Saturday, December 1, 2012

tRNA Synthetase Gene Sharing: Like the Movie Transformers

You’ve seen those amazing multi-purpose kitchen utensils and jackknifes that perform a dozen tasks, but it is all standard fare in biology. From the DNA molecule which stores all kinds of information (you can see examples here, here, here and here) including overlapping genes, to molecules that fulfill various roles depending on the cellular context and gene sharing, biology is the model of efficiency. Call it multi-purpose design, component reuse, optimization of information density, or whatever, it is one of biology’s biggest unsung feats and last week yet another example was published.

You may remember the two key steps in protein synthesis are transcription and translation, where (i) the DNA gene is copied and (ii) the copy is used to encode a string of amino acids, respectively. What your biology teacher did not know, however, is that one of the key enzymes in translation also is part of the massive transcription choreography.

Everyone has heard of the DNA code but few understand how it works. The copy of the DNA gene, known as messenger RNA (mRNA) consists of a string of nucleotides. Those nucleotides are taken three at a time to form a sequence of three letter words, or codons. There are 64 (4^3) different codons and transfer RNA (tRNA) molecules do the reading of these codons. Different tRNA molecules recognize different codons. The magic is that on the other end of each tRNA is glued the correct type of amino acid, corresponding to the codon that that specific tRNA will recognize.

But how did the tRNA molecules come to have the right amino acid glued on? There are enzymes that carry an amino acid and, when they find the right corresponding tRNA, they glue the amino acid onto it. So it is with these enzymes, collectively known as tRNA synthetases, where the heavy lifting occurs. They implement the DNA code.

But the new research has found that the heroics do not stop there. The scientists discovered the details of how one of the tRNA synthetases, when a phosphate group is attached to the right place, undergoes a dramatic structural and functional change. No longer is it busy gluing an amino acid to the right tRNA. Instead, it moves upstream in the assembly line process and helps to regulate the transcription activity. As one of the scientists explained:

If you think about the structural changes that occur in the synthetase we looked at in the study, it’s very much like the movie Transformers, it’s a machine that changes structure and turns into another machine that can accomplish a completely different task—like from a car to a giant robot.

Of course yet another protein is responsible for attaching the phosphate group to the right place, at the right time. But that’s another story. For now, the question is how could this tRNA synthetase have come to have this dual role?

Of course the evolution of a protein, any protein, is problematic simply because successful searches are so unlikely. The fitness landscape is rugged, pitted with myriad local minima that frustrate evolutionary searches. Even by evolutionist’s own optimistic approximations it would never occur in the lifetime of the universe.

And beyond that, there is then the problem of how tRNA synthetases in particular could have evolved. For instance, their role so heavily depends on the intricate process of translation, involving so many other molecular players. To be sure simpler versions of that process can be envisioned, but even simpler versions are complex.

It is not as though a freshly minted tRNA synthetase is going to help much if some sort of translation process is not already in place. And it is even more unlikely that such a translation process would evolve without the needed tRNA synthetases to complete the choreography. Obviously evolution requires some sort of sequence of events providing a gradual build up. But beyond speculation, we have no compelling story to tell for this miracle.

But now, on top of these massive problems, we find that tRNA synthetases can, upon a low entropy phosphorylation, transform to a completely different structure and function. Imagine the serendipity involved.

After successfully navigating the problems discussed above to construct the translation process, and after having constructed protein kinases which attach phosphate groups at convenient places, evolution’s natural selection found that one of the kinases happened to phosphorylate one of the tRNA synthetases at just the right place to perform an incredible transformation operation where the newly formed molecular machine performed just the right function in the completely different process of transcription. This is simply incredible.

Now I would be delighted to learn that I’ve stupidly overlooked some straightforward and compelling evolutionary explanation for all of this. I don’t have a dog in this fight. Perhaps evolution is true, perhaps it is false, or perhaps it is somewhere in between. I don’t care and if there is a scientific explanation of how this world of biology could have spontaneously arisen then I would gladly shout it out.

But instead of explanations all I get is pushback. It’s all my fault for attacking science, we all know evolution is true, and besides god would never make viruses anyway.

It illustrates the enormous gap between evolutionists and the evidence. For evolutionists there are no problems behind the assertion that evolution is a fact. There are only research problems of how evolution occurred. Objective, scientific evaluations of how the evidence actually bears on the theory are elusive. Religion drives science, and it matters.

