tag:blogger.com,1999:blog-37148773.post6918912393846466293..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Another failure: "The Mysterious World of the Human Genome"Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-37148773.post-14911958106280306062016-07-15T08:28:59.716-04:002016-07-15T08:28:59.716-04:00I assume you've read the book from cover to co...I assume you've read the book from cover to cover.<br /><br />Did you learn from reading the book that there are "clearly two sides of the fence" on the subject of epigenetics? If not, do you think you were deceived and mislead because you weren't told about the controversial nature of Frank Ryan's view? <br /><br />Do you think this is the proper way to explain science to a layperson?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43231245113681670312016-07-14T22:40:57.614-04:002016-07-14T22:40:57.614-04:00Not every reader of a genomics/ genetics/ biology ...Not every reader of a genomics/ genetics/ biology book is a scientist or academician. <br /><br />Some are plain joes/ janes who are just out to satisfy their curiosity of the world. Of these laypeople, some haven't touched a book on science for 20 years or more. I am one of the latter group.<br /><br />Sure, going by your scathing review, there seem to be generalizations and oversimplifications in this book, but in order to appeal to the reader like me, scientific accuracy and exactitude may not always work. For with accuracy and exactitude come technical jargon too. And jargon often puts off the lay reader.<br /><br />I hope you get what I'm saying. I guess the author has taken some liberties in order to appeal to a more general audience.<br /><br />And as far as the 'epigentics' topic is concerned, what I've seen from my readings, albeit general in nature, is that there are clearly two sides of the fence: those for epigeenetics and those staunchly against. I guess you might belong to the latter. But I'm not going to dispute you. Not having the requisite technical wherewithal to lean on, there's no way I'm going to ever know who is right, those for or those against.<br /><br />Now however, Amazon tells me you're the author of a university-level textbook on biochemistry, which has run into several editions right from 1994. So it seems you too would be a good author whose book(s) I should read. I shall thus wait for the day you bring out a popular science treatise.<br /><br />I hope I haven't bored youAnonymoushttps://www.blogger.com/profile/06799919869280429041noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41651509703654559682016-03-25T17:36:02.532-04:002016-03-25T17:36:02.532-04:00"..mutant minds...". From an intelligen..."..mutant minds...". From an intelligent designer? Blasphemy !Fair Witnesshttps://www.blogger.com/profile/02096585841391610098noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17662192000491502872016-03-25T01:06:20.145-04:002016-03-25T01:06:20.145-04:00Speaking of another not-so-candid admission of the...Speaking of another not-so-candid admission of the inadequacy of the theory, an exciting new concept emerges.<br /><br />https://www.newscientist.com/article/mg22930660-100-evolution-learn-natural-selection/?cmpid=NLC%7CNSNS%7C2016-2403-GLOB&utm_medium=NLC&utm_source=NSNSAL <br /><br /><i>"We now know that intuition fails us, with feathers, eyes and all living things the product of an entirely natural process."</i><br /><br />Of course, we actually don't now know any such thing. Highly educated minds (never underestimate the power of relentless inculcation) consciously piss themselves away, but in the dark and naked recesses of mutant minds, the doubts persist. And they damn well should. txpiperhttps://www.blogger.com/profile/03645156881353741058noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80500555541252700352016-03-22T12:24:37.171-04:002016-03-22T12:24:37.171-04:00True. Hybridization is so important in some plant...True. Hybridization is so important in some plants I work with that my view can become biased.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5917558770671720242016-03-22T12:22:16.899-04:002016-03-22T12:22:16.899-04:00Big deal. All vertebrates have also undergone at l...Big deal. All vertebrates have also undergone at least two rounds of polyploidization, and teleosts had undergone three. Note that Soltis & Soltis are referring to a polyploidization event at some unspecified time in the past. Allopolyploidy may be responsible for as much as 5% of speciation events in angiosperms according to some estimates, but that's still a fairly small percentage of the total.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3820413047945933742016-03-22T11:09:58.744-04:002016-03-22T11:09:58.744-04:00" Recent developments in genomics are revolut..." Recent developments in genomics are revolutionizing our views of angiosperm genomes, demonstrating that perhaps all angiosperms have likely undergone at least one round of polyploidization and that hybridization has been an important force in generating angiosperm species diversity." -- Soltis & Soltis 2009. <br /><br />Of course, the authors are sweeping the hybridization issue under the polyploidy umbrella, and I can't get further information at the moment without buying the article. <br /><br />I'm not trying to say hybridization is a more important source of variation in plants than is mutation within lineages. Nonetheless, it's big.