Wednesday, April 21, 2010

Codon Correlations: Molecular Recycling

It is well known that the genetic code translates DNA genes into proteins. But the process is immensely complex and new research is revealing some fascinating and challenging details. This process of protein synthesis begins with the unwinding of the DNA double helix. The two strands are separated and an incredible protein machine makes a copy of one of the strands. The copy contains the appropriate gene and, after some editing, the copy is sent to the ribosome where it provides the needed instructions.

The copy of the DNA strand is simply a sequence of nucleotides glued together. At the ribosome the nucleotides are read three at a time. Each triplet of nucleotides is called a codon because it codes for one of the 20 amino acids, according to the genetic code. There are four different nucleotides, so a codon has 64 different possible sequences of the three nucleotides. Since there are only 20 amino acids, several codons code for the same amino acid. In other words, the genetic code is degenerate.

At the ribosome there is a small army of molecular machines, called tRNAs, that read the codons and supply the appropriate amino acid, as per the genetic code. These tRNAs have a codon reader on one end and the corresponding amino acid glued to the other end. (The amino acids are glued onto the tRNAs by an army of proteins--the masters of the genetic code).

The tRNA machines are not always restricted to reading a particular codon, and in general there is not a one-to-one relationship between the codons and the tRNAs. For instance, a particular type of tRNA may read two of the six different codons that code for the serine amino acid. Also, the different tRNA machines are not in equal abundance. Instead, some are common and others are more rare.

One consequence of all this is that a given amino acid sequence (to be used in a protein) can be coded for by many different sequences of codons, which in turn could be read by different tRNAs. Therefore, a given amino acid sequence can use very different tRNAs, depending on the codon sequence used.

It has long been known that the different possible codons, which code for an amino acid, are not merely used at random in gene sequences. Instead, there are patterns though they vary across different genes and different organisms.

For instance, some codons appear more often than others, and genes that are used frequently tend to show a marked preference for the more common codons. And of course this means that certain tRNAs tend to be in greater demand.

The new research has now found another pattern: correlations in the sequence of codons used for a given amino acid along the protein sequence. For instance, consider all the serine amino acids in a protein sequence. What codons are used to code for those different serines?

The research found that the particular codon used for one of the serines, to stay with our example, influences the codon used at the next serine in the sequence. And what is this influence? The two codons tend to be either identical or, if not identical, they tend to be two codons that are read by a common tRNA machine. In other words, gene sequences tend to use the same tRNA machine for successive occurrences of an amino acid--tRNAs tend to be conserved.

This influence tends to wane as the distance between the two codons grows, in the protein sequence. And, as usual, the correlation is by no means consistent across genes or organisms. But the correlation is statistically significant, and the researchers showed that is is not merely a consequence of the well known codon bias.

Indeed, the correlation seems to be stronger in genes that need to be expressed quickly, such as those contributing to rapid growth or to acute stress responses. And finally, the researchers found this pattern of tRNA conservation is strongest for rare tRNAs, particularly in highly expressed genes.

Though many questions remain, all of this makes sense for enhancing the speed and fidelity of protein synthesis. What doesn't make a great deal of sense, as usual, is evolution. With evolution we must imagine a micro world of profound complexity--which we still do not fully understand--just happened to emerge.

33 comments:

  1. CH says: "...all of this makes sense for enhancing the speed and fidelity of protein synthesis. What doesn't make a great deal of sense, as usual, is evolution."

    Right. Because natural selection could never favour speed or fidelity in highly expressed genes. What conceivable fitness advantage could there be to producing the most common proteins quickly and accurately?

    In fact, this idea has been around since the 1980s e.g. Sharp & Li (1987), Sharp & Devine (1989). While it is interesting that there is a codon-to-codon pattern it is not a surprise and certainly not a challenge to evolution.

    Codon bias/preference has long been discussed with respect to level of gene expression in the literature. It is highly compatible with concepts of selection, both purifying and positive.

    Models of 3rd codon position evolution (the position that is commonly synonymous) are used to evaluate population genetic models of how species evolve all the time precisely because of codon bias patterns.

    So - in what sense, Cornelius, does this not make a great deal of sense under an evolutionary interpretation?

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  2. Cornelius,

    When in the history of life did this incredibly complex machinery appear? Was it around in the first creatures 4 billion years ago, or after one of the mass extinctions.

    Abimer,

    How long would it take to evolve such a system? If your estimate exceeds the amount of time prior to the first appearance of this apparatus then it is unlikely to have evolved. This would be a good test of the theory of evolution you support. I look forward to seeing your estimate.

    .

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  3. Peter, here's my guess: It's probably about the same odds that a pile of silica sand would eventually morph into an Intel Core2Quad microprocessor. Just give it *enough* time, and it *could* happen. ;-)

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  4. Jonathan:
    Just give it *enough* time, and it *could* happen.

    Your post prompts me to put in print some questions I have been pondering.

    If there is not enough time for major morphological transformations to occur, then there seems to be no middle ground. If one million years is not long enough, certainly 500 thousand years is "less" long enough, and so on.

