tag:blogger.com,1999:blog-37148773.post3653694571411447203..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Four things that Francis Collins learned from sequencing the human genomeLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger68125tag:blogger.com,1999:blog-37148773.post-33535117117599276462015-08-15T10:43:21.910-04:002015-08-15T10:43:21.910-04:00"No one knows all the roles of isoforms gener..."No one knows all the roles of isoforms generated by all the isoform generating mechanisms"<br /><br />Actually, with V(D)J recombination, we know a lot about its role: it is how antibodies are made. During B-cell production, the V, D, and J units coding for immunoglobulins are randomly spliced together, so that B-cells each carry an antibody with a different specificity. So that explains alternative splicing in one gene.<br /><br />Another interesting aspect of this is how antibody production recapitulates evolution by natural selection. When a B cell first encounters a foreign antigen it can bind to, it is activated and begins to divide rapidly. These cells then undergo affinity maturation, it which random mutations are introduced into the binding site of the antibody, generating a large pool of genetic variation. Forms which bind the antigen less efficiently or lose the ability to bind the antigen no longer receive the proliferation signal and soon get selected out of the B cell population. Forms which bind better continue to receive activation signal and continue to proliferate, increasing in frequency.<br /><br />So by random mutation and non-random selection for better binding variants, antibodies with an increased affinity for the antigen are evolved. Pretty cool, isn't it?<br /><br />Also, it proves wrong the hypothesis put forward by many creationists, notably including Behe, that random mutation cannot create better protein binding domains, but only break them. This is proven wrong billions of times every day across the Earth.Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11496042188140564802015-08-15T09:07:28.318-04:002015-08-15T09:07:28.318-04:00Alternative splicing doesn't just create more ...Alternative splicing doesn't just create more than one protein per gene but creates protein isoforms. It is just one of many mechanisms that generate isoforms and there could be billions if not trillions of these isoforms.<br /><br />There are other isoform generation mechanisms than Alternative Splicing such as V(D)J recombination that is known to have the potential to create billions if not trillions of isoforms. No one thinks those isoforms are spurious just because they get trashed, the trashing process is part of the computation for adaptive immune response.<br /><br />What defines spurious is in the eye of the beholder and beholders who insist something is junk just because it eventually is trashed should consider programmed cell death and apoptosis.<br /><br />No one knows all the roles of isoforms generated by all the isoform generating mechanisms (such as alternative splicing, V(D)J recombination, post transcription editing, post translational modification, etc.). Our high throughput techniques can hardly catalogue even a fraction of them.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63458086634763111422015-08-14T15:49:12.226-04:002015-08-14T15:49:12.226-04:00The author is not a geneticist, biochemist or anyt...The author is not a geneticist, biochemist or anything of the sort, and the book is not about genetics. No source is offered for the "98% junk" claim, there's no bibliographical reference to back it up. So here's just another non-specialist spreading an urban myth. By the way, Shenkin estimates that "only" about 500 million bp are "truly informative", and that they account for less than 2% of the human genome. If that were true, the total length of the human genome would be at least 25 billion bp. I don't think he did his homework well before writing that chapter.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36404921424245096022015-08-14T15:42:20.803-04:002015-08-14T15:42:20.803-04:00It's a claim by a medical ethicist, not a biol...It's a claim by a medical ethicist, not a biologist. But at least it's an actual claim. Better than nothing, but not much better.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80827120515898059462015-08-14T15:39:15.310-04:002015-08-14T15:39:15.310-04:00Ha! You found something. It's fairly old (pu...Ha! You found something. It's fairly old (published in 1992) and pretty obscure (only cited 6 times since 1992), but I think it qualifies. Well done!Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77408580697790329392015-08-14T15:17:45.767-04:002015-08-14T15:17:45.767-04:00See the last two paragraphs on page 274 of this sc...See the last two paragraphs on page 274 of this scientific publication:<br /><br /><a href="https://books.google.com/books?id=7azsCAAAQBAJ&pg=PA274&lpg=PA274&dq=said+that+98%25+of+the+human+genome+is+junk&source=bl&ots=wvmQaGdjlX&sig=qQOMqGNkf6fHRrpFnJMV5wlryus&hl=en&sa=X&ved=0CFAQ6AEwCDgKahUKEwjRyYbU16fHAhUI1B4KHcJnAD0#v=onepage&q=said%20that%2098%25%20of%20the%20human%20genome%20is%20junk&f=false" rel="nofollow">Medical Ethics: Evolution, Rights and the Physician. By H.A. Shenkin, published by Springer</a><br /><br />Gary Gaulinhttps://www.blogger.com/profile/10925297296758439900noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80770849063318243832015-08-14T13:32:34.688-04:002015-08-14T13:32:34.688-04:00the 3 billion base pairs that comprised our mere 2...<i>the 3 billion base pairs that comprised our mere 21,000 genes made up a paltry 2% of the entire genome</i><br /><br />Cite a scientific publication, not an incompetent journalist who doesn't even seem to know that 3 billion bp is the approximate <i>total</i> length of the human genome (2% of that is only 60 million bp). She stupidly repeats an urban myth, which is just what incompetent science reporters do.<br /><br />What geneticists ever said what she claims they said? Names and references, please.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80423801492828858672015-08-14T13:15:29.631-04:002015-08-14T13:15:29.631-04:00Here is how the lies for the devil work.
