Comments for ASA Voices http://www.asa3online.org/Voices A group blog of ASA members Tue, 09 Mar 2010 23:10:02 -0600 http://wordpress.org/?v=2.8.6 hourly 1 Comment on Chromosome 2 Fusion by Charles Austerberry http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-225 Charles Austerberry Tue, 09 Mar 2010 23:10:02 +0000 http://www.asa3online.org/Voices/?p=205#comment-225 One more reference on chromosome fusions: http://www.springerlink.com/content/186u771668271k1r/ This one is useful because it focuses on primate chromosome evolution. Cheers! Chuck One more reference on chromosome fusions:
http://www.springerlink.com/content/186u771668271k1r/
This one is useful because it focuses on primate chromosome evolution.
Cheers!
Chuck

]]> Comment on Chromosome 2 Fusion by Charles Austerberry http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-224 Charles Austerberry Tue, 09 Mar 2010 22:47:05 +0000 http://www.asa3online.org/Voices/?p=205#comment-224 Randy: One interesting recent paper about chromosome fusions reports work on grasses (such as wheat). http://www.pnas.org/content/106/37/15780.abstract Apparently chromosome fusions can happen in different ways, and which mechanism is most likely might depend upon the sort of organism.  In the grasses, insertion of one chromosome into another appears to have happened several times.  Whether via insertion of one into another as in grasses or via fusion of ends (fusion of telomeres) as in mammals, the main difficulty with fusion of entire chromosomes is that after the fusion event you've got a single chromosome with two centromeres (and thus, during mitosis and meiosis, there can be problems with chromosome segregation).  For that reason, people had speculated that in the grasses, the right and left arms of a chromosome might independently insert into two separate recipient chromosomes. The centromere that had been between those arms would fail to insert anywhere and be lost, thus avoiding the problem of adding a second centromere to an existing chromosome.  But, the data in the recent grass paper suggest that entire intact chromosomes have inserted into recipient chromosomes. Maybe inactivation of one of the two centromeres can happen rather quickly, perhaps first through epigenetic silencing, prior to more permanent inactivation via mutation.  Likewise, the telomeric fusion event that apparently led to human chromosome 2 might have been facilitated by quick epigenetic inactivation of one of the two centromeres. Telomeres (which are normally only at chromosome termini) winding up in the middle of a chromosome formed by fusion of two pre-existing chromosomes is likely not a big problem, at least not as big of a problem as having two centromeres.  As Carol Greider might have mentioned at the AAAS talk, the ciliated protists she studied have telomere-like sequences at several internal locations within their micronuclear chromosomes, as does human chromosome 2.  Now it is true that ciliated protists do strange things with their chromosomes when somatic macronuclei develop from germ-line micronuclei.  The micronuclear chromosomes get fragmented into a number of smaller macronuclear chromosomes, which then get telomeres added to their newly-created ends.  But the stable presence of telomere-like sequences in the middle of ciliate micronuclear chromosomes tells me that human chromosome 2 is not unique in having relics of ancient telomeres at internal (non-terminal) locations. Cheers! Chuck Randy:
One interesting recent paper about chromosome fusions reports work on grasses (such as wheat).
http://www.pnas.org/content/106/37/15780.abstract
Apparently chromosome fusions can happen in different ways, and which mechanism is most likely might depend upon the sort of organism.  In the grasses, insertion of one chromosome into another appears to have happened several times.  Whether via insertion of one into another as in grasses or via fusion of ends (fusion of telomeres) as in mammals, the main difficulty with fusion of entire chromosomes is that after the fusion event you’ve got a single chromosome with two centromeres (and thus, during mitosis and meiosis, there can be problems with chromosome segregation).  For that reason, people had speculated that in the grasses, the right and left arms of a chromosome might independently insert into two separate recipient chromosomes. The centromere that had been between those arms would fail to insert anywhere and be lost, thus avoiding the problem of adding a second centromere to an existing chromosome.  But, the data in the recent grass paper suggest that entire intact chromosomes have inserted into recipient chromosomes. Maybe inactivation of one of the two centromeres can happen rather quickly, perhaps first through epigenetic silencing, prior to more permanent inactivation via mutation.  Likewise, the telomeric fusion event that apparently led to human chromosome 2 might have been facilitated by quick epigenetic inactivation of one of the two centromeres.
Telomeres (which are normally only at chromosome termini) winding up in the middle of a chromosome formed by fusion of two pre-existing chromosomes is likely not a big problem, at least not as big of a problem as having two centromeres.  As Carol Greider might have mentioned at the AAAS talk, the ciliated protists she studied have telomere-like sequences at several internal locations within their micronuclear chromosomes, as does human chromosome 2.  Now it is true that ciliated protists do strange things with their chromosomes when somatic macronuclei develop from germ-line micronuclei.  The micronuclear chromosomes get fragmented into a number of smaller macronuclear chromosomes, which then get telomeres added to their newly-created ends.  But the stable presence of telomere-like sequences in the middle of ciliate micronuclear chromosomes tells me that human chromosome 2 is not unique in having relics of ancient telomeres at internal (non-terminal) locations.
Cheers!
Chuck

