Home » The Design of Life » Design of Life: Molecular clock – right twice a day?

Design of Life: Molecular clock – right twice a day?

2006 and 2007 have been years in which a number of key science papers addressed things we know – that ain’t so. One story is the serious challenges to the long contested “molecular clock” theory.

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In the science literature, many adjustments are offered to make the fossil record and molecular data match. Of course, some adjustment is certainly inevitable, but after a while a question arises. One can live with a clock that is routinely ten minutes slow. But if it is variably slow, slower at some times than others, there may come a point when one asks, why consult a clock anyway? Or, more to the point, should this device properly be called a clock?

Read the rest here.

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34 Responses to Design of Life: Molecular clock – right twice a day?

  1. From David Tyler’s commentary:

    The authors are concerned to find out “how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central, especially to paleoanthropology.” This they do with an incisiveness rarely appearing on the printed page of refereed journals.

    But not so rare in alot of other places. Does this mean it’s now “scientifically” legitimate to criticize Darwinism in this area?

    This is a paper that will disturb the Darwinists, but it will offer encouragement to all who want to see less ideology in evolutionary thinking and who want to follow the evidence wherever it leads.

    Isn’t that what ID proponents have been saying for years?
    I suppose Schwartz and Maresca are now going to be accused of being creationists.
    And let’s not forget to fire whoever allowed this paper into a peer-reviewed journal.

  2. On the topic of molecular clocks, let me bring up three additional puzzles:

    1 – There was recently a report of 250 million year old bacteria that was reconstituted. My understanding is that this bacteria seriously challenges the molecular clock hypothesis because genes do not show the 250 million years of ticks that should be in there. Even though this is the product of multiple finds, and careful varification, the conclusion drawn is that there must have been contamination with modern bacteria.

    2 – Hoyle points out that the molecular clock hypothesis is serously challenged by ultra-conserved genes. If a gene is ultra-conserved (99% identical in all vertabrates, for instance) then extrapolating the molecular clock back in time would suggest that these things had an enormous lifespan.

    3 – in “Evidence, a Theory in Crisis” Michael Denton renders an intriguing discussion of the Cytochrome C gene. This gene renders an intriguing map of the tree of life. It is my understanding that the molecular clock hypothesis was developed to explain this “perfect” tree in the Cytochrome C. If the molecular clock hypothesis is invalid, the only other reasonable explanation for the pattern found in the Cytochrome C is that it is intentional — a copyright notice.

  3. a copyright notice…to show that the design wasn’t copied?

  4. ari-freedom, “a copyright notice…to show that the design wasn’t copied?” No, a copyright notice to show that the design was designed — the signature of the designer. I see the pattern in the Cytochrome C as the equivelant of the patterns that are being sent to outer-space (prime numbers, etc.) to indicate that the signal is from an intelligent, rather than random source. Just read the book. It certainly is one of the most important ID books out there.

  5. bFast, you have the name of Denton’s book wrong.

  6. OFFTOPIC

    Hi. I would appreciate some comments regarding a discussion that I am having with an atheist. He has written:

    Hi
    I have just written a post comparing the methodology of ID with the scientific method. It goes into this in a bit more detail than can be done in a comment. I will put it up next week when people are back at their computers.

    But I think where the disagreement comes in is that the Wedge people argue for the legitimacy of a “logical inference” which can’t be evaluated whereas modern science insists on mapping ideas and theory against reality – experiential verification. I discuss the importance of this in Most ideas in science are wrong! I think if we accept that most ideas in science are wrong, and we know that from testing, then surely ideas from “logical inference” are at least as likely to be wrong – but the Wedge people want to protect these from any genuine mapping against reality.

    This guy is a grass scientist and really has it is for ID. I am not sure he has really engaged with ID but perhaps only with ID antagonizers.

    Q1. Is ID testable?

    Q2. Is ID falsifiable?

    Q3. Is ID committing a logical fallacy by using “logical inferences”?

    The longer thread with our discussions is on here:

    http://christiannews.co.nz/200.....mment-1180

  7. Robo, “bFast, you have the name of Denton’s book wrong.”

    Yup, I sure did. The title is “Evolution a Theory in Crisis”.

  8. Robo, let me put in my two cents on your questions:

    Firstly, I do not believe that “theory” is the right term to use when referring to ID. I would suggest that ID is a metatheory, a class that holds many theories. As such, I don’t believe that it is falsifiable. Even if every current theory within that class is falsified, more theories will pop up.

    That said, lets consider three of the theories that are in the ID class: Irreduceable Complexity, Specified Complexity and Haldane’s Dilemma.

    Behe’s theory of Irreduceable Complexity is ABSOLUTELY FALSIFIABLE. If one were to take a bacterium that does not have a flagellum, if one were to add to it single mutational events testing that each mutational event was at least neutral to the bacterium, and ultimately produce a working bacterial flagellum one would be hard pressed to suggest that the flagellum cannot occur by random mechanism. That said, one could argue that if the flagellum fell as a case, there would just be another candidate for irreduceable complexity. While this may be true, the simple reality is that there is an absolutely finite number of possible IC candidates within earth’s living organisms. As there is a finite number of IC candidates, each falsifiable, then the theory of IC is falsifiable. No one ever suggested that falsification must be easy.

