More friam followup
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Hi all,
I think of our discussions as cumulative, so here is somethat that was discussed today that I would like to nail down. We isolated the concept of "misplaced concreteness (Whitehead) which is a version of a "category error" (Ryle) or the violation of a language game (Wittegenstein) or the error of Hypostization. (spelling?)(source?) or Reification (ditto). We will ALWAYS disagree when somebody says that to say that hunger is IN the stomach is an example of misplaced concreteness, but we will never again be confused or ignorant about what is being asserted: that hunger is a complex set of relations that may involve the stomach essentially, but also involves many other things. Even our use of words like probabililty (I probably will go down town today) or (there is a 50 percent chance it will rain today) or causality (guns dont cause crime; people do) lays us open to accusations of misplaced concreteness. Nick Nicholas S. Thompson Research Associate, Redfish Group, Santa Fe, NM (nick at redfish.com) Professor of Psychology and Ethology, Clark University (nthompson at clarku.edu) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://redfish.com/pipermail/friam_redfish.com/attachments/20070615/8d08ad5e/attachment.html |
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I may have mentioned this morning that this is probably important:
http://www.scienceblog.com/cms/node/13465/print Carl Nicholas Thompson wrote: > > Hi all, > > I think of our discussions as cumulative, so here is somethat that was > discussed today that I would like to nail down. We isolated the > concept of "misplaced concreteness (Whitehead) which is a version of a > "category error" (Ryle) or the violation of a language game > (Wittegenstein) or the error of Hypostization. (spelling?)(source?) or > Reification (ditto). > > We will ALWAYS disagree when somebody says that to say that hunger is > IN the stomach is an example of misplaced concreteness, but we will > never again be confused or ignorant about what is being asserted: that > hunger is a complex set of relations that may involve the stomach > essentially, but also involves many other things. Even our use of > words like probabililty (I probably will go down town today) or > (there is a 50 percent chance it will rain today) or causality (guns > dont cause crime; people do) lays us open to accusations of misplaced > concreteness. > > Nick > > Nicholas S. Thompson > Research Associate, Redfish Group, Santa Fe, NM (nick at redfish.com > <mailto:nick at redfish.com>) > Professor of Psychology and Ethology, Clark University > (nthompson at clarku.edu <mailto:nthompson at clarku.edu>) > > > > ------------------------------------------------------------------------ > > ============================================================ > FRIAM Applied Complexity Group listserv > Meets Fridays 9a-11:30 at cafe at St. John's College > lectures, archives, unsubscribe, maps at http://www.friam.org |
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Nature 447, 799-816 - Identification and analysis of functional
elements in 1% of the human genome by the ENCODE pilot project. Here are some of their highlights in their own words: - The human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript and many transcripts link distal regions to established protein-coding loci. - Many novel non-protein-coding transcripts have been identified, with many of these overlapping protein-coding loci and others located in regions of the genome previously thought to be transcriptionally silent. - A total of 5% of the bases in the genome can be confidently identified as being under evolutionary constraint in mammals; for approximately 60% of these constrained bases, there is evidence of function on the basis of the results of the experimental assays performed to date. - Surprisingly, many functional elements are seemingly unconstrained across mammalian evolution. This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism. This pool may serve as a 'warehouse' for natural selection, potentially acting as the source of lineage-specific elements and functionally conserved but non-orthologous elements between species. So, there is no junk DNA, there is no silent DNA, 40% of what's being evolutionarily constrained has no known function, some of what appeared to have a known function is apparently free to change across all known mammal genomes. That's 4 of the 11 highlights. -- rec -- On 6/15/07, Carl Tollander <carl at plektyx.com> wrote: > I may have mentioned this morning that this is probably important: > http://www.scienceblog.com/cms/node/13465/print > > Carl |
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This is what John Mattick (from U. Queensland) has been talking about
all these years. Its sweet to observe heretic science becoming mainstream :) Cheers On Fri, Jun 15, 2007 at 04:22:06PM -0700, Roger Critchlow wrote: > Nature 447, 799-816 - Identification and analysis of functional > elements in 1% of the human genome by the ENCODE pilot project. > > Here are some of their highlights in their own words: > > - The human genome is pervasively transcribed, such that the > majority of its bases are associated with at least one primary > transcript and many transcripts link distal regions to established > protein-coding loci. > > - Many novel non-protein-coding transcripts have been identified, > with many of these overlapping protein-coding loci and others located > in regions of the genome previously thought to be transcriptionally > silent. > > - A total of 5% of the bases in the genome can be confidently > identified as being under evolutionary constraint in mammals; for > approximately 60% of these constrained bases, there is evidence of > function on the basis of the results of the experimental assays > performed to date. > > - Surprisingly, many functional elements are seemingly unconstrained > across mammalian evolution. This suggests the possibility of a large > pool of neutral elements that are biochemically active but provide no > specific benefit to the organism. This pool may serve as a 'warehouse' > for natural selection, potentially acting as the source of > lineage-specific elements and functionally conserved but > non-orthologous elements between species. > > So, there is no junk DNA, there is no silent DNA, 40% of what's being > evolutionarily constrained has no known function, some of what > appeared to have a known function is apparently free to change across > all known mammal genomes. > > That's 4 of the 11 highlights. > > -- rec -- > > On 6/15/07, Carl Tollander <carl at plektyx.com> wrote: > > I may have mentioned this morning that this is probably important: > > http://www.scienceblog.com/cms/node/13465/print > > > > Carl > > ============================================================ > FRIAM Applied Complexity Group listserv > Meets Fridays 9a-11:30 at cafe at St. John's College > lectures, archives, unsubscribe, maps at http://www.friam.org -- ---------------------------------------------------------------------------- A/Prof Russell Standish Phone 0425 253119 (mobile) Mathematics UNSW SYDNEY 2052 hpcoder at hpcoders.com.au Australia http://www.hpcoders.com.au ---------------------------------------------------------------------------- |