]]> Comment on ID not science, should it be called Natural Philosophy? by Ted Davis http://www.asa3online.org/Voices/2010/02/23/id-not-science-should-it-be-called-natural-philosophy/comment-page-1/#comment-223 Ted Davis Tue, 09 Mar 2010 17:44:47 +0000 http://www.asa3online.org/Voices/?p=195#comment-223 Dave, This is a very interesting issue that has not lost its relevance, even though it's largely an historical question.  As you realize, "natural philosophy" was the preferred term for "science," or at least for some aspects of the physical sciences, prior to the 19th century.   "Science" is an old word, going back to Chaucer's time in English (it came to us from Latin via French), but it wasn't widely used to mean the study of nature until ca. 1800 or later.  "Scientist" was coined by William Whewell in 1834, by analogy with "artist" (he said at the time), to identify anyone studying in the various "sciences" that were emerging or were already well established. At that point, teleological arguments were disappearing from scientific literature, esp on the Continent; they survived for another generation (or a bit longer) in England, perhaps b/c the best universities were still church controlled at that point.  There's a lot of controversy among historians, concerning whether the "big picture" (the change from older ways of doing science to newer ways) is really centered on the "scientific revolution" of the 16th & 17th centuries, or on the 19th century when secularization really took over.  In other words, "natural philosophy" was transformed in the "scientific revolution" into something like modern science, but it remained pretty closely tied to theology and natural philosophy until the latter part of the 19th century.  Thus, we have (if I may coin a term that Francis Schaeffer might have liked) "modern modern science" appearing in the 19th century, replacing "natural philosophy" which had been practiced since the ancient world and had been transformed into "early modern science" during the "scientific revolution." This is generating controversy, partly b/c the early modern period ("scientific revolution") is the classic period in my field (it's also the one I was trained in), and some are reluctant to see "modern modern science" appearing later on.  But, I think that's what happened. Dave,
This is a very interesting issue that has not lost its relevance, even though it’s largely an historical question.  As you realize, “natural philosophy” was the preferred term for “science,” or at least for some aspects of the physical sciences, prior to the 19th century.   “Science” is an old word, going back to Chaucer’s time in English (it came to us from Latin via French), but it wasn’t widely used to mean the study of nature until ca. 1800 or later.  “Scientist” was coined by William Whewell in 1834, by analogy with “artist” (he said at the time), to identify anyone studying in the various “sciences” that were emerging or were already well established.
At that point, teleological arguments were disappearing from scientific literature, esp on the Continent; they survived for another generation (or a bit longer) in England, perhaps b/c the best universities were still church controlled at that point.  There’s a lot of controversy among historians, concerning whether the “big picture” (the change from older ways of doing science to newer ways) is really centered on the “scientific revolution” of the 16th & 17th centuries, or on the 19th century when secularization really took over.  In other words, “natural philosophy” was transformed in the “scientific revolution” into something like modern science, but it remained pretty closely tied to theology and natural philosophy until the latter part of the 19th century.  Thus, we have (if I may coin a term that Francis Schaeffer might have liked) “modern modern science” appearing in the 19th century, replacing “natural philosophy” which had been practiced since the ancient world and had been transformed into “early modern science” during the “scientific revolution.”
This is generating controversy, partly b/c the early modern period (”scientific revolution”) is the classic period in my field (it’s also the one I was trained in), and some are reluctant to see “modern modern science” appearing later on.  But, I think that’s what happened.

