Uncommon Descent Serving The Intelligent Design Community

Another windy day in the junkyard …

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From Jason Palmer at BBC News (19 May 2011), we learn, “Protein flaws responsible for complex life, study says.” This time mistakes produce more functional proteins:

Tiny structural errors in proteins may have been responsible for changes that sparked complex life, researchers say.A comparison of proteins across 36 modern species suggests that protein flaws called “dehydrons” may have made proteins less stable in water.

This would have made them more adhesive and more likely to end up working together, building up complex function.

Remarkably, we read,

Natural selection is a theory with no equal in terms of its power to explain how organisms and populations survive through the ages; random mutations that are helpful to an organism are maintained while harmful ones are bred out.But the study provides evidence that the “adaptive” nature of the changes it wreaks may not be the only way that complexity grew.

Natural selection is a theory with no equal – in terms of much belief and little evidence. But it can be supplemented by tiny structural errors that somehow produce co-operation.

The authors suggest then that other adaptations occur that “undo” the deleterious effects of the sticky proteins.

Convenient, that.

Fred Hoyle, wherever you are, check your mail: Your Boeing 747 is ready.

Isn’t this the sort of mess that Steve Fuller says “floored astrology”?

Comments
Elizabeth you stated: 'Obviously our starting points are very different, so I do understand that it must be difficult to see my position as anything other than “suspect”.' Elizabeth, besides materialism being shown to be false by science, you can't even justify doing science, in the first place, with your materialistic 'starting point', so why in blue blazes should I see your 'starting point' as anything other than 'suspect'??? "Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth. As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain." Creation-Evolution Headlines http://creationsafaris.com/crev201102.htm#20110227a This following site is a easy to use, and understand, interactive website that takes the user through what is termed 'Presuppositional apologetics'. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place. Proof That God Exists - easy to use interactive website http://www.proofthatgodexists.org/index.php Nuclear Strength Apologetics – Presuppositional Apologetics – video http://www.answersingenesis.org/media/video/ondemand/nuclear-strength-apologetics/nuclear-strength-apologetics John Lennox - Science Is Impossible Without God - Quotes - video remix http://www.metacafe.com/watch/6287271/ Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place: Dr. Bruce Gordon - The Absurdity Of The Multiverse & Materialism in General - video http://www.metacafe.com/watch/5318486/ Can atheists trust their own minds? - William Lane Craig on Plantinga's evolutionary argument against naturalism - video http://www.youtube.com/watch?v=byN38dyZb-k "But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881 ====================== The Failure Of Local Realism - Materialism - Alain Aspect - video http://www.metacafe.com/w/4744145 The falsification for local realism (materialism) was recently greatly strengthened: Physicists close two loopholes while violating local realism - November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show - July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm --------------------- etc.. etc.. etc..bornagain77
June 5, 2011
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Well, if we are talking about my worldview, ba77, I'm not really sure what to offer. I'm not sure what aspect of it you think I have zero evidence for. In fact, I'm not even sure what you think my worldview is! But as I said, the evidence that the human genome is not deteriorating is the simple evidence that the human population is rapidly increasing!Elizabeth Liddle
June 5, 2011
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Elizabeth, you cannot appeal to evidence that fits just as easily within the theistic worldview to support your own materialistic worldview. You must use direct empirical evidence to make your case for neo-Darwinism, So thus once again I remind you that you simply have ZERO empirical evidence to support your worldview!! notes: The evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders. Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens." I went to the mutation database website cited by John Avise and found: HGMD®: Now celebrating our 100,000 mutation milestone! http://www.biobase-international.com/pages/index.php?id=hgmddatabase I really question their use of the word 'celebrating'. This following study confirmed the detrimental mutation rate for humans, of 100 to 300 per generation, estimated by John Sanford in his book 'Genetic Entropy' in 2005: Human mutation rate revealed: August 2009 Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome. (Of note: this number is derived after "compensatory mutations") http://www.nature.com/news/2009/090827/full/news.2009.864.html This 'slightly detrimental' mutation rate of 100 to 200 per generation is far greater than even what evolutionists agree is an acceptable mutation rate for an organism: Beyond A 'Speed Limit' On Mutations, Species Risk Extinction Excerpt: Shakhnovich's group found that for most organisms, including viruses and bacteria, an organism's rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material. http://www.sciencedaily.com/releases/2007/10/071001172753.htm Even if a truly beneficial random mutation/variation event to the DNA ever did occur, ignoring the fact that that the DNA doesn't solely control encoding for body plans, the 'beneficial mutation' would still be of absolutely no use for a Darwinian scenario because the mutation would be swallowed in the vast ocean of slightly detrimental mutations which are far below the culling power of natural selection to remove