    Dembski’s Specified Complexity case is more easily falsifiable than Behe’s IC case in that a single example of specified complexity (exceding the Universal Probability Bound) which is developed through truly non-directed means is all that is needed to falsify SC. Now, SC is certainly the primary candidate for the “logical inference” argument. (Logical inference is certainly not “proof positive”. If it were, we could not break the sound barrier because mathemeticians proved using logical inference that it could not be done. That said, I fail to see how logical inference merits a cry of “foul”.) Though SC is a logical inference, it still has a very direct pathway to falsifiability. Falsify it, and it will be gone. Plain and simple.

    Walter ReMine points to Haldane’s dilemma, that there are far too much mutational difference between man and monkey to be accounted for by the available generations. Again, this is absolutely falsifiable. All that is needed is a clear, demonstrable path that allows for sufficient mutations to fix. As this would require an average in excess of one mutational event per year, it should be provable.

    Alas, each of these theories in the ID class falsifies the RV+NS hypothesis. If any one of these theories is valid, then RV+NS as the universal explanation is not valid. It appears to me that the scientific community, rather than accepting the challenge of their pet theory, is trying to disqualify the challenge without analysis. I find this attitude to be painfully unscientific.

  9. 2 – Hoyle points out that the molecular clock hypothesis is serously challenged by ultra-conserved genes. If a gene is ultra-conserved (99% identical in all vertabrates, for instance) then extrapolating the molecular clock back in time would suggest that these things had an enormous lifespan.

    Or that the genes were the subject of selection. The theory behind the molecular clock only applies to neutral substitutions.

    3 – in “Evidence, a Theory in Crisis” Michael Denton renders an intriguing discussion of the Cytochrome C gene. This gene renders an intriguing map of the tree of life. It is my understanding that the molecular clock hypothesis was developed to explain this “perfect” tree in the Cytochrome C. If the molecular clock hypothesis is invalid, the only other reasonable explanation for the pattern found in the Cytochrome C is that it is intentional — a copyright notice.

    You’re mis-understanding the molecular clock. It applies to rate of mutation, not the topology of the tree. So, an imperfect molecular clock will still give the right tree, but with branch lengths incorrectly estimated.

    If the clock is too far out, it think can affect the estimated topology, which is one reason why there is still work on improving the estimation methods. But I suspect that using the wrong mutation model would be more important.

    Bob

  10. Cheers bFast for the comments re Robo!

  11. O’Leary, very nice piece. I really enjoyed your article-

    Now on a few things- It seems when (in the article prepared for the school system) you are talking about hemoglobin and its rate of chance- you are more or less describing the deterioration rate of given molecules. One predicts all kinds of things in life simply by looking at a historical record and looking for trends, this is the nature of statistics. For example, someone posted an article a little while back that had a video of Dr. Carter talking about how climatologists are inventing dangerous man made global warming- to support his opinion he showed a climate record that had freezing and warming periods for hundreads of thousands of years. If you looked closely at his chart you saw that not only was there extreme warming and freezing but the warming and freezing happened in almost “clock” like fashion. Now my point is simple- The universe is not random as Darwinian Evolution so often claims and there are limits to what we can expect. While quantum physics allows for any “possibility” there is still the rule of “probabilities” or the way of statisitical averages- it warms- it cools.

    Now, within the biological world we can be sure to see the same sort of averages but we ought not confuse averages with clock work. For example Cambrain Explosion was the first discovery that made DE look really weak because it refuted Darwin’s “clock work” prediction of “slow and gradual change, over long periods of time.” The Cambrian refutes DE’s original prediction so badly in fact, that creationists use it as proof or evidence that all species were created “at the same time.” Now I am not a creationist but their cretique holds merrit- That is that biological origins are a mysterious enterprise indeed, one that seems not to obey any simple natural pattern (like gravity, or the dependable action of a clock). Yet, while change falls within probabilistic rejection regions- CSI does not. The universe therefore seems to have “a mind” of its own- in analogy, it largely adheres to physical laws yet is capable of generating complex specified novelty whenever it feels like it- all at once or slowly over time. The biological clock is somewhat useful or helpful in the sense that it helps us to form a better estimate of rejection regions though this is an issue of probability not of time lines. The real question that gets barried underneath of all the metaphysical imagery is that of “origins”- not of the choatic “general” rate of biological deterioration, erosion or change- But of a very specific change. The formation and diversification of “complex specified information” and it’s root causes. A clock, lest we forget, as a tool ammounts to what we call in philosophy “a circular thought” and in the case of a biological clock that is merely a theory based on little evidence- what we have is “a circular argument.” A clock spins around endlessly- or- it starts at a novel cause or location (12 oclock). NOTHING in the biological clock work theory of change will give us this starting point- and this is in essence why the theroy is lame. No ammount of change variation can probabilisitically give you novel CSI and to use probabilities and disguise them as “a clock” is merely to point out the obvious implications of a preconcieved notion- i.e. DE through retrospect. A prediction is always right when we are guessing the past! But clocks are supposed to move forward.