    Then when we look at the dominate pattern in the fossil record, which is the abrupt appearance of new body plans, I reach the conclusion that indeed direct intervention was required to effect the new body plans.

    In other words, are there truly discontinuities in the history of life?

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  5. Peter, I cannot estimate for you a period of time it would take for the system of protein synthesis to evolve. Your question belies a certain naivety about the underlying science. You are referring to a contingent event of the past, one that will not reoccur in the same fashion ever again, nor can even a similar process occur whilst life exists on earth. We have no way to know the nature of what occurred or the order in which it happened. Even if I had a basis to estimate the time 'required' - and I'm not sure that's even the right approach - I doubt it would be taken with any seriousness by anyone here.

    Also, no one can answer the question you direct to Cornelius. Such things must have been in place for any sort of complex cellular life to have arisen but it is not possible to guess how similar to modern protein synthesis such a system might have been.

    To begin to address your question we need to consider what we need as a rought starting point for protein synthesis. Well, we would need a few RNAs: a coding sequence of some sort, and tRNAs to relate the sequence to amino acids. These are not necessarily immensely complex; only small parts would need to be highly specified. And of course, they need not be much like those we know today.

    To my mind it seems *plausible* that the basics of protein synthesis could have arisen in some form relatively quickly inasmuch as I don't see any particularly grave hurdle to it. I'm sure some people with origin of life expertise could offer some light on this; it is not an area I have ever given sufficient time to (hence, why my above response to Cornelius focuses on codon usage in extant species).

    All we will ever be able to do is guess at possibilities. My apoplogies if this does not sound like a satisfactory answer.

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  6. Doublee says: "Then when we look at the dominate pattern in the fossil record, which is the abrupt appearance of new body plans, I reach the conclusion that indeed direct intervention was required to effect the new body plans.

    In other words, are there truly discontinuities in the history of life?"


    I think these are good questions to ask.

    The fossil record is one useful tool to examine past patterns of life, but it is worth remembering what it does and doesn't do. It is a record that occurs on a geological timescale, not an evolutionary one. As convenient as it would be for the record to faithfully capture a couple specimens of every species every few thousand years, that doesn't happen. Further, it is almost exclusively a record of hard stuff that fossilises reasonably well - and only the hard stuff that ends up in the right place to fossilise. So we can observe things such as skeletal morphology changes (provided enoiugh of a skeleton is found) but little else - barring rare events e.g. Burgess shale.

    Where transitions between species are reasonably quick - e.g. responses to environmental change - we would be rather lucky for any fossils to exist at all, let alone be found.

    It is necessarily speculative to discuss the evolution of new body plans as they are exceedingly rare events. In all of the metazoa, there are only 36 phyla (the division based on body plan) and many are worms. When it comes to body plans, I would certainly expect coarse changes to occur quickly - presumably through drastic changes in genetic components of body plan such as hox genes. Such rearrangements probably occur occasionally, but we would expect virtually all such rearrangements to be either substantially deleterious or to fail to produce a viable zygote at all i.e. they will not produce a new phylum.

    In other words the rarer a type of change is, the more contingency is likely to be involved, and the less those changes could be anticipated or predicted (as opposed to the almost constant fine-tuning evolutionary change and stochastic accumulation of nearly neutral nucleotide substitutions, which can be modelled by population genetics). I can see why this would lead you to assume that direct intervention is required - these processes appear to be quite different in a number of ways - although I do not agree that it is necessary to invoke that explanation.

    Ultimately, If we wanted to look for discontinuities in life, we would be particularly interested in life's genetic history. Of course, there is no way to do so - we have only the extant species and, rarely, some sequences (usually mitochondrial) from recently extinct species. If there were a way, we would have much better answers to questions such as yours than we do.

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  7. Correction to abimer.

    Now, the fossil record is replete with examples of soft-part preservation, with a pantheon crowded with such examples as the Soom Shale, Hunsr├╝ck Shale, Mazon Creek and Messel. And for the Cambrian period, the Burgess Shale is now accompanied by the extraordinary discoveries from China (Chengjiang) and Greenland.

    Check out
    Walcott, the Burgess Shale and rumours of a post-Darwinian world, Simon Conway Morris, Current Biology, Volume 19, Issue 20, 3 November 2009, Pages R927-R931

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  8. Abimer

    "I cannot estimate for you a period of time it would take for the system of protein synthesis to evolve. Your question belies a certain naivety about the underlying science."

    I disagree. My questions shows a fundamental deficiency in evolutionary science. I am holding Evolution to the same standard as any other field that wants to call itself a science. Science must be able to test its theories. To test this theory one needs to understand the process and derive a model. Evolution can not do this. Until it does he has only unsupported hypothesises.

    .

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  9. Peter states:"My questions shows a fundamental deficiency in evolutionary science."

    It does not. You want me to estimate a time period for a unknowable series of historical contingencies. There are plausible scenarios, but even then, what about factors such as population size (affecting the rate at which de novo mutations arise)? Such problems are going to create a very wide confidence interval around any time estimate. This is not equivalent to saying evolutionary biology lacks processes or models.

