Definition of created kind!

Splx, there are apo baramins, mono baramins and baramins of all sorts. But in hypothesis I would go out on the limb of this diagram to asert that by gravity, inertia and mass they could kinda be sorted out to your implementation satifaction. But Lord knows we have not the $$ to even begin to fill in the tabled array.

There was no time for the cell last time I checked and we need not only time but space when not the cell-cycle form to create it first in thought and not in transcendetalism. Now I will not read till I start to read the response. Peace OUt.

BradWhat's the basis for non-mutaitonal adaptive transformations?Wait - plain and simple recombination/reproduction. Yes - I agree.

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[This message has been edited by Tranquility Base, 07-09-2002]

BradPlease try and explain to me what you are saying. I am interested!Are you saying that protein folding issues aren't a barrier to fold to fold evolution? That would be ludicrous but I'm prepared to hear you out.

For a long time I had really pretty much thought that they were, but of late I have realized when trying hard to visualize the interior of a cell(s)(location is what we know of organelles) there was an outside in some topological sense to protein expression. Of old that outside was the my idea of connection to gravity (waves, solitons, Prigogines notions refined etc)but when I was trying to understand why I was failed by L Pierce Williams of Cornell I began to try to assimilate his biogoraphy of Faraday and I realized that there was another "outside" or 'catastrophe set' that could be expressed from immicibility of water and lipids BECAUSE water and oil can create patterns that invert themselves in a dish that is vibrating (cell under mitosis and movement?). I then thought that this and not the issue of denauration was what protiens were being expressed to get beyond in part on thinking that there had to be an equal and opposite force to the code which in DNA i had thought (three thoughts means this is speculative and not even verified to be tested empricalY) was the line or space (of former in the literature acridines) between base pairs going out into the cytoplasm for WHATER FIELD LINES COULD MEAN IN TERMS OF heritibility or just phyiscs (ie in context of this thread more reducion than as said so far from physical chem) and that expression of proteins need go through the endoplasmic reticulum to golgi where this barrier is MEChANCIALLY concentrated and beyond the cell membrane but have ion channels which could alter any organization of field lines up to this point (and this is thought without explict use of mircotubules idea I also have).Thus there is NO central Dogma on this view but the possiblity of "feed back to the genes from the proteins" as Gottlieb had suspected and I had been thinking something of for years since ~1982 which is how I coined term bioentropism to label whatever the physico-chem this is. The Russians tried to hard to work with DNA and solitons in it etc for this is still in line with the denaturation as being the unnnatural outside idea. All I really knew was that there was biology in the woods that I could not find in the literature AFTER I failed to get on with profesional herpetologists who should have at least demuured to me with respect to whole organism knowledge I posses to having passed off for a PhD in letters for reprints from Australa and SA as teen-ager. Hopes this helps. I did not proof it. I Have been waiting for the day when I got to explain this . Thanks for giving me the opportunity. And again thank you. The difference of smooth and rough endoplasmic reticulum would be rather critical for the stage this ontology is in at present and no longer absolutely relies on high-school idea of gravity waves etc.

BradIt is very difficult to understand what you are saying in detail. It sounds interesting and certinly hits on some of the important issues but I can't understand exactly what you are saying!All I am saying is that mutating proteins will almost always have to lose function on the way to becoming a new fold! Hence lack of selectability, hence random drift, hence long time, hence a barrier.Can you please explain your POV in plain English like that? Maybe answer in sections:A. What are you trying to account for?
B. What makes you think there is a deficency in either conventional mainstream or creationist thinking?
C. What is your mechanism?
D. What makes it potentially equal/better than the conventional mechanisms?
E. What makes it empirically equal/better?This is the TB five point 'justification for hypothesising' test every scientist applies to new ideas whether mainstream or creationist.

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[This message has been edited by Tranquility Base, 07-10-2002]

Tranquility and Brad. Im a biology student.What do you think of my definition when I started this topic? Is there a certain lack?"How many new frameshift mutation proteins and new point mutation proteins can be accumulated inside cells or in the interstitial fluid until the organism die. And when they accumulate, how few and short protein systems do they build up max.Tranquility: You are talking about protein folding. Ok, so when a protein with a certain folding will turn into another folding its straight/denatueted. But doesnt these proteins also have active binding sites, so they could bind dangerously to a system. Are all denatueted proteins dangerous? Hence your definition of created kinds.