]]> Comment on Chromosome 2 Fusion by Randy Isaac http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-222 Randy Isaac Mon, 08 Mar 2010 15:50:44 +0000 http://www.asa3online.org/Voices/?p=205#comment-222 <p>Can anyone recommend some useful articles and/or books that discuss the chromosome fusion process? The whole issue of heterozygotic vs homozygotic processes and all the specific mutations and changes that need to happen have presumably been spelled out somewhere but I'm not sure where. Randy</p> Can anyone recommend some useful articles and/or books that discuss the chromosome fusion process? The whole issue of heterozygotic vs homozygotic processes and all the specific mutations and changes that need to happen have presumably been spelled out somewhere but I’m not sure where.

Randy

]]> Comment on Chromosome 2 Fusion by Bernie Dehler http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-218 Bernie Dehler Tue, 23 Feb 2010 22:34:46 +0000 http://www.asa3online.org/Voices/?p=205#comment-218 Thanks Randy- I just looked it up on wikipedia too: http://en.wikipedia.org/wiki/ISCID It looks to be defunct: "As of September 2008 the society's website stated that "ISCID is no longer being managed as an organization".[10]. Its last "Society announcement" and last journal publication being in late 2005,[11] no updates on its essay contests and moderated chats since 2004,[12][13] and no conferences or workshops announced since 2003.[14][15]" Thanks Randy- I just looked it up on wikipedia too:
http://en.wikipedia.org/wiki/ISCID

It looks to be defunct:
“As of September 2008 the society’s website stated that “ISCID is no longer being managed as an organization”.[10]. Its last “Society announcement” and last journal publication being in late 2005,[11] no updates on its essay contests and moderated chats since 2004,[12][13] and no conferences or workshops announced since 2003.[14][15]“

]]> Comment on Chromosome 2 Fusion by Randy Isaac http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-217 Randy Isaac Tue, 23 Feb 2010 20:40:40 +0000 http://www.asa3online.org/Voices/?p=205#comment-217 <a href="#comment-216" rel="nofollow">@Bernie Dehler </a> I'm aware of it, though "familiar" is too strong. It's about 8 to 10 years old, I think, and is an association of ID researchers that Dembski heads. I haven't done any analysis of their work. Randy @Bernie Dehler
I’m aware of it, though “familiar” is too strong. It’s about 8 to 10 years old, I think, and is an association of ID researchers that Dembski heads. I haven’t done any analysis of their work.
Randy

]]> Comment on Chromosome 2 Fusion by Bernie Dehler http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-216 Bernie Dehler Tue, 23 Feb 2010 20:24:14 +0000 http://www.asa3online.org/Voices/?p=205#comment-216 Hi Randy- are you familiar with ISCID ( http://www.iscid.org ) . Is this a new ID-type of science group? Do you have any opinions on this movement/organization? ...Bernie Hi Randy- are you familiar with ISCID ( http://www.iscid.org ) . Is this a new ID-type of science group? Do you have any opinions on this movement/organization?