from a genome. these following studies make this point clear: Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Kondrashov A.S. http://www.ingentaconnect.com/content/ap/jt/1995/00000175/00000004/art00167 The Frailty of the Darwinian Hypothesis "The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,” http://www.evolutionnews.org/2009/07/the_frailty_of_the_darwinian_h.html#more High genomic deleterious mutation rates in hominids Excerpt: Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically (unusually) low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages. http://www.nature.com/nature/journal/v397/n6717/abs/397344a0.html High Frequency of Cryptic Deleterious Mutations in Caenorhabditis elegans ( Esther K. Davies, Andrew D. Peters, Peter D. Keightley) "In fitness assays, only about 4 percent of the deleterious mutations fixed in each line were detectable. The remaining 96 percent, though cryptic, are significant for mutation load...the presence of a large class of mildly deleterious mutations can never be ruled out." http://www.sciencemag.org/cgi/content/abstract/285/5434/1748 All life eventually succumbs to the effects of Genetic Entropy, but humans are especially vulnerable. As This following study reveals: Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally - September 2010 Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study). https://uncommondescent.com/darwinism/sanfords-pro-id-thesis-supported-by-pnas-paper-read-it-and-weep-literally/bornagain77
June 5, 2011
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ba77: Obviously our starting points are very different, so I do understand that it must be difficult to see my position as anything other than "suspect". That's OK, though - it just means that we have to be very careful to ensure that we are not comparing apples and oranges - that we are talking about the same thing when we each use certain words. In a Darwinian framework, as I tried to explain elsewhere, a "deleterious" allele/mutation is simply one that reduces your chances of reproducing successfully in the current environment. So, by definition, in a Darwinian framework, our Genome is, by definition, not deterioriating, because the human population, far from shrinking, is exploding! So in terms of reproductive success, our genomes have never been better. However, that doesn't mean we necessarily live as long (although I don't share Sanford's view of the validity of biblical data wrt to past life-spans), nor even that we have as many children (we don't), but that the net effect on the population, of our current genome, in this environment, is "advantageous". We are populating the world as never before. Nor does it mean that we are not more prone to genetic diseases (we may be) nor more resistant to infection (we may not be). Because of modern medical care, it is actually quite likely that those traits are increasing in our population, and from a certain point of view,that could be described as "degeneration". However, modern medical care is our current environment, and just as a broken vitamin C gene is not "deleterious" in an environment full of fruit, so decreased resistance to disease is not "deleterious" in an environment full of vaccines. I would note, of course, that mutations are extremely common. You and I possess a large number of de novo mutations in our genome. Most of these are harmless. Some may even benefit us. Rather more may be potentially harmful. But the emphasis must be on the "potentially". In the absence of the kind of life-threats our species faced even in the recent past (think how perinatal mortality has come down), any mutation that confers vulnerability to past threats will no longer tend to be "weeded out" by premature death. So in that sense, it is likely that our human genome is "deteriorating" i.e. in the sense that it is no longer well suited to, say, Victorian urban life. But we aren't Victorian urban dwellers! All that matters, in judging the "degeneracy" of a genome is whether, in the current environment, our population is shrinking or not. And sadly, for some populations, it is. Very small populations are at serious risk of extinction because of buildup of mutations that really do reduce the probability of successful reproduction in the current environment. But with the human population standing at 6.92 billion and climbing - well, that's my evidence that Genomes are not Deteriorating!Elizabeth Liddle
June 5, 2011
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Elizabeth, whatever you may think of Sanford's YEC position, the fact is that you cannot produce evidence that Genomes are not Deteriorating. Moreover it is very suspect that you would choose to ignore the extreme poverty of evidence for your very own worldview, while dismissing his solid empirical evidence for genetic deterioration. If you want to look at worldviews by all means let's put all cards on the table and see your materialistic worldview for the absurdity it really is!!!bornagain77
June 5, 2011
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Mung @ #66
Elizabeth Liddle:
I’m not clear why you don’t think the evidence that small incremental changes can have a large effect on body plans has no force.
Ok, let’s start with that. It was not my contention that changes to existing genes cannot have a “large” effect on existing body plans. I’d willingly grant that’s what Carroll shows. I just don’t see how it’s relevant. So to understand each other better we obviously need to concentrate on the latter half of that statement.
Cool.
I understand the context to be the question of the origination of body plans themselves. I don’t see how changing an existing gene, and showing how it effects an existing body plan, tells us anything at all about how body plans themselves came to be, nor how genes which have a large effect on body plans came to be. That’s what I mean when I say these arguments have little or no force. IOW, we can explain B, but what we can’t explain is A, where A is required for there even to be a need for an explanation for B. Does that help?
