tag:blogger.com,1999:blog-3855268335402896473.post3727258366598243582..comments2024-01-23T02:32:28.567-08:00Comments on Darwin's God: De Novo Genes: What are the Chances?Unknownnoreply@blogger.comBlogger39125tag:blogger.com,1999:blog-3855268335402896473.post-37026128460070086912009-12-15T15:26:03.904-08:002009-12-15T15:26:03.904-08:00"Duke, the T-urf13 protein is a trait selecte..."Duke, the T-urf13 protein is a trait selected for by human (read: intelligent) ... an intelligently directed breeding program."<br /><br />I read Randy Wysong's "The Creation Controversey" (1976) about 20 years ago. In it, he claimed that life had been created in a lab (news to me) but that this did not mean abiogenesis was real or that evolution was true, since the people added 'KNOW-HOW' (caps in original) and that the experiment was designed, the materials were designed, etc. He was essentially finding a way to pre-reject any sort of origin of life research and by erroneous extention, to reject any evidence for evolution.<br /><br />The more things change, the more they don't.Doppelgangerhttps://www.blogger.com/profile/07019994267093407424noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-85462534010168576602009-12-15T15:21:48.923-08:002009-12-15T15:21:48.923-08:00Nat:
"Now, 1 trillion wahles might be enough ...Nat:<br />"Now, 1 trillion wahles might be enough to get an adaptation that requires 2 amino acid cahnges, but for 3 you need 1 trillion times 1 million whales. That's harder to come by."<br /><br />There seems to be an overriding yet unacknowledged assumption that many such sequential mutations would have been necessary. <br />As has been alluded to, it is more likley that 'new' proteins are less of an issue in terms of evolution than simply altering the timing or order of expression during development; this also goes for the sequential acquisition of a pre-specified series of amino-acid altering mutations.<br /><br /><br />Oh, and I, too, would like some justification for th e'million million' assertion. Thanks.Doppelgangerhttps://www.blogger.com/profile/07019994267093407424noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-12107395774161979622009-12-09T14:41:13.428-08:002009-12-09T14:41:13.428-08:00Duke, the T-urf13 protein is a trait selected for ...Duke, the T-urf13 protein is a trait selected for by human (read: intelligent) breeders for it's primary trait: Cytoplasmic Male Sterility (CMS). An unfortunate side affect was that it makes the plant susceptible to a fungal toxin. <br /><br />Meaning plants which have this gene will get killed preferentially by a certain fungus. Also plants that have this gene are male sterile. That's two bad things. And not only that, both of them were obtained in an intelligently directed breeding program.Tragic Mishaphttps://www.blogger.com/profile/00561848085559413544noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-47986745442224228732009-12-05T14:12:33.439-08:002009-12-05T14:12:33.439-08:00natschuster : If I make small random changes to my...natschuster : <b>If I make small random changes to my car, I might get lucky, and oneof the changes will imporve my cars performance, but I don't think that it will ever turn my car into a truck.</b><br /><br />The El Camino is a transitional fossil. ;)Thomas Reinardhttps://www.blogger.com/profile/00738492127289675466noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-83340001910747578552009-12-02T17:39:23.397-08:002009-12-02T17:39:23.397-08:00And there are orphan genes, genes that have no kno...And there are orphan genes, genes that have no known homologues, in every group of organism.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-23500478315268472602009-12-02T17:20:39.636-08:002009-12-02T17:20:39.636-08:00The herring gull and the lesser black backed gull ...The herring gull and the lesser black backed gull have been observed interbreeding, along with the yellow legged gull. So they may very well be all one species.<br /><br />And recent events concerning global warming have led to think that scientific consensus, doesn't mean very much.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-4782261131171749692009-12-02T17:18:22.970-08:002009-12-02T17:18:22.970-08:00What I ment by unique was unique, not completely u...What I ment by unique was unique, not completely unique, but having a unique configuration of amino acids. It does happen in individual species. Human proteins are different than chimp protein. And the article I sited that it is not just the time it takes for the new configuration of amino acids to appear, but for them to work through the population. It says >100,000,000 years for human like species. And this is assuming it is neutral, and not bad for rthe species. If it is negative, it will take longer. Something like the sickle cell mutation that gives resistance to malaria by a change in one amino acid in the hemoglobin molecule is what they have in mind, that happens. <br /><br />Now, if evolution has nothing to do with new proteins, then it has to do with contol genes. Reproductive isolation means that changes in the control genes are not overwhelmed by the old, unchanged genes, and have a chance to spread through a population. <br /><br />Now, 1 trillion wahles might be enough to get an adaptation that requires 2 amino acid cahnges, but for 3 you need 1 trillion times 1 million whales. That's harder to come by.