What i get from the information of protein folding on internet, is that point mutations often radically change the protein. Couldnt thus just a point mutation make a totally new alfa-helix instead of a beta-sheat? A new folding thus or are point mutations in most cases causing denatuation.I still think that the certain binding sites of proteins and sugars in combination with different ion-concentration is the most important to focus at.

11 posts in a row by Brad McFall, that's more than enough to make my head spin! -Just a bit of my irrelevant rhetoric, carry on.------------------

ZAURUZYour quoted defintion is pretty confusing. Can you carefully rephrase it and briefly explain it?What's wrong with defining kinds as distinct genomes differentiatable by novel protein families? Sounds simpler than yours - but it may be the same!What do you mean by 'straight'? Wait - OK - you mean extended - yes that is correct - a misfolded protein will be extended and usually aggregate (self-associate) and form giant pieces of junk protein complexes or a 'fibril' hence diseases like Alzhimers.The binding sites are critically dependent on the 'native' (normal) folding. The only purpose of the folding is to get the right3D binding site.Most denatured proteins were once thought to be harmless. this is probably still true but increasing numbers of misfolded proteins are found to (i) form fibrils and plaques and (ii) maybe form simple ion channels (holes) in membranes that cause detrimental effects.The danger of denatured proteins only relates to created kinds indirectly. I can see how one might argue design from it but in evoltuion we are already talking evoltuion of complexity so lack of detrimental denatured proteins will just be selected against. I will grant that it is not a completely pointless arguement. It is not a strong point however.

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[This message has been edited by Tranquility Base, 07-10-2002]

ZAURUZOne in twenty or so mutations can radiacally cahnge the protein - yes. But in every case it is to an unfolded or aggregated state. the recent example discussed here is of a helix interchanging with a strand and this is cerainly not radical as discsussed here previously. In my professinal opinion the authors refer to it as a 'new fold' only becasue the term is not that well defined.Most mutations maintain fold or generate unfolding. Ther is no example in the literature where a really new fold is generated. There was a recent examples where a designed series of mutaitons of 25% of the sequence generated a new fold. I saw the researcher talk on this work about 2 years ago - she won a cash prize for doing this - someone had offered a prize to anyone who could achive this. It was fun and she links her work to Alzhiemer's issues. I've forgotten her name.Can you briefly and clearly explain your point about 'binding sites of proteins and sugars in combination with different ion-concentration'.

I will go into this post and edit --TB- You seem to assume the fold before the function while I the reverse if I got this correct? for when you say "mutating protein" I can not be certain you mean more on the mutation end or the protein end. The notion of "function" at least more from biology than philosophy is tied not notions of analogy and homology yet the molecular equivalent of these organism visions is far from clear. The fold before the function is a category in the creation evolution videos I produced labeled philosophical chemistry in which category I would put Eigen etc (whom I did see lecture but choose not to ask him a question at the end) and could contribute to some of biologic change but I do not go all this way to say that it is the only way for then I land with Cricks notion that RNA selection is reason evolutionist does no longer need consider vital force. That had always seemed to me a cop out. My ideas are not anthema to Wright's notion of using d^2, h^2 and e^2 and to no longer even think that the nature/nuture frame of the answer was every correct. It would not be. So as for dift I have much to say but I have not worked out this "emulation" all the way to Kimura but I am confident enough NOT to follow Provine's historcism of the same biological notion. Wright was rather refereing to whole oranism phentypes and Paulings work. If neopheogeneis is correct it would not be metaphysically incorrect to try to work with function before the fold such that any kind of molecular motion could have potential adaptive significance. I had written to Provine after I got kicked out that he would not win this rejection of me to the extent certainly (all things Wright aside) that adaptations could be thought of as differences in the free path lengths of molecules which no doubt have differences due to enounters and binding to ennzymes and active sites. Maxwells prose provides the means to actual carry this kind of science out but Haldanes use of enzymes and criticism of Wrights lack of dominance in the caluculable progression has along with some history writings of biochem prevented Maxwell's telephone and commentary on APostle Paul from becoming the modem of genomics and protenomics. One only needs recoginze that life is not light or heat. That is not much to ask of the sudent who is living with a science that sees more to mechanics than that cause by gravity. Maxwell wanted us all to understand entopy in this kind of pedagogy and I am on my way to leave Cornell behind in this regard.Q-TB LEtter C- BSM answers^* any mechansim must first be tried out of Newton split between mechanism and geometry. I do not know the dynamics to the ability to calcualte it for I am still at Galileo's stage where he insisted as with the atmosphere that it must be split into layers before any dynamics is defined and Fiegenbaum made the same remand for kinematics to be given before any dynamics be derived but we are talking of cells and not clouds while I do not mind trying to work with a constant kinematics for a geometry that may be taxogenically homogenous (per kind the extent that genetics interats with the notion of clade or kind) due to the circle of chromosmes that form a roseette not being on the electrotonic place coordinations (think ion currents or field lines to start)which is either an asymmetry or irreversibility in addition to any somatically unequality between two divided cells of a common cell back of the division. This visualization combined the geometry of Maxwell's electrotonic functions is enough boundaries to begin to calculate places cells could not divide into yet I do not have an equational handle on the visualzation heuristic necessary to carry out the mechanistic calculations. Feel free to pick my brains as to as much detail as I posses on the possible description of ideal cell. The lipid/water boundary MECHANISTICALLY has the shape it does but this is rather an edge or layer in Galelio's sense of the infinity invovled rather than the "mechanism" invloved persay. The details of how DNA fits into this picture is not finally worked out by me but I have begun to get beyond my first use of torque which could not produce the expansiveness of the present visualization that I have thought more about becuase of your interest in the topic. Thank You.