    I have further explained the basics of what might be needed, which fundamentally appear to be quite modest - not "incredibly complex" as you earlier state.

    "I am holding Evolution to the same standard as any other field that wants to call itself a science."

    Really? Are you? What about criminal forensic science, which frequently attempts to reconstruct typically unknowable past events from the patterns and generalities of controlled, present events? Ultimately such re-creations of actual events are analogies based on probability. Sometimes little can be re-created, and sometimes forensic science is wrong. Yet does it still count as science to you?

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  10. Abimer,

    "You want me to estimate a time period for a unknowable series of historical contingencies."

    Well then, I guess since you don't know how the changes occurred then you therefore can not claim to know how the changes occurred.

    "What about criminal forensic science, which frequently attempts to reconstruct typically unknowable past events from the patterns and generalities of controlled, present events?"

    Everything that happens in a crime scene can be replicated, unlike evolution which conjectures that every creature originated in one universal common ancestor which sprang from the natural laws of physics. If that were true shouldn't we should see spontaneous creation of life more often, rather than never.

    .

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  11. "Well then, I guess since you don't know how the changes occurred then you therefore can not claim to know how the changes occurred."

    If you reread what I wrote above, I stated that this already. I said "[w]e have no way to know the nature of what occurred or the order in which it happened." So I don't know what your point is meant to be. If your alternative is ID, it is no better supported or knowable.

    "Everything that happens in a crime scene can be replicated"

    Well, you can't actually 'replicate' it without committing another crime. You can model a plausible scenario of what might have happened at a crime scene - one that fits all the observations you make of the scene - but you can never actually know what happened such that it could be replicated. It is this uncertainty that is the point - what is determined to be 'fact' in such a situation is really the most plausible scenario from the various possiblities.

    "unlike evolution which conjectures that every creature originated in one universal common ancestor"

    Common descent is one of the best supported ideas in science. It is far from your hyperbolic description "conjecture". CD is supported by lines of independent evidence in geology, geography/biogeography, embryology, genetics, biology/physiology, ecology and phylogenetics.

    "If that were true shouldn't we should see spontaneous creation of life more often, rather than never."

    In a peanut butter jar, perhaps?

    Firstly, the conditions on earth are radically different from the time of the earth's formation - the atmosphere with all of its damaging oxygen is unlikely to be conducive to abiogenesis.

    Secondly, life probably doesn't just appear overnight in a recognisable form. It's gonna need some time in a pool of untapped resources. Time this new life is unlikely to get when competing with extant life with a 4 billion year head start.

    Thirdly, who would know if life did start up and die out every once in a while anyway? Where would you look and what would you look for?

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  12. abimar,

    "So I don't know what your point is meant to be."


    Just reinforcing the idea that evolution is not supported by fact.

    "Well, you can't actually 'replicate' it without committing another crime."

    Actually, you can. You don't have to shoot a person to analyze gun shot physics, etc. Evidence can be gathered from crimes caught on camera.

    "Common descent is one of the best supported ideas in science."

    You must be kidding. Evolution is disproven by scientific evidence, ie. fossil record, dna analysis is inconclusive. There is no tree of life as Darwin speculated. It is always more complicated than the simplistic theory of evolution.

    "In a peanut butter jar, perhaps? "

    You already admitted you don't know how life arose. So the theory of evolution is not an answer.

    .

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  13. Peter, it appears Cornelius Hunter's habit of never replying to any points of consequence is contagious.

    You say: "You must be kidding. Evolution is disproven by scientific evidence, ie. fossil record, dna analysis is inconclusive."

    Please share your wealth of expertise in molecular phylogenetics with me. How has evolution been disproven by 'dna analysis'? Do you have particular taxa you would like to discuss?

    "It is always more complicated than the simplistic theory of evolution."

    On this point we agree - models are always more simple that the reality they attempt to mimic.

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  14. abimer

    "Please share your wealth of expertise in molecular phylogenetics with me. How has evolution been disproven by 'dna analysis'? Do you have particular taxa you would like to discuss?"

    I noticed that you did not include the fossil record in the list of evidence you say supports evolution. That is because you must know that it contradicts evolution. I do know from following this blog that genetic similarities both support and contradict the theory of evolution - so it is a wash and evolution is therefore not strongly supported. I do have some training in statistics. What is you knowledge of statistics? If you are knowledgable in statistics you could never accept evolution because you would understand the the events claimed are astronomically improbable for the simplest life, and impossiblee for the entirerty of life. Every new blog detailing additional complexity is another nail in the coffin of evolution.


    .

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  15. Peter says:"I noticed that you did not include the fossil record in the list of evidence you say supports evolution. That is because you must know that it contradicts evolution.

    I did not exclude it, I focused on one point in order to generate a more fruitful discussion about, hoping you have something specific to debate. FWIW, I disagree that the fossil record contradicts 'evolution'. I have discussed the fossil record and its limitations already in this thread. Again, if you have specific points, please bring them up.

