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Author Topic:   NY Times article on evo-devo
numnuts
Junior Member (Idle past 6113 days)
Posts: 19
Joined: 06-20-2007


Message 1 of 6 (407994)
06-29-2007 5:59 PM


I found this article and I thought I would post it here. I have not looked around to see if it has been done yet. It's a great article to help explain how evolution can work on a macro scale.
http://www.nytimes.com/2007/06/26/science/...
I am also inserting a link to an unrelated picture I just found on My Yahoo of a horse/zebra cross breed. Nothing major just a cool pic.
http://news.yahoo.com/...81/bccee8115b684ff8baf4a26cd3a944c6
I hope someone finds it interesting like me.

I think therefore I am...busy

Replies to this message:
 Message 2 by Brad McFall, posted 07-04-2007 1:55 PM numnuts has not replied

  
Brad McFall
Member (Idle past 5055 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 2 of 6 (408745)
07-04-2007 1:55 PM
Reply to: Message 1 by numnuts
06-29-2007 5:59 PM


Less seperation of genotype and phenotype ?
Dwise gave a rather disconnected notion of "genotype" and "phenotype" in response to numnuts in message 80 in the prior thread
quote:
Re: Evo Devo & horse/zebra cross breed
Basically, evo-devo looks a lot like what Dawkins was saying in The Blind Watchmaker. His Mac program, Blind Watchmaker (in Chapter 3), was based on the idea of small changes in the genotype resulting in large changes in the phenotype.
Slightly tangentially, it seems that a lot of standard creationist misrepresentations about mutations is that they concentrate largely on developmental mutations, in which the mutation is in the phenotype, not necessarily in the genotype. Rather the only mutations that are of interest in evolution are the mutations in the genotype -- ie those that will be carried in the genetic material in the gametes -- , because only those can be inherited.
So part of the name of the game is that the only mutations that count are in the genotype, but selection does not act upon the genotype but rather on the phenotype. So how do we get the phenotype from the genotype? Through development. So in that sense, evo-devo is nothing new; we've known about it all along. What it does appear to contribute, though, is that it tries to figure out just how the genes direct development.
Edited by dwise1, 29-Jun-2007 12:00 PM: Added the slight tangent.
While trying to make concrete my own version of what technology would be like if it could properly extract hierarchic information from biological data. I diagrammed the following:
This gave me surprising access to Conway's "thought process" that has gone unexplained
quote:
http://www.geom.uiuc.edu/.../doyle/mpls/handouts/node39.html
is an exact reproduction of Conway's manuscript. In addition to the 17 types of repeating patterns, Conway's manuscript also gives tables of the 7 types of frieze patterns, and of the 14 types of symmetrical patterns on the sphere. These parts of the manuscript appear to be mainly gibberish. We reproduce these tables here in the hope that they may someday come to the attention of a scholar who will be able to make sense of them.
Here is the combination of Conway and my way of thinking what I hold is Kant's synthetic a priori.
It was only a small step from that visualization to propose that amino acids might actually function to triangulate the phenotype.
This would imply a much tighter relationship between phenotype and genotype than you have represented. It also makes selfish/repetative DNA a possible correlation of somatic mutations, but whether only the two way inteior channeling is being ucovered by EVO-DEVO as Gould suggested (the figure and quote above are from SJ Gould in The Structure of Evolutionary Theory) vs a "one way street" of orthogenesis (and hence also some creationist thought necessarily), I have not determined.
If the triplet code of amino acids function to triangulate the phenotype as represented as Galton's polyhedron or Conway's decagon (as repictured by me) then what you described as "development" may only be 'growth'. In order to make this traingulation work I would suggest that feedback between the gene combinations in a individual and the gene frequencies in a population are causal with guanosine affected microtubule ramifications and seperations of the chormosomes. The numbers in the frieze pattern may be partially encoded guanosine dynamics oriented to the centriole or plant cell wall and gene locations. I dont now. It is just a thought.