Yes indeed. I guess I was taking an example of a genetic account of a fairly radical change in body plan (and that research does contribute a response to a fairly frequently made challenge that Darwinian evolution can't account for major new features, which is the point I thought you were making). However, as you say, the research I cited does not address the whole issue of how multicellular organisms came into being (in a Darwinian framework), although there is research that does (or at least looks promising). None of this is my area of course, although I would argue, not a hundred miles away, neither, which is why I am an interested consumer of the research, being about systems biology, which is much closer to what I do. So I've read a number of interesting papers about it,and I'm trying to find some that aren't behind a paywall (having university access to journals is a huge boon, and I do hope that the trend for open access continues). The general approach seems to be that multicellularity evolved from populations of single-celled organisms that had evolved to live in colonies, which would have necessitated some kind of signalling. That in itself needs an evolutionary account of course (in evolutionary biology, all questions lead further back, of course!) but the idea is that once you have some kind of chemical signalling process i.e. a cell develops differentially depending on chemical inputs from either other organisms or the environment, you have the beginnings of the kind of cell differentiation we see in multicellular organisms. The earliest may have been no more than mats of floating cells, in which the outer organisms developed in a way that gave greater protection from the environment, leaving the inner cells to do something else. Anyway, there is one open access review paper here that you might like: http://people.vanderbilt.edu/~antonis.rokas/pdfs/2008_Rokas_ARG.pdf I hadn't actually read it, but it cites some papers I have read, which is how I found it.
In summary: What needs to be explained is: A. The origination of body plans B. The origination of gene regulatory networks C. The origination of genes which when changed have a large effect on A and B. How can C effect A or B unless A or B exist before C? But if A or B exist before C, what need is there of C?
I think a key concept here is "co-evolution". But, to be specific, gene-regulatory networks are likely to have evolved from the kind of signalling processes that enhance the survival chances of unicellular organisms - the kind of simple chemical signals that emanate from food or threat, and to which a particular physiological response is protective. Once you have that kind of system, you have the potential for incremental tuning of responses to signals that can potentially extend to between-organism signalling. So my hypothesis would be that the beginnings of B preceded A. However, B would also have had to have an effect on the development of the unicellular organism (by definition) in other words must have been some kind of switch mechanism that modulated gene expression. So there's a touch of C in there too. And once you have inter-organism signalling processes (the proximity of another organism modulates gene expression) then you have the potential for A. And once you have A, B's effects can affect both A and C. But, as I say, it's not my field. However, such a system would be easy enough to model, and would make testable predictions.
Now I will say this. I am willing to drop this entire line. Personally I prefer to concentrate on unicellular organisms.
Cool :) Yes, let's keep drilling backwards.
If you’re not willing to accept the modern cell as the starting point then you need to explain how we got from something else to where we are today.
Absolutely. Well, I'd be "willing" in principle to accept the "modern cell as the starting point" if it became impossible to explain how we got from "something else" to the modern cell. But that's a good reason to attempt to explain it!
My own personal area of interest is the cell membrane. If that interests you perhaps you could point me to some sources that explain how it evolved. If not, that’s ok too.
Yes indeed. The most promising approaches as far as I can see right now posit both a "self-replicating" spherical membrane (which is relatively easy to do, given the properties of lipids and their hydrophilic/hydrophobic poles) within a marine environment that is rich in polymers and other compounds. The most prominent researcher in this field, as you probably know, is Joe Szostak http://genetics.mgh.harvard.edu/szostakweb/ The core of his idea seems to be that self-replicating polymers trapped within lipid vesicles might differentially affect the rate of subdivision of the vesicle, leading to "selection" (i.e. greater prevalence) of those vesicles that "inherited" a particular configuration of polymer. But there are also other approaches. (Hey, I've just discovered that the editing marquee window here can enlarged! That might improve my proof-reading!)Elizabeth Liddle
June 5, 2011
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I'll wait until Sanford replies, I think, before I post the text of the email, I sent. But I did invite him to comment on the thread, so I'll keep checking there too!Elizabeth Liddle
June 5, 2011
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I wrote to him, btw, but I haven’t heard back.
Hey, that's great! I hope he'll respond. I am really interested in hearing what he has to say. I need to know if I need to stop claiming he meant one thing if he says he meant another! I would be immensely ashamed if BA77 turned out to be right and I was wrong, lol. Will you share which question(s) you posed?Mung
June 4, 2011
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Elizabeth Liddle:
I’m not clear why you don’t think the evidence that small incremental changes can have a large effect on body plans has no force.