    I do know from following this blog that genetic similarities both support and contradict the theory of evolution - so it is a wash and evolution is therefore not strongly supported.

    I'm sure you won't believe me because of our ideological differences, but this statement is untrue. Cornelius is clever at presenting things is such an incredulous way that it would seem evolution is somehow not valid. This does not change the reality hat most phylogenetics offer good support for evolution. Sure, some analyses offer contradictory results. Mitochondrial gene trees sometimes disagree with nuclear gene trees, for example. However, I know of no field examining empirical data where contrary results do not occur.

    There is an important trend however, one that Cornelius never discusses. That is, as more species are added to analyses and as more genes are sequenced for those species, the phylogenetic trees are becoming better resolved with fewer and fewer conflicts. The vertebrate tree of life is an excellent example in this. Thomson and Shaffer 2010 discuss this:
    http://www.biomedcentral.com/content/pdf/1741-7007-8-19.pdf


    I do have some training in statistics. What is you knowledge of statistics? If you are knowledgable in statistics you could never accept evolution because you would understand the the events claimed are astronomically improbable for the simplest life, and impossiblee for the entirerty of life.

    For what it is worth, I have postgraduate education in statistics and phylogenetics. I wonder what your basis for claiming life is astronomically improbable. My guess is questionable assumptions.

    Every new blog detailing additional complexity is another nail in the coffin of evolution.
    Complexity is a part of the natural world. It is not a coherent argument against evolution.

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  16. abimer,

    " I have discussed the fossil record and its limitations already in this thread. Again, if you have specific points, please bring them up."

    The very first life forms where complex colonies of creatures with photosynthesis; the Cambriann explosion; mass extinctions and rapid appearance of complex, abundant life.

    "phylogenetics offer good support for evolution."

    Of course creatures with similar phenotypes has similar genetics. That is not surprising. However phylogentics only shows similarities. It does not prove that one creature morphed into another, that is an assumption. I believe you are assuming away the problem of proving evolution. That is very convenient. I don't suppose your teachers, which are most likely atheists, and make a living teaching evolution would accurately characterize evolution as an unproven hypothesis. That would be seriously upsetting the gravy train. I know first hand how harmful to ones academic caree that can be.

    "I wonder what your basis for claiming life is astronomically improbable. My guess is questionable assumptions."

    This claim I think is intuitively obviouss. However, for a detailed analysis of the improbablity of life I recommend you read Herbet Yockey. He did a good probablistic calculation for the formation of just one protein. His calculation showed that it was far to complicated to have formed in the hundreds of millions of years available. Multiple that probability times the components in a living cell, and multiply that by the number of life forms in an ecosystem and I believe the probability would be zero. Did they not mention Yockey in your post grad stats work? I wouldn't be surprised.

    .

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  17. Peter, baldly stating 'the Cambrian explosion' is not an argument. Nor 'mass extinctions and rapid appearance of complex, abundant life'. Many explosive periods of evolution appear to be linked to the emergence of novel traits, for example vision and planktotrophy. The emergence of such critical traits alone may be insufficient to explain the mechanisms of such explosions, of course, yet this at least provides a compelling potential cause. However, such phenomena can only be studied using what information can be scraped together of such eras. Our limited knowledge of the mechanisms at play reflects this.

    The cambrian explosion also shows as much failure as success. Many of the new body plans that emerged were failures, spectacularly ephemeral. Why should this be?

    "Of course creatures with similar phenotypes has similar genetics. That is not surprising. However phylogentics only shows similarities. It does not prove that one creature morphed into another, that is an assumption."

    Creatures with superficially similar phenotypes are only genetically similar when they are also closely related. Consider bats and birds, dolphins and fish. Bats and dolphins are genetically much more similar to each other than they are to the birds or fish respectively.

    This is explained by common descent. In other words, evolution unifies all of the disparate observations of the patterns of interrelatedness of species. It is not to say that 'God/designer wouldn't/couldn't have done it that way', but a design hypothesis has no explanatory power here.

    The very closest related species (sister species) are those that have diverged relatively recently from a common ancestor. As predicted by evolutionary theory, they occur in close proximity to each other and morphologically, ecologically and genetically similar. Over time, as divergence increases, one of a couple possibilities happen: either one is forced into a marginal energy niche, one is excluded to a less productive habitat (i.e. higher elevation, higher latitude, lower productivity etc) or one becomes extinct. This happens time and time again and is supported in observations of extant species within ecology and phylogenetics and in fossil records.

    Again, perhaps this is how the designer wants the world to be, but this explanation explains nothing. Evolutionary theory, however, accounts for this in terms of species selection. The biogeography of these species, and the limits of biogeographic possbilities (i.e. the distribution of extant species within their capabilities for migration and their evolutionary relationships) offers powerful evidence for evolution.

    Equally important here, you state "phylogentics only shows similarities". Of course, this is trivially true, but phylogenetics does not stand alone as the evidence for evolution; it complements the other independent lines of evidence. Further, the patterns of similarity shown using phylogenetics are the patterns of nested interrelatedness predicted by naturalistic evolution. Thus when I say phylogenetics offers good support for evolution, I am not simply extrapolating similarity->common descent. It is only part the argument.