This message is a reply to:
 Message 1 by numnuts, posted 06-29-2007 5:59 PM numnuts has not replied

Replies to this message:
 Message 3 by Monk, posted 07-04-2007 5:14 PM Brad McFall has replied

  
Monk
Member (Idle past 3946 days)
Posts: 782
From: Kansas, USA
Joined: 02-25-2005


Message 3 of 6 (408759)
07-04-2007 5:14 PM
Reply to: Message 2 by Brad McFall
07-04-2007 1:55 PM


Re: Less seperation of genotype and phenotype ?
Although the article in the OP presents an interesting update on research thought related to macro evolution through developmental changes, the combination of your diagram, “extraction of hierarchic information from biological data” with Conway’s obscure manuscript on pattern recognition leads to the “EVOlution” and further “DEVelopment” of . . gibberish.
Would Kant consider your art to be “synthetic a priori.” I doubt it, but it’s entertaining nonetheless.

This message is a reply to:
 Message 2 by Brad McFall, posted 07-04-2007 1:55 PM Brad McFall has replied

Replies to this message:
 Message 4 by Brad McFall, posted 07-04-2007 8:01 PM Monk has replied

  
Brad McFall
Member (Idle past 5055 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 4 of 6 (408772)
07-04-2007 8:01 PM
Reply to: Message 3 by Monk
07-04-2007 5:14 PM


