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Author Topic:   AIG has an article up on the nylon-digesting bacteria
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 2 of 27 (98519)
04-07-2004 6:54 PM
Reply to: Message 1 by Biophysicist
04-07-2004 6:38 PM


new hope helps
Do you think it "dishonest" that no biophysicst or biophysical geneticist has tried to ordinate sequence data using sets of harmonic conjugates (Non-Euclidean Geometry by HSM OXTER, FRS UofTORONTO press1942...1968p28...)"A large part of our investigation (eg Chapter v) will be concerned with the geometry of poits on a single line, where there is no scope for incidences. This deficiency is compensated by the possibility of defining ths HARMONIC CONJUGATE of a given point with respect to two given points. (We think of this as a one-dimensional concept, even thouh it requires incidences in two dimensions for its construction and in three dimensions for the proof of its uniqueness.) We shall use the abbreviation H(AB,CD) for the statement that D is the har...")??????????????????????????

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 Message 1 by Biophysicist, posted 04-07-2004 6:38 PM Biophysicist has replied

Replies to this message:
 Message 4 by Biophysicist, posted 04-07-2004 8:29 PM Brad McFall has replied

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 5 of 27 (98767)
04-08-2004 7:05 PM
Reply to: Message 4 by Biophysicist
04-07-2004 8:29 PM


Sure, this is part of my "homework" on Quarternions and I havent quite finished it yet, nor brought the source with me today, but I'll key you up to my memory on it and try to apply it more directly to your post next time. All quotes can be found as done by posters in this thread.
quote:
As usual, it looks like their arithmetic is correct, given the assumptions they've made, about the open reading frame being very long for this new gene.
However, I believe that both the original plasmid and the result of the mutation have been sequenced, and the nylon-digesting gene has indeed been found to be the result of a frame-shift mutation from a previously useful gene.
quote:
I think the way the article keeps trying to deny that a frame-shift mutation could have done this is then dishonest. The best argument they make in that line is that there seems to be an extra mechanism to encourage mutations in that region of the plasmid, which is fairly interesting in its own right.
Also, I don't appreciate their argument that this cannot be considered a "gene duplication --> new gene" event. There can be more than one copy of the plasmid in the cell, so you could easily maintain a mixture of the two probabilistically.
Of course, the real problem with the article is the way it keeps referring to evolution as a process simply based on randomness.
quote:
...)"A large part of our investigation (eg Chapter v) will be concerned with the geometry of poits on a single line, where there is no scope for incidences. This deficiency is compensated by the possibility of defining ths HARMONIC CONJUGATE of a given point with respect to two given points. (We think of this as a one-dimensional concept, even thouh it requires incidences in two dimensions for its construction and in three dimensions for the proof of its uniqueness.)
I noticed that this defintion MIGHT? be useful in detailing frameshift mutations"" without reference to chance prima facie.
quote:
Here's a question: do existing genes have a lower probability of having a frame shift mutation generate a stop codon than would be expected given a random sequence of nucleotides with nominal proportions of A, C, T, and G bases?
As I have contined to do this "homework", I have noticed that your "probabiliy" while possibly "framed" by the 2-D nature of harmonic conjugate would not beenough if bioinformatics could actually be bent to a means of Noneuldeian geometry on the whole rather than just as a formal logic in the debate. This is much more complicated than I had first responded in to your post but it might even be easier to approve of as it use plane duplicity rather than chemical chirality in its proof. Meanwhile the reason I started this work was to address something with AbbyLeever where I assert rotations which need not be limited to a "side" which this would remand as to the acutal seqence location of any old stop codon.
quote:
Of course, the real problem with the article is the way it keeps referring to evolution as a process simply based on randomness.
quote:
AiG always manages to skip right over the natural selection part of evolution and instead focus on the randomness of random mutations. They want to focus on the random chipping of stone and not how the sieve sorts them by size. One is random, granted, but the whole process is not.
A corrollary or theorm in this homed work finds that natural selection might not be understood as to the 3-D proof (more than one cell etc)as disruptive selection could possible be critical here but then remands I had gotton back to AL satifactoruily which I do not gain say at this point even if I personally might so express.

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 7 of 27 (98911)
04-09-2004 12:37 PM
Reply to: Message 6 by Black
04-08-2004 8:41 PM


This is a systemic'" problem with the central dogma and cross national styles of information flow patterns. If it be admitted that more than one protein can do the fermentation then generally one could reason that more than one cell can ORIENT the protein that does the digestion and if one KNEW that the taxonomy economically was defective (personal oberservation) then one could ARGUE the other way around as well. This of course leads to debate and not rebate. Some day we may know more. I dont today.