    In other words this clock is just another easy way to propagate a simplistic visualization that young students can impose on their already misconcieved image of history, to fill in the huge gaps, and ignore the contrary evidence-

    The clock is a vehical one can use to justify and facilitate the “just so story” board of Darwinian Evolution. Afterall, how can you argue with a clock, when it gets the answer to your question right twice a day-

    even when it’s broken.

  12. Robo, allow me to deconstruct the atheist’s rambling

    a “logical inference” which can’t be evaluated

    tell him he is wrong it can certainly be evaluated- poeple have posted cretiques to Dembski’s design inference by the hundreads. If it couldn’t be evaluated no one wold have tried to destroy it. By the way they all to date have failed. Tell him his is confusing towo things. Provability with evaluation. No ID can not be disproven because a designer can create a universe that is meant to fool people into thinking it is not designed or that there is no evidence for design. Therefore, you never can KNOW for sure is there is NOT a designer involved. Now “the design inference” can still be scientifically proven wrong if people can disprove its premises- you see the design inference deos not just say it was designed- it shows us how we reach a design inference’ That is why IT IS SCIENCE. It is a methadology. If you can puncture holes in the methedology then you can make design inferencing scientifically unfruitful. For example if you could show that archaeology is in fact unscientific becasue you can know with any good probability whether somthing is or is not designed, then you can get rid of design inference. But the point is that we know that useing the design inference is highly predictive and therefore very scientific. The fact that it hasn’t been falsified as a useful tool, does not mean that it couldn’t be.

    ID inferencing is almost always right. We know mount rushmore was designed without knowing when or who it was designed by. Look at the example of SETI for a clear cut example. Now there are cases that sit in the middle. ID is not perfect it can be wrong from time ot time- though it is usually right. This is why Dembski’s book he Design Inference sits in the library of congress under the section Probabilities and Mathematics- not religion.

    What ID is now trying to get at is the ultimate question of biological and cosmological origins. In other words is DNA designed? Are the machines in the cell designed? The predictive power of ID where it can be varified with tools- or computer codes or sculptures etc- shows that it is a very powerful tool- and more importantly the method it uses to detect design reaches almost certainty when we apply it to biological systems and the laws and structure of the known universe. If it works almost all of the time then how have we not evaluated its usefulness or scientific relevance? and, if it works so well in all of the cases where it is varified to be correct then why not infer design in the cases where varification is not yet possible? There is no reason – that is why people are so sure about ID’s predictive power and it’s implications for the study of origins.

  13. In short he is saying that we should suspend judgement when we are asking questions about what we dotn know for sure. But science is about explaining answers to questions that we dont know for sure. He is trying to reject the nature of science because at this time (unlike in darwin’s days and up until recently) the science doesnt support his world view. Too bad for him, tell him to get over his idiological bias when he wants to partake in discussions about sicence. If the evidence pointed to their being no designer he would certainly say that “we should fallow the evidence where it goes and the facts are it points away from God.” then he’d say “you can beleive in anyhting you want but we cant teach religious faith in public schools.” Unfortunatly now he is the one displaying the religious faith (or anti- religious faith) and you know this becasue his argument is “lets not fallow the eividence when we dont know absolutly for sure.” Science is not about knowing knowing things for sure- if it was we wouldn’t tech the THEORY of the evolution in schools because it IS NOT A FACT.

  14. Frost et al,
    I think a few of you guys aren’t clear on what a ‘molecular clock’ is. It’s certainly nothing to do with ‘Darwin’s clock like evolution’ or the topology of a cytochrome-C phylogeny.

    A molecular clock is actually just the observation that the number of neutral (so ultra-conserved genes don’t worry us either) mutations that have become fixed after two species diverge increases at an approximately constant rate. If we can calibrate this rate (with fossil or biogeographic data for instance) for a particular split then we can estimate the time since that split occurred.

    There are of course lots of tricks in applying such clocks, and these are usually talked about, and thought about, before they are applied.

    Bob H is right that the having the wrong rate of molecular evolution (the wrong clock) won’t mess up the topology of a tree at all (just the branch lengths) so CytC is no message from the designer. If there are lineages with different rates of molecular evoultion in a single dataset then you can run into problems but thankfully new methods, notably Bayesian phylogenies, allow multiple rates of evolution to included (and, in fact, estimated) in a single analysis.

  15. atavism, the point you miss is that the theory’s usefulness is predicated on the false presuppostion that mutation “time lines” CAN give you complex specified information. And they cant. As far as simple variance between species a totally agree- what we call mico evolution-

    From the student’s text book part-

    Over the course of millions of years, mutations may build up in any given stretch of DNA at a reliable rate.

    This would infact invalidate the concept of Darwinian Evolution becasue it would show non-random variation. Yet, desipte the appearent usefulness for of the thery for ID the fact remains that mutations till need the imgainary MILLIONS OF YEARS to generate SC diversity- even if the mutations are purposive! The evidence that this is happening as the article points out is skimp- and i remind you “highly unlikely”.

  16. Also I used darwin’s clock to invalidate the concept of a clock like fossil record or timeline- you see Darwin got himself into a real logical contradiction when he devised a theory that said everyhting happens in a logical limeline but … it all happened randomly. I mean what a rediculous theory! Now they are looking for evidence of teleological processes with purpose just to validate their efforts to stitch together the broken fossil record. While they are differnt concepts they ultimatly apply to the same thing and are therefore inextricably linked.