54 comments:

  1. Here are some carols for you Dr. Hunter

    John Tesh • We Three Kings • Christmas in Positano, Italy
    http://www.youtube.com/watch?v=TJbfLcD9O9s

    Trans Siberian Orchestra - Christmas Eve/ Sarajevo [Timeless Version]
    http://www.youtube.com/watch?v=MHioIlbnS_A&ob=av2e

    Chris Tomlin - Joy to the world, (joy, unspeakable joy!)
    http://www.youtube.com/watch?v=NLhb3qUA3uc

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    3. Dr Hunter, I don't know if you have seen this video, but this man does a excellent exposition on the theodicy of Darwin's book 'Origin of Species' and he mentions your book 'Darwin's God' very favorably several times in the video. I know you are not one to toot your own horn, but I wish you would repost this video so that more people could understand the exact position that you are coming more easily:

      The Descent of Darwin – Pastor Joe Boot (The Theodicy Of 'Origin Of Species') – video
      http://www.youtube.com/watch?v=HKJqk7xF4-g

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  2. Cornelius

    'This is simply incredible.' You are too generous. I think utterly unbelievable is more accurate.

    If anyone says 'and besides god would never make viruses anyway' to you just explain that death is part of the design. As Genesis says god created plants with the seeds in them. This he did with the very first life form so it must apply to all. He designed generations, and therefore death. And since we know that we are required to worship him, we can conclude that there is death because God wants a relationship, not with the same people for all of our time on earth, but a new 6 billion people every sixty years or so. What else would you expect from a mind that could create these engineering marvels? A relationship with Adam and Eve for all of time hardly seems like the relationship a God that could create the universe would be satisfied with.

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  3. All biological functionality for which DNA sequences serve as necessary conditions (which seems to be all of it) must be explained in terms of a naturalistic theory (i.e., a set of event-regularities) that implies the instantiation of those necessary DNA sequences at the relevant times when said theory is applied to a plausible and relevant set of initial conditions. What articles like this one show is that we are not even done learning WHAT needs to be explained, thus--much less are we close to formulating such a theory.

    That's why there is no evidence for naturalistic UCA. Story-telling is teleological activity, not naturalistic explanation. One can contend that certain events/conditions are "expected" if UCA is true from current theory. But that's not true. Current theory merely imposes certain kinds of constraints on variation, etc. It doesn't even tell us whether extinction of all life on earth would have been inevitable apart from teleological intervention, etc, much less whether the correspondence theory of truth is true.

    A tree-building methodology is not a causal theory. Thus, it, alone, can't imply that hypothetical transitions could have ever exist in terms of a naturalistic causal theory. One must posit kazillions of ad-hoc hypotheses to bridge such "naturalism-of-the-gaps" gaps. And SA requires way less such ad-hoc hypotheses.

    When the only conceivable hypothetical explanations for a set of data require ad-hoc hypotheses, it is no intellectual virtue to posit more ad-hoc hypotheses than is necessary unless one does so to guide NATURALISTIC RESEARCH. Naturalistic UCA is such a working hypothesis. It can be rationally posited to guide research. But there is absolutely ZERO evidence for it, at this time, once you hold it to the requirements of a naturalistic hypothesis. Thus, it is absolutely irrational to claim it is true or the more rational explanation, given current knowledge.

    But even if one uses UCA as a working hypothesis to guide naturalistic research, it still doesn't follow that such naturalistic research is the best use of a society's resources if there are other more pressing societal problems in need of those resources. That requires a different kind of argument.

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  4. Yes, we all marvel at the incredible complexity of living things - a complexity, need I remind you, that has been uncovered slowly and painstakingly by naturalistic science. Do we have a complete picture yet? No, of course we don't and nobody is claiming we do.

    And what is the alternative being offered? God or some unspecified intelligent designer, assuming there's a difference. How does that help? You want science to give you a complete step-by-step account of how every system in every living thing evolved from the year dot - in other words, you want to know how. Your answer is to to speculate about some sort of intelligent agency. That's 'who' not 'how'. You aren't even trying to answer the same question you're asking of science.

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  5. No, Ian, in either case, we're asking WHAT is/are the cause/s for events and states of affairs. And you're wrong in assuming that ID'ists oppose naturalistic research. They don't. They oppose pontificators making assertions in the name of science which are clearly ridiculous.

    Story-telling is teleological activity. But story-telling about the past is teleological activity that even God can't do. What happened in the past can't be changed. It can only be explained more or less parsimoniously in terms or either natural or libertarian causality.

    Whichever explanation is the most parsimonious, thus far, is the best thus far. That doesn't make it true. Because more research can change the data set resulting in a change in the relation of parsimony.