<br /><br />One can quibble about where the hybridization occurs in relationship to speciation itself, but I think two things are important here. <br /><br />First, it seems to me that selection against hybridization can occur only after speciation has happened and the resulting offspring are of low fitness. Of course, inability to hybridize can develop accidentally, too, and can sometimes actually be the cause of the speciation.<br /><br />Second, I think that in plants there may not be the same selection pressure for preventing hybridization as there is in vertebrates. Most individual plants produce a lot more offspring than individual vertebrates, and the seeds produced by one maternal plants have several different fathers. So "wasting" a few as hybrids may have low cost, and sometimes those hybrids will pay off. Plants can't move to seek a better environment; offspring might benefit from having a set of genes that would have been harmful in the parent in its environment. <br /><br />Some plants seem set up for serious hybridization. The variable biological unit we call Kentucky Bluegrass (Poa pratensis) for example, consists of plants that share maternal genetic material but gain additional variation through hybridization; the offspring of hybridization join the interbreeding Poa pratensis unit. Poa pratensis also sets seed apomictically, without sex. <br /><br />Anyway. I should go have breakfast and stop rambling. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19215165696920466592016-03-22T09:43:52.985-04:002016-03-22T09:43:52.985-04:00Hybridizations do occur, of course. There are, for...Hybridizations do occur, of course. There are, for example, about 350,000 species of flowering plants with most lineages stretching back about 200 million years and quite a few hybridization events have occurred in those lineages. I don't know how many but maybe it's as high as 100,000. That's being generous and only counting hybridization events between genuine species that have been reproductively isolated for a long time.<br /><br />So, there would have been one of these events every 20 years somewhere among the many branches of a large tree—mostly between adjacent twigs. In contrast, every new generation of plants has hundreds of new mutations. These events aren't in the same ball park. <br /><br />Frank Ryan suggests that the mating of humans and Neanderthals is an example of hybridization but that's only significant if these are two different species. Otherwise it's no more significant than mating between subpopulations (races) that are part of the same species. <br /><br />(BTW, I don't count artificial selection as part of natural biological evolution.) <br /><br />The issue here is not whether epigenetics, hybridization, and symbiosis occur, it's whether their relative frequency is sufficient to count them as common contributors to change in the frequencies of alleles in a population. In other words, should they be incorporated into standard evolutionary theory or should each event be treated as one-off examples in the history of life? Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68805149539700895762016-03-22T09:16:46.204-04:002016-03-22T09:16:46.204-04:00Epigenetics is trivial. We've known for decade...Epigenetics is trivial. We've known for decades that bacteria inherit methylation at restriction sites and we've known for decades that the progeny of bacteria growing in glucose in the absence of lactose inherit <i>lac</i> repressor and a silenced <i>lac</i> operon.<br /><br />We've known for decades that yeast daughter cells inherit silenced regions of the genome at the Hidden MAT loci (HML or HMR) and we've known for decades that constitutive heterochromatin regions at the centromeres of eukaryotic cells is heritable.<br /><br />Not of this has caused a significant stir among evolutionary biologists because it's trivial on the time scale of evolution. The best thing that can be said about epigenetics is that in a very few rare instances it may actually lead to real genetic changes in the genome but this is an indirect effect that's no different from a lot of other things that may potentiate certain mutations. <br /><br />"Epigenetics" is biology's version of the gluten-free phenomenon. There's a little bit of truth in there somewhere but most of it is hype and misunderstanding promoted by people who epitomize the saying that "a little knowledge is a dangerous thing." Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71109051839220636312016-03-22T04:52:20.176-04:002016-03-22T04:52:20.176-04:00Dear Larry,