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In reply to this post by Nick Thompson
Nick,
Sometimes I can't tell from careful efforts to be rigorous (like the common thread in Whitehead, Ryle and Wittgenstein you point out), whether it refers only to semantics and theories or also refers to physical things. A lack of clarity on whether a subject concerns the forms of mental constructs or the forms of things outside the mind to which we can only point is the most common of the misplaced referents I know of. To me it's highly relevant whether the subject is inside or outside our minds, as the former tend to be projections which can be associated with any other and are limitlessly pliable and extendable, and the latter are not. Does your understanding of category error' include that? Phil Henshaw ????.?? ? `?.???? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 680 Ft. Washington Ave NY NY 10040 tel: 212-795-4844 e-mail: pfh at synapse9.com explorations: www.synapse9.com <http://www.synapse9.com/> -----Original Message----- From: [hidden email] [mailto:[hidden email]] On Behalf Of Nicholas Thompson Sent: Friday, June 15, 2007 5:02 PM To: friam at redfish.com Subject: [FRIAM] More friam followup Hi all, I think of our discussions as cumulative, so here is somethat that was discussed today that I would like to nail down. We isolated the concept of "misplaced concreteness (Whitehead) which is a version of a "category error" (Ryle) or the violation of a language game (Wittegenstein) or the error of Hypostization. (spelling?)(source?) or Reification (ditto). We will ALWAYS disagree when somebody says that to say that hunger is IN the stomach is an example of misplaced concreteness, but we will never again be confused or ignorant about what is being asserted: that hunger is a complex set of relations that may involve the stomach essentially, but also involves many other things. Even our use of words like probabililty (I probably will go down town today) or (there is a 50 percent chance it will rain today) or causality (guns dont cause crime; people do) lays us open to accusations of misplaced concreteness. Nick Nicholas S. Thompson Research Associate, Redfish Group, Santa Fe, NM (nick at redfish.com) Professor of Psychology and Ethology, Clark University (nthompson at clarku.edu) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://redfish.com/pipermail/friam_redfish.com/attachments/20070616/138b2a6c/attachment.html |
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In reply to this post by Roger Critchlow-2
So, the genome seems to be a complex system?, not a passive record
keeping device as needed for the Darwinian model? Finding these other kinds of organization in genes has been long expected by some folks bye the way... simply because the y/n values of 'selection' don't have the requisite variety to distinguish between thousands of variations and circumstances and 'random variation' wouldn't produce the evident 'exploration' of niches evident in evolutionary behavior. Maybe we should consider the alternative models for evolution proposed by people who foresaw the dilemma that there has to be more structure there than the simple ideas of Darwin contemplated. Phil Henshaw ????.?? ? `?.???? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 680 Ft. Washington Ave NY NY 10040 tel: 212-795-4844 e-mail: pfh at synapse9.com explorations: www.synapse9.com > -----Original Message----- > From: friam-bounces at redfish.com > [mailto:friam-bounces at redfish.com] On Behalf Of Roger Critchlow > Sent: Friday, June 15, 2007 7:22 PM > To: carl at plektyx.com; The Friday Morning Applied Complexity > Coffee Group > Subject: Re: [FRIAM] More friam followup > > > Nature 447, 799-816 - Identification and analysis of > functional elements in 1% of the human genome by the ENCODE > pilot project. > > Here are some of their highlights in their own words: > > - The human genome is pervasively transcribed, such that > the majority of its bases are associated with at least one > primary transcript and many transcripts link distal regions > to established protein-coding loci. > > - Many novel non-protein-coding transcripts have been > identified, with many of these overlapping protein-coding > loci and others located in regions of the genome previously > thought to be transcriptionally silent. > > - A total of 5% of the bases in the genome can be > confidently identified as being under evolutionary constraint > in mammals; for approximately 60% of these constrained bases, > there is evidence of function on the basis of the results of > the experimental assays performed to date. > > - Surprisingly, many functional elements are seemingly > unconstrained across mammalian evolution. This suggests the > possibility of a large pool of neutral elements that are > biochemically active but provide no specific benefit to the > organism. This pool may serve as a 'warehouse' for natural > selection, potentially acting as the source of > lineage-specific elements and functionally conserved but > non-orthologous elements between species. > > So, there is no junk DNA, there is no silent DNA, 40% of > what's being evolutionarily constrained has no known > function, some of what appeared to have a known function is > apparently free to change across all known mammal genomes. > > That's 4 of the 11 highlights. > > -- rec -- > > On 6/15/07, Carl Tollander <carl at plektyx.com> wrote: > > I may have mentioned this morning that this is probably important: > > http://www.scienceblog.com/cms/node/13465/print > > > > Carl > > ============================================================ > FRIAM Applied Complexity Group listserv > Meets Fridays 9a-11:30 at cafe at St. John's College > lectures, archives, unsubscribe, maps at http://www.friam.org > > |
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