    But here's the thing. One can research what mutations do under various conditions without positing naturalistic UCA. I have yet to hear one naturalistic-UCA'ist explain to me how PRACTICAL biological knowledge is rendered more practical if naturalistic UCA is true.

    Naturalistic UCA may be eventually shown to be the most parsimonious explanation of the data. But that doesn't mean that the practical knowledge entailed in the discipline of biology is more practical, therefore. It will merely mean that extant and extinct life (except possibly a first common ancestor) originated via descent. It still won't explain free-will, etc.

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  6. "And SA requires way less such ad-hoc hypotheses."

    What's SA?

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  7. "What's SA?"

    Probably "separate ancestry".

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  8. Universal Common Ancestry is a reasonable explanation for the origins of what is observed in biology just as the Big Bang Theory is a reasonable explanation for what is observed in physics. And just as the Big Bang Theory has no direct relevance to many fields of research in physics so UCA has no direct relevance to many fields of research in biology. So what?

    You sound as if you prefer separate ancestry as an explanation. How, in your view, would that be better than UCA?

    As for free will, I'm not sure how either SA or UCA has a bearing. It seems to me that the existence of an omniscient God with knowledge of our future would have much greater implications for that.

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  9. Peter
    we can conclude that there is death because God wants a relationship, not with the same people for all of our time on earth, but a new 6 billion people every sixty years or so

    Interesting theory, how can a perfect being" want" anything? Why does God require worship?

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    1. What do you mean by perfect? An absolute is a human concept that is beyond their comprehension.

      I don't know why god requires worship, other than the Bible tells me so, and all societies that don't worship God are wiped off the face of the earth (Western civilzation at present).

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  10. UCA doesn't explain anything, Ian. It's a hypothesis in need of an explanation. The Big Bang doesn't explain anything either. In fact, the Big Bang fares worse than UCA simply because UCA isn't contrary to any human categories.

    The Big Bang hypothesis, on the other hand, is not even intelligible. It requires us to give up the intuitive principle of individuation for distinct 3-D particles since space itself is conceived of as a 3-dimensionally (3, at minimum, i.e.) extended being, therein. The only way we can intuitively distinguish 3-D particles is via the assumption that 2 distinct 3-D entities cannot extend over the same space simultaneously. But the Big Bang requires this be true if 3-D particles are still to be posited by physics since space is considered to be a 3-D being that can grow and expand.

    That which can grow and expand can not be the spatial reference frame scientists used to consider space to be. There is a reason why scientists say Einstienian relativity is counter-intuitive. Lorentzian relativity is not counter-intuitive, however. But the Big Bang theory is inconsistent with Lorentzian relativity.

    On the other hand, if multiple 3-D particles are to no longer be posited to exist so that the Big Bang hypothesis can be rendered intelligible, then multiple streams of conscious experience can no longer be attributed to but one 3-D entity (assuming they are to be attributed to 3-D entities at all). And that would be space. But if this is the case, isn't obvious that the correspondence view of knowledge is just totally bogus anyway, rendering reason just as illusory as any other approach?

    SA is not an explanation anymore than UCA since it, too, requires lots of ad-hoc hypotheses which we can't even exhaustively enumerate. But many less are required for SA. This is what makes it better in terms of inductive criteria, which is the only rational criteria applicable.

    ID is a species of libertarian (free-will) perspective. Per such world-views, free-will (i.e., libertarian causality) exists and is known to exist intuitively. On the other hand, a worldview that supposes a "world" with only naturally- and/or non- caused events can not account for free-will at all.

    But worse than that, such a world-view can't even account for a correspondence theory of knowledge. One ID-style world-view entails the state of affairs where the correspondence theory of knowledge is an out-working of the fundamental inference that we are designed to seek and attain sufficient satisfaction. The correspondence theory of knowledge is realized to be a necessary condition of satisfaction.

    Per this approach, all specific "knowledge" stands or falls with the validity of that fundamental inference. But that inference is only intelligible if the teleological causal relation is categorical to the human mind. And it seems to be just that. I've never seen anyone account for it any other way, at least.

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  12. Ian, let me address your question, "How, in your view, would that be better than UCA?" a bit further.

    It is obvious that in terms of sheer utility, humans prefer that the concepts that they form about nature apply with some longevity. We hope, for example, that species don't morph into something non-applicable to our existing classification schemes every year or even more frequently. We hope our text-books have useful information for years to come.

    So no one wants biological variation to proceed so far and so fast as to render our concepts and classification schemes in need of continual revision. On the other hand, we see instances of plants, at least, that smack of impressive saltationism. But even these cases are typically characterized by reductions in certain kinds of fitness, etc, from what I've been told. And it is well known that plants are susceptible to easier cases of grafting, etc, than are animals. And this makes sense to us since animals seem to depend on way more conditions because of the greater dynamism of animal existence.

