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Once upon a time, before DNA or RNA, there was TNA … if it ever existed in life forms

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From “Simpler Times: Did an Earlier Genetic Molecule Predate DNA and RNA?” (ScienceDaily, Jan. 9, 2012), we learn,

According to Chaput, one interesting contender for the role of early genetic carrier is a molecule known as TNA, whose arrival on the primordial scene may have predated its more familiar kin. A nucleic acid similar in form to both DNA and RNA, TNA differs in the sugar component of its structure, using threose rather than deoxyribose (as in DNA) or ribose (as in RNA) to compose its backbone.

In an article released online January 9 in the journal Nature Chemistry, Chaput and his group describe the Darwinian evolution of functional TNA molecules from a large pool of random sequences. This is the first case where such methods have been applied to molecules other than DNA and RNA, or very close structural analogues thereof. Chaput says “the most important finding to come from this work is that TNA can fold into complex shapes that can bind to a desired target with high affinity and specificity.” This feature suggests that in the future it may be possible to evolve TNA enzymes with functions required to sustain early life forms.

… research has now shown that a single strand of TNA can indeed bind with both DNA and RNA by Watson-Crick base pairing — a fact of critical importance if TNA truly existed as a transitional molecule capable of sharing information with more familiar nucleic acids that would eventually come to dominate life.

In “Before DNA, before RNA: Life in the hodge-podge world”(New Scientist, 08 January 2012), Michael Marshall notes

That doesn’t mean TNA was the original genetic material, though. Chaput thinks it probably wasn’t, if only because the chemistry of early Earth was so messy that TNA would not have arisen on its own. Rather, many different kinds of genetic material probably formed in a genetic hodge-podge. “The most likely scenario is that nature sampled lots of different things,” says Chaput.

Hmmm. What is “nature” that it should be doing any sampling?

Also,

… there are problems with the hodge-podge world hypothesis. For one thing, there is no trace of TNA or its cousins in modern organisms. For another, although TNA looks simpler than RNA, we can’t be sure it was easier to make some 4 billion years ago because no one has actually made it in the conditions that existed on Earth before life began, says John Sutherland of the MRC Laboratory of Molecular Biology in Cambridge, UK.

TNA has also not been found in life forms today, which is why the media release reads “ if TNA truly existed as a transitional molecule capable of sharing information with more familiar nucleic acids that would eventually come to dominate life.” You be the judge.

89 Replies to “Once upon a time, before DNA or RNA, there was TNA … if it ever existed in life forms

  1. 1
    Petrushka says:

    In the current study, Chaput and his group use an approach known as molecular evolution to explore TNA’s potential as a genetic biomolecule. Such work draws on the startling realization that fundamental Darwinian properties — self-replication, mutation and selection — can operate on non-living chemicals.

  2. 2
    Stu7 says:

    So does that mean we can we now incorporate the Origin of Life question within the modern evolutionary synthesis?

  3. 3
    mk says:

    the minimum to start with is a self replicate molecule. but to do that we need a polymerase protein like rna replicase.
    its a very complex protein that can make a copy of a dna\rna strand.

    also it need to replicate a big number of nucleotides. somthing like couple of hundred.

  4. 4
    EvilSnack says:

    Above all this is the unassailable fact that our knowledge of the chemical make-up of the earth’s surface during the pre-biotic era is conjecture based on assumptions that are for the most part untestable.

    Every scenario about the advent of life on earth begins with the assumption–usually unstated–that unguided abiogenesis is a fact, and goes on to assume–again, without stating that this assumption has been made–that the conditions necessary for unguided abiogenesis are not merely possible, but actually did prevail.

    It would be no different if a prosecuting attorney argued that there is no need to show the defendant was at the scene of the murder, because we already know that he did it.

  5. 5
    Petrushka says:

    Don’t know about the fact part, but it’s a testable hypothesis.. what other testable hypothesis is there?

  6. 6

    There seems to be a general view on this forum that if we can’t actually go back and look, a hypothesis is untestable.

    Or, if we can’t account for a specific phenomena, then a theory is untestable.

    Which isn’t how hypothesis testing works at all, as Genomicus shows in his thread on front-loading. What you do is you predict what you should observe if your hypothesis is true, and, if possible, what differential predictions are made by two alternative hypotheses.

    Support for a hypothesis derived from a theory does not tell you that your theory is correct, but it does provide support for it. Lack of support for a hypothesis derived from a theory tells you that you need to adjust your theory. It doesn’t mean you need to throw out the whole thing, though.

    “Darwinists” are often at fault for not making this clear. We do not, have, and will never have, a complete theory of how life as we observe it came to be. But we do have huge support for a number of theoretical principles, and (IMO) no good reason to suppose that we cannot extrapolate from those principles to events for which we have scant, or no, data.

    But it is perfectly true that we do not know how certain features of living things evolved (and thus, whether they did), nor how life itself got started (and thus, whether it came about through physics and chemistry or by some other means). But nor can we infer that Darwinian evolution and physics+chemistry are NOT the answer, and that is really where “Darwinists” depart from IDists. Not in rejecting ID, but in rejecting ID as the only reasonable default.

  7. 7
    Joe says:

    Elizabeth,

    We wouldn’t say the hypothsis is untestable if you or someone else could tell us how to objectively test it.

    Predictions? Please- predictions borne from stochastic processes is a fool’s errand.

    Oh and is isn’t that we reject Darwinism and NDE, but we reject the claim that they are the only explanations.

  8. 8
    Petrushka says:

    I’m not sure what that even means.

    There isn’t any known historical remnent of first life, so all we can do is explore the chemistry to see what’s possible. We will never know the actual history.

    But we do have quite a bit of historical evidence for the history of plants and animals, plus we have genomes, so we can consider reconstructing common ancestors.

    Plus we can observe evolution in the laboratory. We can study how it works.

    So your question looks. To me Like asking whether the engineering of buildings can be tied to the invention of grass huts. There’s a theoretical link, but the actual history is lost.

  9. 9
    Joe says:

    Well the evolution we observe does not support universal common descent. So that would be one issue…

  10. 10

    Predictions? Please- predictions borne from stochastic processes is a fool’s errand

    Well, no. You can certainly build predictive stochastic models. I’ve just built one myself, as it happens!

    And that’s how weather-forecasting is done.

    Glad to hear you don’t reject Darwinism. It certainly is not the only explanation for the data.

    Are we done?

  11. 11
    Petrushka says:

    It would be news to casinos and professional poker players that stochastic processes don’t lead to useful predictions.

  12. 12
    Petrushka says:

    What evidence is there that some branches of life are unrelated?

  13. 13
    Joe says:

    It is very strange taht every time you say your position makes predictions and you are called on it that you never produce any predictions!

    As for not rejecting Darwinism- obvoulsy it doesn’t say anything to reject…

  14. 14
    Joe says:

    Then tell us about these alleged predictions.

  15. 15
    Joe says:

    Related how? By design or descent? How can we tell?

  16. 16
    Petrushka says:

    I predict that casinos will continue to be profitable, for the same reason that GAs work, and for the same reason evolution works.

    Evolution creates things that never before existed. Their characteristics are not predictable. If you could predict the consequences of sequence changes, design would be possible.

    Try it. Show me that design is possible without evolution.

  17. 17
    Petrushka says:

    What does descent mean among microbes that exchange DNA?

    What multicelled organism are not related by descent?

    Name some.

  18. 18
    Petrushka says:

    If you can’t tell a relationship from descent from a relationship from design, what is the utility of the design hypothesis?

    The designer has not been observed, nor has an instance of design been observed, so it would seem to be an unnecessary hypothesis.

    I find it interesting that the more an ID advocate knows about molecular biology (see Behe) the more likely to accept common descent.

  19. 19

    It is very strange taht every time you say your position makes predictions and you are called on it that you never produce any predictions!

    Weirdly, when we point to Tiktaalik (a stunningly successful prediction) you say it doesn’t count because, I dunno, they didn’t really predict it or something.

    But take any empirical paper in evolutionary biology that reports a positive finding. That will represent a prediction that was successful.

    Because that’s what a positive finding is.