    "This claim I think is intuitively obviouss. However, for a detailed analysis of the improbablity of life I recommend you read Herbet Yockey."
    Are you aware of the assumptions you are making? Here are just some assumptions that one makes when calculating said probabilities: that the nucleotide sequence is strictly specified, that the 'population size' of competing molecules is known, that the contents of a cell are all strictly essential and strictly specified, that the number of possible life-bearing planets is known.

    All of these assumptions are flawed. Hence, the calculation is absolutely not one that can be made without an enormous and meaningless confidence interval.

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  18. Abimer,

    "The emergence of such critical traits alone may be insufficient to explain the mechanisms of such explosions, of course, yet this at least provides a compelling potential cause. However, such phenomena can only be studied using what information can be scraped together of such eras. Our limited knowledge of the mechanisms at play reflects this."

    The fossil record is exactly the opposite of what evolution would predict. It contradicts the theory of evolution. Also, the absence of information is not proof. You can not claim the theory of evolution is true based on evidence you speculate you will find some time in the future. The best you can say is that you do not know how life arouse.

    "The cambrian explosion also shows as much failure as success. Many of the new body plans that emerged were failures, spectacularly ephemeral. Why should this be?"

    Speculation again.

    "The very closest related species (sister species) are those that have diverged relatively recently from a common ancestor. As predicted by evolutionary theory, they occur in close proximity to each other and morphologically, ecologically and genetically similar."

    Again, you are assuming one creature morphed into another, not proving it as I pointed out early. Since the fossil evidence contradicts evolution, then phylogenetics is also contradicted by the fossil record.

    "Again, perhaps this is how the designer wants the world to be, but this explanation explains nothing. Evolutionary theory, however, accounts for this in terms of species selection. The biogeography of these species, and the limits of biogeographic possbilities (i.e. the distribution of extant species within their capabilities for migration and their evolutionary relationships) offers powerful evidence for evolution."

    Actually, it is evolution that explains nothing. The biogeographical data is interesting history of creation, when combined with the overwhelming anthropic principle indicate that life was created by a designer before the universe began 14 billion years ago to create us, the only creatures capable of comprehending the creator.

    "All of these assumptions are flawed. Hence, the calculation is absolutely not one that can be made without an enormous and meaningless confidence interval."

    So you admit you can not calculate the probabilities the theory of evolution is based on. The emperor has no clothes. Evolution is an hypothesis only. With the most conservative estimates for these values the probability of random mutation creating life is still zero. You have no proof to contradict this claim.

    .

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  19. Peter:"The fossil record is exactly the opposite of what evolution would predict. It contradicts the theory of evolution."

    By exactly the opposite, I assume you mean depauperate in early transitional fossils for the metazoa. I say assume because you don't seem to have any detail at all about what you think is wrong.

    If this is what you think, I suggest you examine the fossil record of the Cambrian explosion in Chengjiang and the Burgess Shale.

    I would also suggest that you look at lineages where there is good records of transition. The lack of transitional fossils does not demonstrate much: little is fossilised, little that is fossilised remains well preserved, and little of this is discovered.

    What of lineages such as the horse, whale, bivalves, and humans? There is a better fossil record for these lineages. Do these lineages also show the opposite of the prediction of evolutionary theory?

    Also, the absence of information is not proof. You can not claim the theory of evolution is true based on evidence you speculate you will find some time in the future. The best you can say is that you do not know how life arouse.
    Firstly, I have never claimed to know how life arose, and have repeatedly stated my uncertainty around this. Secondly, the evidence for evolution does not lie on some single claim of non-existent evidence that we hope to one day find. It's strength lies in the multidisciplinary support for the theory. Because it is generally well supported by a number of disparate lines of evidence, where the evidence is lacking and not contrary, it is reasonable to assume that the theory stands.

    Speculation again.

    Not at all. Look at the edicarian fauna - where are they now?

    The biogeographical data is interesting history of creation, when combined with the overwhelming anthropic principle indicate that life was created by a designer before the universe began 14 billion years ago to create us, the only creatures capable of comprehending the creator.

    Do you think something in this paragraph provides evidence for your position? I'm not seeing it.

    "With the most conservative estimates for these values the probability of random mutation creating life is still zero. You have no proof to contradict this claim."

    I doubt that anyone has ever argued that "random mutation" created life. I listed a number of specific assumptions you are making when in your claim. The assumptions are not valid. If you can demonstrate otherwise, go ahead, otherwise it is certainly not up to me to contradict your claim any further than I have.

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  20. Peter, further regarding your probability assertion - in your previous post, you stated that to calculate the probability of evolution one would need to start with the probability of a protein forming and then "[m]ultiple that probability times the components in a living cell, and multiply that by the number of life forms in an ecosystem".

    This, I feel, is a fundamental area where we differ in our understanding. For you, if there is more life and diversity, there is less likelihood that a naturalistic process could have produced it.

