the Pastafarian theory and the pink-flamingo theory and … well, you get the idea.

    Nope, just macro-evolution.

    What “interpretation” have I (or Thornton) given?

    That the ‘resurrected’ protein only validates macro-evolution.

    Your creationist buddies claim that finding a functional protein sequence would require more time than the age of the universe

    Strawman. I would normally ask you to think of how you are wrong but I know by now that would be pointless.

    They think reconstruction could never produce a functional result

    Yet another strawman.

    The Creationists, after all, claim that evolution could not produce any new protein, because of the odds. Thornton’e result is the same but backward—it shows a functional protein despite those same odds.

    And another strawman. Behold, Olorin presents his holy strawman trinity.

    More importantly, list the peer-reviewed global survey for your 99.9999% claim

  27. False analogy. An eclipse is an occurrence, it has no primary biological functionality which can be tested.

    Now that is really desperate. BMWHAHAHAAAAAAAA

    Apparently, you failed english 101. Hint: see the word “expected.

    An expectation, fulfilled or not,cannot constitute a logical contradiction. That’s my beef with what you said.

    Would you be kind enough to list the peer-reviewed global survey from which this 99.9999% claim is derived?

    Sorry, I don’t carry the citation around in my head. It was about 3-4 years ago. The total number of life science researchers was 484,000. The number of dissenters was less than half a dozen. Thus 99.9999%.

    Yes, my appeal is a kind of ad populum argument. Look at it this way. If 1,000 oncologists all told you that you have cancer of the big toe, but Jonathan Wells of the DI said,thought it was merely a cod-liver oil deficiency, which opinion would you follow?

  28. If I have presented strawmwe, please inform me of the true situation with respect to these cr4eatoionist claims.

    I thought not..

  29. Now that is really desperate. BMWHAHAHAAAAAAAA

    If you say so, Oblivious Olorin

    An expectation, fulfilled or not,cannot constitute a logical contradiction. That’s my beef with what you said.

    If you don’t understand how your statement is fallacious, that’s your problem. Frankly, I explain too much with little improvement in your subsequent logic to make such an effort worthwhile.

    Sorry, I don’t carry the citation around in my head. It was about 3-4 years ago. The total number of life science researchers was 484,000. The number of dissenters was less than half a dozen. Thus 99.9999%.

    1. Hmmm, seems your recollection is off since the source gives some 700 creationists as in not “less than half a dozen”
    2. This number assumes that all creationists are out of the proverbial closet. Given the persecution many face, this would not be the case
    3. This is from a 1987 Newsweek article [http://kgov.com/files/docs/Newsweek-1987-God-Classroom.pdf] which specifically states: “By one count there are some 700 scientists with respectable academic credentials (out of a total of 480,000 U.S. earth and life scientists) who give credence to creation-science…”
    4. This is only applicable to the US and to earth and life science but evolution pertains to physics, chemistry, math, medicine, comp sci, engineering, humanities and social sciences
    5. Your claim does not state that this data is US specific
    6. What do they mean by one count? What count was this “one count”?
    7. This was not a peer-reviewed study
    8. This “one count” likely refers to only those in one organization (the CRS) [http://kgov.com/taxonomy/term/26]
    9. Why is Olorin the “research scientist” using a non-peer-reviewed non-study which uses a nebulous “one count”?

  30. You have a peculiar view of scientific theories. …

    Nope, just macro-evolution.

    I agree. You do have a peculiar view of macro-evolution.

    What “interpretation” have I (or Thornton) given?

    That the ‘resurrected’ protein only validates macro-evolution.

    I never mentioned macro-evolution. I’m not sure how you would define macro-evolution of a protein. There were only TWO mutations that launched this ancient protein into a family that is shared by most crown animals.

    But again, there is no “interpretation” here. The structure is what it is. No interpretation required. Yiu look at the sequence the algorithm spits out; you build one according to the sequence, then you test it. Where is the interpretation? You really do not understand something fundamental here, but I’m not sure what it is.

  31. Look at it this way. If 1,000 oncologists all told you that you have cancer of the big toe, but Jonathan Wells of the DI said,thought it was merely a cod-liver oil deficiency, which opinion would you follow?

    Whoever could better explain their diagnosis AND could show empirical evidence without asking me to use my “imaginations.” I cannot accept what a million experts say if it goes against everything I know empirically as an engineer and logically as a rational creature. Thus, if you want to make an argument, first present data which shows ALL the steps taken from an amoeba to a frog in a simulation study. Use all the data from all the sciences which supposedly confirms macro-evolution and create the pathway. Test rigorously and present as a landmark study….I thought not.

    If I have presented strawmwe, please inform me of the true situation with respect to these cr4eatoionist claims.

    Sure thing, as soon as you answer ALL my previous questions. In the mean time, use some of that “research scientist” skills you desperately claim to have and google.

  32. I never mentioned macro-evolution. I’m not sure how you would define macro-evolution of a protein. There were only TWO mutations that launched this ancient protein into a family that is shared by most crown animals.

