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
Well, nothing is "proven" in science (all conclusions must be provisional), but apart from that niggle, yes, of course, and that's exactly what I am saying. In science, we create narratives ("tell stories") but the critics, in the end, are not our readers but the data that either does, or does not, support those narratives. So we seem to be agreed on that :) Where we disagree on is whether I have failed or succeeded! (well not me personally, although I guess I've made the odd small contribution in a very different domain). Shubin's finding of Tiktaalik was a superb demonstration of a scientific narrative predicting something, in a particular place, and that thing being found! That's as good as it gets in science! For what reason do you discount this finding as evidence for Shubin's narrative?Elizabeth Liddle
June 3, 2011
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Elizabeth, you state: 'Science, you might be surprised to hear me say, is all about telling stories.' No Elizabeth, science is about actually proving, by rigorous experimentation, that your narrative is true. On that count you fail miserably. As your 'story telling' citations abundantly testify!!!bornagain77
June 3, 2011
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OK, bornagain77, perhaps we are homing in on our real difference here. Science, you might be surprised to hear me say, is all about telling stories. In other words it's about devising a causal narrative that explains what we see. However, unlike novelists, whose critics are their readers, the ultimate critic of scientific stories are is evidence. And the procedure has two parts: First, scientists tell a story that could explain the data they have. Then they use that story to predict data that they do not yet have. Then they go out and try to find the data that should exist if their story is true. If they don't find it, their story remains a story, and, if they find data that is inconsistent with their original story then they have to change the story. However, if they do find it, then they can claim support for their story as a viable account of the evidence. And, famously, this exactly what Shubin and his colleagues did. They made a story about tetrapod evolution that fit the facts as they had them. And then they used that story to predict that there should be, at a particular level in the geological column, and in a particular kind of habitat, creatures with certain intermediate characteristics, including the beginnings of what would eventually become a "wrist". So they went off to Greenland, where they knew that strata corresponding to the predicted time period and habitat was close to the earth's surface. And they found fossils of the predicted tetrapod. That is the kind of evidence that scientists regard as evidence for their hypothesis - their hypothesis starts as an explanatory "story" that fits the existing data. But that hypothesis must be tested by making a prediction that is subsequently confirmed by new evidence. That's the hard part, and that's the rigorous part. A hypothesis can be a beautiful story, but unless it predicts new evidence, and that new evidence is found, it remains, at best, unsupported, and at worst, infirmed, and must be changed or discarded completely. So that a piece of evidence that I count as evidence. Let's look at what you regard as contrary evidence - the negative evidence of the lack of evidence that a fruit-fly can evolve into anything other than a fruit-fly. It may surprise you to know that evolutionary theory not only does not predict that fruitflies will turn into anything other than fruitflies, it predicts that all their descendents will be fruitflies! That's why biological nomenclature is arranged in a nested hierarchy. What may be a species, at one time point, may subdivide into sub-species at another level, and sub-subspecies at yet another level. But the sub-sub-species is still a member of the original species, which we might now re-term a "genus" or some other term. So a dog's descendents will always be dogs, just as the descendants of the carnivora ancestor of both dogs and cats will always be carnivora, and the descendents of the mammalian ancestors of carnivora will always be mammals. As for the experiment that involved irradiating fruitfly - why on earth would anyone expect that inflicting gross damage to the genome would result in viable organisms? This is simply not the mechanisms by which novel evolutionary features are proposed to evolve. On the other hand, much more slight mutations to an existing genome can result in some wonderfully adaptive novelties. Look at these extraordinary, closely related, insects: http://www.google.co.uk/search?tbm=isch&hl=en&source=hp&biw=1079&bih=835&q=treehoppers&gbv=2&aq=f&aqi=&aql=&oq= (I just discovered them recently). And here is a paper on the genetics of these extraordinary features: http://www.nature.com/nature/journal/v473/n7345/abs/nature09977.html This is an excellent example of what I would consider positive evidence for standard evolutionary theory. I would be interested to know why you think it is not.Elizabeth Liddle
June 3, 2011