Ok, let's start with that. It was not my contention that changes to existing genes cannot have a "large" effect on existing body plans. I'd willingly grant that's what Carroll shows. I just don't see how it's relevant. So to understand each other better we obviously need to concentrate on the latter half of that statement. I understand the context to be the question of the origination of body plans themselves. I don't see how changing an existing gene, and showing how it effects an existing body plan, tells us anything at all about how body plans themselves came to be, nor how genes which have a large effect on body plans came to be. That's what I mean when I say these arguments have little or no force. IOW, we can explain B, but what we can't explain is A, where A is required for there even to be a need for an explanation for B. Does that help? Would you like me to attempt to develop an analogy? In summary: What needs to be explained is: A. The origination of body plans B. The origination of gene regulatory networks C. The origination of genes which when changed have a large effect on A and B. How can C effect A or B unless A or B exist before C? But if A or B exist before C, what need is there of C? Now I will say this. I am willing to drop this entire line. Personally I prefer to concentrate on unicellular organisms. If you're not willing to accept the modern cell as the starting point then you need to explain how we got from something else to where we are today. My own personal area of interest is the cell membrane. If that interests you perhaps you could point me to some sources that explain how it evolved. If not, that's ok too.Mung
June 4, 2011
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Mung, me too, but you asked me for some examples from Carroll, which I didn't have to hand, so I gave you some papers instead, all of which give examples of genes, or gene regulatory network implicated in the evolution of diverse body plans by means of regulation of hox genes. Two of the citations I gave you are full text. I couldn't find an open access source for the other. As for the book - well, the whole book is about the role of hox genes and regulatory gene networks in specifying body plans. And right now, I'm not clear why you don't think the evidence that small incremental changes can have a large effect on body plans has no force. It seems to me it is the major message of Carroll's book, and I have given you three references in support. But then we seem to disagree with the message of Sanford's book too, so perhaps that is telling :) (I wrote to him, btw, but I haven't heard back). Anyway, the Averof 1995 Nature paper references an earlier paper in Current Biology, which is behind a firewall, unfortunately, but continues the story of investigating divergence in hox genes that led to crustaceans and arthropods. The Science paper (Davidson and Erwin 2006) is about the role of Gene Regulatory Networks, and reports evidence suggesting that these were laid down prior to the diversification and placed strong constraints on evolution of new body plans down that lineage (hence their bilateral ground plan). The other Nature paper (Ronshaugen et al, 2002) reports evidence for "that links naturally selected alterations of a specific protein sequence to a major morphological transition in evolution", again the divergence of insects from the line that would become crustaceans.Elizabeth Liddle
June 4, 2011
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Elizabeth, with respect, I try not to play the "here, read all these links and maybe you'll find something in them that makes the point I'm trying to make" game. Do you have something specific in mind from one of these? Make it one that I can access for free, please. And like I said, I have a copy of the book. If you can just tell me what to look for. Perhaps something specific that you remember that stuck out in your mind. I've told you that I think it does not cease to have force, perhaps you can explain why you think it does for you.Mung
June 4, 2011
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No, Mung, I don't think that a small tweak to a gene in an existing organism can make it, for example, become an arthropod rather than a vertebrate. It's not what I'm claiming, and I apologise if you misread me. What I am claiming is that findings in "evo-devo" show us that genes are hierarchical, and that the same genes, in creatures with radically different body-plans, are nonetheless key to those body plans, and how they develop depends, as you say, on "switches". And no, I'm not "just spouting talking points". Why on earth would I? If something I say doesn't make sense to you, I'm only too happy to try to clarify. I can't actually find my copy of Endless Forms right now (I think it is buried in my son's bedroom somewhere) so I can't give you a citation that I can guarantee comes from there. I can cite some primary literature however (and did so above). Here are a three more: http://www.imbb.forth.gr/people/averof/averof_lab_2011/publications_files/1995%20Nature.pdf http://www.sciencemag.org/content/311/5762/796.short (paywall, unfortunately) http://blogimages.bloggen.be/tsjokfoto/attach/16147.pdf (found a pdf posted somewhere for this one).Elizabeth Liddle
June 4, 2011
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Mung, if it can be shown that a small change in a gene results in a large change in body plan, the objection that changes in body plan cannot have evolved by means of incremental changes to DNA ceases to have force, no?
No, it does not cease to have force. That's why am trying to take you along this path, so that you will be able to understand why. I'm just asking that we take this and look at it in depth. You use it as a somewhat flippant response to BA77, but it does not carry the force you think it does. Using it in an argument might work against people who don't know better, but to others it looks like you're just spouting talking points.
Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.