    The reason why evolutionary biologists will disagree with you on this is because speciation can be understood as a rational process, where geneflow in large or demic populations or isolated subpopulations is insufficient relative to mutation pressure to prevent reproductive isolation.

    Such a process can be wholly neutral to selection, although selection may increase the likelihood or rate at which a genetic basis for speciation could occur (via various mechanisms such as pleiotropy, epistasis etc). This is not even to consider other factors in higher species such as sexual selection.

    Mallet (2008) discusses the ease with which speciation occurs and the lack of sufficiently distinct barriers between species as population genetic processes occur.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607318/

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  21. Abimer,

    "By exactly the opposite, I assume you mean depauperate in early transitional fossils for the metazoa. I say assume because you don't seem to have any detail at all about what you think is wrong."

    I was refering to the earliest life forms - stromatolite fossils discovered in rocks 3.5 billion years old. These complex colonies of creatures were capable of oxygenic and anoxygenic photosynthesis. This evidence is directly the opposite of what evolution would predict. However, you do say that you can not explain how first live arose. We are in agreement on this point. If evolution can not describe the mechanism for this ecosystem, I don't see why more diverse ecosystems could be explained.

    "This, I feel, is a fundamental area where we differ in our understanding. For you, if there is more life and diversity, there is less likelihood that a naturalistic process could have produced it."

    This is basic probability. If a life form is dependant on eating other life forms to survive, then the probability of the hunter life form surviving is dependant on the probability of the prey's existance. Therefore the probability of the existance of the hunter life form is multiplied by the probability of the existance of the prey life form. Now take all such relationships in an ecosystem. If we start with Yockey's calculation for the probability of a protein, then you can see that likelihood of an ecosytem happening by random chance is zero given the finite age of the universe.

    "The reason why evolutionary biologists will disagree with you on this is because speciation can be understood as a rational process, where geneflow in large or demic populations or isolated subpopulations is insufficient relative to mutation pressure to prevent reproductive isolation."

    I believe you are a little off topic here. In this paragraph and the following ones you assume that an ecosystem exists. That of course is assuming away the question, and not addressing the idea of the probability of an ecosystem coming into existance.

    .

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  22. However, you do say that you can not explain how first live arose.

    And you believe you can?

    In this paragraph and the following ones you assume that an ecosystem exists. That of course is assuming away the question, and not addressing the idea of the probability of an ecosystem coming into existance.

    Once again, the fundamental difference here is that you believe that random mutation has to produce highly specified nucleotide sequences independent of selection. Furthermore, if you genuinely believe you can calculate the probability of an ecosystem using your hunter/prey example, you have no understanding of how natural systems work.

    I believe you are a little off topic here.

    This discussion is not off topic at all, it is directly on topic because I am suggesting that the addition of diversity to natural systems is a rational process that can be understood by naturalistic means, while you seem to believe that any change is exponentially unlikely. Your POV is demonstrably untrue.

    Equally important here are the assumptions I discussed above that you make in calculating the probabilities of life (assumptions which you completely ignored). You seem to believe that proteins and ecosystems absolutely have to be the way they are, or they could not function. This is absolutely false. I suggest you supplement your theoretical statistical approach with some basic ecology, an understanding of mutation, and natural selection.

    The problem here is not that I am "assuming" an ecosystem, it is that you don't understand ecosystems at all. Ecosystems are assemblages of interacting species, often robust and buffered against deleterious effects of change. However, ecosystems are not precise or specified systems. Nor are proteins. This is why your calculation is not meaningful.

    Let's start with the protein: I can tell you that in an alignment of 400 small mammals, there is only 25% identity in the cytochrome b nucleotide sequence. 25% - and only within small mammals not across all metazoan life! 25% in a sequence that is highly expressed and central to metabolism. Thus any assumption that nucleotide sequences are highly specified such that probability calculations like that which you suggest are possible are enormous assumptions to be making.

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  23. Abimer,

    "Once again, the fundamental difference here is that you believe that random mutation has to produce highly specified nucleotide sequences independent of selection."

    It is clear that you have no understanding of how probability works, irregardless of selection. There are nearly an infinity of possible permutations of chemical that go into making life. That fact that there is selection is irrelavant. What you fail to understand is that all the random mutations have to occur before seleection. Unless you are saying there is some mechanism which weeds out the unhelpful combinations before selection. That sounds like ID to me, or perhaps theocratic evolution.

    "However, ecosystems are not precise or specified systems. Nor are proteins. This is why your calculation is not meaningful."

    Nonsense. The point is simple, even though you can not grasp it - the more parts in a system the smaller the likelihood that it assembles randomly.

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  24. It is clear that you have no understanding of how probability works, irregardless of selection.

    A prerequisite to any valid statistical anaylsis is understanding its assumptions. You have failed to understand your own assumptions.

    There are nearly an infinity of possible permutations of chemical that go into making life.

    And many different permutations appear to work.

    What you fail to understand is that all the random mutations have to occur before seleection. Unless you are saying there is some mechanism which weeds out the unhelpful combinations before selection.