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Elizabeth you equate story telling for evidence; for instance you state: 'Neil Shubin gives a detailed, empirically supported account of the evolution of “novel body plans” including the very important (for our ancestry) evolution of the four limb patterns.' So you are saying that Shubin provided undeniable evidence that a four limbed creature evolved from some creature that did not have four limbs, yet clearly Shubin did not do this, he only 'told a story' that you happily believed.,,, As well, Shubin seems to have some serious, serious, issues with rampant 'just so' story telling, instead of solid science, as is clearly noted here: Evolutionary biologist Neil Shubin claims that the human breast evolved from fish teeth. (5:08) - Colbert Report http://www.colbertnation.com/the-colbert-report-videos/147281/january-14-2008/neil-shubin Yet even though he clearly did not demonstrate anything he conjectured, you have 'dishonestly' implied that he did have undeniable evidence, what you should have 'truthfully' said, but forgot to do, was that Shubin traced a convoluted pathway using pre-chosen genetic similarity to arrive at his predetermined conclusion!!! But alas, when I cut out all the story telling and show you decades of work trying to change a fruit fly into anything other than a fruit fly, all to no avail, this is of no import to you... because??? because??? Well because by golly, Shubin, and company, have told you such wonderful stories that confirms your predetermined conclusion!! This is EXACTLY how you ARE NOT suppose to practice science!!! ============== There is no evidence that mutations to DNA will effect body-plan morphogenesis in a significant novel, and positive, way; …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells Darwin’s Theory – Fruit Flies and Morphology – video http://www.youtube.com/watch?v=hZJTIwRY0bs Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010 Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.bornagain77
June 3, 2011
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No, indeed, bornagain77, I am not looking to you to "cosign [my] rationalizations", as should be very clear from my posts. I am simply putting it to you that what you are attributing to my apparent inability to accept what you consider lack of evidence may instead be my view that there is a great deal of evidence. However, one problem we seem to have between us, is that I notice that a lot of your posts, which you present, it seems as evidence that infirms the Darwinian model of evolution, are in fact posts about physics and cosmology. I simply do not see these as counter arguments to evolutionary theory. Why should the weirdness of existence be an argument against the processes by which existence unfolds? I am not arguing against an some transcendental reality that we might call God. I'm simply arguing for Darwinian processes as an account of biological diversity, as I would argue for chemical processes as an account of chemical reactions. There is simply no conflict between a transcendental view of reality and modern biology. Your other sources have been to writers who claim there is no evidence for various evolutionary hypotheses. I dispute the claims made by those writers, because I am aware of the work of many scientists, including Neil Shubin and Sean Carroll, who cite, and indeed provide, direct empirical evidence that I consider strongly support evolutionary theory. So when you say that "there is no evidence", can you explain why you discount this evidence? Neil Shubin gives a detailed, empirically supported account of the evolution of "novel body plans" including the very important (for our ancestry) evolution of the four limb patterns. And Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans. Again, by what reasoning do you dismiss this empirical evidence? Far from asking you to "cosign [my] rationalizations" I am asking you to defend your own position, namely, that there is "no evidence". In what sense is the above "no evidence"? Cheers LizzieElizabeth Liddle
June 3, 2011
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Elizabeth, if you are looking for me to cosign your rationalizations, you ain't going to find it. The evidence is clear and unmistakeable, indeed goes to the core of how reality is actually constructed in the first place!!!bornagain77
June 3, 2011
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bornagain77: no I'm not upset, don't worry! It's just that by assuming that I'm being dishonest you are consistently missing the points I'm trying to make. Obviously we are in deep disagreement, but I suggest that this is not because either of us are dishonestly looking at (or failing to look at) the evidence. It's that we each seem to be referring to very different bodies of evidence, and, indeed, have very different ways of even evaluating what is "admissible" evidence. So by making the assumption of good faith, perhaps we can drill down to what that evidence is, and why you think it supports your position, and why I think it supports mine. I am, as I think you know, a scientist, and so I have, I guess, a particular slant on evaluating evidence. I would contend it is a rigorous one. And, using the evaluation tools at my disposal, I think the evidence for evolutionary theory is extremely strong. I simply disagree with you that there is "no evidence" and I've given you a couple of books that cite a lot of the primary findings. Let's try to move on from the question as to who is the blinkered one here to what the arguments and evidence for each case actually are. OK? Cheers LizzieElizabeth Liddle