Re: Less seperation of genotype and phenotype ?
It is not "art". Monk, what do consider Kant's synthetic a priori to be. Please be specific. Do you hold it exists at all?? If not then why respond as if you knew what Kant would have thought.
If you read the article on Conway you would see that authors of that piece had little intuition of how Conway was moving in thought from the plane (the purpose of their paper) via symmetry groups on a strip to the sphere.
I have been trying to imagine if something OTHER than cladistic 3item analysis can be used to fullfill the call for a new programtic representation of hierarhic data in biology ( I linked here
quote:
/Documents/hierarchicalhomologyPDF.pdf
Part of the real difficulty is extracting hierarchical information out of a pedagogic process that continues to present largely interms of data tables. This artilce by Nathanael Cao, Rene Zaragoeta Bagils, and Regine Vignes-Lebbe shows why database normal forms may be directing biogeographical research where the notion of "rooting" presently obtains. I had visualized this "extra row" to be programmed, possibly with MSTs, once a collection locality (semaphoront vs. holomorph) is streched to include another point in biogeographic space (into an area of endemism). Order is not free. Bertrand Russell's "Principles of Mathematics" applies to this data placement aspect.http://axiompanbiog.com/comparisons.aspx
).
Originally I used pictoral represenation of the symmetry groups you saw in my "art". After I had decided how the different symmetry groups could be synthetically combined to create an input output device for the powerball I came across Conway "manuscript". The diagrams in the side of that table made sense interms of the already placed symmetry groups (with the exception of 1 or 2 permantely placed) in view of the motion of powerball that I had made the decisions on. This device has external sphere so the relation between the human and the hand excersier in terms of torque would indeed manifest it self as groups in the sphere VIA the partial 3-D diagrams provided by Conway bewteen the freize patterns and the sphere groups. This is the immediate effect of the a priori in math that Kant writes of. If you want to say that it is a delusion and deviant than you had better be sure you have a comparable vision else you will inevitably be made to look the fool you might have claimed. If you think you have a more sophisticated view of Kant than me, pray tell, I am all ears.
Elisabeth Lloyd in "The Strucutre and Confirmation of Evolutionary Theory" while discussing Dawkins, notes that even Dawkins admitted (in 82) that Wright's interdemic selection could produce "superior adaptations" than selection alone. Wright tried to inform Provine (and I think Gould as well) that they had the wrong idea of the phenotype. I was only suggesting that the idea that the phenotype is large changes of small changes in the geneotype is probably wrong.
I would not discard the benefit of mathematical intution before its consequences have been worked out. What is exiting is that this notion fully permits Gould's interpreation of internal channels in evo-devo AND provides a means to ascertain if Galton's term, "transilient variation" exists.
The blueprints I have provided may indeed provide a new approach to interpreting gene sequence data. It may be that there is no real "code" as in the computer metaphor for heritable information but rather protein expression is a topological triangulation of the organisms traits and that finding "the code" between DNA-RNA-and proteins was just a consequence of our view of the 2-D surface structure of individuals which express "the gibberish" in what Conway was finding with mutltiplicative frieze patterns.
The hierarchic data extraction can commence if the taxi stops between places on a squares' corners
http://axiompanbiog.com/comparisons.aspx
are isomorhpic to panbiogeographic tracks or the binary trees he has encoded are explained by post Gondwanna distribtions rather than Pleistocene climatic cycle changes.
This is not an average post I have produce here. Please be advised.
If there is NO (inguistic)CODE and amino acids FUNCTION to TRIANGULATE phenotypes (this provides a superior benefit to the organism able to so use proteins because the indiviual despite being taken apart at each generation can retain environmental(developmental) details experienced in phylogeny IN ONTOGENY) I can explain how Gould was mistaken to think that there was a 'hardening' of adaptationism. There was not. There was a failure to visualize morphological form mathematically as D'Arcy Thompson recommended commence. Gould had it out for the American school of Hyatt and Cope. I am simply turning recapitulation on its head (you can do this with symmetry in the plane, that's what your supposed to do to recognize them)and having a mechanism such that phylogeney can recapitulate ontogeny.
Wouldnt it be something if the repatitive nature of freize patterns was the same phenomenon as repetative DNA?? Why to you scoff by arguing about philosophy before you seem to have recognized what I had tried to indicate?
So I was just trying to show that the phenotype and genotype can be understood as ONE rather than having to explain one term in terms of the other.
Traditionally this can be aswered by simply pointing out that measuring the mutation parameters are usually done differently than gene frequency changes. Saying that is only the status quo.
Galton wrote (in Gould SETH p 347)
quote:
No variation can establish itself unless it be of the character of a sport, that is, by a leap from one position of organic stability to another, or as we may phrase it, through "transilient" variation. If there be no such leap the variation is, so to speak, a mere blend or divergence from the parent form, towards which the offspring in the next generation will tend to regress; it may therefore be called a "divergent" variation... I am unable to conceive the possibility of evolutionary progress except by transiliences, for, if they were merely divergences, each subsequent generation would tend to regress backwards towards the typical center"
Computer programs for constructing phylogenetic trees do not work because they do not discriminate against these "centers" (places of rotational symmetry) they simply "root" the structure and orient the characters by outgrouping. Conway's skectches permit one to travel on purely internal "channels" of constraint, mentally, among classes of forms.
By relating the repetition of the pattern to track width it is possible to introduce a non-Platonic shape DETERMING the outerbounds. If you are not ready for that step simply work on the suggestions about the patterns and numbers of chromosomes. If just that works somewhat Dakwins seperation of vehicle and gene will not work because the ANALYSIS is fully geometrical and will trump his algorithmic insistance of engneering for the simple difference of pure vs applied math.
If you insist on following up nonsensical things bring that over to thread on me. I will explain this furhter there.
Here is how I expressed the device BEFORE I read Conway's notes;
Your paper,“Hierarchical representation of hypotheses of homology”, I found on SEBA is highly significant to me.
It seems to show up a truth in Russell’s statement,
“The things we have got to take as premises in any kind of work of analysis are the things which appear to us undeniable - to us here and now, as we are - and I think on the whole that the sort of method adopted by Descartes is right; that you should set to work to doubt things and retain only what you cannot doubt because of its clearness and distinctness, not because you are sure not to be induced into error, for there does not exist a method which will safeguard you against the possibility of error. The wish for perfect security is one of those snares we are always falling into, and is just as untenable in the realm of knowledge as in everything else. Nevertheless, granting all this, I think Descartes’s method is on the whole a sound one for the starting-point.”
(“The Philosophy of Logical Atomism” in Logic and Knowledge:Essays 1901-1950 by Bertrand Russell, Capricorn Books, G.P. Putnam’s Sons, New York, 1971)
We do not seem to have computer programs for biogeography and taxonomy that do not simply try to not be induced into error.
The need for your synthesis is prescient if Papavero and Llorente-Bousquets’ “atomo logico”
(Papavero, N. and J. Llorente Bousquets eds. 1993. Principia Taxonomica: Una introduccion a los fundamentos logicos, filosoficos y metodologicos de las escuelas de taxonomia biologica)
is conceived as homogenous with Russell’s logical atomism. The failure to perceive the particulars of your added row may indeed be more fundamental than a software solution.
I am trying to forge a synthetic operating system around 3 Euler angles and 7 symmetry groups of 3-D space
(picture in attached document, this)
so as to extract hierarchic data. Perhaps your solution(s) is to be preferred quantitatively nonetheless. My attempts are going to involve serial port programming of blue tooth enabled power balls so as to convert angles into two dimensions.
As you already know, Malte Ebach
(“3item is also no longer available. A far better program Nelson05 is
out that does three-item analysis and subtree analysis. The program is
free. Please email Rene Zarageta or Nat Cao for a free copy.”
)
recommended I contact you two. My interest is principally in your “computer program” that can read and understand your representation but I also wanted to get deeper into its precursors and especially, 3Item stuff. Any information on your up and coming work or Nelson05 would be greatly appreciated. I can do some JAVA programming but I am not (yet) a “computer geek”. My interest has been in herpetology instead.
The difference, between my approach and yours, if there is any, may depend on what is to become of Russell’
.”The reason I call my doctrine logical atomism is because the atoms that I wish to arrive at as the sort of last residue in analysis are logical atoms and not physical atoms. Some of them will be what I call ”particulars’ - such things as little patches of colour or sounds, momentary things - and some of them will be predicates or relations and so on. The point is that the atom I wish to arrive at is the atom of logical analysis, not the atom of physical analysis ” (Russell page 179 op.cit.)
As I have been corresponding with Dr. Georgi Gladyshev (academy@endeav.org)