  17. Frost122585 –

    atavism, the point you miss is that the theory’s usefulness is predicated on the false presuppostion that mutation “time lines” CAN give you complex specified information.

    Huh? I’ve never seen that claimed in the molecular clock literature. Can you show me where it’s stated?

    Bob

  18. Bob, its sused to support the standard theory of evolution- i cant find a copy of ther work online right now- but my point is that mutation is not shown to produce CSI- so the only place where the thoery could work is among simple viriation among species- but the evidence for a stochasitc clock is not only skimp but as i pointed out its illogical-

    can you show me where in the literature its stated that the theory is not trying to explain evolution of universal common ansestry? Or can you show me in the literature where the authors clearly state that the theory cant account for CSI?

    My point is an implicit one- I wish i had a copy of the original theory though.

  19. That said, one could argue that if the flagellum fell as a case, there would just be another candidate for irreduceable complexity.

    You have this backwards. If you can provide even one case where you can show IC evolved naturally, IC ceases to be a barrier evolution can not cross.

    Dembski’s Specified Complexity case is more easily falsifiable than Behe’s IC case in that a single example of specified complexity (exceding the Universal Probability Bound) which is developed through truly non-directed means is all that is needed to falsify SC.

    Take ten decks of cards (including the jokers), shuffle 1000 times, and there are more than 10^1200 possible outcomes. Beating the the UPB is simple. The issue is the “specified” part, and I have seen no test to tell whether a given 540-card deck is “specified” or not based upon the order of the cards in the deck.

    As this would require an average in excess of one mutational event per year, it should be provable.
    At current known rates of random replacement mutations in the genome, every human will be born with some 5-13 of them, IIRC. So, that does not seem too much of a barrier.

    Alas, each of these theories in the ID class falsifies the RV+NS hypothesis.

    Technically, none of those hypothesis are in the ID class, they are arguments about evolution. An argument in the ID class would be one that provides some effect or measure of ID.

    In addition, since there are some 10-15 different processes that cause inheritable variation in an organism and at least three more that affect the selection among these variations, making claims about RV+NS will not affect evolutionary theory as a whole.

  20. one brow, you have no idea what you are talking about. Evolutionary theiry as we all know it is the Darwnian vrsion that says two tings- one, everything evolves via mutations and coption and two, it is all random-

    The second part is the philosophical attachment that ID hates- Intelligence is defined scientifically in one sense as being about to match ends to means– pick a goal then make it happen and this is why and how an ID can produce specified complexity-

    Darwin was a fool becasue he wanted to account for a very logical theory of all things being connected but say that is all happned randomly- this is illogical and improbable-

    Irreducible complexity is a major problem for evolution and it in effect a positve case for ID–

    the reason why is that ID is the antithesis of DE. Why? Becasue DE was invented to replace theistic creationism and paleo- ID. In this world there are only two natrualistic explanations- one is methedological materialism and the other is Intellgient Design. Anyting that counts against one counts for the other.

    And how you can call specifeid compelxity just a problem for evolution is beyond me. It is at the heat of THE DESIGN INFERENCE. This is the methedology whereby we infer design- not rule out DE but INFER ID (positive).

    Read Denton’s book sometime and you might well realize that Evolution is A Theroy In Crisis.

  21. Please read this for the indepth cretique of DE and the POSITIVE case for design-

    http://www.discovery.org/scrip.....38;id=2177

  22. Evolutionary theiry as we all know it is the Darwnian vrsion that says two tings- one, everything evolves via mutations and coption and two, it is all random-
    Well, the biology blogs I have been reading discuss some 10+ ways of inducing change and at least three methods of selection. Of course, if by “mutation” you mean “any change at all”, you’re statement is correct, but its not very useful.

    The second part is the philosophical attachment that ID hates- Intelligence is defined scientifically in one sense as being about to match ends to means– pick a goal then make it happen and this is why and how an ID can produce specified complexity-
    Well, scientifically, that sense of intelligence is only useful if you what the end (goal) is. You can measure the intelligence in mice in a maze because you know their goal is to get the food. By your own words, you can’t determine intelligence unless you state the goal up front. As far as I know, ID does not state the goal of this intelligence.

    Darwin was a fool
    How unkind, and apparently untrue.

    this is illogical and improbable-
    Illogical and improbable things happen every day. The order of cards in a well-shuffled deck is neither logical nor probable.

    Irreducible complexity is a major problem for evolution and it in effect a positve case for ID–
    I disagree, and see no reason that it should be.

    In this world there are only two natrualistic explanations- one is methedological materialism and the other is Intellgient Design.
    Methodological materialism is not an explanation at all, it is a process used for finding explanations. Alternatives processes would includes supernatural searches, decision by revelation or fiat, and blind guessing.

    And how you can call specifeid compelxity just a problem for evolution is beyond me. It is at the heat of THE DESIGN INFERENCE.
    The Design Inference is a based upon knowledge of the goals of the supposed designer. Until Intelligent Design has advanced to the point where you can look internally at an information string and make a design inference based upon the string alone, ignoring it’s surroundings, it will never function without a knowledge of the goals of the putative designer.