June 3, 2011
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oops, I meant "make the assumption that the other is posting in good faith"? cheers LizzieElizabeth Liddle
June 3, 2011
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Elizabeth, the problem for you is that you want to have your cake and eat it to. You have no evidence, thus you make up any excuse you can, and push your problem back, under the rug to a former age of 'miracles' if you will, but this is not science Elizabeth, what you are doing is rationalization in the face of all contrary evidence. You get upset that I call you on not honestly facing the evidence, but that is in fact what you are doing!!!,,, Moreover, if you really cared to follow the evidence where it leads, instead of making up more and more extremely far fetched excuses for your 'preferred' worldview, you would find that the problem traces back to the inability of material processes to generate ANY amount of non-trivial functional information/complexity! And once you see that "information' is the insurmountable problem, then you can then follow the evidence deeper, to try to answer the question, 'Where does the information come from?", and you will find that all of reality itself reduces to information, of a 'infinite' (mind of God) Theistic order, and thus indeed, all of reality (the entire material universe) must originate from the 'infinite information' that originates from the purposeful intent of the infinite Mind Of God. notes: It is also very interesting to note that the quantum state of a photon is actually defined as 'infinite information': Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) --- Concept 2. is used by Bennett, et al. Recall that they infer that since an infinite amount of information is required to specify a (photon) qubit, an infinite amount of information must be transferred to teleport. http://www.cas.umt.edu/phil/faculty/duwell/DuwellPSA2K.pdf The following articles show that even atoms (Ions) are subject to teleportation: Of note: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. 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),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp 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. http://www.freerepublic.com/focus/news/2171769/posts Moreover Elizabeth, from the preceding experiments, and other experiments, 'information' is shown to be 'conserved' to a greater degree than energy; Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. (This experiment provides experimental proof that the teleportation of quantum information in this universe must be complete and instantaneous.) http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html ,,, thus Elizabeth, since we have no reason to believe that purely material processes, according to the first law of thermodynamics, will ever create energy, then thus how much more so shall we not expect purely material processes to create 'information' which exceeds energy in its rank of conservation??? etc.. etc.. etc..bornagain77
June 3, 2011
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bornagain77: I'd be grateful if you wouldn't impugn my honesty. Wrong, I may well be (I am frequently wrong), and biased I may be too, but I am not dishonest, and I am far more interested in finding a model that fits the data than in defending an a priori view, or even my own ego. Still, no problem - I often encounter the same accusations of dishonesty levelled at IDists, and I get just as cross. It seems to me we get nowhere by assuming the other "side" is posting in bad faith. So please can we agree to at least make that assumption, for the time being? Yes, there is good evidence that bacteria reached an optimal peak several hundred million years ago, around which they continue to move between adjacent sub-peaks. That doesn't mean their ancestors were at that peak two or three billion years ago. Nor does it mean that we are descended from bacteria of any kind (we aren't).Elizabeth Liddle
June 3, 2011
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Well Elizabeth let's take a closer look: For a clear instance of your inability to honestly face the truth Elizabeth, you hold that simpler life gradually changes, by purely 'natural' processes, into more and more complex life, but when we look as far back as we can, through the wildly changing environment of the earth's deep past, we find that bacteria look exactly the same as they did hundreds of millions of years ago; Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial microbial. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 ,,, i.e. if neo-Darwinism were true, this extreme stasis should not be present, and to make excuses for why there is no change is certainly not facing the evidence honestly Elizabeth!!! further notes; The Paradox of the "Ancient" (250 million year old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland's work: “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961 Dr. Cano's work on ancient bacteria came in for intense scrutiny since it did not conform to Darwinian predictions, and since people found it hard to believe you could revive something that was millions of years old. Yet Dr. Cano has been vindicated: “After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber." https://uncommondescent.com/intelligent-design/reductionist-predictions-always-fail/comment-page-3/#comment-357693 In reply to a personal e-mail from myself, Dr. Cano commented on the 'Fitness Test' I had asked him about: Dr. Cano stated: "We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.": Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. Here is a revisit to the video of the 'Fitness Test' that evolutionary processes have NEVER passed as for a demonstration of the generation of functional complexity/information above what was already present in a parent species bacteria: Is Antibiotic Resistance evidence for evolution? - 'Fitness Test' - video http://www.metacafe.com/watch/3995248 Thus Elizabeth, your conjectures fail on all fronts they are tested!!!bornagain77
June 3, 2011
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bornagain77, #31 No, my posts relate to empirical results, bornagain77. But you are very good at citing your sources, and I will try to cite some of mine. One source worth referring to, and it contains a lot of references to primary empirical sources, is Sean Carroll's book, "Endless forms most beautiful". Another is Neil Shubin's "Your Inner Fish". http://www.amazon.com/Your-Inner-Fish-Journey-3-5-Billion-Year/dp/0375424474 http://www.amazon.com/Endless-Forms-Most-Beautiful-Science/dp/0393327795/ref=sr_1_1?ie=UTF8&qid=1307106039&sr=1-1-spellElizabeth Liddle
June 3, 2011
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@bornagain, #25
Elizabeth Liddle you state; ‘in a population that is already at near-optimum,’ And exactly why do you say that bacteria are near optimum complexity, and cannot improve any further over their current ‘optimal’ state (as the evidence now demands you say), when you in fact hold, according to your own neo-Darwinian worldview, the completely contrary view that bacteria are not of optimum complexity and that all life evolved from bacteria??? You can’t have it both ways Elizabeth, either bacteria are of the optimal complexity allowable for any particular bacterium, because they were designed that way, or bacteria are not of optimum functional complexity and can evolve by neo-Darwinian means, ‘naturally’, to greater and greater heights of integrated functional complexity.
Good question, bornagain77, but one with a good answer :) In fact, several. Biologists do not hold that all life descended from bacteria. In fact, only modern bacteria descended from ancient bacteria. What biologists hold is that both bacteria and all other living things descended from a common ancestor that was probably simpler than either. Second: fitness is multidimensional, and while it is convenient to talk about a 2 or 3 dimensional "fitness landscape" because that is easy to visualise, in fact there are countless dimensions along which a population can "move". However, there will also be local "maxima" occupied by particular populations, and populations of populations, and these include bacteria. But my fundamental point is related to Gould's point about "punctuated equilibrium". Once a population is at equilibrium, most "directions" will be down, and so "selective pressures" will tend to be conservative (sharks are a good example). But if that equilibrium is broken, by an environmental change of some kind, populations will tend to "move" to a new optimum. At that point, a much larger proportion of what would otherwise have been either neutral or "Very Slightly Deleterious" mutations will be "Very Slightly Beneficial". So the fact that in a population at equibrium, most mutations are VSDMs or neutral doesn't extrapolate to populations in flux.Elizabeth Liddle
June 3, 2011
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Elizabeth you ask; 'well I did read your post, but I don’t find your sources very convincing! Did you read the rest of mine?' Well Elizabeth, I did not think you find it 'convincing' since it does not sit well with your neo-Darwinian worldview. But alas for you Elizabeth, my post are the actual empirical results, whereas your posts are merely conjecture. You keep alluding to the fact that your materialistic conjectures are 'demonstrated',,, Yet I never find any citation from you so as to counter Behe and Axe's work. ,,, You know Elizabeth, you can believe whatever you want, as you clearly demonstrate that you are intent on doing, but that is not science, and the blunt truth is, when the rubber meets the road, that you have ZERO empirical evidence to back up all your 25 cent word rhetoric!!!bornagain77
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Bornagain77: well I did read your post, but I don't find your sources very convincing! Did you read the rest of mine?Elizabeth Liddle
June 3, 2011
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Joseph:
Lizzie, Darwin chose it to cause confusion. And he was corrected in his own time. Unfortunately that has been lost and “natural selection”still remains.