Your biggest mistake is in thinking that these genes act as a specification for a body plan. But isn't it the case that really they just act as a switch and the specification is somewhere else? Maybe you were just using sloppy language to describe a complex subject. It happens. But you really seam to think that a small tweak to one or two genes here and there can specify radically different body plans, and you seem to think that this is demonstrated by Carroll in Endless Forms. I just want to find out of this is what Carroll actually demonstrates in the book you cite, or if you're just winging it. I have the book, let's take a look. Can you provide an example?Mung
June 4, 2011
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Mung, if it can be shown that a small change in a gene results in a large change in body plan, the objection that changes in body plan cannot have evolved by means of incremental changes to DNA ceases to have force, no? So the two questions are intimately connected.Elizabeth Liddle
June 4, 2011
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Elizabeth, I noticed that you highlighted the word 'evolution' in post 57; That reminded me of this observation by Phil Skell: 'I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.' (Phil Skell, "Why Do We Invoke Darwin?," The Scientist, 2005, Vol. 19(16):10 (2005) (emphasis added).) And in this following video, at the 7:00 minute mark, Dr. Behe demonstrates the mere 'narrative gloss' characteristic of the word 'evolution', by removing the word 'evolution' from a piece of peer-reviewed literature, and showing that it had no effect on the core finding of the research!: Michael Behe - Life Reeks Of Design - video http://www.youtube.com/watch?v=Hdh-YcNYThY So Elizabeth, how much was 'narrative gloss', in Koonin's paper, and how much was actual evidence that neo-Darwinism can actually create functional information. Once you see the fact that there is ZERO empirical evidence that purely material processes can create integrated functional information, then you may perhaps start to see how bankrupt neo-Darwinism is of true explanatory power!!!bornagain77
June 3, 2011
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Another busy day in the junkyard! Elizabeth Liddle @53:
Well, I think answers to the first shed light on the second. Obviously we can’t, in most cases, do genetic analyses of long extinct species.
So your answer then is the former, correct? Not that I had any doubt.
Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.
Existing genes, existing body plans. So what does this tell us about how such genes and body plans came about in the first place? Does Carroll address that question?
Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.
Cite time. If you can. Please cite an example of Sean Carroll showing how a small change in a gene specifies a radically different body plan. I have the book, so you don't have to type it up unless you want to. Just give me a reference. And please address the question, if you can, how does changing an existing gene and watching how it affects body plan development actually tell us how such genes and body plans came about in the first place? THAT is the $64,000 question.Mung
June 3, 2011
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Such as this testable hypothesis Elizabeth??? This following study is very interesting for the researcher surveyed 130 DNA-based evolutionary trees to see if the results matched what 'natural selection' predicted for speciation and found: Accidental origins: Where species come from - March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel's team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation - but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak." http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 So Elizabeth how do you like that 'falling out of the sky' bit???bornagain77
June 3, 2011
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bornagain77: yes, Koonin is an interesting guy. Nice link! Note though that he makes it absolutely clear in his paper, and in the interesting discussion below,that he is drawing an analogy. I think it's a bit strained myself, but his "Biological Big Bang" model seems to stand on its own merits. It is, however, an evolutionary model:
I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements.
(my bold) It makes a fair bit of sense to me, and should generate testable hypotheses.Elizabeth Liddle
June 3, 2011
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So Elizabeth, basically, by refusing to honestly address the evidence, you are saying that nothing can falsify your worldview. i.e. You hold one very, very, shaky 'verified prediction' for materialism, in the face of many more directly. and concretely 'verified predictions' for Theism.,,, Well I don't know exactly what your thinking, but what you are doing certainly IS NOT science!, perhaps God, who does know exactly what you are thinking, will help you sort it all out when you die and meet Him: It is also very interesting to point out that the 'light at the end of the tunnel', reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world 'folds and collapses' into a tunnel shape around the direction of travel as an observer moves towards the 'higher dimension' of the speed of light, with the 'light at the end of the tunnel' reported in very many Near Death Experiences: Traveling At The Speed Of Light - Optical Effects - video http://www.metacafe.com/watch/5733303/ The NDE and the Tunnel - Kevin Williams' research conclusions Excerpt: I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn't walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn't really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different - the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.(Barbara Springer) coast to coast – Blind since birth – Vicki’s NDE http://www.youtube.com/watch?v=e65KhcCS5-Y Near Death Experience – The Tunnel, The Light, The Life Review – view http://www.metacafe.com/watch/4200200/bornagain77
June 3, 2011