for a few years now and I would like to reach a conclusion for physical atoms as well as logical ones so that I may attempt to integrate his work into the modern evolutionary synthesis.
My Grandfather was the first science teacher at SUNY Fredonia, in 30s (to the 70s) after completing a PHD in genetics with Sturtevant’s flies (temperature-effective periods) in Charles Zeleny’s lab. I got interested in biology because of him. Sewell Wright was also there in the Mid-West. Will Provine did not seem, to me ( he was supposed to be overseeing my worm snake project but instead was too involved in writing Wright’s biography(in the 80s))to resolve Wright’s response to a failure(gene combination vs gene frequency) ( Stephen Gould also asserts differently) to find non-linearity in populations. I subsequently showed Will, Gladyshev’s work, but he seems to have ignored also that even though supramolecular chemistry had subsequently appeared on the Cornell campus since then.
Again, any ideas or information about reading and writing hierarchic information to digital media would be invaluable. If you have a free copy of Nelson05, I would like that too.
Best,
Brad.

This message is a reply to:
 Message 3 by Monk, posted 07-04-2007 5:14 PM Monk has replied

Replies to this message:
 Message 5 by Monk, posted 07-05-2007 9:42 PM Brad McFall has replied

  
Monk
Member (Idle past 3946 days)
Posts: 782
From: Kansas, USA
Joined: 02-25-2005


Message 5 of 6 (408903)
07-05-2007 9:42 PM
Reply to: Message 4 by Brad McFall
07-04-2007 8:01 PM


Re: Less seperation of genotype and phenotype ?
Brad McFall writes:
If you read the article on Conway you would see that authors of that piece had little intuition of how Conway was moving in thought from the plane (the purpose of their paper) via symmetry groups on a strip to the sphere.
That's true. The article you quoted notes that the Conway manuscript appears as gibberish and has not yet been understood by scholars.
These parts of the manuscript appear to be mainly gibberish. We reproduce these tables here in the hope that they may someday come to the attention of a scholar who will be able to make sense of them.
Yet you merged a jpg file of the manuscript that know one has yet made sense of with some sketchy notes and symbols that you wrote on a piece of paper and voila! You posted the merged document as Kant's synthetic a priori?
Perhaps you should first decipher the Conway manuscript before using it to posit something from Kant.
On the other hand, your comment:
So I was just trying to show that the phenotype and genotype can be understood as ONE rather than having to explain one term in terms of the other.
Makes sense and is better understood than a cut and paste jpg.
Edited by Monk, : Spelling