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-82754096563700041902009-12-01T19:17:01.604-08:002009-12-01T19:17:01.604-08:00First of all, large organisms do have unique prote...<b>First of all, large organisms do have unique proteins, so evolution happened at the level of the protein as well. </b><br /><br />Reference? How many novel proteins are there between chimpanzees and humans? Gorillas and humans? Macaques and humans?<br /><br /><b>And evolution of forms requires changes in the genes that control development, which is probably much harder to get right than changing proteins.</b><br /><br />Reference? <br /><br />This is actually completely backwards from the case as I understand it. If you look at a list of the proteins used to construct us, we are virtually identical to chimpanzees, gorillas, cats, dogs, mice (of course the exact structure of the protein varies, but it's the same protein in a slightly different shape). Can you find a record of a <i>de novo</i> protein evolving in mammals? The only instance I can think of (ignoring the immune system, which is evolved to produce and react to novel proteins in the form of anti-bodies) is the venom in platypuses' spurs (and I might be wrong about that). Can you find a reference of a new protein evolving in mammals? If you find a reference, I'll discuss it, but until then...<br /><br />Current evolutionary theory holds that most metazoan evolution happens through reproductive isolation, which causes the populations to lose their ability interbreed; we can see this played out in real time in ring species such as the Herring Gull/Lesser Black-Backed Bull. Novel proteins don't play any major part at all in animal speciation (although if you find a reference, I'll be happy to change my story.) I'll joyously defend the scientific consensus, but don't ask me to defend your mis-interpretation of the consensus.<br /><br /><b>What I should have said about the article was that two specific amino acids necessary to create a new adaptation would take along time.</b><br /><br />Well, first off, you're assuming that the species you're talking about is asexual, where they first have to find one amino acid change, and then find the other after the first moves to fixity in the species. In a sexual species (like almost every animal in the world), things don't work that way. The two amino acid changes can arrive separately and then be mixed together in some fortuitous offspring. This is a real, observed effect.<br /><br />Second, how long? Let me give you a back-of-the-envelope calculation. According to current thinking among people who've actually studied the physical world, whales separated from the rest of the hoofed mammals around 53 million years ago. Let's just say, for argument's sake, that throughout that time whales had a stable population of one million individuals, each with a lifespan of 50 years. I'm making these numbers up for illustration, using a ridiculously small population (considering the number of whales who existed up to historical times) and a ridiculously long life (considering that many of the early whales were small meat eaters like hoofed wolves). That is, I'm fudging the numbers in your favor by several orders of magnitude. <br /><br />There have been<br /><br />5.3e7 years * (5e1 years/whale)^-1 * 1e6 whales = <b>1.06e12 whales </b><br /><br />since the lineage began.<br /><br />There's your trillion whales. Of course (unless you show otherwise), I'm going to say there are no new proteins in whales, just refinements in existing proteins inherited from their common mammalian ancestors. The numbers are there, though.<br /><br /><b>And I must say I agree with jimbo. Your civility is refreshing.</b><br /><br />Thank you very much. I'm really seeing this as a two part exercise; explaining the ideas as clearly and succinctly as possible and (more difficult and more important) not losing my temper doing it ^_^.<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-36464792640357033012009-12-01T15:50:01.137-08:002009-12-01T15:50:01.137-08:00Duke:
First of all, large organisms do have uniqu...Duke:<br /><br />First of all, large organisms do have unique proteins, so evolution happened at the level of the protein as well. And evolution of forms requires changes in the genes that control development, which is probably much harder to get right than changing proteins.<br /><br />What I should have said about the article was that two specific amino acids necessary to create a new adaptation would take along time.<br /><br />And I must say I agree with jimbo. Your civility is refreshing.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-3650688013571439032009-12-01T15:05:15.227-08:002009-12-01T15:05:15.227-08:00Duke,