  20. 20
    mk says:

    elizabeth

    we can also fund a fail predication of the evolution theory. like a genes that can be found in a far species.

    the intellgegent design also has a positive prediction: a very complex system the cant be bild in a step by step mechaisem

  21. 21

    Yes, indeed, that’s an excellent example. And, as a result, the theory had to be modified (though not Darwin’s part, interestingly).

    Hence HGT.

    the intellgegent design also has a positive prediction: a very complex system the cant be bild in a step by step mechaisem

    I don’t see why not. Why not?

  22. 22
    Upright BiPed says:

    Because a “very complex system” (on massive observation) requires the constraint of recorded informational input.
    Recorded information requires abstract representations and transfer protocols; two material objects that must be coordinated even though they do not interact, and each must both be present in order for information transfer to take place.

    By definiton, such systems are beyond “step by step” configuration.

  23. 23
    Upright BiPed says:

    Aternatively, you can show that informational control is not required for the complex systems under question, or that information transfer does not require representations and protocols.

  24. 24

    By definiton, such systems are beyond “step by step” configuration.

    Please explain why an intelligent designer could not assemble such a thing “step by step”?

    Or are you simply saying that the intermediate steps will be non-viable?

    That it has to be assembled at the work bench, as it were? In which case, how does it reproduce?

  25. 25
    Upright BiPed says:

    Please explain why an intelligent designer could not assemble such a thing “step by step”?

    Have you become an ID proponent Dr Liddle?

    Such systems cannot be assembled ‘step-by-[unguided] step’.

  26. 26

    No, I’m not (right now) arguing that they can.

    I’m simply querying mn’s apparent comment that an intelligent designer couldn’t.

    If it’s a prediction, anyway. But I may have misunderstood his/her post. That’s why I asked.

  27. 27
    mk says:

    elizabeth:

    “And, as a result, the theory had to be modified”

    so the theory can accept anything?

    “I don’t see why not. Why not?”

    because if you want to make a new protein you will need huge amount of amino acid sequence. if you want a protein that can bind 2 substrate, you will need minimum 2 binding site, so one binding site will be useless.

  28. 28
    Upright BiPed says:

    Aternatively, you can show that informational control is not required for the complex systems under question, or that information transfer does not require representations and protocols.

    So, there will be no counter-examples offered here today, nor will the lack of such mean anything whatsoever to your conclusions.

  29. 29
    Petrushka says:

    Another chicken and egg argument?

  30. 30

    so the theory can accept anything?

    No, that’s what I said. It had to be modified.

    That’s the thing about science – you fit models to data, not data to models.

    And in this case, the part of the model, the theory of evolution, that had to be modified, was the part that said that all genetic information is passed down from parent to offspring. In fact “genes” were originally defined that way – as the unit of longitudinal inheritance, the “gen…” root being the same as the gen in “generations”.

    Then it was found that some genetic sequences just didn’t fit a longitudinal pattern of transfer – that there was also “Horizontal” gene transfer, or HGT.

    That isn’t a problem for the basic Darwinian algorithm – Darwin didn’t even know about genes, or where heritable variance came from – but it did mean that the idea that all genetic novelty came from copying infidelities was challenged.

    Drift is another relatively new part of evolutionary theory, as is evo-devo, and population-level selection, and symbiosis.

    So evolutionary theory is constantly “evolving” – the “evolving synthesis” as someone dubbed it (can’t remember who). As it should and must. Far from being “able to accept anything” it must be constantly modified to accommodate new data.
    And it can

  31. 31
    Jammer says:

    I can comprehend how an intelligent origin of life can be falsified?by showing that natural laws and chemistry, in and of themselves, with no (observable) intelligent input, are capable of creating life from non-life.

    That’s easy, at least theoretically.

    My question is: How can the belief that life was not intelligently designed be falsified in the laboratory? What finding(s) would disprove the notion of a design-free origin of life?

    I’ve seen answers along the lines of, “If we discovered a message encoded in our DNA that said, ‘You are designed,’ then I’d accept that life was designed, and my abiogenesis beliefs are wrong.”

    But isn’t this answer basically C.S.I., the very metric that design-deniers pretend is meaningless? Sure, the specification is (unreasonably) limited to previously existing human language, but it’s the exact same concept, no? A complex and specific sequence of DNA denoting information.

    So, then, it would seem to me that the real issue isn’t whether C.S.I. is an indicator of design?it clearly is. The real issue is just what it is that can be classified as C.S.I.

    Design-deniers would accept the discovery of an encoded message written in a human constructed-language as evidence of intelligent design, yet they wont accept the discovery of an entire, mind-blowingly brilliant language as evidence of intelligent design.

    Does that strike anyone else as being kind of, sort of, maybe a little bit irrational?

  32. 32
    mk says:

    elizabeth

    “No, that’s what I said. It had to be modified”

    so there is no prediction that can falsified the theory?

    where is the limit that there you will say that the theory is worng?

    if we find a gene that is similar to the same gene in monkey and dog insted of humans, what you will say in this case?

  33. 33

    Yes, there are great many predictions that can falsify the theory. You just gave an example. As a result, the theory had to be modified.

    In other words, it was wrong.

    It wasn’t very wrong, and now it’s less wrong than it was.

    That’s how theories are developed – they are constantly refined and modified.

    Occasionally a major plank of the theory has to be revised, but it is extremely rare for an entire theory to be abandoned, and so far, the fundamental Darwinian insight: that populations of self-replicators that replicate with heritable variance in reproductive success in the current environment will tend to adapt to that environment, remains extremely powerful. Indeed it is so powerful, it is more a syllogism than a theory – hard to see how it could not be true, and it has, of course, been directly observed, as most people here will agree.

    But the entire theory of evolution, with all its bits and pieces, from genetics to cladistics and all stations in between and beyond, is constantly subject to testing, falsification, and subsequent refinement.

  34. 34
    mk says:

    elizabeth

    You just gave an example. As a result, the theory had to be modified.”-

    modified but not falsified

    if anything can fit to the theory, what will not fit?

    give an example

    Indeed it is so powerful, it is more a syllogism than a “theory – hard to see how it could not be true, and it has, of course, been directly observed, as most people here will agree.”-

    there is no observation of a new protein or new system yet.

    its only a belife

    can you give an example of an evidence that cant be explain by intellegent design?

  35. 35
    bornagain77 says:

    Of related note:

    Science and Pseudoscience – Imre Lakatos – exposing Darwinism as a ‘degenerate science program’

    “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture

    ‘Before you can ask ‘Is Darwinian theory correct or not?’, You have to ask the preliminary question ‘Is it clear enough so that it could be correct?’. That’s a very different question. One of my prevailing doctrines about Darwinian theory is ‘Man, that thing is just a mess. It’s like looking into a room full of smoke.’ Nothing in the theory is precisely, clearly, carefully defined or delineated. It lacks all of the rigor one expects from mathematical physics, and mathematical physics lacks all the rigor one expects from mathematics. So we’re talking about a gradual descent down the level of intelligibility until we reach evolutionary biology.’ ?
    David Berlinski

    In fact, by the criterion laid out by Lakatos in the following audio lecture, Darwinism is found, in reality, to be a ‘degenerate science program’, i.e. a ‘pseudoscience’;

    Science and Pseudoscience – Lakatos – audio
    http://richmedia.lse.ac.uk/phi.....nce128.mp3

    The following evidence shows Darwinism to be a ‘degenerate science program’ using Lakatos’s criteria

    Predictions of Materialism compared to Predictions of Theism within the scientific method:
    https://docs.google.com/Doc?docid=dc8z67wz_5fwz42dg9

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information
    https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

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

    Here is how neo-Darwinian evolution avoids falsification from ‘anomalous’ genetic evidence:

    A Primer on the Tree of Life – Casey Luskin – 2009
    Excerpt: The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified.
    http://www.discovery.org/a/10651

    How to Play the Gene Evolution Game – Casey Luskin – Feb. 2010
    http://www.evolutionnews.org/2.....ution.html

    Pattern pluralism and the Tree of Life hypothesis – 2006
    Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.
    http://www.pnas.org/content/104/7/2043.abstract

    Here is how neo-Darwinian evolution avoids falsification from the fossil record;

    Seeing Ghosts in the Bushes (Part 2): How Is Common Descent Tested? – Paul Nelson – Feb. 2010
    Excerpt: Fig. 6. Multiple possible ad hoc or auxiliary hypotheses are available to explain lack of congruence between the fossil record and cladistic predictions. These may be employed singly or in combination. Common descent (CD) is thus protected from observational challenge.
    http://www.evolutionnews.org/2.....es_pa.html

    The Fossil Record and Falsifiable Predictions For ID – Casey Luskin – Audio
    http://intelligentdesign.podom.....6_42-07_00

  36. 36

    Well, the part of the theory that had to be modified was falsified.