This message is a reply to:
 Message 4 by Brad McFall, posted 07-04-2007 8:01 PM Brad McFall has replied

Replies to this message:
 Message 6 by Brad McFall, posted 07-05-2007 10:38 PM Monk has not replied

  
Brad McFall
Member (Idle past 5055 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 6 of 6 (408910)
07-05-2007 10:38 PM
Reply to: Message 5 by Monk
07-05-2007 9:42 PM


Recapitulation
Thanks Monk for this considered and non-enflaming response.
I suppose I could have just made the claim that genotype and phenotype are more unified than I understood Dwise1 to have represented, but then, without any evidence, my post would not be any different than the numerous kinds of responses ones finds in other creation/evolution discussion boards.
Seeing that you are not really disputing in the conclusion, I’ll leave that for Dwise1 to comment on if he so chooses, I will respond to your other content in another post linked back to this one.
And just to be clear, after completing
quote:
sketchy notes and symbols
in trying to think WHY Conway would start his pages with 2-D symmetry then mess up (scratch out)writing the series of 1-D symmetries which have a page of non-spherical symmetries (on the same “gibberish” as in the 1-D notes) BEFORE listing the symmetries on the sphere, I had an idea how the focus would be on (a,b,c,d) frieze patterns in the plane as a mathematical thought process and I came to visualize this mathematical maturity in terms of things of biology that I felt still had not been properly mathematized. THAT led me to recommend to DWise1 that his invocation of Dawkins may be too strong.
The actual issue this comes to regarding the relation of phenotype and genotype (see THE PERSISTENCE OF THE FISHER-WRIGHT CONTROVERSY) is, why can not co -ordination of epistatic terms be terms of ordinations of Frieze patterns in a plane divided among the chromosomes? Answering this query in the affirmative is why I can say that genotype and phenotype may be a tighter unity than reductionism leads to. Saying this without the background of the thought (former “art”) is really quite senseless. That is why I do not respond to each and every poster on EVC. I do not want to be perceived as the boy who cries wolf. If epistatic terms can be ordinated mathematically following the procedure that Conway et al triangulated a polygon, found binary trees for the duration of, and connected pathways between two points of . then it becomes significantly possible to think that one may be in possession of a resolution of the dispute between Fisher and Wright that no one has yet to have thunked up. I can now explain, by way of a simple diagram Fisher sent to Wright (in the 30s?), that indeed Fisher may have suffered from, in his words, “an adaptive oversight” and that Gould made too much of “adaptive hardening” on the same account of this math not be used in biology. I do not have to assume the use of my pet ideas of transfinites etc . Simple “mathematical maturity” will do and a concern for proper presentation of a hierarchic datum.
This, if true, would erase, thousands of pages of dispute in biology over the last century and require a complete re-writing of the creation/evolution debate. I hate to make such a proud sounding claim but I have no other way to explain how good it made me feel to have realized this. This, I might added was released from my own subconscious, if I may say so, because I read in the paper of homology representations that those authors were claiming a computer program could be written that moves “OUT” of the matrix/square data structure.
That claim is squarely in my thoughts on Kant, there was no other place in my thoughts for it. I have given enough years to thinking about form-making and translation in space, and enough of the literature to know that I am not learning new areas of endeavor but spinning circuits around the same lump of leaven. Usually the circle is so large that only the creation side makes a visible showing, this time the trajectory was tight enough to remain secular. Sorry.
I will respond to your other concerns on this matter in my next post. Thanks again. That is now available here
EvC Forum: All about Brad McFall II.
Edited by Brad McFall, : fixed link
Edited by Brad McFall, : finished next post

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 Message 5 by Monk, posted 07-05-2007 9:42 PM Monk has not replied

  
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