    Macro-evolution of a protein: novel functionality due to accumulated nearly neutral mutations with an overall increase in functional information for said protein resulting in increased beneficial functionality of the organism.

    You are using an example of protein micro-evolution as evidence for macro-evolution. This is an extrapolation beyond the data.

  33. Sure thing, as soon as you answer ALL my previous questions.

    You’ll have to get a new line to disguise your lack of ability to answer a question you don’t like. This line is wearing so thin that everyone can see through it.

  34. Notice, gentle readers, that Olorin was the one who originally did not answer multiple direct questions in multiple previous posts. He then wants his questions answered and if not, he claims that it is due to the “lack of ability to answer a question you don’t like.” Pot calling kettle black and damned if you do, damned if you don’t. Recall also that Olorin consistently does not directly engage with the bulk of any reply post but latches on to a few sentences and makes a fallacious mountain out of a molehill. Keep consistent Olorin.

  35. Sorry, I don’t carry the citation around in my head. It was about 3-4 years ago. The total number of life science researchers was 484,000. The number of dissenters was less than half a dozen. Thus 99.9999%.

    1. Hmmm, seems your recollection is off since the source gives some 700 creationists as in not “less than half a dozen”

    The DI’s “700 list” is such a fragrant pile4 of horse puckey that even they have stopped promoting it actively. I thought everyone knew that. A number of people on the list have asked to be taken off when they found out they were on it. Were they taken off? Noooooo.

    Please note the conditions on my claim of half a dozen: PhD’s in the life sciences who are engaged in actual research in the life sciences. I stand by half a dozen evolution denialists, among life-sciences PhD’s engaged in life-sciences research. There’s Douglas Axe, Ann Gauger, Jonathan Wells, Michael Behe, and who else? Name a few—-if you can.

    Note also that the DI list has hardly grown at all since it was first published The “Steve List,” of scientists endorsing evolution has several times as many names as the DI list after only a couple of years. The Steve List, unlike DI’s, is limited to life-sciences researchers having appropriate PhD’s, and you must be named Steve (or Stephan or Stephanie)

    So all I can say is MWAHAHAHAHAAAAAAAAAAAAA.

  36. Macro-evolution of a protein: novel functionality due to accumulated nearly neutral mutations with an overall increase in functional information for said protein resulting in increased beneficial functionality of the organism.

    Sorry, that was a trick question to expose your abysmal lack of knowledge. The concept of macro-evolution does not apply to proteins. Asking about macro-evolution in a protein is like asking about the number of cylinders in a 747 airliner engine. Go look up the definition of “macro-evolution” sometime, instead of relying upon faulty imagination grounded in ignorance.

  37. Whoever could better explain their diagnosis AND could show empirical evidence without asking me to use my “imaginations.” I cannot accept what a million experts say if it goes against everything I know empirically as an engineer and logically as a rational creature.

    Get real.

  38. You are using an example of protein micro-evolution as evidence for macro-evolution. This is an extrapolation beyond the data.

    Why do you now say that this protein was only “micro” evolved? Seems a reversal of your previous position.

    Here is why the reconstruction is evidence for evolution and against creation. Creationists[1] like to say they have an “orchard” model of life, as opposed to the nested “tree” of evolution. The reconstruction algorithm came up with a single ancestral form of the protein. That is it found a tree relating all the modern proteins to a single progenitor protein. If the algorithm had instead found several unrelated ancestors at the base, then this would have been evidence for the orchard model. Finding a tree rather than an orchard is therefore evidence for evolution and against creation. No extrapolation required.

    As an illustration, the same algorithm has been used to reconstruct an earliest version of The Canterbury Tales from hundreds of modern copies, all of which vary from each other. The algorithm found a single ancestor. If, instead, we had input modern copies of The Canterbury Tales, and some modern copies of Shakespeare’s Richard II, we would come up with at least two very different ancestors, or, more likely, a fault indication saying that it could not find an ancestor.

    It is this result that indicates an evolutionary tree rather than an creationist orchard—i.e., separately created early forms. So let me know where is there any “extrapolation” in that? You seem to have some queer ideas about this whole area.

    ===================

    [1] At least those who admit at least some amount of evolution has taken place.

  39. I mentioned earlier that macro-evolution is a term that has not been applied to proteins. I can still find no references to this usage. However, last night while I was reading the facts about the Cambrian (rather than Stephen Metyer’s fictional account), I noted that Wallace Arthur, one of the founders of modern evo-devo, mentions that a few people have applied this term to individual genes. However, he notes[1] that none of them have defined the term in this sense, and that any such usage would be meaningless. The reason is that gene mutations—and protein mutations as well—are spread uniformly from minor to major phenotypic effects. There are no cut-off points or clusters that could separate “micro” from “macro” mutations.

    ==================

    [1] Wallace Arthur, TheOrigin of Animal Body Plans (Cambridge U. Press 1999), p. 16.

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