    Read Denton’s book sometime and you might well realize that Evolution is A Theroy In Crisis.
    I might instead recognize that the book makes unconvincing arguments.

    Thank you for the link, I have read it before.

  23. Bob O’H:

    You’re mis-understanding the molecular clock. It applies to rate of mutation, not the topology of the tree. So, an imperfect molecular clock will still give the right tree, but with branch lengths incorrectly estimated.

    I understand perfectly. The cytochrome C molecule shows both the tree and the branch lengths being correct! Ie, take any two members of the animal kingdom, and compare their molecular distance from any member of the plant kingdom and the distance will be the same. The distance between a pea and a mosquito is the same as a pea and me. Take any two vertibrates and compare their molecular distance to an invertibrate, and you will find that they are the same. Ie, the distance between a trout and a flea is the same as the distance between me and a flea.

    The fact that the cytochrome C gene is both a tree and a balanced tree requires either designer’s intention or a perfectly ticking molecular clock. All recent findings relative to the molecular clock hypotheis is that the clock does not tick perfectly. The speed of the clock is clearly influenced, for instance, by the generation rate of the organism in question. As such, the molecular clock hypothesis will not render the balanced tree seen in the cytochrome C gene.

    Don’t believe me, get Denton’s book and read it. He discusses the molecular clock hypothesis as it relates to the cytochrome C very clearly.

  24. Frost,

    I’m afraid you still don’t quite get it. The molecular clock is a tool for timing the age of splits between lineages. That is all. It’s not a mechanism for the introduction of information into systems. The text you quoted is actually the rather uncontroversial claim that if mutations have a small chance of occurring in each generation then over many generations mutations (with or without benefit) will accrue.

    bFast,

    Ah, what you’re talking about is an “ultramteric” or highly clock like tree. And it’s much easier to answer questions because what you say Denton says is not true. You can go and get the some cytC sequences from NCBI (http://www.ncbi.nlm.nih.gov/sites/entrez) and check it out yourself. (the differences from a completely clock-like tree are due to some of the things you talk about and because the molecular clock is probalistic, much like an atomic clock, so has a certain degree of slop. So, no, no copyright notice there.

  25. One Brow, sorry a havent had time to respond- here is a quick one as im short on time-

    None of your responses to my comments are worthy of reply because you merely asserted things are failed to explain how TDI is not a positive case for design. But don’t feel bad, being wrong is a rough disposition to be in.

    A deck of cards being shuffled is not in the slightest illogical- we know how and what is going on- and moreover it requires an ID because cards have information value and are designed by humans that is what makes them Specified. A mountain forming for example is improbable as a whole but has no specificity or complex function that can be understood in a purposive intellectual way. As an end it matches no purpose by which we can certainly say an intelligent agent would have designed for. A car or a computer program or a watch is however clearly designed.

    Darwin was a fool because unlike the shuffling of cards by intelligent agents – the formation of genetic code cannot be mathematically random yet his tree of life required a highly organized purposive agent. I would point you to no free lunch but I can tell from your last response that you are already very familiar with all of the literature and are simply intent on rejecting the concept of intelligence a priori- what a pitty. I predict you wont be with this blog for very long. Darwin was wrong. Face it. And so are you. Evolutionary theory has moved on from the days of the Cambrian explosion which showed evolution must happen quickly- which is the antithesis of Darwin’s prediction of slow gradual change over long periods of time. I wont debate the facts with you- but feel free to religiously believe whatever you like. The nature of the biological clock is a way of trying ot formalize evolutionary change in a way that makes CSI seem likely. If there is a evolutionary clock than evolution is not random be definition but if there is no dependable clock we are only dealing with probabilities and it still is not random but it is even less likely to account for CSI because it would have no dependable driving force.

    Now methodological materialism is ultimately an explanation because whether all things evolved from common ancestry or not – that is merely a description of what happened. It does not tell us what moved and cause the changes. It could be god therefore you have theistic evolution. But if you believe that all of the answers are to be found within the physical stuff of this reality you then explain everything through chance and necessity. If on the other hand you are an intelligent person and can see that the universe is more than matter and has laws- then you have to explain where the laws and SC came from. In that case you have only one known option. We call it ID.

    As far as intelligence and goals are concerned- we as human being know what ends we want to accomplish and it allows us to design things loaded with huge amounts of SC. Unfortunately no natural unintelligent process has be show to produce SC. None. Therefore we conclude that biological examples of SC requires a process that is not only intelligent but capable of design.

    The design inference is once again A POSITVE CASE FOR DESIGN because it defines what design is and how we infer it. Sorry, your wrong and that you fail to deny this is merely a testament to you absolute bigotry.

  26. None of your responses to my comments are worthy of reply
    Yet, I am reading a reply.

    because you merely asserted things are failed to explain how TDI is not a positive case for design.
    Perhaps, had you read my post more carefully, you would realize that I agreed with you a design inference would be possible under certain conditions that you yourself laid out (knowledge of the goals of the designer), but that so far the ID movement has not met the stadard you described.