    That’s why it had to be modified.

    “It” (the data) didn’t “fit the theory”. The theory had to be fitted to the data. That’s what science does – fits models to data, not data to models.

    And no, I can’t give you an example of evidence that can’t be explained by Intelligent Design. That’s why Intelligent Design has no explanatory power – a theory that can explain everything, explains nothing.

    The theory of evolution, conversely, cannot explain everything, and when it comes up against something it cannot explain, it has to be modified. That’s the discipline of the scientific method – you fit models to data, and if the data doesn’t fit, you modify the model.

    But if your model can, in principle, explain anything, then it is unfalsifiable, so not scientific.

  37. 37
    bornagain77 says:

    Here is how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations:

    More Biogeographical Conundrums for Neo-Darwinism – March 2010
    http://www.evolutionnews.org/2.....f_the.html

    The Case of the Mysterious Hoatzin: Biogeography Fails Neo-Darwinism Again – Casey Luskin – November 5, 2011
    Excerpt: If two similar species separated by thousands of kilometers across oceans cannot challenge common descent, what biogeographical data can? The way evolutionists treat it, there is virtually no biogeographical data that can challenge common descent even in principle. If that’s the case, then how can biogeography be said to support common descent in the first place?
    http://www.evolutionnews.org/2.....52571.html

    Many more instances of Darwinism avoiding falsification from the empirical data, by ad hoc models, are found in this following site:

    Darwin’s Predictions – Cornelius Hunter PhD.
    http://www.darwinspredictions.com/

    Whereas in contrast to there being no identifiable falsification criteria for neo-Darwinism (at least no identifiable falsification criteria that neo-Darwinists will accept), here is a very rough outline of the basic falsification criteria for Intelligent Design:

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

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

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    Moreover here is the true principle governing all biological adaptations (a principle that is certainly very antagonistic to Darwinism, and very friendly to Intelligent Design)

    “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.co.....evolution/

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    Here is a rough outline of future predictions for Intelligent Design:

    A Positive, Testable Case for Intelligent Design – Casey Luskin – March 2011 – several examples of cited research
    http://www.evolutionnews.org/2.....45311.html

  38. 38
    Stu7 says:

    I was expanding on the statement that you quoted:

    Such work draws on the startling realization that fundamental Darwinian properties — self-replication, mutation and selection — can operate on non-living chemicals.

    If “fundamental Darwinian properties” were at work on non-living chemicals — in other words if non-living chemicals were “evolving”, utilising the very mechanisms used by living organisms — surely it should / could form part of the wider evolutionary synthesis?

  39. 39
    bornagain77 says:

    further note:

    Is evolution pseudoscience?
    Excerpt:,,, Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other?pseudosciences — astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many.
    http://creation.com/is-evolution-pseudoscience

    Music and Verse:

    Sara Groves – Miracle (Official Music Video) – Music Videos
    http://www.godtube.com/watch/?v=FM1CEFNU

    1 Corinthians 2:9
    However, as it is written: “No eye has seen, no ear has heard, no mind has conceived what God has prepared for those who love him”–

  40. 40
    mk says:

    elizabeth

    Well, the part of the theory that had to be modified was” falsified.”

    ok. the chicken have a gene called har1, that is more similar to the chimpanzee version than to the human version. the evolution is now false?

    And no, I can’t give you an example of evidence that can’t” be explained by Intelligent Design. That’s why Intelligent Design has no explanatory power – a theory that can explain everything, explains nothing.”

    not realy. a falsification for the id theory will be if you find a step by step mechanisem to a ic system

    if we have a ic system like abcd, you can find an ab system or abc system.

  41. 41
    Joe says:

    Elizabeth:

    Weirdly, when we point to Tiktaalik (a stunningly successful prediction) you say it doesn’t count because, I dunno, they didn’t really predict it or something.

    Weirdly I explained why Tiktaalik isn’t a prediction and obvioulsy you have some mental issues and cannot grasp reality.

    Ya see Shubin said he was looking for evidence of the transition, which occurred BEFORE tetrapods lived. Tiktaalik was found AFTER tetrapods existed and therefor is the wrong speciman.

  42. 42
    Joe says:

    Hey Petrushka,

    We design casinos without the use of evolution…

  43. 43

    ok. the chicken have a gene called har1, that is more similar to the chimpanzee version than to the human version. the evolution is now false?

    No. How would that falsify evolution? Let’s say your first cousin and your very distant 60th cousin lots of times-removed both have blue eyes, but you have brown.

    Does that mean your first cousin is more closely related to your distant cousin than to you? Nope.

    So the nested hierarchy is not violated, even though both your first and remote cousin share the blue-eyed gene, and you don’t have it.

    Same with this gene. If it was underwent some beneficial mutation in a descendent of the common ancestor between chimps and humans that was not an ancestor of chimps, then you would expect it to diverge rapidly from the version shared by chickens and chimps. So chickens and chimps will have similar sequences, and humans different ones.

    What would be more problematic for our current understanding of evolution would be to find a functional sequence closely shared by chickens and chimps, but not by any other primate.

    It would not necessarily falsify the whole theory, but some additional gene transfer mechanism, or gene convergence mechanism, would have to be proposed to explain it.

    not realy. a falsification for the id theory will be if you find a step by step mechanisem to a ic system

    Why would that falsify ID? Why couldn’t the designer have designed the “ic” system step by step?

  44. 44

    And, weirdly, I explained why it was, but you didn’t get it.

    You are making the “why are there still monkeys” error.

  45. 45
    Joe says:

    Wrong again, as usual, Elizabeth. I am just going by what Shubin said.

    Also logic says that you do not go looking for the transition AFTER it occrred as there isn’t any reason that a transitional form should exist many millions of years AFTER the transition occurred.

    But all that is moot because obvioulsy you have reading comprehension issues.

  46. 46
    Joe says:

    For Elizabeth:

    Shubin said- SHUBIN SAID- he was looking where he did because he had data that put the transition from fish to tetrapods between 385- 365 million years ago.:

    Chapter 1 of “Your Inner Fish” tells us why:

    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

    However new data has tetrapods appearing over 390 million years ago, meaning his data was out-dated and is wrong.

    And yes a transitional HAS to be found- IN TIME- between the alleged parent and alleged child species. And yes parent, transitional and child species can overlap- all transitionals can overlap. However any given transitional absolutely HAS to exist (or had to have existed) between the alleged parent and alleged child.

    Right now Shubin’s find shows fish-> tetrapods-> fishapodes, whereas the theory requires fish-> fishapods-> tetrapods, not that Elizabeth can understand that…

  47. 47
    Joe says:

    To falsify ID all one has to do is demonstrate that a designer is not required. That is how it is done in archaeology and forensics…

  48. 48

    As I said, Joe, you are making the “why are there still monkeys?” error.

    You certainly don’t go looking for a transition before you think it had occurred. You can look after it, for as long as you like, though (hence “living fossils”). That’s because a “transitional fossil” is not an actual populatoin that is directly between some known ancestor and some known modern (or later) population, but which represents a population that branched off between the two and has intermediate characteristics. So where would you expect to find tetrapods with the fishiest characteristics? In litoral deposits dating from not too long (but it doesn’t matter exactly how long) after the conjectured divergence.

    So they checked out where such litoral deposits would be at the earth’s surface, dating from the right sort of date. And they found them.

    The fact that there are also other, earlier, ones (as we know from the trackways) is irrelevant. They used a hypothesis to predict where a population of fishy tetrapods would still be living and have left fossils close to surface. They got it right.

    Science +1.