Oh I have to disagree, there, Joseph. I think it was a very apt analogy in its day. I just think it has acquired a misleading life of its own since. I presume you agree that, for example, a modern poodle, say, has the characteristics it has because those characteristics were consistently bred for by breeders? In other words, those dogs with the desired characteristics were selectively bred from? In other words, certain naturally occurring variants increased the probability that the individual would be chosen by the breeder as a breeding animal, i.e. would increase the animal's chances of reproductive success (within the context of the breeding farm). Yes? So all Darwin did was to extrapolate this particular example to what happens naturally - characteristics that increase an individuals chance of reproductive success will tend to be propagated through the population. The only difference is that in the wild, the probability of a characteristic leading reproductive success doesn't depend on whether a dog-breeder likes that characteristic, but on whether it increases the organism's chance of surviving, finding a mate, or rearing its offspring successfully to maturity. Hence "natural" selection by analogy to the "artificial" selection by breeders.Elizabeth Liddle
June 3, 2011
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Elizabeth states: 'So the question is: can those accumulations result in “useful, multipart systems”, and I’d say there is abundant evidence that they, and indeed, for the way that the accumulation happens.' see post 27!!!bornagain77
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further notes; Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution "Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use." http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge.html The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.” Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”) Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009 Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites) http://www.evolutionnews.org/2009/10/nature_paper_finally_reaches_t026281.html When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/bornagain77
June 3, 2011
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Joseph @ #21:
Lizzie- 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.
Well, I would have to disagree with you! Certainly genetic accidents can "accumulate" as I'm sure you would agree, and you would probably agree that genetic "accidents" that confer reproductive advantage will tend to accumulate at the expense of those that do not. So the question is: can those accumulations result in "useful, multipart systems", and I'd say there is abundant evidence that they, and indeed, for the way that the accumulation happens. You probably know about "hox" genes, that specify, extremely simply, such matters as which end of the developing embryo is front and which the back, given chemical inputs from neighbouring cells. There are also fairly basic genes that determine, again, given chemical inputs from neighbouring cells, whether the dividing embryo will have radial or bilateral symmetry. This is so simple that it's directly analogous to the features that determine whether a growing snowflake will be columnar or flat. And once it's started growing in a particular manner, the growth pattern itself is a determining factor in what happens next. Now obviously I accept that you do not think such evidence is valid, but I would have to disagree. We know a lot about the genes that specify whether a forelimb becomes a flipper, a wing, or an arm, or whether a skin cell becomes a tooth, a scale, a hair, or a feather. I think the best way to conceive of the developmental process is as a nested "decision tree" where the initial "decisions" (Head or tail? four segments or five?) are very simple, but once down one of the branches of the tree, what has already developed interacts with what may be slight variants of regulatory genes and others to determine which of a subset of possibilities is executed.Elizabeth Liddle
June 3, 2011
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Lizzie, Darwin chose it to cause confusion. And he was corrected in his own time. Unfortunately that has been lost and "natural selection"still remains. However we now know that it is but a minor player in the scheme of life.Joseph
June 3, 2011
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Elizabeth Liddle you state; 'in a population that is already at near-optimum,' And exactly why do you say that bacteria are near optimum complexity, and cannot improve any further over their current 'optimal' state (as the evidence now demands you say), when you in fact hold, according to your own neo-Darwinian worldview, the completely contrary view that bacteria are not of optimum complexity and that all life evolved from bacteria??? You can't have it both ways Elizabeth, either bacteria are of the optimal complexity allowable for any particular bacterium, because they were designed that way, or bacteria are not of optimum functional complexity and can evolve by neo-Darwinian means, 'naturally', to greater and greater heights of integrated functional complexity. ,,, But to further highlight the sheer absurdity of your position, even if we grant that you must always 'descend' from the optimal function complexity of a bacterium before you can ascend to anything more functionally complex than a bacterium, and test for that extremely charitable allowance to the almighty power of evolution to succeed in such a convoluted, circuitous, manner, this is what we find: These following articles refute Richard E. Lenski's 'supposed evolution' of the citrate ability for the E-Coli bacteria after 20,000 generations of the E-Coli from his 'Long Term Evolution Experiment' (LTEE) which has been going on since 1988: Multiple Mutations Needed