    But don’t feel bad, being wrong is a rough disposition to be in.
    How fortuitous for me that I am not wrong.

    A deck of cards being shuffled is not in the slightest illogical- we know how and what is going on- and moreover it requires an ID because cards have information value and are designed by humans that is what makes them Specified.
    I believe, if you will check the literature on information more carefully, you will find that is not what is printed on the individual card that carries information referenced by CSI, but rather the order of the cards in the deck. This is true whether you refer to Shannon or Kolmoogorov-Chaitan theory.

    A mountain forming for example is improbable as a whole but has no specificity or complex function that can be understood in a purposive intellectual way. As an end it matches no purpose by which we can certainly say an intelligent agent would have designed for. A car or a computer program or a watch is however clearly designed.
    One could argue that mountains serve the very useful function of altering the weather patterns of the world. Does that suddenly make them designed?

    We think of a car or a computer as designed because of their simplicity, not their purpose.

    Darwin was a fool because unlike the shuffling of cards by intelligent agents – the formation of genetic code cannot be mathematically random yet his tree of life required a highly organized purposive agent.
    The genetic code isn’t random, because natural selection and sexual selection are not random forces. So, your claim of foolishness appears to be unfounded.

    I would point you to no free lunch but I can tell from your last response that you are already very familiar with all of the literature and are simply intent on rejecting the concept of intelligence a priori- what a pitty.
    As I have said before, I’m perfectly open to the concept of intelligently designed things where it can be demonstrated, including the genetic code. However, so far ID has not even come up with a set of goals for this designer, which you yourself said was needed.

    I predict you wont be with this blog for very long.
    What will be, will be.

    Darwin was wrong. Face it. And so are you.
    I would never try to stop you from holding that opinion.

    Evolutionary theory has moved on from the days of the Cambrian explosion which showed evolution must happen quickly- which is the antithesis of Darwin’s prediction of slow gradual change over long periods of time.
    I was not aware that we had a definitive listing of pre-Cambrian life forms, nor that 80 million years, or even 30 million, was considered “quickly”.

    I wont debate the facts with you-
    Then we will have little to discuss.

    but feel free to religiously believe whatever you like.
    Thank you.

    The nature of the biological clock is a way of trying ot formalize evolutionary change in a way that makes CSI seem likely. If there is a evolutionary clock than evolution is not random be definition but if there is no dependable clock we are only dealing with probabilities and it still is not random but it is even less likely to account for CSI because it would have no dependable driving force.
    What is the amount of CSI in the genome of a human, or a malarial parasite? Can you give me a number of the measure? Is it within the reach of 1000 gene-duplication events?

    Now methodological materialism is ultimately an explanation because whether all things evolved from common ancestry or not – that is merely a description of what happened. It does not tell us what moved and cause the changes. It could be god therefore you have theistic evolution.
    Methodological naturalism would not be able to tell the difference between theistic evolution and undirected evolution, correct.

    But if you believe that all of the answers are to be found within the physical stuff of this reality you then explain everything through chance and necessity.
    Another possibility is that you accept chance and necessity even when you have no direct explanation.

    If on the other hand you are an intelligent person and can see that the universe is more than matter and has laws- then you have to explain where the laws and SC came from. In that case you have only one known option. We call it ID.
    Many intelligent people feel that we need to go no further than matter to explaing where the laws of matter come from.

    As far as intelligence and goals are concerned- we as human being know what ends we want to accomplish and it allows us to design things loaded with huge amounts of SC. Unfortunately no natural unintelligent process has be show to produce SC. None. Therefore we conclude that biological examples of SC requires a process that is not only intelligent but capable of design.
    Again, you have pointed out the need for knowledge of goals in order to determine SC exists. Has the ID movement put forth a list of goals for its putative designer? If not, you don’t have a purpose, so you don’t have the specification of CSI.

    The design inference is once again A POSITVE CASE FOR DESIGN because it defines what design is and how we infer it.
    I never claimed otherwise. I just noted you were missing a component that you yourself pointed out was needed.

    Sorry, your wrong and that you fail to deny this is merely a testament to you absolute bigotry.
    I am fairly sure you don’t know me well enough to have any authority in your claim that I am a bigot.

  27. one brow said

    “You have this backwards. If you can provide even one case where you can show IC evolved naturally, IC ceases to be a barrier evolution can not cross.”

    This nonsense. If a particular alleged case of IC can be shown to have evolved naturally it says nothing about the other cases. This particular case is no longer IC. The other cases are completely independent. The opposite is what is true. If there is one case standing that has no means of natural evolution then it is still IC and the concept is still valid.

    Now for practical purposes, if 20 cases of IC have been proffered and say 5-10 have been shown to have evolved naturally then the argument would be mute. The argument could be used that the others will fall and it is just a matter of time. But if not one has fallen, then the argument gains strength over time.

    As far as I know not one has fallen yet. There has been a lot of wild speculation but no proof. But proving that one is not IC says nothing about the concept in general or the other cases.

  28. one brow (#26): “I was not aware that we had a definitive listing of pre-Cambrian life forms, nor that 80 million years, or even 30 million, was considered “quickly”.”

