tag:blogger.com,1999:blog-4948885059517209129.post7276437195409116837..comments2023-10-29T08:04:00.488-07:00Comments on Quintessence of Dust: Introns and designStephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.comBlogger41125tag:blogger.com,1999:blog-4948885059517209129.post-16502380886837720172010-06-01T15:29:18.295-07:002010-06-01T15:29:18.295-07:00Hi Brad. No, I haven't. He got the last word, ...Hi Brad. No, I haven't. He got the last word, and I'm fine with that. I thought the discussion here was more enlightening, anyway.Stephen Mathesonhttps://www.blogger.com/profile/05057004085073574659noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-54688454997797631492010-06-01T09:54:56.401-07:002010-06-01T09:54:56.401-07:00Steve, have you ever followed up on Mike's rep...Steve, have you ever followed up on Mike's replies to this post?Bradnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-69758792699703584342010-04-05T08:02:18.564-07:002010-04-05T08:02:18.564-07:00Arthur, It appears as if you once again misunderst...Arthur, It appears as if you once again misunderstood. MG's hypothesis is that introns is one of the factors that facilitated mammalian-like multicellular complexity. He acknowledged that bacteria can form multicellular assemblages in his response to Steve.<br /><br />See here:<br />http://designmatrix.wordpress.com/2010/03/31/cell-plans-and-evolution/#more-2255Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-30214111363226504402010-04-05T06:23:48.310-07:002010-04-05T06:23:48.310-07:00Steve,
I notice in your discussion of multicellul...Steve,<br /><br />I notice in your discussion of multicellularity in bacteria that you did not mention bacteria like filamentous cyanobacteria, myxobacteria, and some magnetic bacteria. These all have multicellular lifestyles (even obligatorily multicellular) that are quite akin to what we see in filamentous fungi, oomycetes, and the like. That these bacteria have such clear multicellular developmental programs really makes it hard to argue that introns in protein-coding genes are important for multicellularity in a general sense.Arthur Hunthttp://www.aghunt.wordpress.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-8975699554051521592010-04-04T22:29:41.616-07:002010-04-04T22:29:41.616-07:00Looks like Mike responded:
http://designmatrix.wo...Looks like Mike responded:<br /><br />http://designmatrix.wordpress.com/2010/04/04/the-general-rule/Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-28020851896394402832010-04-04T16:37:54.444-07:002010-04-04T16:37:54.444-07:00Art,
I'm not sure Steve would mind you taking...Art,<br /><br />I'm not sure Steve would mind you taking on Mike here. But even if he did, there's always your own blog. We sports enthusiasts are willing to travel vast distances to see a good fight.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-77875541835498658292010-04-04T14:32:44.666-07:002010-04-04T14:32:44.666-07:00Arthur, just curious, which of those organisms in ...<i>Arthur, just curious, which of those organisms in that table do you think has "overlaps", in terms of intron number, density, size, etc, with multicellular critters?</i><br /><br />Fully half of the 14 organisms in the table that have intron numbers greater than Drosophila are not multicellular plants or animals. I haven't bothered to check into genome sizes, but it's a fair bet that most or all have gene numbers that are lower than Drosophila. <br /><br /><i>"...as a general rule, introns are far more common in multicellular genomes than single-celled genomes..."</i><br /><br />That's not what the data say.<br /><br />Bilbo, seeing that this is Steve's blog, I'm going to limit my further participation in this thread to back-and-forth with Steve (if there is any). So I guess I won't be having much to say about MG's efforts to rescue his hypothesis.Arthur Hunthttp://www.aghunt.wordpress.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-27451345145288287782010-04-03T23:35:02.747-07:002010-04-03T23:35:02.747-07:00Notice also how he is carefully avoiding answering...Notice also how he is carefully avoiding answering my specific questions. It's bizarre.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-90928398198490779482010-04-03T23:22:40.652-07:002010-04-03T23:22:40.652-07:00Alan, try clicking on the big "Intron" w...Alan, try clicking on the big "Intron" word in his cloud on the sidebar (try reading the whole thing this time :))<br /><br />Bilbo, I'm more interested where Arthur takes the "more data" from, as he has previously failed to provide any data that contradict the MG hypothesis. <br /><br />Arthur, just curious, which of those organisms in that table do you think has "overlaps", in terms of intron number, density, size, etc, with multicellular critters?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-22443802531243659292010-04-03T20:37:43.337-07:002010-04-03T20:37:43.337-07:00Hi Art,