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Elizabeth, as to your citation, here is another citation that directly parallels it; I like this following paper for though it is materialistic in its outlook at least Dr. Eugene Koonin, unlike many materialists, is brutally honest with the genetic evidence we now have. The Biological Big Bang model for the major transitions in evolution - Eugene V Koonin - Background: "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable; http://www.biology-direct.com/content/2/1/21 Biological Big Bangs - Origin Of Life and Cambrian - Dr. Fazale Rana - video http://www.metacafe.com/watch/4284466 It should be noted that Dr. Koonin tries to account for the origination of the massive amounts of functional information, required for the Cambrian Explosion, and other 'explosions', by trying to access an 'unelucidated and undirected' mechanism of Quantum Mechanics called 'Many Worlds'. Besides Dr. Koonin ignoring the fact that Quantum Events, on a whole, are strictly restricted to the transcendent universal laws/constants of the universe, including and especially the second law of thermodynamics, for as far back in time in the universe as we can 'observe', it is also fair to note, in criticism to Dr. Koonin’s scenario, that appealing to the undirected infinite probabilistic resource, of the quantum mechanics of the Many Worlds scenario, actually greatly increases the amount of totally chaotic information one would expect to see generated 'randomly' in the fossil record. In fact the Many Worlds scenario actually greatly increases the likelihood we would witness total chaos surrounding us as the following points out: The Many Worlds interpretation of Quantum Mechanics, that Koonin has used in his paper, is in fact derived because of the inability of 'materialistic scientists to find adequate causation for quantum wave collapse (adequate causation that did not involve God!): Quantum mechanics Excerpt: The Everett many-worlds interpretation, formulated in 1956, holds that all the possibilities described by quantum theory simultaneously occur in a multiverse composed of mostly independent parallel universes.[39] This is not accomplished by introducing some new axiom to quantum mechanics, but on the contrary by removing the axiom of the collapse of the wave packet: http://en.wikipedia.org/wiki/Quantum_mechanics Perhaps some may say Everett’s Many Worlds in not absurd, if so,, then in some other parallel universe, where Elvis happens to now be president of the United states, they actually do think that the Many Worlds conjecture is absurd,, and that type of 'flexible thinking' I find to be completely absurd!!! And that one 'Elvis' example from Many Worlds is just small potatoes to the levels of absurdity that we could draw out if Many Worlds were actually true. The Absurdity Of The Many Worlds Hypothesis - William Lane Craig - Last 5 minutes of this video http://www.metacafe.com/watch/4784630 Though Eugene Koonin is correct to recognize that the infinite probabilistic resource found in ‘Quantum Mechanics’ does not absolutely preclude the sudden appearance of massive amounts of functional information in the fossil record, he is very incorrect to disregard the ‘Logos’ of John 1:1 needed to correctly specify the ‘precisely controlled mechanism of implementation’ for the massive amounts of complex functional and specified information witnessed abruptly and mysteriously appearing in the ancient genomes of these ancient fossils. i.e. He must sufficiently account for the ’cause’ for the ‘effect’ he wants to explain. And as I have noted previously, Stephen Meyer clearly points out that the only known cause now in operation, sufficient to explain the generation of massive amounts of functional 'digital' information, is intelligence: Stephen C. Meyer – What is the origin of the digital information found in DNA? – August 2010 - video http://www.evolutionnews.org/2010/08/stephen_meyer_on_intelligent_d037271.html This following paper corroborates Koonin's observation of irreconcilable differences being found in the genetic evidence with Darwinian evolution: Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html I would like to point out that this, 'annihilation' of Darwin's genetic tree of life, article came out on the very day that Dr. Hillis, a self-proclaimed 'world leading expert' on the genetic tree of life, testified before the Texas State Board Of Education that the genetic tree of life overwhelmingly confirmed gradual Darwinian evolution. One could almost argue it was 'Intelligently Designed' for him to exposed as a fraud on that particular day of his testimony instead of just any other day of the year.bornagain77
June 3, 2011
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Well, bornagain77, I don't think the evidence you cite in anyway calls into question the import of Shubin's find. It's perfectly true that Darwin envisaged a very slow and steady process, and that what we see instead is a process that is far more rapid than Darwin foresaw (remember that Darwin had no idea about the mechanics of inheritance). But we now know from both genetics and mathematical models much more about the dynamics of fitness landscapes, and that "punctuated equilibrium" is a common pattern, as observed in the fossil record. Sudden extinction events and periods of comparatively rapid radiation turn out to be consistent with the dynamics of adaptive evolution, especially now that we know what we know about the role of drift (something that Darwin did not consider). And I'm afraid I simply disagree with the interpretations expressed in your cited sources.Elizabeth Liddle
June 3, 2011
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Mung:
Honest question. Does he show how small changes to existing genes can specify radically different body plans, or does he show how it came to be the case that small changes to genes came to specify radically different body plans? Do you see the distinction and do you agree it’s a valid one? Don’t you think it’s the latter question that needs to be answered, rather than the former?