Nobody h...Here is how the lies for the devil work.<br /><br />Nobody has ever been attributed in person by the "98% of Your DNA is Junk" but all over the lies are being repeated: <br /><br /><a href="https://www.youtube.com/watch?v=uX7Okcqe8eU" rel="nofollow">"98% of Your DNA is Junk"</a><br /><br /><a rel="nofollow">The Race Is Over<br />The great genome quest is officially a tie, thanks to a round of pizza diplomacy. Yet lead researcher Craig Venter still draws few cheers from his colleagues</a><br /><br />"Junk. Barren. Non-functioning. Dark matter. That’s how scientists had described the 98% of human genome that lies between our 21,000 genes, ever since our DNA was first sequenced about a decade ago. The disappointment in those descriptors was intentional and palpable.<br /><br />It had been believed that the human genome — the underpinnings of the blueprint for the talking, empire-building, socially evolved species that we are — would be stuffed with sophisticated genes, coding for critical proteins of unparalleled complexity. But when all was said and done, and the Human Genome Project finally determined the entire sequence of our DNA in 2001, researchers found that the 3 billion base pairs that comprised our mere 21,000 genes made up a paltry 2% of the entire genome. The rest, geneticists acknowledged with unconcealed embarrassment, was an apparent biological wasteland."<br />Jasshttps://www.blogger.com/profile/00012083978513644307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43348896959251761202015-08-14T11:17:30.645-04:002015-08-14T11:17:30.645-04:00If two populations of the same species are geograp...<i>If two populations of the same species are geographically isolated from each other, they are likely to experience somewhat different selective environments.</i><br /><br />The reference to "two populations" is the part I somehow glossed over in your original comment. I was therefore trying to figure out how reproductive isolation would arise as a byproduct of selection in the absence of geographic barriers. (I figured this could happen, but very rarely relative to the situation where two or more populations are geographically separated.)<br /><br />You've recommended the book before, and believe me, I've taken note. I'd prefer for a Kindle edition to become available, though. :-)judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27309383477856483062015-08-14T10:51:15.855-04:002015-08-14T10:51:15.855-04:00judmarc,
If there's a central message of Coyn...judmarc,<br /><br />If there's a central message of Coyne & Orr's book <i>Speciation</i>, that's it. If two populations of the same species are geographically isolated from each other, they are likely to experience somewhat different selective environments. In the lab, populations under different selective regimes tend to evolve partial reproductive isolation. The selection isn't directed at isolation but at other characters, and the isolation arrives as an incidental product of selection for other things. You could explain that by pleiotropy, hitchhiking, or perhaps something else, but that's the observation. For examples (and for much else) I recommend the book.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22800235872515710912015-08-14T09:11:49.522-04:002015-08-14T09:11:49.522-04:00No, I could not find anyone arguing in favor of it...<i>No, I could not find anyone arguing in favor of it either. It was more like there were a small number of experienced scientists who cautiously accepted the 98% figure, in which case they believed it was possibly true. But they were not well enough convinced for it to be an issue worth arguing over.</i><br /><br />Hmm. When I attempted to replicate your study, I was not able to find any scientist claiming that 98% of the human genome is junk, not even at the level of "cautiously accept(ing)" that "it was possibly true." . I <i>did</i> find websites from the likes of TIME, FoxNews, and catholic.org that repeated the claim that 98% of the genome is <i>non-coding</i>, and who confused this with "junk". But obviously you would have rejected this data as irrelevant to the question being investigated. Right?Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76595880953980941402015-08-14T06:40:54.438-04:002015-08-14T06:40:54.438-04:00Hi John, would like to know a little more about wh...Hi John, would like to know a little more about what this means if you would be kind enough to explain: <br /><br /><i>it's fairly likely that isolation will arise as a byproduct of selection</i><br /><br />An example (doesn't need to be actual) would likely do.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2099537754361273332015-08-14T01:14:59.372-04:002015-08-14T01:14:59.372-04:00I say again: can you find anyone making the claim,...I say again: can you find anyone making the claim, however tentatively, that 98% of the human genome is junk? If so, who is that person?