    I’m not going to rudely accuse you of having “comprehension issues” as you do me, but I do suggest you actually read the primary literature. Also that you check out what is meant by a “transitional” fossil.

  49. 49
    Joe says:

    Elizabeth:

    As I said, Joe, you are making the “why are there still monkeys?” error.

    Prove it or shut up. I understand that transitional forms can exist after the transition has been made and that has NOTHING to do with what I am saying.

    So read it AGAIN , for the FIRST time:

    Shubin said- SHUBIN SAID- he was looking where he did because he had data that put the transition from fish to tetrapods between 385- 365 million years ago.:

    Chapter 1 of “Your Inner Fish” tells us why:

    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

    However new data has tetrapods appearing over 390 million years ago, meaning his data was out-dated and is wrong.

    And yes a transitional HAS to be found- IN TIME- between the alleged parent and alleged child species. And yes parent, transitional and child species can overlap- all transitionals can overlap. However any given transitional absolutely HAS to exist (or had to have existed) between the alleged parent and alleged child.

    Right now Shubin’s find shows fish-> tetrapods-> fishapodes, whereas the theory requires fish-> fishapods-> tetrapods, not that Elizabeth can understand that…

    Shubin did NOT say he was looking for a ”
    transitional fossil”- he clearly states he was looking for evidenec of the transition.

    As I said you have reading comprehension issues.

  50. 50
    Joe says:

    Elizabeth:

    So where would you expect to find tetrapods with the fishiest characteristics?

    You do it as Shubin said- first you find out when there were fish and no tetrapods, then you find out when there were fish and tetrapods and you search BETWEEN those two dates, duh.

    What the theory of evolution expects is fish-> fishapod-> tetrapod

    what we have right now thanks to Shubin is:

    fish-> tetrapod-> fishapod

  51. 51
    mk says:

    So the nested hierarchy is not violated, even though both “your first and remote cousin share the blue-eyed gene, and you don’t have it.”

    so how can we falsify the nested hierarchy? give me an exmple

    secondly, nested hierarchy doesnt prove evolution. cars models have nested hierarchy. but they dont have commondescent. even if they are self replicate.

    What would be more problematic for our current” understanding of evolution would be to find a functional sequence closely shared by chickens and chimps, but not by any other primate”

    not realy. you always can say rhat the gene came from horizontal gene transfer, or was cut from the organism because mutation.

    It would not necessarily falsify the whole theory, but some” additional gene transfer mechanism, or gene convergence mechanism, would have to be proposed to explain it”

    so again, anything can happan.

    and last thing, my native language is not english, so sorry if im not spell well some words.

  52. 52
    Joe says:

    The War of 1812-> if I wanted to find evidence for the transition between peace and the war of 1812 do I look in documention for the year 1850 or do I look in documentation that pre-dates the war?

    If I wanted to study the transition between two US Presidents do I focus my study on the period two years after the election?

    If I wanted to study the transiton between caterpillars and butterflies, what am I doing wrong by studying what butterflies eat?

    ???

  53. 53
    mk says:

    i forgot somthing

    “Why would that falsify ID? Why couldn’t the designer have designed the “ic” system step by step?”

    good question. the answer is because even intellegent design cant do that. think about car turn into airplan in functional way. its ipossible.

  54. 54
    bornagain77 says:

    Of related note:

    Lenski’s work has also shown that ‘convergent evolution’ is impossible because his work has shown that evolution is ‘historically contingent’. This following video and article make this point clear:

    Lenski’s Citrate E-Coli – Disproof of Convergent Evolution – Fazale Rana – video (the disproof of convergence starts at the 2:45 minute mark of the video)
    http://www.metacafe.com/watch/4564682

    The Long Term Evolution Experiment – Analysis
    Excerpt: The experiment just goes to show that even with historical contingency and extreme selection pressure, the probability of random mutations causing even a tiny evolutionary improvement in digestion is, in the words of the researchers who did the experiment, “extremely low.” Therefore, it can’t be the explanation for the origin and varieity of all the forms of life on Earth.
    http://www.scienceagainstevolution.org/v12i11f.htm

    The loss of ‘convergent evolution’, as a argument for molecular sequence similarity in widely divergent species, is a major blow to neo-Darwinian story telling:

    Implications of Genetic Convergent Evolution for Common Descent – Casey Luskin – Sept. 2010
    Excerpt: When building evolutionary trees, evolutionists assume that functional genetic similarity is the result of inheritance from a common ancestor. Except for when it isn’t. And when the data doesn’t fit their assumptions, evolutionists explain it away as the result of “convergence.” Using this methodology, one can explain virtually any dataset. Is there a way to falsify common descent, even in the face of convergent genetic similarity? If convergent genetic evolution is common, how does one know if their tree is based upon homologous sequences or convergent ones? Critics like me see the logic underlying evolutionary trees to be methodologically inconsistent, unpersuasive, and ultimately arbitrary.
    http://www.evolutionnews.org/2.....37841.html

    Origin of Hemoglobins: A Repeated Problem for Biological Evolution – 2010
    Excerpt: When analyzed from an evolutionary perspective, it appears as if the hemoglobins originated independently in jawless vertebrates and jawed vertebrates.,,, This result fits awkwardly within the evolutionary framework. It also contradicts the results of the Long-term Experimental Evolution (LTEE; Lenski) study, which demonstrated that microevolutionary biochemical changes are historically contingent.
    http://www.reasons.org/origin-.....-evolution

    Convergence: Evidence for a Single Creator – Fazale Rana
    Excerpt: When critically assessed, the evolutionary paradigm is found to be woefully inadequate when accounting for all the facets of biological convergence. On the other hand, biological convergence is readily explained by an origins model that evokes a single Creator (reusing optimal designs).
    http://www.reasons.org/converg.....le-creator

    Bernard d’Abrera on Butterfly Mimicry and the Faith of the Evolutionist – October 2011
    Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe (science) that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible.
    http://www.evolutionnews.org/2.....51571.html

    Convergence Drives Evolution Batty – Fazale Rana – September 2010
    Excerpt: The multiple, independent origin of echolocation in these animals (twice in bats and once in toothed whales) exemplifies convergence,,, When examined from an evolutionary perspective, convergence doesn’t make much sense.,,, the latest research demonstrates that—again, from an evolutionary perspective—the genetic and biochemical changes that account for the emergence of echolocation in bats and dolphins is identical. Given the random nature of the evolutionary process, this recent discovery doesn’t match what evolutionary biologists would expect to find. But both the discovery and convergence make sense if life stems from the work of a Creator.
    http://www.reasons.org/converg.....tion-batty

    Common Design in Bat and Whale Echolocation Genes? – January 2011
    Excerpt: two new studies in the January 26th issue of Current Biology, a Cell Press publication, show that bats’ and whales’ remarkable ability and the high-frequency hearing it depends on are shared at a much deeper level than anyone would have anticipated — all the way down to the molecular level.
    http://www.evolutionnews.org/2.....42291.html

    Bat and Whale Echolocation Genes Point to Common Design – February 2011 – Podcast
    http://intelligentdesign.podom.....9_16-08_00

  55. 55
    Petrushka says:

    So how many data points were used to make the age estimate? What do you think the error bars would look like?

    What percentage of the tetrapods that ever liived have been recovered as fossils?

  56. 56

    Prove it or shut up. I understand that transitional forms can exist after the transition has been made and that has NOTHING to do with what I am saying.

    Good. So your argument is simply that he had the earlier window boundary a bit too late?

    How does that invalidate his prediction? Just meant he was aiming at a wider target than he thought.

    And yes a transitional HAS to be found- IN TIME- between the alleged parent and alleged child species.

    Well, not in the way that palaeontologists use the term.

    They aren’t even looking for populations in direct line between two known populations, merely for ones that branched off between the two.

    As I said you have reading comprehension issues.

    Possibly. But not on the evidence you have supplied. From where I am standing it is you have misunderstood the nature of palaeontological research.

    You are a very rude man, Joe. I think I’ll take another break. Perhaps in the mean while you can locate your manners.

  57. 57

    So the nested hierarchy is not violated, even though both “your first and remote cousin share the blue-eyed gene, and you don’t have it.”

    so how can we falsify the nested hierarchy? give me an exmple

    Well, I gave you an example – a gene that was common to chimps and chickens but not found in any other primate.

    secondly, nested hierarchy doesnt prove evolution. cars models have nested hierarchy. but they dont have commondescent. even if they are self replicate.