for E. Coli - Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Michael Behe's Quarterly Review of Biology Paper Critiques Richard Lenski's E. Coli Evolution Experiments - December 2010 Excerpt: After reviewing the results of Lenski's research, Behe concludes that the observed adaptive mutations all entail either loss or modification--but not gain--of Functional Coding ElemenTs (FCTs) http://www.evolutionnews.org/2010/12/michael_behes_quarterly_review041221.html Lenski's e-coli - Analysis of Genetic Entropy Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment. http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria Lenski's work actually did do something useful in that it proved that 'convergent evolution' is impossible because it showed that evolution is 'historically contingent'. This following video and article make this point clear: Lenski's Citrate E-Coli - Disproof of Convergent Evolution - Fazale Rana - video (the disproof of convergence starts at the 2:45 minute mark of the video) http://www.metacafe.com/watch/4564682 The Long Term Evolution Experiment - Analysis Excerpt: The experiment just goes to show that even with historical contingency and extreme selection pressure, the probability of random mutations causing even a tiny evolutionary improvement in digestion is, in the words of the researchers who did the experiment, “extremely low.” Therefore, it can’t be the explanation for the origin and varieity of all the forms of life on Earth. http://www.scienceagainstevolution.org/v12i11f.htm Even more crushing evidence can be gleaned from Lenski's long term evolution experiment on E-coli. Upon even closer inspection, it seems Lenski's 'cuddled' E. coli are actually headed for genetic meltdown instead of evolving into something, anything, better. New Work by Richard Lenski: Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal. http://www.evolutionnews.org/2009/10/new_work_by_richard_lenski.html The following shows that we can actually watch the 'final act' of Genetic Entropy, 'mutational meltdown', in the laboratory for small asexual populations (bacteria, yeast, etc.): The Mutational Meltdown in Asexual Populations - Lynch Excerpt: Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown,,, http://www.oxfordjournals.org/our_journals/jhered/freepdf/84-339.pdf and of course no matter what convoluted route you want to take for bacteria, the bottom line is that no bacteria has EVER passed the fitness test against its parent strain!! Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 further note: Again I would like to emphasize, I’m not arguing Darwinism cannot make complex functional systems, the data on malaria, and the other examples, are a observation that it does not. In science observation beats theory all the time. So Professor (Richard) Dawkins can speculate about what he thinks Darwinian processes could do, but in nature Darwinian processes have not been shown to do anything in particular. Michael Behe - 46 minute mark of video lecture on 'The Edge of Evolution' for C-SPAN https://uncommondescent.com/intelligent-design/michael-behe-lecture-recommend/comment-page-1/#comment-361037bornagain77
June 3, 2011
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Joseph @ #22 Actually I sort of agree with you that it's a bad term, although I understand entirely why Darwin chose it - he was making the fairly simple point that just as farmers and breeders deliberately select desirable traits, traits that "naturally" confer greater fecundity will be automatically "selected". But it tends to result in tautologies like "selection selects", so I try to avoid it where I can. The Darwinian principle is simply this: When things replicate with variance, variants that replicate better will become more prevalent. Which isn't even a theory really, its more like a syllogism.Elizabeth Liddle
June 3, 2011
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Also "natural selection" is an oxymoron as mature does not select. Natural selection is a result, ie differential reproduction due to heritable variation.Joseph
June 3, 2011
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Lizzie- 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.Joseph
June 3, 2011
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@ nullasalus: Further to my point above, I would make the additional point that "the environment" should probably be taken to include the context of the rest of the genotype. Just as homozygosity for one allele might reduce the probability of breeding, while heterozygosity increases it, so an allele in one genetic context may increase reproductive success, but reduce it in another. For example, we know that both schizophrenia and ADHD are highly heritable (estimates are over 50%) and yet Genome Wide Association Studies (GWAS) show that while individual alleles have a statistically significant odds ratio (over 1, which would indicate no association)), they rarely hit even hit two. In other words, while "risk alleles" exist, the vast majority of bearers of those alleles will not develop the disorder, and indeed, the alleles in a different genetic context may confer some benefit. I also thought of a (totally hypothetical example) of the homozygosity thing that might make my point clearer: Let's say that a particular allele slightly increased testosterone expression in women, and in so doing greater enthusiasm for sex. And let's say that when heterozygous for that allele, there is no measurable effect on fertility, but where homozygous, fertility is impaired (but sexual enjoyment increased). That allele would tend to reach homeostasis, because heterozygous individuals would tend to have more babies (more sex) but homozygous individuals fewer (even more sex, but fewer babies). Do we call that allele a "flaw" or not? Is it a bug or a feature? From the PoV of evolution, it's a net feature, but the cost of