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TBQ-A. BSManswers^%I have been trying to account for what is either in the classic genetics literature as "thermophene" or its historically simpler precursor as it had showed me not only that Wright arbitrarly choose the standard deviation to create his statistical procedure with and at the same time provides the references needed to update or change Fisher's fudamental theorem. I have been rather stalled becasue trying to work out the philsophy of all this and not the simple "you say causation and I say correlation" incantation I realized contra physicist Cambell that biologist MAY BE (dont question me on this I really dont know) looking at S U M of two temperatures when looking at color patterns in anmials when not also organelles in plants which Cambell asserts with some numbers does not exist even under any uniforma association for if true I would have to do serious battle with Einstien's mind for which I am not ready to committ Kuhn's p 102 to posterity and possibly slip in a Mickey Mouse Mistake. I need to write something on the "evolution of dominance" I am only confident up the existence of lethals at this point of accountibility.

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I dont really see any problem with current creationism I had only wanted to take a more active role but it seems that my own ideas indepenet of the revival will fit in with creationism in about 20 yrs for I am working on the less abstract level with how to think of mutations and x-rays and electro pollution bioassays as one. There is NO apriori reason that with IT information Maxwell's vortexs can not be ad hoc adapted to an emirical determination.

BradWhen I say 'mutating proteins will lose function on the way to a new fold' what is there to misunderstand? On the way to a new fold mutations will almost invariably end up unfolding the protein and leading to loss of funtion. So then there is nothing to select for and hence the gene will drift to randomness. Hence one might as well start with random DNA.NEW EDIT: So I sort of agree that genes would more likely evolve before folds for this reason above or that actually, most proteins should have the same fold - just like antibodies all share the immunoglobulin fold and yet perform billionso of functions. That would be the expectation of evolution.What do you mean by 'Letter C' - do you mean my point C? What about ABD&E? EDIT - OK there's more!What has Newtonian mechanics got to do with it?
And what is this 'it' anyway? What are you trying to explain?
You are not making any sense.
Why bother about the cell shape when we're talking about the origin of tens of thousands of protein families?EDIT:1. What are your 'thermophenes'. The only Google hits on the entire internet are your posts here!!
2. Why do you drop all these names (of scientists) as if we all know the intricacies of this obscure piece of research?
3. Are you trying to explain pattern formation eg the zebra stripes?
4. Do you really think your answer to A explained what you are trying to account for?That last paragraph made my day Brad - thanks.