…Bernie

]]> Comment on Chromosome 2 Fusion by Randy Isaac http://www.asa3online.org/Voices/2010/02/23/chromosome-2-fusion/comment-page-1/#comment-215 Randy Isaac Tue, 23 Feb 2010 19:18:45 +0000 http://www.asa3online.org/Voices/?p=205#comment-215 No, I hadn't read Borger. Interesting paper. I'm not convinced his conclusions follow from his data. Certainly it seems reasonable, and I believe it has long been known, that there are factors that modulate the mutation rate and type in different portions of the genome. In his article on anitbody formation, Craig Story notes the enhanced mutation rate precisely at the region that determines affinity. So no one really claims that all mutations are purely random in the mathematical sense with equal probability. But noting that there are mechanisms that make some mutations more probable doesn't eliminate mutations from being a marker for common ancestry. Those studies focus on regions where the mutations are reasonably well understood and where independently identical mutations are extremely unlikely. This is being used very effectively in the genographic project sponsored by National Geographic. Randy No, I hadn’t read Borger. Interesting paper. I’m not convinced his conclusions follow from his data. Certainly it seems reasonable, and I believe it has long been known, that there are factors that modulate the mutation rate and type in different portions of the genome. In his article on anitbody formation, Craig Story notes the enhanced mutation rate precisely at the region that determines affinity. So no one really claims that all mutations are purely random in the mathematical sense with equal probability. But noting that there are mechanisms that make some mutations more probable doesn’t eliminate mutations from being a marker for common ancestry. Those studies focus on regions where the mutations are reasonably well understood and where independently identical mutations are extremely unlikely. This is being used very effectively in the genographic project sponsored by National Geographic.

Randy

]]> Comment on Welcome and Some New Guidelines by Terry M. Gray http://www.asa3online.org/Voices/2010/02/09/welcome-and-some-new-guidelines/comment-page-1/#comment-214 Terry M. Gray Tue, 23 Feb 2010 16:53:34 +0000 http://www.asa3online.org/Voices/?p=163#comment-214 <a href="#comment-213" rel="nofollow">@Allan Harvey</a> Your comment illustrates some of the difficulties of all this. You seem to be fully adapted to the brave new world of Web 2.0. Some of our users are wanting to go back to the old way and so we are trying to come up with email based solutions for them. Your particular need is different from either of those and are the result of folks not recognizing that they are veering into a new topic. Sorry for the inconvenience of the emails. I am guessing that if the posts were on-topic, you wouldn't mind get emails of comments. Please bear with us. I have moved the veered off comments to a new post. Also, since you are so savvy, I'd encourage you to set up some mail filters to deal with these sort of things. All my "asa3online.org" related email now goes to a separate mail folder that I only occasionally look at. @Allan Harvey

Your comment illustrates some of the difficulties of all this. You seem to be fully adapted to the brave new world of Web 2.0. Some of our users are wanting to go back to the old way and so we are trying to come up with email based solutions for them. Your particular need is different from either of those and are the result of folks not recognizing that they are veering into a new topic. Sorry for the inconvenience of the emails. I am guessing that if the posts were on-topic, you wouldn’t mind get emails of comments. Please bear with us. I have moved the veered off comments to a new post. Also, since you are so savvy, I’d encourage you to set up some mail filters to deal with these sort of things. All my “asa3online.org” related email now goes to a separate mail folder that I only occasionally look at.

]]> Comment on Welcome and Some New Guidelines by Allan Harvey http://www.asa3online.org/Voices/2010/02/09/welcome-and-some-new-guidelines/comment-page-1/#comment-213 Allan Harvey Tue, 23 Feb 2010 16:06:10 +0000 http://www.asa3online.org/Voices/?p=163#comment-213 It would be nice if there were a way to "turn off" the feature where the original poster gets an email for each comment. My earlier comment on "Richard Dawkins: Good Scientist, Bad Philosopher" got turned into a post of its own, which was fine. But now I'm getting multiple emails a day of follow-ups for a discussion that has veered off the original topic. I'd rather just look at the blog site every day or two to see comments instead of getting these emails. Ideally this could be a check box where the author of the post gets to choose whether or not to get these notification emails. It would be nice if there were a way to “turn off” the feature where the original poster gets an email for each comment.

My earlier comment on “Richard Dawkins: Good Scientist, Bad Philosopher” got turned into a post of its own, which was fine. But now I’m getting multiple emails a day of follow-ups for a discussion that has veered off the original topic. I’d rather just look at the blog site every day or two to see comments instead of getting these emails. Ideally this could be a check box where the author of the post gets to choose whether or not to get these notification emails.

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