Epigenetics is not trivial when there ...Dear Larry,<br />Epigenetics is not trivial when there is epigenetic inheritance over several generations.<br />Hybridizations occur frequently in wild plants. Wheat, potato, tomato, cabbages, etc. are hybrids.<br />New symbiosis have been observed in the lab (Pak, J.W., and Jeon, K.W. (1997). J. Eukar. Microbiol. 44, 614-619)<br />Anonymoushttps://www.blogger.com/profile/16070497729266515629noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36755498176759388782016-03-21T17:39:00.553-04:002016-03-21T17:39:00.553-04:00I'm glad he knows it. He should have looked o...I'm glad he knows it. He should have looked over the video based on his book, and featuring him prominently, before it went out. More people will watch the video than read the book.Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22025272023288912722016-03-21T17:33:28.730-04:002016-03-21T17:33:28.730-04:00In humans, and many other complex species, genes o...<i>In humans, and many other complex species, genes occupy only a small fraction of all of the DNA, and are separated by long intervals of noncoding DNA. Some of this noncoding DNA functions in the control of how genes are used, but a lot of it is what is called "junk." This junk accumulates by various mechanisms and often contains long repetitive tracts with no information content. I will generally ignore this junk, but it is worth mentioning in order to have a picture of the structure of our genomes as archipelagoes of islands (genes) separated by vast areas of open sea (junk.)</i> Sean B. Caroll, "The Making of the Fittest" p. 76)<br /><br /><i>Most dark matter contains no instructions and is just space-filling "junk" accumulated over the course of evolution. In humans, only about 2 to 3 percent of our dark matter contains genetic switches that control how genes are used.</i> Sean B. Carroll, "Endless Forms Most Beautiful" p. 112 Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43226089761218001102016-03-21T15:44:42.021-04:002016-03-21T15:44:42.021-04:00I just watched "What Darwin Never Knew" ...I just watched "What Darwin Never Knew" again, and the errors surrounding junk DNA and the number of human genes jumped out at me. It's everywhere! Sean Carroll should know better.Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39043296376854252072016-03-21T14:37:45.646-04:002016-03-21T14:37:45.646-04:00"The author is Frank P. Ryan, a physician...&..."The author is Frank P. Ryan, a physician..."<br /><br />No need to elaborate...nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53985848048796214142016-03-21T12:45:37.408-04:002016-03-21T12:45:37.408-04:00They don't belong in the same league.
It don&...<i>They don't belong in the same league.</i><br /><br />It don't think they belong to the same category. I would have accepted gene transfer between symbionts as a genuine mechanism on a molecular level, but in all other cases we are talking just about adaptations and in some instances drift.<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7552213152370901672016-03-21T09:50:11.970-04:002016-03-21T09:50:11.970-04:00The author is only referring to symbiosis events t...The author is only referring to symbiosis events that affect the evolution of the genome. Of course he covers endosymbiosis and the importance of mitochondria and chloroplast but he also refers to other examples such as the association of algae and fungi to form lichens and the association of rhizobial bacteria with legumes. In the latter examples, the emphasis is on the genetic changes in each of the organisms that make up the symbiosis.<br /><br />He refers to a third kind of symbiosis such as the adaptation of hummingbirds to feed on nectar. I dismiss those examples as trivial—they are not substantially different from any other kind of adaptation to the environment.<br /><br />If we take only the serious examples of symbiosis, including but not confined to endosymbioses, then this is hardly a ubiquitous phenomenon nor one that has occurred repeatedly over the history of life affecting a large number of genes.<br /><br />Your quibble is noted ... perhaps I should have said about once every 100 million years and usually confined to a small clade. The message I'm trying to convey is that there's a huge, huge, difference in both time and extent between mutation and symbiosis as important creators of diversity. They don't belong in the same league. <br /><br />Read the book if you want to continue the discussion. He also talks about transposons and viruses as examples of symbiosis but that's really just semantics. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52822598347699774992016-03-21T09:01:45.538-04:002016-03-21T09:01:45.538-04:00Symbiosis happened only a few times in three billi...<i>Symbiosis happened only a few times in three billion years.</i><br /><br />You mean endosymbiosis here, right? Or actually you mean endosymbiosis where the endosymbionts end up as organelles of the host. Because there are certainly more examples of symbiosis and even obligatory endosymbiosis around.Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.com