the feature is a proportion of the population for which it is a bug; the allele prevalence will stabilise at a level at which the number extra fecund heterozygous individuals is balanced by the number of less fecund homozygous individuals. However, for the individual homozygous woman, however, it might be either bug or feature, depending on how great their desire for babies was. For some, great sex without worry of pregnancy might be win-win! For others, a mixed blessing. And for the individual heterozygous woman it might be great nuisance, certainly in a pre-contraceptive era. So I think it's important to distinguish between the value of the allele to the individual (and we can probably usefully use words like "flaw" in that context), and the "value" (in deliberate scare quotes) of the allele from an evolutionary PoV. "Selection coefficient less than 1) is probably a better term, if a bit technical, but you still have to remember that selection coefficient remains a function of context, where context includes both the external and internal environment, including the rest of the genome.Elizabeth Liddle
June 3, 2011
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It is true, bornagain77, that in a population that is already at near-optimum, most changes will be deleterious. When things are pretty good, there is nowhere to go but down :) But that doesn't mean that during the climb to that optimal peak, a much greater proportion of changes would have been beneficial. In fact, that is the heart of the theory - that where genotypic variation results in variance in reproductive success, the most successful variants will become the most prevalent.Elizabeth Liddle
June 3, 2011
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as to; 'The value of an allele is a function of its phenotypic effects' There is no evidence that mutations to DNA will effect body-plan morphogenesis in a significant novel, and positive, way; ...Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies further notes: Getting Over the Code Delusion (Epigenetics) - Talbot - November 2010 - Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism: http://www.thenewatlantis.com/publications/getting-over-the-code-delusion The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion." http://eyedesignbook.com/ch6/eyech6-append-d.html Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 The Gene Myth, Part II - August 2010 Excerpt: So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.,,, So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used.,,, Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html etc.. etc..bornagain77
June 3, 2011
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as to: as the vast majority of gene variants are near-neutral in effect. ,,,but not quite neutral; the vast majority of mutations are shown to be 'slightly detrimental'; Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html ,,, the vast majority of mutations being "Slightly Detrimental" means that the vast majority of mutations are far below the power of natural selection to remove from a genome until it is too late, i.e. long before the effects of 'slightly detrimental mutations' are noticed by natural selection they will spread throughout the entire population. Evolution vs. Genetic Entropy - video http://www.metacafe.com/watch/4028086bornagain77
June 3, 2011
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Exactly. In a Darwinian context, the only quality criterion for a trait is: does it increase or reduce the probability that, in this environment,I will reproduce successfully? Of course that criterion is completely orthogonal to the subjective effects, in a sentient organism, of that trait. For example, not being able to reproduce, may, conceivably, improve the quality of my life. But from a Darwinian perspective, it's a flaw. Of course nothing is quite as simple as that (although that's the basic Darwinian principle, I would say); for example there are some alleles that increase the probability of reproduction when heterozygous, but reduce it when homozygous. In a sexually reproducing population, there will tend to be a few homozygous individuals that get the rough end of the deal, but the allele still propagates through the population because heterozygous individuals reproduce better (although there will be an optimal level of frequency in the population, clearly). In that sense, from the individuals point of view, heterozygosity is a benefit, but homozygosity, probably a flaw (unless it confers something fun as well). But what is inherited, will be the allele, not the homozygosity! To take your last point: You don't have to tell a story at all. I'm just giving a more precise definition of the concept of a "flaw" in Darwinian terms. It's probably a bad word to use, in fact, because it has absolutist baggage. The value of an allele is a function of its phenotypic effects and the current environment. It's not a static quantity. And in many cases its only inferable statistically anyway, as the vast majority of gene variants are near-neutral in effect.Elizabeth Liddle
June 3, 2011
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Then we’d have to record allele frequencies in the population over time, and see which alleles became more frequent and which less. Right, but at that point you wouldn't be determining the features and flaws of the flower, but of successive generations. And the simulations you'd run would have to make assumptions about the environments, among other things. Do you run simulations with the 'this was done by a breeder' environment in mind? I have no doubt you can tell a good story about the flower, if the sky's the limit as far as hypothetical environments and histories and who-knows-what is involved, to overlay over any actual data gathered.nullasalus
June 3, 2011
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