    Thus, we can typically explain such plant saltations as degenerative more easily than we can as transitions to better-adapted organisms. This resonates, analogically, with our sense of how entropy grows over time.

    On top of this, DNA sequencing is virtually irresistably interpreted as a function-producing code, which is analogous to functions/routines in computer programs, which are intelligently-designed.

    When we look at the fossil record, we see lots of variation on a theme, but little to no radical variation connected by transitional fossils that are convincingly indicative of evolutionary descent. This is precisely what classifying creatures like ourselves prefer. If phenotypic gradualism applied to a UCA-generated biosphere and all extant and extinct phenotypes were availabe to us for classification, class boundaries would be arbitrary.

    There are several kinds of analogies that apply to ID-style SA:

    1) Designers configure for functionality
    2) Designers tweak already existing designoids
    3) Designers use common design
    4) The most conspicuous cases of specified sequencing conditioning conspicuous functions are language and DNA. Language is designed communication
    5) "Reproduction" is analogous production. Descent is truly "reproduction" if by "reproduction" we only include "themes" that can include variation. Of course, such essentialism may fail even with SA. But it's not clear that essentialism fails in every sense, to me.

    The only analogy that applies to at least most of the biota, per UCA, is that most "reproducing" organisms arose from one or more parent organisms themselves. I say "most," because abiogenesis is a kind of singularity that truncates the pattern at some point.

    So UCA, per se, is not as analogy-rich as ID-style SA is. If a naturalistic causal theory is conceived that not only accounts for observed variation, but also "predicts" the phenotypes of fossils at the relevant times from the relevant initial conditions, then naturalistic UCA will be the best explanation. For it will then be the more parsimonious view.

    But I hope you realize you're not even close to having any kind of biological variation theory with that much predictive power. Indeed, as CH's post shows, we're still learning what NEEDS to be accounted for by such a theory.

    No deductive theory (i.e., one that depends on natural causality past some set of initial conditions) can account for everything SA'ists or UCA'ists believe. But SA'ists posit way less ad-hoc hypotheses and have a much more analogy-rich approach than does UCA.

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  13. I guess I should be more specific as to what I mean by natural causality in the contexts above. In those contexts, I mean causality that involves not only event regularities, but which don't involve consciousness or sentience. One could, e.g., posit that God directs evolution via natural desires that motivate accordingly.

    But I assume you are not positing any such thing. And I, like most, want to limit divine providence as much as possible. In my opinion, this is what even Dembski's explanatory filter implies we tend to do. Thus, even those like Van Til once posited that, though God sustains all things in existence, creatures are "gifted" with the capacity to evolve as per UCA. Now, I see that as a clear contradiction, for if God has to create particles in their actual locations at every given instance, it is obvious those particles are not gifted with any motion-causing power at all. Dembski seems to be agreeing with me that induction requires that we try to minimize God's providential intervention into the created order.

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  14. In one sense, I think it's more parsimonious to attribute conscious, sentient impulsiveness to all beings to account for their causal capacity. But I don't attribute libertarian causality to them. E.g., I assume my dogs are conscious, sentient and impulsive. But I don't see any evidence that they are rational or libertarianly-causal. Their psychological causality seems to be accounted for by instinct and experience-generated associations that condition particular sentient experience attended with corresponding impulses, just like much of my own psychological causality seems to be.

    To me, attributing the creatio-continua view of God's providence to phenomenon is less parsimonious than the alternative unless one can intelligibly think of why continued existence, per se, needs a continual cause. But this would mean, for theists, that even God must cause his own existence. And that seems unintelligible unless that causality is unconsciously rendered. Regardless, causality, per se, is explicable without positing creatio-continua, per my understanding.

    Modern biologists tend to deny that conscious experience is even attributable to a single being or any beings. And that renders conscious experience quite mysterious. And yet consciousness is supposedly a condition of real knowledge about real beings, nevertheless. The whole epistemology of many modernistic scientists is counter-intuitive and, therefore, arbitrary.

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  15. Jeff,


    4) The most conspicuous cases of specified sequencing conditioning conspicuous functions are language and DNA. Language is designed communication


    Therefore DNA is designed communication or therefore DNA uses symbolic representation?

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  16. Neither. What I meant was that classes of biological "activity" are functions of DNA just as communication is the function of language. Function is inferred to be intelligently-designed in many instances even by atheists. Indeed, atheistic biologists have as much difficulty ridding their biological rhetoric of teleological language as do theistic biologists.