    No, nested hierarchy does not prove evolution, although it strongly suggests common ancestry, and without common ancestry, Darwinian evolution can only explain evolution within branches that do share ancestry.

    Cars, however, do not show nested hierarchy of features – they are full of violations, not surprisingly, as they are not generated by Darwinian processes (although the process has some things in common). Take, for instance, the adoption of an innovation such as ABS, or air conditioning in many lines simultaneously, not just the lineage in which it was first introduced. In other words we don’t simply see HGT in cars we see Horizontal phenotypic feature transfer.

    What would be more problematic for our current” understanding of evolution would be to find a functional sequence closely shared by chickens and chimps, but not by any other primate”

    not realy. you always can say rhat the gene came from horizontal gene transfer, or was cut from the organism because mutation.

    Well, that might be an explanation, although that would be difficult to sustain if it served a similar function in both species. And impossible to sustain if it was found in a related location.

    It would not necessarily falsify the whole theory, but some” additional gene transfer mechanism, or gene convergence mechanism, would have to be proposed to explain it”

    so again, anything can happan.

    Not sure what you mean. If data that cannot be explained by the current version of the theory are found, then the theory has to give. It does so all the time – that’s why it now includes HGT and drift, and evo-devo, none of which were envisaged by Darwin, who didn’t even know about genes.

    But certainly some hypothetical findings would be very difficult to reconcile with our current understanding, and might require wholesale readjustment of the theory. Hard to imagine just what, though. I guess finding the first chapter of genesis encoded in some highly conserved sequence might do it 🙂

    and last thing, my native language is not english, so sorry if im not spell well some words.

    No problem 🙂

  58. 58
    Joe says:

    Elizabeth,

    I made my argument. Obvioulsy you were too busy making up false accusations and couldn’t be bothered to read what I actually posted. Then you say I am being rude when in fact it is YOUR rudeness that is displayed by not even addressing what I post.

    And now you are going to run away, again. Typical.

    Shubin said- SHUBIN SAID- he was looking where he did because he had data that put the transition from fish to tetrapods between 385- 365 million years ago.:

    Chapter 1 of “Your Inner Fish” tells us why:

    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythings” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10 (bold added because obvioulsy the meaning of that sentence eludes evos)

    However new data has tetrapods appearing over 390 million years ago, meaning his data was out-dated and is wrong.

    And yes a transitional HAS to be found- IN TIME- between the alleged parent and alleged child species. And yes parent, transitional and child species can overlap- all transitionals can overlap. However any given transitional absolutely HAS to exist (or had to have existed) between the alleged parent and alleged child.

    Right now Shubin’s find shows fish-> tetrapods-> fishapodes, whereas the theory requires fish-> fishapods-> tetrapods, not that Elizabeth can understand that…

    (and another prediction is fulfilled, thanks Lizzie)

  59. 59
    Joe says:

    Elizabeth,

    We will add nested hierarchies to the growing list of things you do not understand.

  60. 60
    EvilSnack says:

    It would help to distinguish what I said from what I did not say.

    I did not say that the inability to observe the pre-biotic conditions of earth disproves unguided abiogenesis.

    What I said was that Darwinists hold, as an incontrovertible fact, that the advent of life on earth was an unguided process, that this belief affects their argumentation a related topic, and that that in the face of our inability to observe anything at all about conditions that held when this process took place, their certainty is unjustified.

    And yes, I do hold that any claim that “X happened at a certain point in the past” must necessarily be tentative when neither X nor anything like X has been observed, and the conditions in the past are not knowable beyond the vaguest guesswork.

    I most certainly did not say that unguided abiogenesis was conclusively disproven, merely that it is not conclusively proven.

    But if we are going to go for testable hypotheses, fine:

    What will we observe if life on Earth began as a result of unguided processes, with no involvement of any kind by any intelligent agency?

    What will we observe if life on Earth began as a result of processes of which one or more were guided by intelligent agents?

    Either side can answer these ones.

  61. 61

    Well, perhaps you could take the time to read what I actually posted, rather than just repost what you already posted.

    Because there really isn’t any point in responding to you unless you do.

  62. 62
    Joe says:

    Elizabeth,

    I read what you posted and it is irrelevant to the point I am making and does not even address what Shubin said.

    Now in his book either he was lying or making up a story but according to what he said he would not have been looking where he did if he knew that tertrapods already existed in strata much earlier.

    IOW Liz you aren’t responding to me now, so if you run away there won’t be any difference.

    So I will keep repeating what I say until you actually respond to it and stop with the irrelevant distractions.

  63. 63
    Petrushka says:

    Again, the estimate of the transition period was made on the basis of fossils found prior to Tik. More data has obviously widened the window.

  64. 64
    Joe says:

    Elizabeth:

    You certainly don’t go looking for a transition before you think it had occurred.

    You need to know when it occurred. ya see according to Shubin he thought he was looking in strata that pre-dated tertrapods. He was wrong.

    You can look after it, for as long as you like, though (hence “living fossils”).

    That is false as there isn’t anything that says transitional forms should remain in existence millions of years after the transition occurred.

    Obvioulsy you are just making stuff up again.

    That’s because a “transitional fossil” is not an actual populatoin that is directly between some known ancestor and some known modern (or later) population, but which represents a population that branched off between the two and has intermediate characteristics.

    Again he did NOT say he was looking for a transitional fossil. He said he was looking for evidence of THE TRANSITION and he said he was looking for evidence of the transition is strata in which he thought it occurred. However we now know the transition occurred much earlier which means he was looking in the wrong place.

    So where would you expect to find tetrapods with the fishiest characteristics?

    Only in strata between the transition of fish and tetrapods, which is where Shubin thought he was looking. Yet he was wrong.

    In litoral deposits dating from not too long (but it doesn’t matter exactly how long) after the conjectured divergence.

    1- It was at least many millions of years after and
    2- No one even knows when it occurred.

    So you lose, again.

  65. 65
    Joe says:

    Again, I know all of that and it does not change anything I have posted.

  66. 66

    I have responded to it, Joe, in 7.1.1.1.4.

    I will rephrase here:

    Firstly, if you accept that “transitional” populations can survive, relatively unchanged, long after the “transition” then your only real criticism of Shubin seems to be that he set the earliest boundary of his critical window rather late. In other words, he set the window rather narrower than he need have done, and at the later (safer) end of it. That makes no difference to the success of his prediction.

    Secondly, in response to your repeated claim that:

    And yes a transitional HAS to be found- IN TIME- between the alleged parent and alleged child species. And yes parent, transitional and child species can overlap- all transitionals can overlap. However any given transitional absolutely HAS to exist (or had to have existed) between the alleged parent and alleged child.

    I am simply disagreeing that this is how palaeontologists use the term “transitional”. It normally does not refer to a fossil that is directly inline between “parent” and “child” population anyway, and need not even be from a population that lived between those two populations in terms of time.

    For example, to take the definition given in Wiki:

    A transitional fossil is any fossilized remains of a lifeform that exhibits characteristics of two distinct taxonomic groups. A transitional fossil is the fossil of an organism near the branching point where major individual lineages (clades) diverge. It will have characteristics typical of organisms on both sides of the split, but because of the incompleteness of the fossil record, there is usually no way to know exactly how close it is to the actual point of divergence.

    “Near the split” does not necessarily mean near it in time but near in characteristics.

  67. 67
    Joe says:

    No Elizabeth, you have not responded to what I have posted.

    Firstly, if you accept that “transitional” populations can survive, relatively unchanged, long after the “transition” then your only real criticism of Shubin seems to be that he set the earliest boundary of his critical window rather late. In other words, he set the window rather narrower than he need have done, and at the later (safer) end of it. That makes no difference to the success of his prediction.

    then why didn’t he just go to a local stream and find one? Heck if there isn’t any time limit then they should be still be here.

    And again Shubin did NOT say that he was looking for a transitionl fossil, you are pathetically mistaken. He said he was looking for evidence of THE TRANSITION.