    Mutation happens first, but selection is precisely the mechanism that weeds out deleterious mutations and combinations. It does so at the population level - differential reproductive success. Bad combinations and mutations happen all the time, the individuals bearing these differences have a lower chance of survival and thus reproducing.

    Unhelpful combinations also include neutral mutations, which are left unaffected by selection (other than linked selection, see Gillespie 2000). Their fate belongs in the domain of genetic drift. We frequently observe population processes involving neutral mutations in molecular evolution - more frequently than selection in fact!

    That sounds like ID to me, or perhaps theocratic evolution.

    What I have described is naturalistic evolution.

    Nonsense. The point is simple, even though you can not grasp it - the more parts in a system the smaller the likelihood that it assembles randomly.

    I grasp it Peter, I really do. But my argument is this: Your point only stands if the system at hand is strictly specified. Otherwise it is just a collection of loosely specified and/or unspecified stuff. If there are clear processes than control how much of said stuff comes together there is nothing miraculous or improbable about it.

    In summary, for your point to be valid, any nucleotide change to a protein coding sequence would have to render it useless, and the loss or gain of any species to an ecosystem would have to destroy it. These things do not happen because these systems are not specified in the way you assume they are.

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  25. Abimer,

    "A prerequisite to any valid statistical anaylsis is understanding its assumptions. You have failed to understand your own assumptions."

    What you don't understand is that I'm talking about the rise in complexity and you seem to fixed with the existing life forms.

    "Mutation happens first, but selection is precisely the mechanism that weeds out deleterious mutations and combinations."

    Again you are assuming an existing biological system that handles minor variations in dna, but does not add new complexity.

    "Unhelpful combinations also include neutral mutations, which are left unaffected by selection (other than linked selection, see Gillespie 2000). Their fate belongs in the domain of genetic drift. We frequently observe population processes involving neutral mutations in molecular evolution - more frequently than selection in fact!"

    ditto

    "I grasp it Peter, I really do. But my argument is this: Your point only stands if the system at hand is strictly specified. Otherwise it is just a collection of loosely specified and/or unspecified stuff. If there are clear processes than control how much of said stuff comes together there is nothing miraculous or improbable about it."

    Unfortunately you do not. You have no idea of the complexity needed to bring change into a living system. Take for instance the complexity of the eye. All the parts need to go together to work. They can not work alone. In order for the eye to work the probability of all the chemicals coming together in just the right way, from our lens to the receptors in our brain is zero, or as realistically close as one can calculate.

    "In summary, for your point to be valid, any nucleotide change to a protein coding sequence would have to render it useless, and the loss or gain of any species to an ecosystem would have to destroy it. These things do not happen because these systems are not specified in the way you assume they are."

    Again you are talking about existing systems and not the rise of complexity which is necessary to explain the "evolution" of life.

    .

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  26. "What you don't understand is that I'm talking about the rise in complexity and you seem to fixed with the existing life forms. "

    I was responding to your comments on ecosystems, which has everything to do with existing life forms.

    But so what? This was your response to me saying you haven't addressed the assumptions you are making - and you still haven't. You somehow seem to think that you can apply a meaningless calculation and not address it's assumptions because you are discussing the origins of complexity. How does this not apply to the rise of complexity?

    Again you are assuming an existing biological system that handles minor variations in dna, but does not add new complexity.

    How so? I was discussing speciation. That is hardly minor dna variations, and is absolutely about adding complexity to a system.

    Unfortunately you do not. You have no idea of the complexity needed to bring change into a living system....In order for the eye to work the probability of all the chemicals coming together in just the right way, from our lens to the receptors in our brain is zero, or as realistically close as one can calculate.

    What model of evolution says the eye in all its parts just happened to come together one day? Because if you're not saying that, you are obviously wholly unaware of the models of eye development that even Behe has acknowledged are broadly reasonable.

    There are lots of different eyes in nature that work in lots of different ways. Once again, the idea that every single component must be exactly as it is or the eye couldn't work is plainly untrue, or there would be only one eye in nature. Sure you can't remove parts of a working eye and expect it to work, but this is an evolutionary prediction. The concept of irreducible complexity is entirely bunk, it was wholly pre-empted by Muller in 1918 (p 463-4 and expanded in the 1930s) long before the ID movement was conceived. Muller demonstrated how natural selection builds interlocking complexity, the concept that Behe misinterprets as irreducible complexity.

    Again you are talking about existing systems and not the rise of complexity which is necessary to explain the "evolution" of life

    No, this applies to the rise of complexity as well, because the same processes are at play. So either you have to believe that every nucleotide substitution is substantially deleterious (hint: I've already demonstrated that nothing could be further from the truth) or you must admit that there is not the specificity that your calculation requires.

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  27. Abimer,

    "I was responding to your comments on ecosystems, which has everything to do with existing life forms."

    Obviously wrong. Ecosystem have to come into existance too.