    Naturalistic UCA is a hypothesis that will be more parsimonious if someone can conceive of a theory of mutations that both explains observed variation as well as predicts the relevant phenotypes at the relevant times from the relevant initial conditions. We're not even in the ball bark on that yet.

    All they're doing now is making ridiculously over-simplified assumptions to see if that approach gets them anywhere. And they're failing EVEN at that. But that was expected by rational people, because over-simplified assumptions are just polyanna.

    Thus, we currently have NOTHING inductive going on in the project. We're in the very beginning phases of winnowing out over-simplistic assumptions (which could only be true if tons of other ad-hoc hypotheses are true), and even that has been time-consuming and expensive. The next phase will probably cost a fortune and turn up precious little (if anything) relevant to the hypothesis in years at a time.

    When one actually stops to consider the enormity of the "explanation" problem in need of solution, it is no wonder that we've gotten nowhere in 150 years. The confusion about UCA is that there is an infinite number of trees that are consistent with UCA. You have to have a theory that predicts not only ONE tree, but one that 1) predicts observed variation, and 2) implies the relevant phenotypes arise at the relevant times.

    It's a pipe-dream. War will probably destroy too much accumulated human knowledge again long before meaningful progress is made in such a huge project. Indeed, war will result in part BECAUSE of such huge wastes of society's resources. It's a waste because HOW mutations affect health, etc (i.e., the utility of science) can be determined without spending the extra money required to prove UCA and a putative historical tree. This is the very kind of greed that causes war.

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  17. Jeff

    Neither. What I meant was that classes of biological "activity" are functions of DNA just as communication is the function of language. Function is inferred to be intelligently-designed in many instances even by atheists. Indeed, atheistic biologists have as much difficulty ridding their biological rhetoric of teleological language as do theistic biologists.


    Scientists understand the the use of teleological language is merely metaphorical, a way to help communicate ideas. When we say "Electric current chooses the path of least resistance" that doesn't mean electricity is doing conscious choosing. Apparently you are too uneducated to grasp the difference.

    Naturalistic UCA is a hypothesis that will be more parsimonious if someone can conceive of a theory of mutations that both explains observed variation as well as predicts the relevant phenotypes at the relevant times from the relevant initial conditions. We're not even in the ball bark on that yet.

    More ignorance. In many cases we can deduce general principle like insular dwarfism, isolated populations with limited physical resources will tend to diminish in physical size. What we can't predict are the exact morphological changes due to the random nature of the genetic variations. It's no different than predicting in the long run a casino will always win money on roulette due to the favorable house odds even though the specific sequence of numbers that arise aren't predictable.

    All they're doing now is making ridiculously over-simplified assumptions to see if that approach gets them anywhere. And they're failing EVEN at that. But that was expected by rational people, because over-simplified assumptions are just polyanna.

    I see another Creationist in dire need of a Biology 101 course.

    When one actually stops to consider the enormity of the "explanation" problem in need of solution, it is no wonder that we've gotten nowhere in 150 years. The confusion about UCA is that there is an infinite number of trees that are consistent with UCA. You have to have a theory that predicts not only ONE tree, but one that 1) predicts observed variation, and 2) implies the relevant phenotypes arise at the relevant times.

    Science does predict one tree, and that tree has been confirmed to well over 99.999999% certainty. We don't have to predict specifics for the reasons already given.

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    1. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.

      (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society, Vol. 87:991-1024 (2012).)

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  18. Jeff,

    It's a pipe-dream. War will probably destroy too much accumulated human knowledge again long before meaningful progress is made in such a huge project

    Good point. I wonder if my credit card company will buy that argument





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  19. V, I shouldn't have to tell you this, but your credit card company doesn't make it's business plans based on the status of the current fit of evolutionary speculation to the data to be explained evolutionarily.

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    1. Perhaps not,though if there was a profit to be made they might. Maybe I misunderstood, the war ,caused by the greed of scientists, will destroy human knowledge but not our credit rating.

      Have you run the numbers on what exactly the amount of money wasted on UCA research is?

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    2. V, if tax-funded science should have some practical value to those who fund it (and that seems pretty plausible, eh?), and if the ascertained truth of UCA has no discernable practical value whatsoever (and it doesn't), then any research that MERELY seeks to demonstrate UCA as opposed to understanding the workings of biological systems for practical ends is a sheer waste of the tax-payers' money. The way UCA'ists show their posterior on sites like this one demonstrate that belief in UCA is about as rabidly religious/metaphysical in quality as it gets.