I appreciate your willingness to engage and...Duke,<br /><br />I appreciate your willingness to engage and answer questions. On other parts of the Internet I've been, evolution proponents mock and insult those who ask questions about it. Thank you for your civility and willingness to explain things repeatedly.<br /><br /> -jimboUnknownhttps://www.blogger.com/profile/11394074243845982832noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-51132554448536101232009-12-01T03:56:04.997-08:002009-12-01T03:56:04.997-08:00According to this model, it would take a really lo...<b>According to this model, it would take a really long time for a two amino acid change to happen in humans.</b><br /><br />You're being careless in your terms; a two amino acid change is trivially easy. Each of us has proteins that are two amino acids different from our parents due to random mutation. (I have the math for that, if you want to see it). <br /><br />Read the article again; this is about the creation, from nothing, of a completely new protein that didn't exist previously, not the modification of an existing protein. (To use creationist terms, we're talking about an observed instance of protein <i>macro</i>-evolution, where as the "two amino acid change" you're denying with this comment is <i>micro</i>-evolution.)<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-11436611612429044262009-12-01T03:41:23.292-08:002009-12-01T03:41:23.292-08:00I undertand that a single amino acid in a protein ...<b>I undertand that a single amino acid in a protein chnages on the average once per every 1,000,000 organisms in a species. That means that if a beneficial chnage requires that two amino acids change, then you need a trillion individuals to get it. Bacteria can do that. Blue whales can't.</b><br /><br />Yes! You're exactly right! You've made the correct evolutionary prediction. Blue whales don't create new proteins as they evolve, and this goes for all "higher" animals.<br /><br />Unfortunately, that doesn't have anything to do with their speciation. Evolution and speciation in metazoans is a matter of chromosomal re-arrangements and re-shaping of existing proteins, not creation of new proteins. (Rather, I should say, that evolutionary theory predicts that speciation in metazoans comes from re-shuffling of genetic material and not from <i>de novo</i> proteins. If you wanted to <i>disprove</i> neo-darwinian evolutionary theory, you could do it by finding lots and lots of new proteins in human that don't exist in chimpanzees!)<br /><br />Do you see why I say bringing up speciation was red herring? It doesn't touch on this article.<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-8477215710509286872009-11-29T17:06:44.552-08:002009-11-29T17:06:44.552-08:00According to this model, it would take a really lo...According to this model, it would take a really long time for a two amino acid change to happen in humans.<br /><br /><br /><br />http://www.genetics.org/cgi/content/full/180/3/1501natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-53959024773271040812009-11-29T16:51:32.350-08:002009-11-29T16:51:32.350-08:00I undertand that a single amino acid in a protein ...I undertand that a single amino acid in a protein chnages on the average once per every 1,000,000 organisms in a species. That means that if a beneficial chnage requires that two amino acids change, then you need a trillion individuals to get it. Bacteria can do that. Blue whales can't.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-71591658357475408022009-11-29T16:45:02.169-08:002009-11-29T16:45:02.169-08:00Duke:
All the cases mentioned may very well be ju...Duke:<br /><br />All the cases mentioned may very well be just part of the normal variation within one species.<br />The literature often calls theses possible incipient species not clearly a new species.<br /> <br /><br />Now, one problem with the car to truck scenario is that some the random changes will not work unless anyother corresponding change happens at the same time. An how many changes do you need to effect some real change that is an advantage? And the majority of copies won't have any change. So you need and lots and lots of copies. For organisms that reporduce quickly, like bacteria that might work. But for whales and humans it becomes a problem. <br /><br />And again, I'm not convinced that the case mentioned could turn corn into a new species.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-55181915562406950182009-11-29T16:02:13.333-08:002009-11-29T16:02:13.333-08:00Duke:
"You've said that it takes "a...Duke:<br /><br />"You've said that it takes "a million million" random arrangements to find a functional protein, right? What I'm trying to show is that that number, a million million, 1e12, is actually quite small next to the number chances to find it. That's what I was getting at with the whole 4e20 corn plants thing; that is far, far larger than 1e12. If you look at the number of corn plants that are created every year, you see that there are well over 4e8 times more corn genomes than your 1e12 number."<br /><br />You are comparing apples and oranges and not making sense. Let me suggest you wait for AG to make his points.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-78050004144307673712009-11-29T14:38:09.945-08:002009-11-29T14:38:09.945-08:00If I make small random changes to my car, I might ...<b>If I make small random changes to my car, I might get lucky, and oneof the changes will imporve my cars performance, but I don't think that it will ever turn my car into a truck.</b><br /><br />Really? You can't see turning your car into a truck in small steps? Your <i>car</i> into a <i>truck</i>? Really?<br /><br />Are you serious?<br /><br />Of course, your thought experiment of turning a car into a truck is wildly wrong, betraying a gross misunderstanding of what your opponents believe. What you'd actually be doing is copying your car, repeatedly, thousands upon thousands of time, with minor variations. Those copies in the second generation that cease to function are destroyed; those that are better at performing whatever you need them to do are kept (in the case of the car-to-truck transition, this might be hauling cargo rather than carrying passengers) to breed the third generation. Repeat as necessary. This sort of thing does happen and has been demonstrated happening.<br /><br />And we have seen new species come about, both in the lab and in the field; check out Wikipedia and Google with "Speciation" to get your learning process started. <br /><br />I notice that you didn't say what, exactly, you find untenable in the bacteria-whale transition. Do you not have any specifics? What have you learned about what biologists say about that process?<br /><br />Duke<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-6673675995407860922009-11-29T10:30:32.001-08:002009-11-29T10:30:32.001-08:00Duke:
The appearence of this new protein will not...Duke:<br /><br />The appearence of this new protein will not allow the corn to become a new species. It is more likely to make the corn become extinct. And evben if it didn't drive the corn to extinction, I;m not convinced that it could turn the corn into a new species. If I make small random changes to my car, I might get lucky, and oneof the changes will imporve my cars performance, but I don't think that it will ever turn my car into a truck.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-57867032110471849202009-11-29T09:35:58.018-08:002009-11-29T09:35:58.018-08:00The point of controversy is whether this mechanism...<b>The point of controversy is whether this mechanism can explain how bacteria can turn into blue whales. That is an evolutionists claim, but they haven't demonstrated that it is possible.</b><br /><br />And I feel that they have demonstrated it is possible, because I've looked at the evidence, whereas I suspect that you have not.<br /><br />What about the proposed evolution of the whale do you find untenable? <br /><br />Please, be specific. Where does the scientific consensus break down for you?<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-58049213465198249382009-11-29T06:54:46.315-08:002009-11-29T06:54:46.315-08:00Duke:
ID people, creationists, etc. have conceede...Duke:<br /><br />ID people, creationists, etc. have conceeded that microevolution does take place. Trivial changes in extant organisms happen. The point of controversy is whether this mechanism can explain how bacteria can turn into blue whales. That is an evolutionists claim, but they haven't demonstrated that it is possible.natschusterhttps://www.blogger.com/profile/13127240463824366637noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-37746398606622407662009-11-29T00:55:29.289-08:002009-11-29T00:55:29.289-08:00AG:
"maybe you could support your claims abo...AG:<br /><br />"maybe you could support your claims about mutational loads as the concept pertains to plant mitochondria. I would be interested in specific studies and data that are consistent with your (otherwise unsupported) assertions."<br /><br />Hmm, I didn't think I would need justification that ~10^-3 mutations/site/year would be a big mutational load on the corn mitochondria genome. What new explanation do evolutionists have for this?Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-63833056360776575752009-11-28T20:44:53.339-08:002009-11-28T20:44:53.339-08:00Isn't this new protein bad for the corn? Doesn...<b>Isn't this new protein bad for the corn? Doesn't it lead to sterility and vulnerability to a virus? So how can this mechanism be the one that leads to a new species? I'm curious.</b><br /><br /><br />Whether or not the protein is good or bad for corn is irrelevant; it's a new protein that has a new function, and it appears to have come about through unplanned, undirected, "natural" causes. Evolutionary theory requires this to happen at least occasionally, and if it did happen, it would invalidate intelligent design "theory". <br /><br />It seems to me that, at this point, mentioning forming a new species is a bit of a red herring; no one in this discussion is saying there was a speciation event, and no one in the more general community says that new proteins are sufficient or even necessary to make a speciation event (if I recall correctly, we don't have <i>any</i> new proteins when compared to chimpanzees, although I might be wrong on that). <br /><br />It's like coming in on two auto mechanics discussing a carburetor, and saying "You can't get to Philly, the bridge is washed out." We're discussing two completely different things that are only tangentially related.<br /><br />At least it seems that way to me. I could be wrong, or expressing myself unclearly.<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-52368935800069358642009-11-28T20:33:51.028-08:002009-11-28T20:33:51.028-08:00Cornelius Hunter:
I thought you were saying you e...Cornelius Hunter:<br /><br /><b>I thought you were saying you each mitochondria generates something like a new protein / year. If you're not saying that, then what are you saying? You haven't spelled out the details so I'm left trying to figure out what you are thinking.</b><br /><br />Ah, yes. This is a common problem with me. I have such problems communicating what I think to others; I sometimes suspect I must as Asperger's Syndrome or something. Let me try a different tack.<br /><br />You've said that it takes "a million million" random arrangements to find a functional protein, right?<br /><br />What I'm trying to show is that that number, a million million, 1e12, is actually quite small next to the number chances to find it. That's what I was getting at with the whole 4e20 corn plants thing; that is far, far larger than 1e12. If you look at the number of corn plants that are created every year, you see that there are well over 4e8 times more corn genomes than your 1e12 number. And this is for the nuclear corn DNA, not for corn mitochondrial DNA or chloroplastic DNA.<br /><br /><b>OK, so sometimes the mutations generate new proteins. You'll still need more details. At about what frequency does this occur?</b><br /><br />I'm terribly sorry, but I'm going to have to turn this back on <i>you</i>. Where did you get that "million million" number? I'm relying on <i>you</i> for frequency of useful proteins from random searches; that's the one thing I didn't look up. What's your reference?<br /><br /><b>Do we have any reason to think so many mutations can occur in so short a time? </b><br /><br />Yes, we do. Every time DNA gets copied, errors are made. This is simple, brute fact. That's what we were getting at with that whole "Platonic ideal" thing.<br /><br /><b>What you're saying seems to make no sense, but perhaps I just don't have all the details yet.</b><br /><br />I think the fact this doesn't seem to make sense is my fault for adding <i>too many</i> details. Let my try to simplify it.<br /><br />You said that you have to search 1e12 random arrangements to find a functional protein.<br /><br />I showed that there are far, far more random arrangements occurring in nature, since each corn plant, each mitochondria and each chloroplast is, in part, a random arrangement. <br /><br />To me, this answers your question about where the new protein comes from. You set a limit as how likely finding any protein with any function is (a million million) and I showed that there are far more chances to find a protein that that.<br /><br />Is that clearer?<br /><br />DukeDuke Yorkhttps://www.blogger.com/profile/12847805422765204747noreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-14086803729067312532009-11-28T19:19:09.315-08:002009-11-28T19:19:09.315-08:00Cornelius, maybe you could support your claims abo...Cornelius, maybe you could support your claims about mutational loads as the concept pertains to plant mitochondria. I would be interested in specific studies and data that are consistent with your (otherwise unsupported) assertions.<br /><br />And please, try to point to studies of plant mitochondria. A general blanket reference to nuclear genes won't cut the mustard here.<br /><br />(We'll get to the unsupported claims that are behind your ideas about protein evolution later.)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3855268335402896473.post-32320092601101397672009-11-28T18:28:59.366-08:002009-11-28T18:28:59.366-08:00Duke:
"Really? Please, just show me where I&...Duke:<br /><br />"Really? Please, just show me where I'm wrong, so I can see your point of view."<br /><br />I thought you were saying you each mitochondria generates something like a new protein / year. If you're not saying that, then what are you saying? You haven't spelled out the details so I'm left trying to figure out what you are thinking.<br /><br />"a corn mitochondrion doesn't generate a new protein every year. Each mitochondrion has some random variation from its parent; that random variation may or may not enable it to produce a novel protein."<br /><br />OK, so sometimes the mutations generate new proteins. You'll still need more details. At about what frequency does this occur? Do we have any reason to think so many mutations can occur in so short a time? What you're saying seems to make no sense, but perhaps I just don't have all the details yet.Cornelius Hunterhttps://www.blogger.com/profile/12283098537456505707noreply@blogger.com