Well, I think answers to the first shed light on the second. Obviously we can't, in most cases, do genetic analyses of long extinct species. We can however do experiments with extant species and observe the effects of tampering with genes that are implicated in the embryological time table that determines body plans, as well as examine genetic phylogenies. There's a paper relevant to your second point here: http://icb.oxfordjournals.org/content/38/6/829.abstract The developmental perspective on genetics is fascinating, and of course extremely relevant to practical research into developmental disorders.Elizabeth Liddle
June 3, 2011
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Elizabeth you say Shubin's fossil is an amazing 'predicted' find. Well lets look at a couple of falsified predictions that call into question the severe import that you want to place on this one fossil; notes; ,,,,13. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God's fifth day of creation. - The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short "geologic resolution time" in the Cambrian seas. - Materialistic Basis of the Cambrian Explosion is Elusive: BioEssays Vol. 31 (7):736 - 747 - July 2009 Excerpt: "going from an essentially static system billions of years in existence to the one we find today, a dynamic and awesomely complex system whose origin seems to defy explanation. Part of the intrigue with the Cambrian explosion is that numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time." ---"Thus, elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists." http://www.evolutionnews.org/2009/06/bioessays_article_admits_mater.html Deepening Darwin's Dilemma - Jonathan Wells - Sept. 2009 Excerpt: "The truth is that (finding) “exceptionally preserved microbes” from the late Precambrian actually deepen Darwin’s dilemma, because they suggest that if there had been ancestors to the Cambrian phyla they would have been preserved." http://www.discovery.org/a/12471 Deepening Darwin's Dilemma - Jonathan Wells - The Cambrian Explosion - video http://www.metacafe.com/watch/4154263 14. Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record - Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. - Here is a page of quotes by leading paleontologists on the true state of the fossil record: https://docs.google.com/document/pub?id=15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg Here are four more pages of quotes, by leading experts, on the fossil record here: Creation/Evolution Quotes: Fossil Record #1 - Stephen E. Jones http://members.iinet.net.au/~sejones/fsslrc01.htmlbornagain77
June 3, 2011
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No, bornagain77, the evidence does NOT "fall apart on scrutiny". Shubin et al predicted that a creature like Tiktaalik would be found in a particular place in Greenland, it it was. This is a spectactular example of new data supporting a prior hypothesis. The hypothesis was not that no other tetrapods would be found, nor that Tiktaalik was the earliest tetrapod. And virtually no fossil is likely to be in a direct line of descent to modern species. There are likely to be no living descendents of Tiktaaliks.Elizabeth Liddle
June 3, 2011
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Elizabeth @40:
And Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.
Honest question. Does he show how small changes to existing genes can specify radically different body plans, or does he show how it came to be the case that small changes to genes came to specify radically different body plans? Do you see the distinction and do you agree it's a valid one? Don't you think it's the latter question that needs to be answered, rather than the former?Mung
June 3, 2011
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correction; which unwittingly, to you, was falsified a few years back,bornagain77
June 3, 2011
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Elizabeth, you alluded to a 'prediction', which you unwittingly was falsified a few years back, as quote, 'That’s as good as it gets in science!' Now Elizabeth verified, and falsified, predictions are indeed 'about as good as it gets in science!' and are a very, very strong indication of a hypothesis veracity towards the truth.,, So Elizabeth please note that earlier in this post I presented this evidence; The following articles show that even atoms (Ions) are subject to teleportation:
Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
So Elizabeth materialism, which is the basis of neo-Darwinian thought, predicted, for thousands of years, that the foundational basis of reality was a solid indestructible particle that has always existed. Whereas Theism, particularly Christian Theism, in John 1:1-3, predicted that The Word (Logos) was/is the foundational basis of reality; i.e. Theism predicted 'information' as the foundational basis of reality and moreover that prediction was confirmed at the expense of falsifying the very foundation of reality that neo-Darwinism affirms!!! As you said Elizabeth 'That’s as good as it gets in science!'