I'm enjoying watching the fight. Bet...Hi Art,<br /><br />I'm enjoying watching the fight. Better than watching my Pistons lose. I was wondering if you're going to respond to Mike's latest thread.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-55744699429224539712010-04-03T09:53:44.674-07:002010-04-03T09:53:44.674-07:00More data that contradicts MG's "clue&quo...More data that contradicts MG's "clue" can be found in <a href="http://nar.oxfordjournals.org/cgi/content-nw/full/35/14/4737/T2" rel="nofollow">Table 2</a> of <a href="http://nar.oxfordjournals.org/cgi/content/full/35/14/4737" rel="nofollow">this paper</a>. Focus on the first two columns, and notice that there is considerable overlap between the extents intron contents of many unicellular organisms and animals (even without normalizing for genome sizes or gene numbers).<br /><br /><i>"First, as a general rule, introns are far more common in multicellular genomes than single-celled genomes,"</i><br /><br />I don't think so.Arthur Hunthttp://http//www.aghunt.wordpress.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-45470019733718774522010-04-03T00:54:01.662-07:002010-04-03T00:54:01.662-07:00It seems Mike Gene has decided:
(quote)
No, the ...It seems Mike Gene has decided:<br /><br />(quote)<br /><br />No, the issue of introns is not central to my position. I raised the issue after reading Steve’s review of Meyer’s book, as I thought some people might be interested in a different approach than the usual evolution vs. design template. The intron issue is just one facet of my front-loading thesis and I once again demonstrated that a teleological perspective can a) generate testable hypotheses that are b) supported by some evidence.<br /><br />(unquote)<br /><br />and has switched moderation on (at least for me) at his blog. Not sure where the demonstrations took place that Gene refers to.Alan Foxhttps://www.blogger.com/profile/16470368958109056177noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-74278334587241350512010-04-02T15:10:05.607-07:002010-04-02T15:10:05.607-07:00I have no idea what you're talking about. I do...I have no idea what you're talking about. I don't disagree with the Roy's conclusion at all, and neither does MG, and neither does Roy's conclusion contradict MG's hypothesis.<br /><br />It looks like all you did here was completely ignore my response. See my above response and let me know if you have any questions.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-39838667538994948312010-04-02T15:08:40.679-07:002010-04-02T15:08:40.679-07:00This comment has been removed by the author.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-65386380290909990512010-04-02T14:54:11.513-07:002010-04-02T14:54:11.513-07:00Hi Ashe,
You said recently:
"MG's wordi...Hi Ashe,<br /><br />You said recently:<br /><br /><i>"MG's wording is more accurate.<br /><br />"First, as a general rule, introns are far more common in multicellular genomes than single-celled genomes,”"</i><br /><br />MG's wording does not accurately represent what Drs. Scott Roy and Walter Gilbert said in the paper I linked to above. To repeat: <br /><br /><i>""We find: (i) <b>intron density in the plant-animal ancestor was high,</b> perhaps two-thirds that of humans and three times that of Drosophila; and (ii) intron density in the ancestral bilateran was also high, equaling that of humans and four times that of Drosophila.""</i><br /><br />If you don't mind my prying, I wonder why you accept MG's opinion and not that of Roy and Gilbert. Is there something about the approach the latter use that calls their conclusions into question?<br /><br />Thanks.Arthur Hunthttp://www.aghunt.wordpress.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-33361044038976948032010-04-02T08:17:07.217-07:002010-04-02T08:17:07.217-07:00MG's wording is more accurate.
"First, ...MG's wording is more accurate. <br /><br />"First, as a general rule, introns are far more common in multicellular genomes than single-celled genomes,”Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-27353480837584741342010-04-02T05:39:52.077-07:002010-04-02T05:39:52.077-07:00Mike Gene points to a quote in a 1999 Scientific A...Mike Gene points to a quote in a <a href="http://www.scientificamerican.com/article.cfm?id=what-is-known-about-the-f" rel="nofollow">1999 Scientific American Article</a> where Sandro J. de Souza is quoted:<br /><br /><b>In general, nuclear introns are widespread in complex eukaryotes, or higher organisms. Simple prokaryotes and eukaryotes (such as fungi and protozoa) lack them.</b><br /><br />Does <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44KPSG8-2&_user=10&_coverDate=01%2F02%2F2002&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=05dc371b9ccc580f6c47b98f662bcb62" rel="nofollow">Introns in protein-coding genes in Archaea</a> indicate ongoing developments?Alan Foxhttps://www.blogger.com/profile/16470368958109056177noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-66465955089453535682010-04-01T17:09:08.397-07:002010-04-01T17:09:08.397-07:00Still doesn't contradict MG's hypothesis, ...Still doesn't contradict MG's hypothesis, since he regards ancestors as exceptions that prove the rule, see his discussion on chaonoflagellates and chlamy.<br /><br />You might be interested in this quotation:<br /><br />"Protein-coding genes have, on average, 8.3 exons per gene and are intron-rich relative to other unicellular eukaryotes and land plants (15) (fig. S21); only 8% lack introns (Table 1) (1). The average Chlamydomonas intron is longer (373 bp) than that of many eukaryotes (16), and the average intron number and size are more similar to those of multicellular organisms than those of protists (fig. S21) (1, 17)."<br /><br />http://www.sciencemag.org/cgi/content/abstract/318/5848/245Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-39169923742888509692010-04-01T16:36:03.856-07:002010-04-01T16:36:03.856-07:00Hi Ashe,