    "You somehow seem to think that you can apply a meaningless calculation and not address it's assumptions because you are discussing the origins of complexity. How does this not apply to the rise of complexity? "

    A rough estimate is always better than no estimate, which is what you are offering. Try reading Yockey, you might understand how it's done. You obviously don't understand how to make probabilistic calculaitons based on chemical structures. I can understand why your teachers rabidly avoid this topic. If they tried to make a moderately realistic probability then evolution would become a laughing stock.

    "There are lots of different eyes in nature that work in lots of different ways."

    True enough, but it is a wild guess to assume that one type of eye could evolve into another. Do you know of any humanoids or mammals for that matter that ever had compound eyes? You are assuming eyes evolved without any proof.

    .

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  28. A rough estimate is always better than no estimate...Try reading Yockey, you might understand how it's done.

    And a demonstrably wrong estimate is always wrong.

    You obviously don't understand how to make probabilistic calculaitons based on chemical structures.

    I won't put much faith in your ability to do so when you refuse to so much as consider your assumptions.

    I can understand why your teachers rabidly avoid this topic.

    Even more assumptions.

    But you still haven't addressed the core problem of your first set of assumptions. As I said in the last post:

    "...either you have to believe that every nucleotide substitution is substantially deleterious (hint: I've already demonstrated that nothing could be further from the truth) or you must admit that there is not the specificity that your calculation requires."

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  29. Abimer,

    "And a demonstrably wrong estimate is always wrong."

    "I won't put much faith in your ability to do so when you refuse to so much as consider your assumptions."

    Your defense of not providing a probabilistic calculation for the field of science which is based on probability tells me that you are deep in denial. No other field of science would make a probabilistic claim and fail to provide a calculation. It is your claim that life arose because of random variations in dna which are later selected for in nature. The onus is on you to support your claim with a probabilitistic calculation. You can not say that you don't like the assumptions, or a calcution is impossible and claim the random mutation is the force responsible for creating life. You have proven nothing. All that is left is an elaborate just-so story.

    .

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  30. "Your defense of not providing a probabilistic calculation for the field of science which is based on probability tells me that you are deep in denial."

    Great - let's start up with the pop psychology now. I'm sure this is another area you are excellently schooled in. Well, whatever helps you avoid the argument Peter...

    At this point, this 'discussion' is just comical. No matter what I write, you won't actually engage with the assumptions of your probabilistic calculation, you'll just write another empty paragraph. You won't seriously consider the reasons that I won't make a probabilistic calculation, you'll just tell me I'm in denial.

    I suggest, by the way, you look up what a just-so story is, before you flippantly throw it around. It is an empty insult and a favourite of ill-informed creationists with nothing to say. In fact, I have been honest about the gaps in my knowledge and the gaps in the broad scientific understanding of abiogenesis.

    At the same time, what I have attempted to do is demonstrate that what we know of the continuing processes of evolution are rather different than what you portray in your calculation. This is the basis of my rejection of your probability calculation. But what do you care about that? Your ignorant calculation makes you happy.

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  31. This comment has been removed by the author.

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  32. here's the link to this , since the powers of 10 are a little difficult in post above

    "Probaility of Abiogenesis"
    http://www.evolutionfaq.com/articles/probability-life

    as you can see its not the imcomprehensible thing after all when one looks at the total volume of the Oceans of the Earth , Volcanic vents & the billions of chemical reactions taking place each day , 24hrs a day in this constant agitated state .

    Supplementing with the Iron Sulphur World theory shows some surprises at just how fast the first complex moelules can form in early Earth conditions ,
    http://en.wikipedia.org/wiki/Iron%E2%80%93sulfur_world_theory

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  33. The calculation which supports the creationist argument begins with the probability of a 300-molecule-long protein forming by total random chance. This would be approximately 1 chance in 10to390th. This number is astoundingly huge. By comparison, the number of all the atoms in the observable universe is 10to80th. So, if a simple protein has that unlikely chance of forming, what hope does a complete bacterium have?

    If this were the theory of abiogeneisis, and if it relied entirely on random chance, then yes, it would be impossible for life to form in this way. However, this is not the case.

    Abiogenesis was a long process with many small incremental steps, all governed by the non-random forces of Natural Selection and chemistry. The very first stages of abiogenesis were no more than simple self-replicating molecules, which might hardly have been called alive at all.

    For example, the simplest theorized self-replicating peptide is only 32 amino acids long. The probability of it forming randomly, in sequential trials, is approximately 1 in 10to40th, which is much more likely than the 1 in 10to390th claim creationists often cite.

    Though, to be fair, 10to40th is still a very large number. It would still take an incredibly large number of sequential trials before the peptide would form. But remember that in the prebiotic oceans of the early Earth, there would be billions of trials taking place simultaneously as the oceans, rich in amino acids, were continuously churned by the tidal forces of the moon and the harsh weather conditions of the Earth.

    In fact, if we assume the volume of the oceans were 10 to 24th liters, and the amino acid concentration was 10-6M (which is actually very dilute), then almost 10to31th self-replicating peptides would form in under a year, let alone millions of years. So, even given the difficult chances of 1 in 10to40th, the first stages of abiogenesis could have started very quickly indeed.

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