    The War of 1812-> if I wanted to find evidence for the transition between peace and the war of 1812 do I look in documention for the year 1850 or do I look in documentation that pre-dates the war?

    If I wanted to study the transition between two US Presidents do I focus my study on the period two years after the election?

    If I wanted to study the transiton between caterpillars and butterflies, what am I doing wrong by studying what butterflies eat?

    ???

    And nice of you to ignore all of other posts refuting your nonsense of this…

  68. 68

    Feel free, Joe.

    But I remain of view that it is one of a list of things you do not understand.

    I guess we will have to agree to differ.

  69. 69
    Joe says:

    Well Elizabeth I have provided support for my claim. OTOH you have provided nothing.

    Here it is- AGAIN:

    Eric B Knox, “The use of hierarchies as organizational models in systematics”, Biological Journal of the Linnean Society (1998), 63: 1–49

    Descent with modification would lead to a hierarchy based on “first life”, which as you can see is not a nested hierarchy- that is if you bother to read the paper.

  70. 70
    mk says:

    elizabeth

    “Well, I gave you an example – a gene that was common to
    chimps and chickens but not found in any other primate”

    an erv called herv-k was found in gorila and chimpanzee but not in humans.

    they have also 100 copies ofervs called pterv1 and not a single one in humans!

    we found a slug with genes for photosynthese and more.

    the evolution is wrong?

    “Take, for instance, the adoption of an innovation such as ABS, or air conditioning in many lines simultaneously, not just the lineage in which it was first introduced”

    its called “convergent evolution” and living organisem have this also. the eye was evolved somthing like 40 times without a commondesent.

    “If data that cannot be explained by the current version of the theory are found, then the theory has to give”

    but like i sayed, anything can fit to the theory.

    there is no spot that you will say: “the theory is now false”

  71. 71

    then why didn’t he just go to a local stream and find one? Heck if there isn’t any time limit then they should be still be here.

    Because clearly in this case there was reason to expect a time limit (there are no living animals that have the intermediate characteristics proposed). Hence his later boundary. He needed to look between the earliest likely date and the latest likely date.

    It turns out he made that window slightly narrower than it need have been. Didn’t matter – he still found them.

    And again Shubin did NOT say that he was looking for a transitionl fossil, you are pathetically mistaken. He said he was looking for evidence of THE TRANSITION.

    Well, finding a transitional fossil is evidence that the transition occurred, and, moreoever, informative about the nature of the transition.

    Your analogies are not analogous. We are talking about a branching tree here, not a single timeline.

    And I’m sorry, but I simply do not accept that you have “refuted” anything. I am not ignoring your posts (though I said I would), as you can see, but I’m not going to address every one.

  72. 72
    Joe says:

    Eliabeth:

    Because clearly in this case there was reason to expect a time limit (there are no living animals that have the intermediate characteristics proposed).

    1- He had no idea what characteristics he would find

    2- There are transitional forms around today- ie fish that are air breathers and fish that can travel on land.

    3- There isn’t any reason why a species such as Tiktaalik today as opposed to just a mere twenty or more million years after the transition.

    It turns out he made that window slightly narrower than it need have been. Didn’t matter – he still found them.

    Actually the “window” was totally shattered, which means his erasoning for looking where he did was also shattered.

    As he knew the only time period in which it is guaranteed to find a transitional form is BETWEEN two periods. What he found was after that and therefor could just be a hybrid.

    That said “transitional form” is nothing more than “it looks like a transitional to me” and that is because of OUR classification system.

    BTW I am not using anologs- I am using what Shubin said aling with logic- the same logic Shubin used-> you do not go looking for evidence of the transition millions of years after-the-fact. And you cannot place some aribitrary time limit on the existence of the transitionals.

    As I said either you think Shubin is a liar or just a story-teller…

  73. 73

    1- He had no idea what characteristics he would find

    Well, no. He was specifically looking for animals with characteristics intermediate between known early tetrapods and late Silurian fish. That was the “gap” he wanted to fill, and he identified the time window in which he was likely to find those animals; the kind of deposit (litoral) in which they would be found; and where that kind of deposit happens to be close to the surface today. The answer was a particular spot in Greenland. And there he found fossils of animals with exactly those intermediate characteristics.

    2- There are transitional forms around today- ie fish that are air breathers and fish that can travel on land.

    Yes, indeed, and they are probably descended from an ancestor that diverged from the those same early fish. But what Shubin was looking for were animals that lived earlier than the earliest known tetrapods, not their likely descendents.

    Actually the “window” was totally shattered, which means his erasoning for looking where he did was also shattered.

    Not sure what you mean by this. He found the animals with the predicted characteristics in his predicted window. That he might have found similar animals had he looked in slightly earlier strata is irrelevant. That someone has done so (or at least their tracks) is very exciting, and sheds new light on the timescale. It doesn’t “shatter” anything, it merely fills in some more of the jigsaw puzzle in an unanticipated way. If the jigsaw is a picture of a tree, he found a particular piece of a branch. We know know that there is another branch that hadn’t been known about earlier. In all likelihood there are probably a great many, but whether we will find fossils of all of them is unknown – not likely, though.

    As he knew the only time period in which it is guaranteed to find a transitional form is BETWEEN two periods. What he found was after that and therefor could just be a hybrid.

    Possibly. In some ways it probably was – speciation isn’t a rapid process in geological terms, and some hybridisation will go on even after two populations have diverged. But if you are suggesting that Tiktaaliks are the hybrid offspring of some later tetrapod and a fish – well that seems unlikely to me. Does it really seem likely to you?

    But you are still not using the word “transitional” in the way generally used by palaeontologists, which maybe why you are (IMO) misinterpreting Shubin. And you are never, of course “guaranteed” to find a transitional form (on either the regular meaning of the word, or yours).

    As I said either you think Shubin is a liar or just a story-teller…
    3- There isn’t any reason why a species such as Tiktaalik today as opposed to just a mere twenty or more million years after the transition.

    You seem to have missed out a word or so here. But if you mean “there isn’t any reason why there aren’t Tiktaaliks today”, sure there isn’t. There are fish today, after all.

    That said “transitional form” is nothing more than “it looks like a transitional to me” and that is because of OUR classification system.

    Well, no, it isn’t. The concept is certainly closely bound up with the classification system, but fitting a new kind of organism into the classification system isn’t just a question of saying “it looks like a transitional to me”. It’s usually done by quite sophisticated classification algorithms with statistical tests for the likelihood of any output tree.

    BTW I am not using anologs- I am using what Shubin said aling with logic- the same logic Shubin used-> you do not go looking for evidence of the transition millions of years after-the-fact. And you cannot place some aribitrary time limit on the existence of the transitionals.

    Well, your examples of wars and caterpillars were analogies, surely? And I’m precisely NOT “plac[ing] and arbitrary time limit on the existence of the transitionals”. I’m saying that if you want to find a transitional form i.e. one that has characteristics of two existing taxa, then the first place to look (if you haven’t found one) is in strata that lie, temporally, between the time you think the ancestral population lived, and the time you think the other population lived, because whether they subsequently surved for eons afterwards or went rapidly extinct, you know that they must have been extant during that intervening period.

    In other words, the window tells you where to look; it’s the characteristics that tell you whether it’s a transitional. If, instead of Tiktaaliks, Shubin and al had just found, say pandericthyses, or acanthostegas, they’d have found tetrapods from time between known populations of those two animals, but they wouldn’t have found transitional fossils. However, in fact, they found Tiktaaliks, which were.

    As I said either you think Shubin is a liar or just a story-teller…

    I think he’s neither. But I do think you have misunderstood him.

    Anyway, I appreciate the more civil tone. Thanks.

    Cheers

    Lizzie

  74. 74
    Joe says:

    Elizabeth:

    He was specifically looking for animals with characteristics intermediate between known early tetrapods and late Silurian fish.

    then you have to look between the two eras, just as Shubin said. And guess what? Tiktaalik was not found between the two eras.

    That was the “gap” he wanted to fill, and he identified the time window in which he was likely to find those animals; the kind of deposit (litoral) in which they would be found; and where that kind of deposit happens to be close to the surface today.

    His time window was the wrong window.

    The answer was a particular spot in Greenland.