My comments about introns in "lower...Hi Ashe,<br /><br />My comments about introns in "lower" eukaryotes speaks to this remark by MG:<br /><br /><i>"Let me now provide a couple of clues to support the hypothesis that introns facilitated the evolution of multicellular life.<br /><br />First, as a general rule, introns are far more common in multicellular genomes than single-celled genomes." </i><br /><br />It's pretty clear that, "as a general rule", introns are not necessarily "far more common in multicellular organisms than single-celled genomes".<br /><br />I guess I could have made more clear the connection between my comments and MG's claims. Sorry about that.Arthur Hunthttp://www.aghunt.wordpress.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-15786787236814401262010-04-01T12:33:11.807-07:002010-04-01T12:33:11.807-07:00IMO, the paper Arthur references doesn't contr...IMO, the paper Arthur references doesn't contradict Mike's hypothesis, it complements it. It just studies genomic complexity from the point of view of intron loss. <br /><br />That the early ancestors of eukaryotes had such genomic complexity, which may have lead to the origin of spliceosomal introns and the spliceosomal machinery, fits well with an evolutionary path that was "front-loaded". The early ancestors were therefore phenotypically plastic, followed by the evolution of modern organisms whose forms were stabilized by selection. Since those were the initial conditions (intron-rich ancestral genome), the ratio between intron losses and gains increased in many lineages, resulting in the observed trends towards losses. <br /><br />A protein functions "arsenal" of a higher organism contains more<br />functions than the arsenal of a simpler one. And the functions are produced via a network of alternative splicing events with higher complexity.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-57076247995459542372010-04-01T12:11:11.963-07:002010-04-01T12:11:11.963-07:00Oops, that was Dan, not Doug.Oops, that was Dan, not Doug.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-32504457755701211542010-04-01T12:08:41.375-07:002010-04-01T12:08:41.375-07:00Alexander and Doug,
Mike Gene is the only guy I k...Alexander and Doug,<br /><br />Mike Gene is the only guy I know working on the front-loading hypothesis. He would say that the way you preserve elements for multicellularity in prokaryotes is by making them useful in the prokaryotes.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-83853028789603660112010-04-01T09:52:36.879-07:002010-04-01T09:52:36.879-07:00Hi Bill,
Mike doesn't start with a conclusion...Hi Bill,<br /><br />Mike doesn't start with a conclusion, he starts with a hypothesis, where fishing for supporting evidence is allowed.<br /><br />I've never tried poofing a bacterium, but I imagine it would be easier than poofing a wombat. ;)Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-82900364633048324102010-04-01T09:13:21.914-07:002010-04-01T09:13:21.914-07:00Hi Prof. Matheson,
I appreciate your responding t...Hi Prof. Matheson,<br /><br />I appreciate your responding to Mike's ideas. For those of us who follow his blog, it's more interesting when others challenge his views. And it's had the added benefit of flushing Art out of the bushes. I'll be curious to see if Mike responds to him as well. <br /><br />One question: I can't help but notice your strong antipathy to a design perspective. I'm curious if part of that is rooted in your Reformed theology, which I believe takes a very dim view of Natural theology.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-2463152939947054422010-03-31T11:05:15.264-07:002010-03-31T11:05:15.264-07:00Hi Steve,
You asked:
Can we agree that introns an...Hi Steve,<br />You asked:<br /><br /><i>Can we agree that introns and mobile elements are very likely to have played a decisive role in eukaryotic and/or metazoan evolution? </i><br /><br />Just speaking of introns for now (to keep with the theme of the OP), I would say, in a word, no.<br /><br />The way I look at this, there are three options: introns played a decisive role in multicellularity, some property of multicellularity played a decisive role in the dynamic of intron evolution in multicellular organisms, or there is no connection between the two (any perceived connection is actually just coincidence). If we are to presume some sort of cause-and-effect, then I think a better case can be made for the second of these options than the first. Specifically, I think that regulatory changes were more important for the evolution of multicellularity than were the sizes of proteomes (which, if I read things correctly, is the outcome of the expansion of number, size, and functioning of introns). And it is quite possible that regulatory changes, especially those that affect RNA metabolism, promoted subsequent intron evolution.<br /><br />As an aside, <a href="http://www.ncbi.nlm.nih.gov/pubmed/15687506" rel="nofollow">here</a> is another study that contradicts MG's assertions, starting with the very base of the eukaryotic tree. From the abstract:<br /><br /><i>"We find: (i) intron density in the plant-animal ancestor was high, perhaps two-thirds that of humans and three times that of Drosophila; and (ii) intron density in the ancestral bilateran was also high, equaling that of humans and four times that of Drosophila."</i>Arthur Hunthttp://www.aghunt.wordpress.comnoreply@blogger.com