tag:blogger.com,1999:blog-3855268335402896473.post8990043317241366282..comments2024-01-23T02:32:28.567-08:00Comments on Darwin's God: Fish Have a Toolbox and Several Other FindingsUnknownnoreply@blogger.comBlogger24125tag:blogger.com,1999:blog-3855268335402896473.post-49575649066635094052014-07-11T00:09:30.814-07:002014-07-11T00:09:30.814-07:00Sorry for the delay. I discussed this here:
http:...Sorry for the delay. I discussed this here:<br /><br />http://darwins-god.blogspot.com/2014/07/heres-that-protein-protein-interaction.htmlCornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-23704360382516962062014-07-06T08:58:34.493-07:002014-07-06T08:58:34.493-07:00Cornelius Hunter: No, you are confusing single res...<b>Cornelius Hunter</b>: <i>No, you are confusing single residue replacement with multiple residue replacement. </i><br /><br />The model in Behe 2004 is *one* or more potentiating mutations followed by an enabling mutation. Behe assume potentiating mutations are nearly always detrimental, when most of the time, they are nearly neutral, and sometimes beneficial. <br /><br />Behe: The majority of nonneutral point mutations to the gene will yield a null allele (again, by which we mean a gene coding for a nonfunctional protein) because most mutations that alter the amino acid sequence of a protein effectively eliminate function.<br /><br />As we have already shown, single mutations are commonly not detrimental to function. Behe cites Reidhaar-Olson, who say "At some positions only one or two residues are functionally acceptable; at other positions a wide range of residues and residue types are tolerated." He also cites Bowie 1989: "The identities of approximately one-third of the residues in Arc repressor are functionally important, about one-half are structurally important, and the remainder are unimportant for either structure or function." Lim & <br />Sauer: "The random alteration of hydrophobic core positions in the N-terminal domain of lambda-repressor, both individually and in combination, shows that there are many ways of repacking the core of the protein." And so on. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-56333996727759650962014-07-06T08:39:28.000-07:002014-07-06T08:39:28.000-07:00Z:
No, you are confusing single residue replaceme...Z:<br /><br />No, you are confusing single residue replacement with multiple residue replacement. Your original point, in attempting to refute Behe's uncontroversial point that protein-protein binding is a hard problem for evolution, was that proteins typically can sustain a significant number of (multiple) substitutions. This is not generally true. When I pointed this out to you, you responded with citations stating that typically, only about a third of residues, if altered, affect the protein function significantly. So *single* substitutions can occur at most locations. That is true, but it does not imply that a protein can sustain very many multiple substitutions. There's quite a bit if data on that, showing that function rapidly falls off with only a few substitutions.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-72206101576479807882014-07-06T06:39:49.705-07:002014-07-06T06:39:49.705-07:00Cornelius Hunter: Well for starters that is false....<b>Cornelius Hunter</b>: <i>Well for starters that is false.</i><br /><br />Axe et al., A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease, Biochemistry 1998: "Exhaustive-substitution studies, where many amino acid replacements are individually tested at all positions in a natural protein, have proven to be very valuable in probing the relationship between sequence and function. The broad picture that has emerged from studies of this sort is one of functional tolerance of substitution."<br /><br />Guo et al., Protein tolerance to random amino acid change, PNAS 2004: "the probability that a random amino acid replacement will lead to a protein's functional inactivation ... was found to be 34% ± 6%."<br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-49532587406920326972014-07-05T19:54:38.716-07:002014-07-05T19:54:38.716-07:00Z:
As proteins are generally tolerant of many mut...Z:<br /><br /><i>As proteins are generally tolerant of many mutations, there will usually be ...</i><br /><br />Well for starters that is false.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-40955788687673730622014-07-05T18:07:23.584-07:002014-07-05T18:07:23.584-07:00Cornelius Hunter: For instance, he took the exampl...<b>Cornelius Hunter</b>: <i>For instance, he took the example of protein-protein binding surfaces and showed how traditional evolution does not have the resources to evolve them. But again, no harm. </i><br /><br />There are many problems with Behe & Snoke 2004, among them: <br /><br />* "Traditional evolution" includes recombination, including sexual recombination, which Behe fails to incorporate into his model. <br /><br />* As proteins are generally tolerant of many mutations, there will usually be a large variety of different versions of the same protein even before duplication, some of which may have the potentiating mutation. <br /><br />* The potentiating mutation may be functionally neutral or even have some advantage. <br /><br />* Most protein-protein binding evolved early in the history of life, when the supposed rarity of 10^-20 is not a significant hurdle. <br /><br />* Potentiating mutations have been observed. See Blount et al., Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 2008. <br /><br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-73889117027330020572014-07-05T08:51:43.285-07:002014-07-05T08:51:43.285-07:00Zachriel:
however, he never showed such a thing ....Zachriel:<br /><br /><i>however, he never showed such a thing ...</i><br /><br />Can you explain what you mean here? Why do you say that?Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-4273416105383016602014-07-05T04:54:51.572-07:002014-07-05T04:54:51.572-07:00Cornelius Hunter: To this day there are myriad bio...<b>Cornelius Hunter</b>: <i>To this day there are myriad biological structures for which we do not know how they evolved, and we have no detailed description of a series of numerous, successive, slight modifications, leading to the structure. </i><br /><br />We don't have to know everything to know some things. There is ample evidence of transitions, including the evolution of complex structures. <br /><br /><b>Cornelius Hunter</b>: <i>For instance, he took the example of protein-protein binding surfaces and showed how traditional evolution does not have the resources to evolve them. But again, no harm. </i><br /><br />If he had, it would require either revising or discarding the current theory of evolution, however, he never showed such a thing. That's why his claims have never had any effect on evolutionary theory. <br /><br /><b>Cornelius Hunter</b>: <i>Evolution would be false according to that 1982 paper. </i><br /><br />The hypothesis would have been falsified, and that would mean either revising or discarding the then current theory of evolution. <br /><br /><b>Cornelius Hunter</b>: <i>The new answer is horizontal gene transfer, which evolution is supposed to have created against all odds so that evolution could happen. </i><br /><br />As we can directly observe horizontal gene transfer, it's not such as leap to think that it worked in the past. For most taxa, the phylogenetic tree is not difficult to discern, even if there are some genes that don't match the tree. <br /><br /><b>Cornelius Hunter</b>: <i>So I think evolutionists have presented some flawed ideas for how evolution could be falsified. </i><br /><br />Evolutionary theory makes all sorts of predictions, and they are tested every day, with no reference to creationism. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-12463341363792182642014-07-04T09:56:41.537-07:002014-07-04T09:56:41.537-07:00Ian:
So I think evolutionists have presented some...Ian:<br /><br />So I think evolutionists have presented some flawed ideas for how evolution could be falsified. But it is, nonetheless, falsifiable. It would be false if creationism or design were demonstrated to be true, or highly likely. This is what evolutionists consistently ask for when challenged: "If you have a better theory then we'll drop evolution."<br /><br />This makes sense, because evolution is proved by contrastive thinking. It is the failure of creationism and design that proved evolution, and so it requires a proof of creationism or design to falsify evolution.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-66802844093712994502014-07-04T09:50:48.900-07:002014-07-04T09:50:48.900-07:00Ian:
Darwin presented another criterion, regardin...Ian:<br /><br />Darwin presented another criterion, regarding utilitarianism which was at the foundation of evolution:<br /><br />"The foregoing remarks lead me to say a few words on the protest lately made by some naturalists, against the utilitarian doctrine that every detail of structure has been produced for the good of its possessor. They believe that very many structures have been created for beauty in the eyes of man, or for mere variety. This doctrine, if true, would be absolutely fatal to my theory. "<br /><br />This criterion reveals some of the underlying metaphysics. But the criterion is not very good because it is not scientific (something Darwin later mentions).<br /><br />Popper criticized evolution for not being falsifiable at one point, and David Penny tried to address that in an influential 1982 paper. Penny presented an example (protein sequence comparisons) he said would have falsified evolution, had the results come out differently. But 30 years later the results did come out differently. Evolution would be false according to that 1982 paper. But now Penny has changed the criterion. So his 1982 falsifiability criterion was not genuine. You can read about it here:<br /><br />http://darwins-god.blogspot.com/2011/07/david-pennys-reversal-and-why.html<br /><br />continued ...Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-5248405237823810672014-07-04T09:36:42.897-07:002014-07-04T09:36:42.897-07:00Ian:
Falsification of evolution is tricky. Darwin...Ian:<br /><br />Falsification of evolution is tricky. Darwin presented a criterion ("If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.") but it wasn't a very good one because it is so difficult. How can one prove a universal negative dealing with a theory that is so flexible? Indeed the passage in which that criterion appears is a good demonstration of that flexibility.<br /><br />To this day there are myriad biological structures for which we do not know how they evolved, and we have no detailed description of a series of numerous, successive, slight modifications, leading to the structure. But such ignorance does no harm to evolution.<br /><br />Behe's work is a good example. For instance, he took the example of protein-protein binding surfaces and showed how traditional evolution does not have the resources to evolve them. But again, no harm.<br /><br />It seems Darwin's criterion is either too difficult to demonstrate, or if one does demonstrate it, we just set it aside, assuming that a solution will come some day. One way or another, the theory is protected.<br /><br />continued ...Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-11325243677780138122014-07-03T18:47:44.684-07:002014-07-03T18:47:44.684-07:00Marcus One wonders what it would take to falsify ...<i><b>Marcus</b> One wonders what it would take to falsify the theory.</i><br /><br />You're all highly knowledgeable about science in general and evolution in particular, CH especially. What would <i>you</i> look for as a falsification?Anonymoushttps://www.blogger.com/profile/11311738457332907931noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-45919159625039108482014-07-02T08:49:32.154-07:002014-07-02T08:49:32.154-07:00One wonders what it would take to falsify the theo...One wonders what it would take to falsify the theory.Marcushttps://www.blogger.com/profile/05905104887549850614noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-48556265347025764732014-06-29T16:18:53.918-07:002014-06-29T16:18:53.918-07:00You guys are freaking morons. This is scary.You guys are freaking morons. This is scary.Rebel Sciencehttps://www.blogger.com/profile/11762287159937757216noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-9153715316314846152014-06-29T10:06:54.097-07:002014-06-29T10:06:54.097-07:00Scientists determine electric organs in fish are d...<i>Scientists determine electric organs in fish are due to convergent evolution, and how they adapted from muscle.</i><br />Funny, I must have missed this world shaking proof.Rebel Sciencehttps://www.blogger.com/profile/11762287159937757216noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-49499617670868688802014-06-29T08:09:59.214-07:002014-06-29T08:09:59.214-07:00Glenn: I even appreciate Scott's willingness t...Glenn: I even appreciate Scott's willingness to help prove your point about teleological arguments:...<br /><br />If you think I've proved Cornelius' point, then it would seem my comment has gone over your head. <br /><br />"Purpose", in teleological arguments, refers to something endowed by a source. Yet, I said that good ideas are good, regardless of their source. So, your response seems to indicate you cannot recognize this philosophical assumption, even after I pointed it out to you. <br /><br />For example, I'm a computer scientist, not a cancer researcher. Despite this fact, let's hypothetically assume I decide to create a drug for the purpose of curing cancer. I then order laboratory mice that have cancer and administer my drug. Given the above, it would come as no surprise that my drug doesn't actually serve the purpose of curing cancer, despite the fact that I developed it for that specific purpose.<br /><br />IOW, any treatment that was actually successful would be successful because it embodied the "knowledge" of how cancerous cells multiply, how they can be identified and how cell death can be induced in just those cells, while excluding healthy cells. IOW, curing cancer occurs when the right transformations of matter occurs, which is independent of anyone's purpose. Ideas are jugged by their contents, not the source. <br /><br />To use another example, let say an actual researcher decided to find away to extend human life. As such, she might develop a drug protocol specifically for that purpose, then order middle aged mice for testing. Since all ideas start out as conjectures, she might find that her protocol doesn't actually extend the life of her test mice beyond their normal lifespan. But, for the sake of illustration, let's assume it does actually extend their life by a year. However, a year after ordering them, the mice supply company called and apologies for what must be the obvious mixup that occurred. It ends up, the mice she received weren't actually healthy middle aged mice but actually had been given cancer for testing as in the previous hypothetic experiment. They assumed her mice should be dead long ago, but in our hypothetical experiment, they were not! It ends up, the researchers protocol ended up curing the cancer in those mice, which was not her original purpose. This is an unexpected consequence. <br /><br />Again, curing cancer occurs when the right transformations of matter occurs. That's independent of anyone's desire, including whether or not any researcher's treatment was developed for that specific purpose. To reiterate, we judge ideas by their contents, not their source. <br /><br />On the other hand, your response to my comment suggests you think the exact opposite. For my comment to be teleological, you must assume an idea solves a problem due to having been endowed that purpose, not it's contents. Some authoritative source wanted it to work that way, so it did. But, as I've illustrated above, that doesn't survive rational criticism. Scotthttps://www.blogger.com/profile/11193595678064010528noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-74751097291289931342014-06-28T17:54:48.844-07:002014-06-28T17:54:48.844-07:00Good points Glenn.Good points Glenn.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-30454871586853631702014-06-28T17:21:04.785-07:002014-06-28T17:21:04.785-07:00Thanks Dr. H.