    Wrong answer. Had he known that tetrapods exiosted at that time he would not have looked there. That is according to his logic and reasoning.

    But what Shubin was looking for were animals that lived earlier than the earliest known tetrapods, not their likely descendents.

    Exactly. Unfortunately that isn’t what he found. And that is what I have been saying.

    What Shubin found lived many millions of years AFTER/ LATER than tetrapods.

    He found the animals with the predicted characteristics in his predicted window.

    So the theory predicts fish-> tetrapods-> fishapods? Or is it that you don’t know what you are talking about.

    Shubin was looking for the water to land transition. For all he knows, because of the time-line of the find, he found a land-to-water transition.

    One more time-

    Shubin had his “window” based on two things he thought he knew- 1) the era in which there were fish and no tetrapods and 2) the era in which there were tetrapods. Those are HIS words, Elizabeth.

    However we now know that Shubin’s “window” was the wrong window because his data points were wrong.

    And there is NOTHING in the theory of evolution that says transitional forms will exist millions of years AFTER the transition. If they existed millions of years after the transition there isn’t anything preventing them from still existing.

    Data for the window was wrong- strange that you cannot grasp that simple fact.

  75. 75
    Petrushka says:

    Joe: does God not exist because some YEC believers have said the earth is 6000 years old and some have said 10,000?

    Your argument is every bit as silly.

  76. 76
    Joe says:

    Yeah, I admit that you do know quite a bit about silly arguments, but in this case your example does not fit.

    If we were to find Tiktaalik-like things in strata before there were tetrapods and after there were fish, then yes, Tiktaalik was just a very long-lived transitional.

    But according to Shubin he wanted to find something that existed between the time of fish and the time of tetrapods:

    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythings” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

    Those are his words, from his book. Even my 9 year old understands what it means…

  77. 77

    then you have to look between the two eras, just as Shubin said. And guess what? Tiktaalik was not found between the two eras.

    Yes, it was. 8 is between 6 and 9, right? It is also between 4 and 9.

    Turns out we now have evidence for tetrapods at 5 as well. Cool, but that doesn’t invalidate Shubin’s prediction or his find.

  78. 78

    and after there were fish

    There are still fish.

  79. 79
    Chas D says:

    Eric B Knox, “The use of hierarchies as organizational models in systematics”, Biological Journal of the Linnean Society (1998), 63: 1–49

    Descent with modification would lead to a hierarchy based on “first life”, which as you can see is not a nested hierarchy- that is if you bother to read the paper.

    It’s just the way he draws ’em. Drawing a species family tree – the cone with ‘first life’ on the left and ‘modern life’ on the right – is not a nested hierarchy, it is true, any more than a line of babushka dolls on a shelf is nested. But stack them, and they are.

    See fig 4-6 on page 12. Take a cone of descent (Fig 4), turn it end-on (Fig 5g), and group the latest descendant inside its recent ancestors, then draw those ancestors’ ancestors around them and so on, and the hierarchy is revealed, nested at the base of the cone.

    Fig 4 is the non-nested hierarchy of parent-child couplings. Fig 5 is the succession of nested hierarchies that pattern of descent would yield. Fig 6 is the ‘coupled model’, where he attempts to draw the descent hierarchy in a way that yields the nested hierarchy in cross-section.

    It’s just different ways of representing the same tree of descent. The point for cladistics is that you do not have the tree (fig 4), you only have the cross-section of current organisms (fig 5a-g, the nested hierarchy you would recover at successive points in time). But (if you are lucky) you have enough information in fig 5 (nested) to reconstruct figs 4 (non-nested) and 6 (coupled).

  80. 80
    Joe says:


    And guess what? Tiktaalik was not found between the two eras.

    Elizabeth:

    Yes, it was.

    No, it was not. It was found after tatrapods already existed. he was looking for something that existed before tetrapods existed.

    8 is between 6 and 9, right?

    By that analogy, Shubin found 11.

    We do not have any evidence Tiktaalik lived before tetrapods. Shubin was looking for something that existed before tetrapods.

    So simple my 9 year old gets it.

  81. 81
    Joe says:

    Elizabeth:

    It’s just the way he draws ‘em.

    ALL are man-made constructs- ALL of them. And the way descent with modification works it is not a nested hierarchy.

    And yes it all different representations of the same thing- the point is HOW they are all constructed- what is the basis for each drawing. And if the basis is descent with mod then the parent-child non-nested hierarchy is the drawing to use.

    OTOH if you want to use some arbitrary method of construction then it is clear it is not based on descent with modification and that ruins your whole claim.

  82. 82
    Joe says:

    Sorry Chas…

  83. 83
    Chas D says:

    And yes it all different representations of the same thing- the point is HOW they are all constructed- what is the basis for each drawing. And if the basis is descent with mod then the parent-child non-nested hierarchy is the drawing to use.

    Well, you have seen HOW they are constructed. Look at a real tree. A real tree is also a tree of descent – lineages of cells. On a flat sheet, draw the buds, then follow the branches back. When you get to a node, draw the single branch around its two descendant buds. Follow other branches back, and again when you get to a node draw around it, encircling everything that depends on that branch, and so on.

    Bingo-you have a nested hierarchy. So, we know what a tree of descent gives – a nested hierarchy. We can reconstruct the branching pattern of the tree from the nested hierarchy alone – it is a 2D representation of the order of branching. And since we still have the tree, we can check that this is indeed the right branching pattern.

    Next, we look at some data where we ONLY have the buds (eg modern organisms). We try to draw a nested hierarchy. If we can’t, we have NOT supported a tree. If we can, we HAVE. Simple. In practice, it’s not always fully congruent, but the fundamental principle is that IF there was a real tree of descent, THEN the buds will group as a nested hierarchy. If it wasn’t, they won’t.

    OTOH if you want to use some arbitrary method of construction then it is clear it is not based on descent with modification and that ruins your whole claim.

    Arbitrary? What’s arbitrary about grouping molecular markers held in common in a dataset? Could not be less arbitrary. The test is whether this non-arbitrary grouping produces a tree – it’s based on descent, with or without modification. If a tree is recovered, common descent is strongly supported. If common descent wasn’t routinely supported, this would be a worthless method of phylogenetic analysis.

  84. 84
    Joe says:

    Chas-

    In order to have a nested hierarchy you need to have the “consist of and contained by” criteria:

    http://www.isss.org/hierarchy.htm

    Nested and non-nested hierarchies: nested hierarchies involve levels which consist of, and contain, lower levels. Non-nested hierarchies are more general in that the requirement of containment of lower levels is relaxed. For example, an army consists of a collection of soldiers and is made up of them. Thus an army is a nested hierarchy. On the other hand, the general at the top of a military command does not consist of his soldiers and so the military command is a non-nested hierarchy with regard to the soldiers in the army. Pecking orders and a food chains are also non-nested hierarchies.

    Animal kingdom consists of and contains animals. The alleged common ancestor of chimps and humans does not consist of nor conatain chimps and humans.

    As for molecular markers- there are only 4 possibilities for any one site and you have no idea how many times sites have changed and then changed back or converged.

    Trees are not necessarily a nested hierarchy. A family tree isn’t a nested hierarchy.

  85. 85
    Maus says:

    Fomr 3.1.1

    There seems to be a general view on this forum that if we can’t actually go back and look, a hypothesis is untestable.

    Elizabeth, the notion that something is ‘testable’ is the notion that you can slap it on a lab-table and doit or fail to do so. That is the common understanding of such things. As you have it, it is testable if we can navel-gaze over intuitions as a means of empirically testing a theory. And it must be empirical or it is not science. Remember well that Science is the intersection of Philosophy and Engineering. Absent the engineering, the empirical testing, it is just Philosophy. With all the good and bad that this entails.

    Support for a hypothesis derived from a theory does not tell you that your theory is correct, but it does provide support for it.

    If the hypothesis is not a necessary consequence of the theory then the hypothesis is based on mere intuition and is independent of the theory. Affirming consistency with the hypothesis cannot support the thoery it is independent from, and refuting a hypothesis on such a basis cannot refute the theory in any manner. This is fine if, again with Philosophy, the notion is that a Scientific theory is a Wetlanschauung; a philosophy; and non-empirical.