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  20. Thorton: When we say "Electric current chooses the path of least resistance" that doesn't mean electricity is doing conscious choosing.

    Jeff: Whoever said that? I don't. I say "takes the path of least resistance," not "chooses ..."

    Thorton: What we can't predict are the exact morphological changes due to the random nature of the genetic variations.

    Jeff: Right. Thus, the one tree that must have obtained if UCA is true is just one of an infinite set of logically possible trees. What we don't know, however, is that any such UCA tree is logically possible using the event regularities you want to extrapolate back in to the past. IOW, we can story-tell genealogical histories, but we can't generate one by applying any naturalistic theory to the relevant Precambrian initial conditions. We can't even show any such tree is logically possible.

    Thorton: It's no different than predicting in the long run a casino will always win money on roulette due to the favorable house odds even though the specific sequence of numbers that arise aren't predictable.

    Jeff: Wrong. We can run the numbers and demonstrate that mathematically as well as observe it. We don't know the other is even logically possible.

    Thorton: Science does predict one tree, and that tree has been confirmed to well over 99.999999% certainty. We don't have to predict specifics for the reasons already given.

    Jeff: That's about as confused as it gets, Thorton. Tree-building rules don't need to correspond to mutational effects. That's why tree-building rules have precisely zero implications about the logical possibility of naturalistic UCA.

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  21. Jeff

    Right. Thus, the one tree that must have obtained if UCA is true is just one of an infinite set of logically possible trees. What we don't know, however, is that any such UCA tree is logically possible using the event regularities you want to extrapolate back in to the past.


    Take a beginning biology or genetics class. Not only does science know it is possible, we've identified the one that was actually formed to an incredible degree of accuracy.

    IOW, we can story-tell genealogical histories, but we can't generate one by applying any naturalistic theory to the relevant Precambrian initial conditions.

    No one knows enough about the relevant Precambrian initial conditions to make such a claim. Certainly not Creationists who do no research and produce no results.

    We can't even show any such tree is logically possible

    Pity for you that it's already been done as I already provided evidence for.

    Wrong. We can run the numbers and demonstrate that mathematically as well as observe it.

    Please do so then. Give me the winning roulette numbers in order for next week in Las Vegas. I'd love to be a multi-millionaire.

    That's about as confused as it gets, Thorton.

    But the confusion is all your Jeff. Take a beginning science class.

    Tree-building rules don't need to correspond to mutational effects. That's why tree-building rules have precisely zero implications about the logical possibility of naturalistic UCA.

    I see you're also completely ignorant of how best fit cladistic trees are generated, and of the Consistency Index tests that can be performed.

    Do you understand anything about actual evolutionary theory, anything at all?

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  22. Thorton: Please do so then. Give me the winning roulette numbers in order for next week in Las Vegas. I'd love to be a multi-millionaire.

    Jeff: The calculations produce probabilities, not precise predictions for the next card shuffle, etc. The probabilities tell us what one can reasonably expect over the long run. You know this, and yet you show your posterior thinking it becomes you. Wow!

    Thorton: I see you're also completely ignorant of how best fit cladistic trees are generated, and of the Consistency Index tests that can be performed.

    Jeff: Cladistic trees are not generated based on what scientists know mutations + environment will produce over millions of years, given the assumed event regularities in operation over the time-frames. And that's why cladistic trees have no implications as to whether naturalistic UCA is even logically possible, much less plausible.

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  23. Jeff

    Thorton: Please do so then. Give me the winning roulette numbers in order for next week in Las Vegas. I'd love to be a multi-millionaire.

    Jeff: The calculations produce probabilities, not precise predictions for the next card shuffle, etc. The probabilities tell us what one can reasonably expect over the long run. You know this, and yet you show your posterior thinking it becomes you. Wow!


    Which is exactly what I said, yet you continue with the ridiculous demand that ToE give you a causal connection for every last step in a 500 MYO evolutionary history. You're just not very bright.

    Cladistic trees are not generated based on what scientists know mutations + environment will produce over millions of years, given the assumed event regularities in operation over the time-frames.

    They're based on the best fit to the empirically collected evidence, a bet fit that by every statistical test known indicates a UCA.

    You're not knowledgeable of evolutionary theory even a tiny bit. Don't you think you should read and understand at least a little on the topic before spouting off nonsense?

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  24. Cladistic tree-building rules are not known to correspond to the phenotypical/extinction effects caused by mutations and environment. I'm amazed you don't realize this.

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  25. "Of course yet another protein is responsible for attaching the phosphate group to the right place, at the right time. But that’s another story."