    The actual period involved was much shorter than you seem to think. From Valentine, 1995, Late Precambrian Bilaterians: Grades and Clades: “The application of absolute dates to the boundaries of the stages of the lower Cambrian remains a difficult stratigraphic problem, but it is likely that the most critical stages, the Tommotian and Atdabanian, are probably only 8-10 [million years] in duration; over 50 metazoan orders first appear in the [fossil] record during that interval.”

    You imply that the duration of the Cambrian Explosion is not really “quick”. From a review article by Valentine, Jablonski and Erwin (1999); Fossils, Molecules and Embryos: New Perspectives on the Cambrian Explosion: “Understanding the events surrounding the Cambrian explosion remains a major challenge. ….Among the chief challenges of the Cambrian explosion are to understand the evolution of the developmental systems…., to find the reason(s) that so many different lineages produced novelties in such concert, and to understand why the explosion was such a brief episode rather than constituting an ongoing flood of major novelties.”

  29. One Brow, at 26:

    Re:

    The genetic code isn’t random, because natural selection and sexual selection are not random forces.

    –> The usual expression is RANDOM VARIATION + Natural Selection [RV + NS]. Namely that the DNA code is held to initially vary at random — as opposed to based on natural regularities resting on inter-atomic forces or the like [cf Kenyon and his abandonment of the biochemical predestination thesis of his work by that name, based on Bradley's studies], or intentional actions of agents.

    –> NS can indeed “explain” the survival — on average — of the fittest [most often by eliminating unfit variations and stabilising a population], based on the deleterious effects of most random variation by mutation of one form or another.

    (I exclude variability due to the range of genetic factors and genes that allow for a range of diverse features in a population. This can for instance lead to microevolution by elimination of variability in a sub-population, or by re-infusion of said variability. The features of Caribbean people as the various races mixed it up are a case in point. I recall the reaction of a dentist when he first saw certain features in my teeth that are characteristic of indians, for instance. I have predominantly african features, with others that are recongisabley caucasian and indian. Caribbean exotic beauties who often do so well in contests are one result of this. But note, we are reshuffling information inthe population, not generating it de novo, at least in any truly significant, body-plan innovation level.)

    –> But, equally, is has nothing to say to their arrival as functionally viable organisms with body plans and cellular functions based on DNA-coded functionally specific complex information well beyond the Dembski universal probability bound.

    –> Thus, RV + NS is unable to address competently and in technical details, body-plan level biodiversity, starting with say the Cambrian life revolution in the fossil record. [Where did the credibly 100 mn base prs of incremental information-carrying capacity for the innovation of say an arthropod, come from?]

    –> Next, on origin of life we note that it is generally estimated that 300 – 500 thousand DNA base pairs is is the requisite for a minimally viable unicellular organism. Thus, origin of life models have just as impassable an information hurdle that they have not properly addressed. [Cf my always linked through my name for an intro level discussion of this and the previous issue.]

    –> Next, I take issue with the characteristation of NS as being a FORCE. it is a result: in a given environment, some organisms are able to arrive, survive eat and reproduce better than others, so they tend to dominate the population. That is a result, not a causative force.

    –> Finally, NS is in significant part a statistical result, i.e it is inescapably in major part random. Thus, for instance so humble and reliably darwinist a source as Wiki notes on NS:

    . . . Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. If these phenotypes have a genetic basis, then the genotype associated with the favorable phenotype will increase in frequency in the next generation.

    –> the highlighted tells the tale.

    GEM of TKI

  30. one brow (#19): “Beating the UPB is simple. The issue is the “specified” part, and I have seen no test to tell whether a given 540-card deck is “specified” or not based upon the order of the cards in the deck.”

    If specified complexity were actually in principle not quantifiable or measurable, then science would have nothing real to say about it. For metaphysical naturalists this means it doesn’t exist. But observation of living organisms reveals huge amounts of ordered complexity which can be roughly measured and compared, organism to organism. A man has more than a mouse and a mouse has more than an amoeba and an amoeba has more than a bacterium. This is common sense aided by intuition.

    I will quote Dembski on specified complexity: “Life is both complex and specified. The basic intuition here is straightforward. A single letter of the alphabet is specified without being complex (i.e., it conforms to an independently given pattern but is simple). A long sequence of random letters is complex without being specified (i.e., it requires a complicated instruction-set to characterize but conforms to no independently given pattern). A Shakespearean sonnet is both complex and specified.”

    The first component of specified complexity is great improbability given the total sequence space. This is the criterion of complexity, which is another term for the amount of Shannon information. The second component in the notion of specified complexity is the criterion of specificity. The idea behind specificity is that not only must an event be unlikely (complex, high Shannon information), it must also conform to an independently given, detachable pattern.

    Specified complexity is a characteristic that can in principle also be scientifically quantified and measured. Leslie Orgel used the term specified complexity (meaning much the same thing) in his book The Origins of Life (1973): “Living organisms are distinguished by their specified complexity. Crystals fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.” Charles B. Thaxton discussed the quantification of specified complexity in his book From The Mystery of Life’s Origin: Reassessing Current Theories (1984). He points out that “…only certain sequences of amino acids (out of all randomly possible) in polypeptides and bases along polynucleotide chains correspond to useful biological functions. Thus, informational macro-molecules may be described as being and in a specified sequence.”