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 Message 6 by Black, posted 04-08-2004 8:41 PM Black has not replied

Replies to this message:
 Message 8 by Loudmouth, posted 04-09-2004 12:58 PM Brad McFall has not replied
 Message 17 by Biophysicist, posted 04-16-2004 7:45 PM Brad McFall has not replied

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 11 of 27 (99485)
04-12-2004 6:08 PM
Reply to: Message 9 by Trixie
04-09-2004 7:26 PM


Re: Random Mutation
T,
I was headed to the issue of behaviorial neophenogenesis which creationism remands be solved in some way that DID not seperate descent and mechanisms but I have not tried to do the same reasoning on this "bug" level. In terms of research I am in the same state I was when Mammuthus and I were discussing strong vs weak PE. There is a tendency to assume that one FIRST addresses the mutation before one shows how some adaptibility IS an adaptation and this rather than the effects of chance are my better guess at what's going on even in GOuld's reading of the "synthesis" but I really dont know. I do know it does not need to be first or foremost. It must be addressed at the end at least. The possiblity of applying "design" at the bug level is much easier as many people have indeed spent many more hours thinknig of cats, cows and hippos for instance given any bird. There was a claim prior (to Provine-Johsonson debate)(to say nothing of my own educated "protestations") that the Baldwin effect, Stablizing Selection and genetic assimilation step or stem from the same cause. The kinematics may be seperable while the mechanics are not. I am in possesion of a physical means to manipulate this trio conceptually and given time I will explain the analysis again. I have already discussed ALL of the relevant individual issues in various threads here (there may have been a few things I said on other web sites that had not been repeated here but I doubt it as to evolutionary interest).

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 Message 9 by Trixie, posted 04-09-2004 7:26 PM Trixie has not replied

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 23 of 27 (101015)
04-19-2004 7:22 PM
Reply to: Message 18 by NosyNed
04-16-2004 10:21 PM


Re: It's not ok to just say no.
Let it, I didnt bring the working paper(s)(which I see now would have been useful for biophysicist which I was working on and from before I posted. The issue is NOT about information INCREASE as I was led onto on TrueSeekers (as to any or all prior online info) but if information itself goes the way from protein to DNA and there are plenty of people using a more "heuristic" approach (than my application of track width to grades (not CLADES!!) across discontinuous spaces) who HAVE ALREADY been documenting in this vein, I simply extend the reasoning INTO the creationis position. I do not repose too soon. Read Gottleib's book on NEOPHENOGENESIS if you want to grow your own thought on biology in a different landscape than Ernst Mayr for standard reference for instance. I CAN THINK of the 1957 seperation of clade interms of Crick's force of base pairs but the creationist reading writes Volta's side and not Galvani's to which I am personal inclined so it is not easy for me to compose the creationist position correctly easily from within KNOWN ideas of biological change. It can be done. That is all that is needed for DEBATE. Biophysicist would be wrong to think that creationism wont work for I have been able to redisplay with baraminiology things herpetological that had already "played" themseleves out in my childhood. One needs a sharp enough magestria to note that Gould's punctuation speaks acutally AGAINST the notino of grades being disconitnuous as baraminology can logically direct but IS done at the expense of an UNADUJDIACATED claim to age and area against Gould's but not necessarily Fisher's notion of Natural Selection which the Pacific Ocean already WAS for Croizat BEFORE Huxley thought the time for anagensis that Gould streches out statistically. Time as Bridgman understood it IS necessary to sort out the material differences an Einstein could bring to this notion of adaptions FROM adaptabilities but whether they are theorized from a discontinuous (my preference and that which best supports creationist concepualization) or a continuous (any old decent with or without slopy mechanical seperations wrongly (in my opinion) permitted)one there ARE claims that behavior migh morph BEFORE any gene frequnecy changes. The issue is if the grade is thus arithemetically described can the geometry be also convergent or track narrowing within any lineage and can not adaptabilities CHANGE the genetics (not the INFORMATION!)to the DNA level of base pair mathematically equivlanet to clade abstract space seperation. Not only do I assert this is possible conceptually which anyone with an ability to read biology can find out but I am working out the consequences of a use of thermal contact as the cause of both the failure to incorporte Croizat, the seperation of the word "Clade" with the warm bloods, and the rightful justice of the creationist position on the physical discontinuites in the GENE data. The work on multiple gaped alingments would not be uncalled for. I however KNOW that there is NOTHING wrong with creation and biology in general BECAUSE I know that a grade<>clade no matter what Gould said. As for the nylon thing this gets a bit more complicated as to the issue of frame shifts and unlike the general direction which even Nosy ought not to warn posters of of my ability to speak on for regardless of how the cell cuts there is still the mathmatical use of catstrophe theory WIHTHIN creationist taxonomy that is not available to the evolutionist. I try not to take the readers this far as there is not *that* much exictment%% about creationism here on EvC and I dont want others to simply be disinclined to post for feeling a kind of religous connativity.
Ned, while it is true that some of my posts ought not worry one. This thread should! I am not mad, just using the icon for affect. I'll try to edit down my working papers to some essentials for the B in our midst.

This message is a reply to:
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