Many good points:
1) Darwin shifts t...Thanks Dr. H.<br />Many good points:<br />1) Darwin shifts the burden of proof to those who do not accept his theory: "Prove to me there are not 100 blue faeries hovering somewhere above the South Pacific Ocean; and if you can't prove it, then you are either uneducated (don't understand the theory) or you are a creationist."<br />2) when the only argument for evolution of highly complex electric organs with no common ancestor is that they MUST have evolved independently six times without small incremental changes, it really is past time to consider a new explanation for their existence.<br />3) the concept of a "genetic toolbox" is a teleological argument employed to keep a explicitly non-teleological theory from sinking; kind of like trying to keep the Titanic afloat with those little plastic armbands kids wear in swimming pools.<br /><br />I even appreciate Scott's willingness to help prove your point about teleological arguments: Scott wrote: "Good ideas, including electric organs, are good regardless of their source. Evolution converges on them because they are good ideas. They solve problems." Thanks Scott.Glenn Jhttps://www.blogger.com/profile/05974895763468680337noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-2928445644411134712014-06-28T10:26:12.902-07:002014-06-28T10:26:12.902-07:00Good ideas, including electric organs, are good re...Good ideas, including electric organs, are good regardless of their source. Evolution converges on them because they are good ideas. They solve problems. <br /><br />This is in contrast to assumption that ideas have to come from an authoritative source. Scotthttps://www.blogger.com/profile/11193595678064010528noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-51882975490417551132014-06-28T08:15:04.664-07:002014-06-28T08:15:04.664-07:00Darwin: Hence in the several fishes furnished with...<b>Darwin</b>: <i>Hence in the several fishes furnished with electric organs, these cannot be considered as homologous, but only as analogous in function.</i><br /><br />As Darwin was aware, muscular neurons are homologous, even if they are in different anatomical structures. Anatomic structures don't become homologous just because the cellular structures are. <br /><br /><b>Darwin</b>: <i>It is incredible that the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation.</i><br /><br />And this basic rule still applies. <br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-83471104743810632862014-06-28T08:02:53.719-07:002014-06-28T08:02:53.719-07:001. Darwin hypothesized that electric organs in fis...1. Darwin hypothesized that electric organs in fish are due to convergent evolution, adapted from muscle. <br />2. Scientists determine electric organs in fish are due to convergent evolution, and how they adapted from muscle. <br />3. Mapou: This fully falsifies Darwinian evolution. <br /><br />Darwin falsified Darwin 150 years ago! <br /><br />-<br />xposted from AtBC<br />Zachrielhttps://www.blogger.com/profile/16081260898264733380noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-85360579855023699152014-06-28T06:55:11.201-07:002014-06-28T06:55:11.201-07:00Aristotelianism lives on today as a property of ID...Aristotelianism lives on today as a property of ID's designer. It's "Design" needs to be explained. <br /><br />For example, how did the designer know exactly what genes would result in the right proteins that would result in the electric origins of fish? Or did he simply will them into existence?<br /><br />If the latter, that would be the spontaneous creation of knowledge since fish build copies of themselves, including those very electric organs, using the instructions in their genes. And, according to Cornelius, spontaneous origins is absurd. <br /><br />So, it would seem that the designer is either itself complex entity, because it contains the knowledge of what genes would results in just the right proteins, which would result in just the right biological adaptations, or that same knowledge was spontaneously created.<br /><br />Which is it? Better yet, which option am I not considering? <br /><br />Anybody?Scotthttps://www.blogger.com/profile/11193595678064010528noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-14823742233259824042014-06-28T06:47:00.085-07:002014-06-28T06:47:00.085-07:00Absurdity?
But good ideas are good regardless of...Absurdity? <br /><br />But good ideas are good regardless of where they came from, right? Or perhaps you judge ideas according to their source?Scotthttps://www.blogger.com/profile/11193595678064010528noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-19980495878128555992014-06-28T02:54:53.972-07:002014-06-28T02:54:53.972-07:00When I heard this reported on the radio my first t...When I heard this reported on the radio my first thought was to wonder how long it would be before it appeared here - <i>et voila!</i>.Anonymoushttps://www.blogger.com/profile/11311738457332907931noreply@blogger.com