    So the concept of specified complexity has a seriously considered history in science.
    In principle it can be measured, because there is a general relationship between information and entropy. Thaxton goes on to say “If we want to convert a random polymer into an informational molecule, we can determine the increase in information (as defined by Brillouin) by finding the difference between the negatives of the entropy states for the initial random polymer and the informational molecule.” Brillouin information is closely related to Shannon information.

    This shows that specified complexity is not purely subjective but is as intuition tells us, an objective indicator. For amino acid polymers this is of how tightly the physical system must be constrained (specified) in order to obtain a functional protein.

    one brow (#22): “The Design Inference is a based upon knowledge of the goals of the supposed designer. Until Intelligent Design has advanced to the point where you can look internally at an information string and make a design inference based upon the string alone, ignoring it’s surroundings, it will never function without a knowledge of the goals of the putative designer.”

    The presence of specified complexity is a reliable empirical marker of design of some sort. To detect the presence of specified complexity does not require knowledge of goals or purposes of that design, just that it is improbable (complex) and patterned (specified).

  31. 31
    xcdesignproponentsists

    bFast:

    No, a copyright notice to show that the design was designed — the signature of the designer. I see the pattern in the Cytochrome C as the equivelant of the patterns that are being sent to outer-space (prime numbers, etc.) to indicate that the signal is from an intelligent, rather than random source.

    So evidently you are not only able to posit the existence of a Designer, but you have somehow have sufficient evidence to make inferences about his/her/its character. Apparently, he/she/it likes leaving messages in genomes that would have gone unnoticed for millions of years of human existence.

  32. One Brow,

    “One could argue that mountains serve the very useful function of altering the weather patterns of the world. Does that suddenly make them designed?”

    As with almost anyhting in life there are cases that fall into the grey area. The point is that as design theorists we infer design only when the sample and evidence reaches the point when we can say for sure that there is specificity. Now the parameters change depending on what kind of a situation and sample we are dealing with. Take SETI (search for extraterestrial intelligence) they will infer design or aline life if they get a highly improbable arrangement of radio pulses or waves that ARE IN A SPECIFIED PATTERN. How do they define such a pattern – well they look at what we know about what Darwin called THE PRESENTLY ACTING CAUSE of intelligence- look at computer programs and high tech machinery. We see such machinery in the cell and see super highly improbability and we go AHA! Design. Its really quite simple i cant see where you confusion comes in. This also goes along way to explaining your question of “what are the ends? Well, if we see SC and it is with in a living organism we can deduce that its there to help the thing live. I mean is this really that mysterious? Why are cars an example of intelligently designed ends to means? Beause they (like most technology) help to facilitate the extension of the human life. They did’t get there by accident either- we can presently see the intelligence acting in their construction.

    As I have said before, I’m perfectly open to the concept of intelligently designed things where it can be demonstrated, including the genetic code.

    It sure doesn’t seem like it.

  33. Atavism:

    bFast,

    Ah, what you’re talking about is an “ultramteric” or highly clock like tree. And it’s much easier to answer questions because what you say Denton says is not true. You can go and get the some cytC sequences from NCBI (http://www.ncbi.nlm.nih.gov/sites/entrez) and check it out yourself. (the differences from a completely clock-like tree are due to some of the things you talk about and because the molecular clock is probalistic, much like an atomic clock, so has a certain degree of slop. So, no, no copyright notice there.

    I find it personally frustrating when the links provided call for a financial investment on my part. Now, Denton certainly renders a very small part of the cytochrome C molecular tree, but his data does show some amount of “slop”. His data does how, however, an absolute inability to estimate a branch’s generation time (time from birth to offspring) by studying the cytochrome C tree. Everything that I have read about the molecular clock says that its rate is directly subject to generation time. As such, the cytochrome C molecule should be useful as a tool for estimating that time. Rather, the portion of the cytochrome C that Denton rendered, though it shows “slop”, does not show generation time.

    Two possibilities exist, as far as I can see. One is that Denton has been dishonestly selective about the branches of the tree that he rendered, and the other is that the cytochrome C gene does not provide an indication of generations. If the latter is the case, then the molecular clock, as currently understood by science, does not explain the cytochrome C.

    I add to this the recent discovery of 250 mya bacteria. Bacteria 250 million years ago should render significant differences from modern bacteria in genes where the molecular clock ticks. My understanding is that it does not. My understanding is that the lack of motion of the molecular clocks has caused the scientific community to seriously question whether the found bacteria is really 250 million years old — even though new finds have been discovered about 5 times, and significant care has been taken to assure that the found bacteria would not be contaminated by modern bacteria.

  34. This article seems on topic:

    http://www.arn.org/blogs/index....._evolution

    “The older molecular dates would predict an abundance of long branches, and a long delay of diversification within each long branch after a branch’s origin. However, studies using morphological data of both fossil and extant taxa demonstrate that there are few or no such lineages with a long evolutionary lag time. This discrepancy is so systemic and widespread that it cannot be explained by the difference between minimum age constraint (represented by actual fossils) and the timing of origin that can be hypothetically estimated by molecules in marsupial and placental evolution.”

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