    I know next to nothing about this process, but i was wondering if you could point me in the right direction where i might learn more. It seems to me that this orchestration of when a phosphate group arrives at the right place, at the right time must be akin to the process air traffic controllers use to land airplanes at busy airports.

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  26. Thorton: They're based on the best fit to the empirically collected evidence, a bet fit that by every statistical test known indicates a UCA.

    Jeff: Empirical data is only evidence for a hypothesis if the data holds a certain relationship to the hypothesis. The hypothesis is naturalistic UCA. What empirical data holds what relationship to that hypothesis that renders that data evidence for it? And please don't make the obvious mistake of reasserting some aspect of the hypothesis in need of explanation, confusing it for data that is evidence for the hypothesis.

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  27. Jeff

    Thorton: They're based on the best fit to the empirically collected evidence, a bet fit that by every statistical test known indicates a UCA.

    Jeff: Empirical data is only evidence for a hypothesis if the data holds a certain relationship to the hypothesis. The hypothesis is naturalistic UCA. What empirical data holds what relationship to that hypothesis that renders that data evidence for it?


    Poor Jeff, still doesn't understand the scientific method.

    Hypothesis prediction: If UCA is true we should see evidence of a branching nested hierarchy in the fossil and genetic records. Furthermore the twin nested hierarchies thus created should strongly correlate.

    Empirical data: We do see strong evidence of a branching nested hierarchy in the fossil and genetic records. Furthermore the twin nested hierarchies thus created do strongly correlate.

    Is this proof? No, because science doesn't do 'proof'. We will never know for 100% sure because things like HGT cause the genetic signature to become indistinct the further back in time we try to analyze. But what we can see gives a huge amount of strongly confirming evidence for the UCA hypothesis.

    Tell us Jeff, what is your scientific evidence for SA? I keep asking but you keep forgetting to provide any.

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    1. From http://evolution.berkeley.edu/evosite/lines/IVDhierarchies.shtml:

      Nested Hierarchies

      Common ancestry is conspicuous.
      Evolution predicts that living things will be related to one another in what scientists refer to as nested hierarchies—rather like nested boxes. Groups of related organisms share suites of similar characteristics and the number of shared traits increases with relatedness. This is indeed what we observe in the living world and in the fossil record and these relationships can be illustrated as shown below.

      (see link above for the diagram that goes here)

      In this phylogeny, snakes and lizards share a large number of traits as they are more closely related to one another than to the other animals represented. The same can be said of crocodiles and birds, whales and camels, and humans and chimpanzees. However, at a more inclusive level, snakes, lizards, birds, crocodiles, whales, camels, chimpanzees and humans all share some common traits.

      Jeff: Note that, Thorton? These researchers know a priori, apparently, that crocodiles and birds have a common ancestor, and that whales and camels have a common ancestor, and that humans and chimps share a common ancestor. But I suppose if you can know such things a priori, you might as well claim to know UCA is true a priori as well. Why not, right? I mean, if you're gonna show your posterior right out there in broad daylight, go for the gusto! Right?

      Such hierarchical classification indicates nothing about the phenotypical/extinction effects of mutations plus environment in the past. And though you are still utterly ignorant of the fact, apparently, if naturalistic UCA is true, it is true because of the NATURAL effects of mutations and environment, NOT humanly-devised cladistic tree-building rules!

      As for the fossil record, you are dead wrong. It was admitted not too many blogs back that the fossil record is used to calibrate the trees. It's admitted in the literature as well. Worse, known stratigraphic ranges are not known to be actual stratigraphic ranges. And actual stratigraphic ranges are not known to be existential ranges. The ad-hoc hypotheses involved in such high-level assumptions are ubiquitous.

      Science is supposed to be methodologically skeptical. Not so with UCA'ists. They'll believe any number of ad-hoc hypotheses are true if it will help them believe their dogmatism.

      You're utterly confused and, apparently, ignorant of the circular reasoning that is standard fare for UCA'ists.

      And that doesn't mean they're wrong. It means there is no evidence for UCA. It is held up by an enormous number of ad-hoc hypotheses. And this means that the hypothesis is no more plausible than the plausibility that all those ad-hoc hypotheses are true. And that, in turn, means naturalistic UCA is UTTERLY implausible, given our current knowledge of event regularities and past environmental conditions.

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    2. Lots of blithering from you Jeff, but still no scientific evidence for your claimed SA.

      When will you be writing to all those scientific journals, colleges and universities, and working research labs telling them evolution is dead wrong?

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    3. dancing queen:
      When will you be writing to all those scientific journals, colleges and universities, and working research labs telling them evolution is dead wrong?