    Lack of support for a hypothesis derived from a theory tells you that you need to adjust your theory. It doesn’t mean you need to throw out the whole thing, though.

    Confirmation Holism, and an ugly thing. This is true whether or not the hypothesis was derived by necessity, or intuition about a weltanschauung.

    “Darwinists” are often at fault for not making this clear. We do not, have, and will never have, a complete theory of how life as we observe it came to be.

    Then you must agree, by the same argument, that one cannot state that Darwinsm is a fact. If it is not now, nor can ever be, complete and describe all possible inputs then it may reasonably state that it is necessary, but you have exlicitly stated that it is not, nor ever can be, shown as sufficient. At such a point if you make the leap from ‘justified’ to ‘fact’ then you have gone straight into the religious Faith side of things.

    … and that is really where “Darwinists” depart from IDists. Not in rejecting ID, but in rejecting ID as the only reasonable default.

    In general ID only states that mutations that have an external cause are necessary. Of course if you put internal, Darwin, and external mutations together then quite obviously the two together are sufficient. And thus via deductive hypothesis testing and confirmation holism: ID is Darwinism.

    And thus, in contradiction, Darwinism is sufficient and a fact that may be taught by government mandate without fear of theocracy so long as we include external mutations. If you wish to divorce ID and Darwinism you need to divorce Science and Philosophy; where Philosophy is, and should be, known as ‘respectable’ religioon when we assert a philosophy as a fact.

  86. 86
    Chas D says:

    nested hierarchies involve levels which consist of, and contain, lower levels.

    The set of an ancestral species and all its descendants consists of and contains that species and all its descendants. The set of one of its descendant species and all its descendants sits right within the first set, since the first set includes the rest by definition. And so on. These successive hierarchies are nested. An ancestor is not a nested hierarchy. It sits at the top of a descendant hierarchy, the full set of which forms the outer set of all descendants. Sets-of-all-descendants at successively lower levels sit inside (are nested within) the superior set. If A gives rise to B and C, then B and C are nested hierarchically within {A,B,C}, thus {A,{B,C}}, not within A alone. You are simply confusing two kinds of hierarchy that can be used to represent the same branching pattern of descent.

    The alleged common ancestor of chimps and humans does not consist of nor conatain chimps and humans.

    The set of any common ancestor and its descendants consists of and contains that ancestor and all its descendants. Ergo, if there was a common ancestor to chimps and humans, we would expect to be able to recover such a hierarchy from examination of modern DNA, and reconstruct the non-nested hierarchy from a nested arrangement of descendants. If there wasn’t, we would not. Nobody is suggesting that the common ancestor of chimps and humans would be a nested hierarchy. You need the descendants as well. Humans and chimps nest separately within the outer set of ancestor-and-humans-and-chimps.

    As for molecular markers- there are only 4 possibilities for any one site and you have no idea how many times sites have changed and then changed back or converged.

    As I have pointed out a few times now – I’m beginning to wonder if you’re just messing with me! – molecular phylogeny is not solely dependent on point features. If there is a clear common sequence, then your bases having been through many intermediate mutations is not that relevant. It causes under-counting of changes, but does not fatally undermine the whole tree. Often, we can simply looking at a binary signal, Present and Absent. We cannot use degraded sites, but if we find a site we can identify, it must either be little-degraded or convergent. And widespread convergence at the nonfunctional molecular level is highly unlikely. The idea that the sequences could have both wibbled around phase space and ended up identical is the usual extravagant swerve from you, Joe. You would have to assert convergence of every sequence that supports common descent, and there is no support for such an improbable hypothesis. Why not just common descent? Simple, obvious, and involves no desperate mental gymnastics. All other options are ludicrous fantasy, on the data. Your designer is trying to trick us.

    Trees are not necessarily a nested hierarchy. A family tree isn’t a nested hierarchy.

    Gene trees are though, even in families. You get a gene from mum OR dad, not both. Any surviving set of genes forms a nested hierarchy back up to the sequence from which they all descend, whichever path they took. But anyway, I am not talking of family trees, but trees at species level and above. Despite sex operating within the species, descent resolves to a ‘vegetative’, branching structure above it.

  87. 87
    Joe says:

    The set of an ancestral species and all its descendants consists of and contains that species and all its descendants.

    Right, that is the nested hierarchy based on “all life”.

    It sits at the top of a descendant hierarchy, the full set of which forms the outer set of all descendants.

    Just as the general sits at the top of a military command, ie a non-nested hierarchy.

    The set of any common ancestor and its descendants consists of and contains that ancestor and all its descendants.

    But you don’t have any idea what those are.

    Ergo, if there was a common ancestor to chimps and humans, we would expect to be able to recover such a hierarchy from examination of modern DNA,

    Heresay.

    Look one can construct a nested hierarchy out of just about anything.

    Trees are nested hierarchies and my dad’s genes do not consist of nor contain my genes.

    So in what way are gene trees a nested hierarchy? I take it you have never heard of recombination…

  88. 88
    Chas D says:

    Chas: The set of any common ancestor and its descendants consists of and contains that ancestor and all its descendants.

    Joe: But you don’t have any idea what those are.

    Totally not the point! This is easing you gently through the features one might expect to find in a real tree of descent. Then one uses these concepts to try and establish whether a dataset containing hypothetically commonly descended organisms actually fits that pattern. Of course you don’t know what the organisms are! You want to see how their descendants relate, if at all, and you do so by trying to reconstruct a tree from the buds back.

    Chas: Ergo, if there was a common ancestor to chimps and humans, we would expect to be able to recover such a hierarchy from examination of modern DNA,

    Joe: Heresay.

    Heresy? Hearsay? You didn’t spot the conditional in that sentence. IF there was such an ancestor, that makes a prediction about the relationships we would expect to recover from modern genes.

    Look one can construct a nested hierarchy out of just about anything.

    Trees are nested hierarchies and my dad’s genes do not consist of nor contain my genes.

    The set of your those genes you got from your dad and their homologues in him can be formed into a nested or a non-nested hierarchy according to whim. The simple hierarchy is: A gene in your dad and a descendant of that gene in you. Your dad’s copy is hierarchically above you. The nested hierarchic set constructed from the ancestor and all its descendants is: {dad’s copy{your copy}} The outer set is everything, the inner the lower levels.

    If you have a sister and a kid who also had the gene, the nested hierarchy would be

    {dad’s copy{your copy{kid’s copy},sister’s copy}}

    The non-nested hierarchy is
    dad’s copy
    your copy,sister’s copy
    kid’s copy

    Same data, different drawing.

    So in what way are gene trees a nested hierarchy?

    In the above way. In the sense that “an ancestor and all its descendants” can apply to a species, or a haplotype gene, or an asexual lineage, and each descendant node is itself “an ancestor and all its descendants”, nested in the higher tree. Gets a little more complex with sex:

    I take it you have never heard of recombination…

    Recombination does indeed mess up trees. But it is not guaranteed to operate, and does so quite gently – average one crossover per chromosome, so a gene can stay intact for many generations. It may also function as a long-term haplotype due to inversions. And recombination makes no difference at homologous sites. They are homologous due to common descent, incidentally.

    Ultimately, the braided threads of sexual networks resolve into vegetative species branches, and at that level, recombination doesn’t make a difference.

  89. 89
    Joe says:

    This is easing you gently through the features one might expect to find in a real tree of descent.

    I would expect the offspring to have the same features as their parents. And that is what we see 99.9999999% of the time. The time when there is a difference is a loss of a part.

    So that doesn’t help you.

    You didn’t spot the conditional in that sentence. IF there was such an ancestor, that makes a prediction about the relationships we would expect to recover from modern genes.

    It’s heresay because you assume that the pattern observed can only be explained if they had a common ancestor.

    If you have a sister and a kid who also had the gene, the nested hierarchy would be

    {dad’s copy{your copy{kid’s copy},sister’s copy}}

    1- my kid may not have a copy from my dad

    2- my kid could have a copy that better resembles my dad’s copy than my copy does

    3- My kid’s copy could match my sister’s copy.

    One more time- how are you constructing your gene tree?

    If you had no idea what the actual relationships were, how could you do it?

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