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59945450550722382972015-08-13T21:16:13.772-04:002015-08-13T21:16:13.772-04:00Did you find anyone at all arguing in favor of the...<i>Did you find anyone at all arguing in favor of the claim? I didn't.</i><br /><br />No, I could not find anyone arguing in favor of it either. It was more like there were a small number of experienced scientists who cautiously accepted the 98% figure, in which case they believed it was possibly true. But they were not well enough convinced for it to be an issue worth arguing over.Gary Gaulinhttps://www.blogger.com/profile/10925297296758439900noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48553302661523841322015-08-13T20:31:47.033-04:002015-08-13T20:31:47.033-04:00So you did find some information that 98% of human...<i>So you did find some information that 98% of human genome being junk was claimed you just don't like that it was never attributed to one person or as Larry would put it: " no knowledgeable scientist would make such a claim."</i><br /><br />No, I'm afraid you can't read. I found nobody making the claim that 98% of the genome is junk. I found only people (like you) making the claim that somebody else, always unspecified, thinks that 98% of the genome is junk. This is the equivalent of the urban legend, the sort of thing that always happens to a "friend of a friend" but never to anyone real. You have nothing.<br /><br /><i>What I would really like to see from you and the followers of devil is how the mechanism of the evolution works especially including the random genetic drift. I know you have been married to this, so explain how it works and why Coyne is not buying it. Why he is against it? </i><br /><br />Short answer: he isn't against it, and I have no idea where you got that notion. I see no need to explain to you how evolution works; it's a big subject, and you can always read a text if you want. If you were actually interested in learning I might be more forthcoming, but you have displayed your pride in ignorance too many times here.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35450464844400499352015-08-13T20:24:41.262-04:002015-08-13T20:24:41.262-04:00I found that fisheries bureau description of drift...I found that fisheries bureau description of drift to be mighty poor. What they describe isn't drift; it's founder effect. Founder effect is a form of drift but by no means the typical case. Sampling error happens in every generation in every finite population, simply because that population doesn't perfectly reproduce the exact frequency of every allele from parent generation to offspring generation.<br /><br />Now, what Coyne thinks of drift is simple: it fixes alleles at a much slower rate than selection, so that speciation due entirely to drift will happen much more slowly than speciation due to selection. And while two populations wait to become incompatible through drift, it's fairly likely that isolation will arise as a byproduct of selection, and thus speciation by drift will seldom happen. Note that here we're talking about plain vanilla allopatric speciation, in which both geographically separated populations are of reasonable size, not tiny peripheral isolates.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61158098973088745762015-08-13T20:19:27.120-04:002015-08-13T20:19:27.120-04:00It tested true, but it was also true that many who...<i>It tested true, but it was also true that many who repeated the claim were arguing against that possibility.</i><br /><br />Did you find anyone at all arguing in favor of the claim? I didn't.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24584625905046268692015-08-13T20:04:10.791-04:002015-08-13T20:04:10.791-04:00so explain how it works and why Coyne is not buyin...<i>so explain how it works and why Coyne is not buying it. Why he is against it?</i><br /><br />How it works, from a fisheries bureau:<br /><br /><i>Genetic drift is random changes in gene frequency that occur because of sampling error. Sampling error can be natural, or it can be manmade. Natural sampling errors are those which occur when earthquakes, floods, landslides, or other natural disasters subdivide a population and isolate small groups of organisms. This process is a major force in the evolution of new species.</i><br /><br />What Coyne thinks: He's not "against it," since plainly random stuff happens, so he'd very likely agree with the first part of the quote above. He might not agree with the last sentence - he might not feel drift should be assigned such a major (direct) role in evolution of new species. By "direct" I mean that it is plain drift opens up new evolutionary pathways, but Coyne may feel it is not directly responsible for the changes at the end of the pathway where a new species emerges.<br /><br />(I'm a layperson, so the foregoing may have mistakes, for which I am solely responsible.)judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54744219814517304042015-08-13T19:02:14.232-04:002015-08-13T19:02:14.232-04:00Gary, when you tested it, what was the result?