!!! But Elizabeth, though that ought to severely shake your belief in anything based on materialism in the first place, it gets far worse if we dig just a bit deeper into the predictive power of theism compared to materialism; ,,,The materialistic and Theistic philosophy make, and have made, several natural contradictory predictions about what evidence we will find. These predictions, and the evidence we have found, can be tested against one another within the scientific method. Steps of the Scientific Method http://www.sciencebuddies.org/science-fair-projects/project_scientific_method.shtml For a quick overview, here are a few: 1. Materialism predicted an eternal universe, Theism predicted a created universe. - Big Bang points to a creation event. - 2. Materialism predicted time had an infinite past, Theism predicted time had a creation. - Time was created in the Big Bang. - 3. Materialism predicted space has always existed, Theism predicted space had a creation (Psalm 89:12) - Space was created in the Big Bang. - 4. Materialism predicted that material has always existed, Theism predicted 'material' was created. - 'Material' was created in the Big Bang. 5. Materialism predicted at the base of physical reality would be a solid indestructible material particle which rigidly obeyed the rules of time and space, Theism predicted the basis of this reality was created by a infinitely powerful and transcendent Being who is not limited by time and space - Quantum mechanics reveals a wave/particle duality for the basis of our reality which blatantly defies our concepts of time and space. - 6. Materialism predicted the rate at which time passed was constant everywhere in the universe, Theism predicted God is eternal and is outside of time - Special Relativity has shown that time, as we understand it, is relative and comes to a complete stop at the speed of light. (Psalm 90:4 - 2 Timothy 1:9)- 7. Materialism predicted the universe did not have life in mind and life was ultimately an accident of time and chance. Theism predicted this universe was purposely created by God with man in mind - Every transcendent universal constant scientists can measure is exquisitely fine-tuned for carbon-based life to exist in this universe. - 8. Materialism predicted complex life in this universe should be fairly common. Theism predicted the earth is extremely unique in this universe - Statistical analysis of the hundreds of required parameters which enable complex life to be possible on earth gives strong indication the earth is extremely unique in this universe. - 9. Materialism predicted much of the DNA code was junk. Theism predicted we are fearfully and wonderfully made - ENCODE research into the DNA has revealed a "biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.". - 10. Materialism predicted a extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. Theism predicted only God created life on earth - The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial mutations whatsoever. (M. Behe; JC Sanford) - 11. Materialism predicted a very simple first life form which accidentally came from "a warm little pond". Theism predicted God created life - The simplest life ever found on Earth is far more complex than any machine man has made through concerted effort. (Michael Denton PhD) - 12. Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11) - We find evidence for complex photo-synthetic life in the oldest sedimentary rocks ever found on earth - 13. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God's fifth day of creation. - The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short "geologic resolution time" in the Cambrian seas. - 14. Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record - Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. - 15. Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth - Man himself is the last generally accepted major fossil form to have suddenly appeared in the fossil record. - references: https://docs.google.com/document/pub?id=1ubha8aFKlJiljnuCa98QqLihFWFwZ_nnUNhEC6m6Cys As you can see when we remove the artificial imposition of the materialistic philosophy, from the scientific method, and look carefully at the predictions of both the materialistic philosophy and the Theistic philosophy, side by side, we find the scientific method is very good at pointing us in the direction of Theism as the true explanation. - In fact it is even very good at pointing us to Christianity: General Relativity, Quantum Mechanics, Entropy & the Shroud Of Turin - video http://www.metacafe.com/watch/5070355bornagain77
June 3, 2011
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For a clear instance of your inability to honestly face the truth Elizabeth...
That's right Elizabeth. You are a WONDERFUL person, and the sooner you come to accept that fact the better off we'll all be. You simply MUST honestly face the truth. Cheers.Mung
June 3, 2011
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There isn’t any evidence that genetic accidents can accumulate in such a way as to give rise to useful, functional multi-part systems. That means there couldn’t have been any climbing.
You've never heard of climbing downhill?Mung
June 3, 2011
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Elizabeth you state: 'Shubin’s finding of Tiktaalik was a superb demonstration of a scientific narrative predicting something, in a particular place, and that thing being found!' And yet once again your evidence falls completely apart upon scrutiny; The supposed 'evidence' for the evolution of fish to land dwelling creatures is not even close to the conclusive evidence evolutionists pretend that it is: Tiktaalik- Out Of Order Excerpt: One of the problems with an evolutionary interpretation of the fishapods is that these creatures appear to be out of order. http://www.reasons.org/OutofOrder Tiktaalik Blown "Out of the Water" by Earlier Tetrapod Fossil Footprints - January 2010 Excerpt: The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr. http://www.evolutionnews.org/2010/01/tiktaalik_blown_out_of_the_wat.html This following article has a excellent summary of the 'less than forthright' manner in which Darwinists handle anyone who dares to tell of falsifications to their paltry evidence for 'transitional' fossils: Evolutionary Biologists Are Unaware of Their Own Arguments: Reappraising Nature's Prized "Gem," Tiktaalik - Casey Luskin - September 2010 http://www.evolutionnews.org/2010/09/evolutionary_biologists_are_un038261.html But alas Elizabeth, you are left with nothing but story telling once again!!!bornagain77
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