      Evolution is neither wrong nor right. It just is what it is.

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    4. Thorton, one of the really stupid things UCA'ists always (and I mean EVERY TIME I've argued with them) resort to is to say that ID'ists content that UCA or some hypothetical, naturalistic, genealogical relationship is "wrong," or "impossible." But induction doesn't prove things impossible.

      Rather, logical induction has criteria by which an explanation is knowably better (i.e., more warranted in terms of analogy, parsimony, fewer ad-hoc hypotheses required, etc) than its competitors as PER the current state of knowledge of the relevant data. Many UCA'ists incessantly make indicative truth assertions about evolution for which there is no naturalistic explanation yet at all, much less a plausible one. This is what ID'ists oppose. They don't claim UCA or hypothetical natural lineages can be ABSOLUTELY proven impossible.

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  28. thorton:
    If UCA is true we should see evidence of a branching nested hierarchy in the fossil and genetic records. Furthermore the twin nested hierarchies thus created should strongly correlate.

    Why? Just saying so is not enough. Also we do NOT see a branching nested hierarchy wrt prokaryotes. Not only that gradual evolution does not expect a nested hierarchy as the existence of transitional forms would ruin such a scheme.

    IOW thorton is either totally clueless
    or just a pathological liar.

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    1. Joe, I've seen one evolutionist define nested hierarchy in such a way that there is only a nested hierarchy inconsistent with SA IFF you ASSUME that all the hypothetical transitions existed. IOW, as I explained (to no avail, of course!) to Thorton above, the hypothesis of naturalistic UCA is only plausible if kazillions of ad-hoc hypotheses for which there is currently no evidence are true.

      Never mind the fact that naturalistic UCA, when conceived a-teleologically, is not even inconsistent with conscious thought being virtually totally illusory in the first place. In short, the atheist's approach to epistemology can't even provide warrant for believing science about a "world out there" is possible.

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    2. Jeff,

      Just about anything can be placed into a nested hierarchy. They are entirely man-made constructs- meaning they ain't so special.

      But yes, the existence of all the transitionals would absolutely ruin the nice neat sets that we now observe.

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  29. When you pin them down, though, Joe, they'll go to a more specific definition of nested hierarchy that, though they apparently haven't thought about it, is actually better fitted to evolution from separate ancestors. They seem to forget that no one argues against evolution per se. It's the particular extrapolations they posit that are unwarranted by any rational criteria applied to the relevant data.

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  30. Jeff

    They seem to forget that no one argues against evolution per se.


    My but you're a clueless noob. Arguing against evolution is ALL the IDiots ever do. IDiots propose no hypotheses, do no research, publish no results. It's "evolution is wrong so ID wins by default!!" 100% of the time.

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    1. Dancing queen thorton's ignorance is showing again.

      Do you really think that your bluffing equivocations mean something? Really?

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    2. Well, no, Thorton. Some ID'ists may believe UCA is false. But they also know it can't be PROVEN false.

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    3. JeffDecember 5, 2012 4:54 PM

      Well, no, Thorton. Some ID'ists may believe UCA is false. But they also know it can't be PROVEN false.


      I've already given you observations that *if made* would falsify the idea. Not science's problem you're too ignorant to understand that unfalsified doesn't mean unfalsifiable.

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    4. But you were wrong about your supposed "falsifications." UCA could be true if observed fossil succession is uncorrelated with existential ranges and all major morphological gaps were bridged by single saltations. There is no falsifying UCA, because UCA, per se, doesn't imply any specific tree or mode/tempo of evolution.

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  31. Jeff

    But you were wrong about your supposed "falsifications".


    Still too stupid to get that unfalsified doesn't mean unfalsifiable I see. Keep trying.

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    1. Evolutionism isn't even testable, so how can it be falsified?

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    2. Thorton,

      You're still too stupid to realize that NO one has deduced implications from the hypothesis of naturalistic UCA that we could actually corroborate the hypothesis by. So you're still too stupid to realize that naturalistic UCA is not KNOWN to be falsifiable. You can assert it baldly as long as you wish. But it will just add further proof (as if any more was needed) that you're just too stupid.

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    3. Poor Jeff, still too stupid to get that unfalsified doesn't mean unfalsifiable.

      Some IDiots just don't have the brainpower I guess. That's why they're philosophy students and not scientists.

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  32. Poor Thorton, still too stupid to realize that if there are no implications derivable from the hypothesis of naturalistic UCA that can be tested, naturalistic UCA is not known to be falsifiable. That's mind-bogglingly stupid.

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