It...<i>Gary, when you tested it, what was the result?</i><br /><br />It tested true, but it was also true that many who repeated the claim were arguing against that possibility.Gary Gaulinhttps://www.blogger.com/profile/10925297296758439900noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61975879928456985292015-08-13T19:01:43.599-04:002015-08-13T19:01:43.599-04:00John Harshman,
What I would really like to see ...John Harshman, <br /><br />What I would really like to see from you and the followers of devil is how the mechanism of the evolution works especially including the random genetic drift. I know you have been married to this, so explain how it works and why Coyne is not buying it. Why he is against it? <br />Jasshttps://www.blogger.com/profile/00012083978513644307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29967907327076230572015-08-13T18:42:04.699-04:002015-08-13T18:42:04.699-04:00John Hirschman,
I googled, as Lies suggested. I f...John Hirschman,<br /><br /><i>I googled, as Lies suggested. I found many statements that 98% of the genome is junk. But all of them were made as strawman claims to argue against, and never attributed to any particular person. That is, the only people saying that 98% of the genome is junk were people who wanted to claim that there's no junk.</i><br /><br />So you did find some information that 98% of human genome being junk was claimed you just don't like that it was never attributed to one person or as Larry would put it: " no knowledgeable scientist would make such a claim."<br /><br />You see John, the ten famous icons of evolution were never attributed to one person including the Muller-Urey experiment. Not the actual results that supposedly their experiment resolved like the problem with the origins of life. But it was being sold as such. <br /><br />You see John, in the world of lies for devil it is not the proof or disproof you have that matters. It is how you sell it. <br /><br />Arnold Swarzenegger once said that you can sell even the worst possible product if you just know how to do it.<br /><br /> He was referring to himself as not having any acting abilities and speaking with the heavy German accent.Jasshttps://www.blogger.com/profile/00012083978513644307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38833954964534284012015-08-13T09:10:09.174-04:002015-08-13T09:10:09.174-04:00Gary, when you tested it, what was the result?Gary, when you tested it, what was the result?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90349830089810452902015-08-13T08:07:18.828-04:002015-08-13T08:07:18.828-04:00"1.My friends are the very knowledgeable scie..."1.My friends are the very knowledgeable scientist who think you are just another (?) you fill in."<br /><br />Hahahahaha. I laughed for like a whole 20 seconds. Ohmyjebus...Uncivilized Elkhttps://www.blogger.com/profile/12876539220615373258noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19707111282362885342015-08-12T22:21:51.742-04:002015-08-12T22:21:51.742-04:00"Don't you get it? You've lost. "..."Don't you get it? You've lost. "<br /><br />Where did Diogenes lose? Where has the Central Dogma been falsified?<br /><br />Let's assume it has been falsified. What do you think this means for the field of evolution?Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81372220887129258172015-08-12T21:40:46.278-04:002015-08-12T21:40:46.278-04:001.My friends are the very knowledgeable scientist ...1.My friends are the very knowledgeable scientist who think you are just another (?) you fill in.<br /><br />2. Why would you add another layer to the complexity to your already weak, weak assumptions? Don't you get it? You've lost. You had lost before this issue. Why would someone like you do it? Give me one really good reason and I will leave you alone.Jasshttps://www.blogger.com/profile/00012083978513644307noreply@blogger.com