tag:blogger.com,1999:blog-37148773.post1626223333359903444..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: IDiots, suckers, and the octopus genomeLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger14125tag:blogger.com,1999:blog-37148773.post-48104473197787794612015-08-27T12:24:26.971-04:002015-08-27T12:24:26.971-04:00All of which shows that the creationist position i...All of which shows that the creationist position is sustained by their laziness to search and find. In an era pf easy access to information no less.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13005964713358186022015-08-26T11:17:04.666-04:002015-08-26T11:17:04.666-04:00Sometimes I think the biggest problem with science...Sometimes I think the biggest problem with science today is that press releases tend to be sensationalist. Journalists get confused, laymen get confused, and wicked people misuse every result possible.<br /><br />This is especially true for the life sciences and economics, since there are so many interests involved. How can we expect the general public to trust science like this?roxhttps://www.blogger.com/profile/07204669572707780537noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3740833402928342022015-08-26T09:56:54.921-04:002015-08-26T09:56:54.921-04:00Carl, that's a cool article but let's keep...Carl, that's a cool article but let's keep in mind that many of these so-called orphan genes have not been shown to have a function. They may be transcribed regions and they may produce some protein but that doesn't mean they are real genes with a confirmed biological function. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84128300833087495062015-08-26T02:33:29.445-04:002015-08-26T02:33:29.445-04:001. Origin and Spread of de Novo Genes in Drosophil...1. Origin and Spread of de Novo Genes in Drosophila melanogaster Populations<br />http://www.sciencemag.org/content/343/6172/769.abstract<br /><br />Abstract:<br />Comparative genomic analyses have revealed that genes may arise from ancestrally nongenic sequence. However, the origin and spread of these de novo genes within populations remain obscure. We identified 142 segregating and 106 fixed testis-expressed de novo genes in a population sample of Drosophila melanogaster. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames, with natural selection playing a significant role in their spread. These results reveal a heretofore unappreciated dynamism of gene content.<br /><br />2. Emergence of a New Gene from an Intergenic Region<br />http://www.sciencedirect.com/science/article/pii/S0960982209014754<br /><br />Abstract:<br />It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and transcript processing would be unlikely to evolve in parallel with a new gene function [1, 2] . We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5–3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes [3–8] . The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5′ regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.<br /><br />Check Fig: 3 of the above paper. It shows how enabling mutations led to the emergence of this gene from non-coding DNA in the mouse lineage.<br /><br />3. Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori<br />http://www.sciencedirect.com/science/article/pii/S001457931500705X<br /><br />Abstract:<br />Orphan genes (OGs) which have no recognizable homology to any sequences in other species could contribute to the species specific adaptations. In this study, we identified 738 OGs in the silkworm genome. About 31% of the silkworm OGs is derived from transposable elements, and 5.1% of the silkworm OGs emerged from gene duplication followed by divergence of paralogs. Five de novo silkworm OGs originated from non-coding regions. Microarray data suggested that most of the silkworm OGs were expressed in limited tissues. RNA interference experiments suggested that five de novo OGs are not essential to the silkworm, implying that they may contribute to genetic redundancy or species-specific adaptation. Our results provide some new insights into the evolutionary significance of the silkworm OGs.<br /><br />Casey Luskin & Co. are 100% wrong. Orphan genes are not evidence for ID. They arise by the normal processes of mutation, selection etc and their ancestral sequences can be traced.Anonymoushttps://www.blogger.com/profile/04852803503240037336noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8956862839309868542015-08-25T19:36:46.497-04:002015-08-25T19:36:46.497-04:00For a non-technical introduction to where new gene...For a non-technical introduction to where new genes come from, here's an article I wrote last year, and a TED-Ed video that emerged from it:<br />http://www.nytimes.com/2014/04/29/science/the-continuing-evolution-of-genes.html<br />https://www.youtube.com/watch?v=z9HIYjRRaDECarlhttps://www.blogger.com/profile/03829168960578664919noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29602677217855083332015-08-25T13:40:12.199-04:002015-08-25T13:40:12.199-04:00Here's the paper:
Functional proteins from a
...Here's the paper: <br /><a href="http://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf" rel="nofollow">Functional proteins from a<br />random-sequence library</a>. <br /><br />Creationism is bunk. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32268334888199522952015-08-25T09:50:52.522-04:002015-08-25T09:50:52.522-04:00The Szostak lab found functional proteins (four di...The Szostak lab found functional proteins (four different ones) in a pool of about 10^11 random sequence proteins (sequences that were 80 amino acids in length). And they only tested for one function (bind ATP), they could have tested for thousands of additional functions, such as chemical catalysts and binding to countless other molcules. They also only tested at one temperarure. Who's to say what else could be found in that pool of random sequence proteins?Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65349556026241780982015-08-25T09:02:22.887-04:002015-08-25T09:02:22.887-04:00 Twenty years ago I would have said that its absol... Twenty years ago I would have said that its absolutely impossible for a randomly chosen sequence to be transcribed and translated into a functional protein but it seems to me there is fairly good evidence that its happened. <br /> If this turns out to be true we can forget all the other arguments made in the Evo ID debate. This makes them all superfluous. This observation alone would completely demolish the ID position, and we could all go homeAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79377350443157938402015-08-25T07:25:54.240-04:002015-08-25T07:25:54.240-04:00There are bound to be some genes that fall outside...There are bound to be some genes that fall outside the limit of the statistical techniques used to infer sequence homology. Luskin has no comment on the greatly superior number of genes with sequence similarity, except when he feels like saying "it's Common Design". So, orphan genes indicate genes that had to be designed from scratch, apparent homologs those that could be reused. It's all evidence of Design, heads I win tails you lose. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23932322457187394642015-08-25T02:01:20.031-04:002015-08-25T02:01:20.031-04:00Long story short: they are the result of long peri...Long story short: they are the result of long periods of accumulating mutations in already existing genomic sequences.<br /><br /><br />They don't pop "out of nowhere".Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44871564568953846722015-08-24T21:07:46.128-04:002015-08-24T21:07:46.128-04:00Eric,
Here is a nice review of the topic of orpha...Eric,<br /><br />Here is a nice review of the topic of orphan gene evolution:<br /><br />http://www.nature.com/nrg/journal/v12/n10/abs/nrg3053.htmlDave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43347585530572247362015-08-24T20:34:27.041-04:002015-08-24T20:34:27.041-04:00Work in ants reveals that some orphan genes come f...Work in ants reveals that some orphan genes come from non-coding DNA that acquires a promoter. There are other sources:<br /><br />"Some can be traced to highly divergent products of gene duplications, overlapping or anti-sense reading frames (overprinting), domesticated transposons, resurrected<br />pseudogenes, or early frameshift mutations [citations]. Others may arise de novo from non-coding sequence."<br /><br />-- Arendsee et al. 2014, http://www.cell.com/trends/plant-science/pdf/S1360-1385%2814%2900193-9.pdfAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34203039244558976682015-08-24T20:12:32.480-04:002015-08-24T20:12:32.480-04:00Sorry, I'm new to this genetics thing, so may ...Sorry, I'm new to this genetics thing, so may I ask: Where do "orphan" genes come from? They are the genes that are organism-specific & distinguish that organism from even its nearest relatives. Casey thinks they actually do, as it were, come out of nowhere. In fact, they come out of "somewhere". What's the somewhere?Anonymoushttps://www.blogger.com/profile/08407210117304897641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71685439961730028492015-08-24T17:03:33.182-04:002015-08-24T17:03:33.182-04:00"Little facts like those don't stop the I..."Little facts like those don't stop the IDiots from sensationalizing the results of every new genome sequence."<br /><br />Indeed. Without their "this new finding is a major problem for Darwinism" spin, they would have no reason to post about the the genome in the first place. It's not as if they are writing for an audience that is interested in learning science, so the spin is the whole point! <br />Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.com