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[This message has been edited by Tranquility Base, 07-11-2002]

[QUOTE]Originally posted by Tranquility Base:
[b]BradWhen I say 'mutating proteins will lose function on the way to a new fold' what is there to misunderstand?[/QUOTE][/b]I was imagining that you visualized the bonded angle between amino acids danglin randomly ( in the pre-fold thermodynamic space, which for any change over time even the transients stanges could be "stored" in 'gene information' if one is teleomatic about the Aristotle the likes of Mayr agrees to...)and this could indeed be the whole of the physical chem reality in this instance under discussion but my first read thought is to think of the proteins and not the mutations they may in the 10-6 mutation rate be a part of for which I am working out "mechanisms" relative to effect of protein motion on the entire translation/transciption (messengerRNA) that I bound out with the lipid/water barrier but see the motion of the proteins as forming the potential for change that actually become adaptions when all of a given developement is or would be the final cause to use Aristotle's 'philosophy' to say something rather even more explicit. Otherwise I guess I understood what you meant. I was happy to see you pick up on the reproduction/ recombination difference. What is crucial for me is loosing HOMOLOGICAL function for my larger program is to try to provide what NZ Panbiogeographers have claimed corrallary wise that Croizat's notion of biogeographic homology is not an artifact and the possibility of orthogenesis is always lurking somewhere in the my mind's eye so to say.

quote:

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[BOLD]
On the way to a new fold mutations will almost invariably end up unfolding the protein and leading to loss of funtion.

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[/B] yOU ARE THINKING ACROss generations here and I had not gone that far yet except insofar as I would have been actually describing only an idividual and not a population. Notion of bioentropism would be tied up with the physiological genetics and not the tranmission genetics of this time of slacked protein as you represent it when not a down right instatiation of the kinetic theory of gasses. I belive this work is on the way if not to change Fisher's Theorm at least to sharpen in physcio-chemical terms his notion of environmental degredation that I think but do not know that Provine Chalked up to Fisher and not Wright. One can not forget that Wright and Fisher used different approaches to the same conclusions in some instances. Without my details being filled in, your default (in my letters) is most eminently correct. [QUOTE][b]
So then there is nothing to select for and hence the gene will drift to randomness.[/QUOTE][/b]. There is at least the different REPULSIONS contribution to the calculation of the virial (which DNA by torque but not BASE pairing could contribute)in the molecular velocities distributions per celluar Internal vs central vs centric environment PER NORM OF RXN [QUOTE][b]Hence one might as well start with random DNA.[/QUOTE][/b]. I start from geometry and a Circle of DNA and not an a posteriori reality that randomly you are free to conduct justifiable research on. But random in this sense is indistinguisable from Rene Thom's notion of a catastrophe set of interacting chemicals which could be random in every respect of molecular velocities I may or may not have enumerated and yet posses such distinctions as the cusp and butterfly that I have not ruled out are not responsible for the existence of tangent reference froms in morphometrics when not consisttuting metrics of morphogeny iteself. The field of Macrothermodynamcis would have this for its object and not tranditional physics nor phsical chemsitry. But you are free to reason as Eigen does. I do not and Cricks panspermia is too far away from me to be usable yet.What do you mean by 'Letter C' - do you mean my point C? What about ABD&E? EDIT - OK there's more!YesWhat has Newtonian mechanics got to do with it?If Crick was so certain he was working from a FORCE then the randomness you speak of aside from any dream heretofore of MAxwells demon means that entirely within Cricks lexicon there Should be an equal and opposite "force" to the code. On the other hand one might try to be a descartian though I do not know that this would acutally get beyond Maxwells vortex + virial in the critical periods of developemtn. Phenomenolgically this makes sense. Newton wrote about coasts of visibles and coasts of audibles and I have thought in analogy coasts of Maxwell's electrotonics andthis was when Newton was discussing the difference of a fish and a lizard brain. I have not been able to agree with Dawkins that genes are before brains then I would not have been able to have thought in the same sense that I could not outwit GOD for god could have changed the parameters even before I measured them to verify what I had thought but then again Mach was correct to think that every good dynamics needs a perpetuation and the impressed force we both source sinks somewhere that would need defition before we could continue to reliably communicate etc. Kant made the division of ethics,phyics and .. while Newton divided geometry and mechanics and HM Morris asked me to please keep the math and biology ligusitically seperable. That is all I am trying to do. This would be inline with woodger andI presume the Cambridge Theoretical Biology Club that I would prefer to be addressing here rather than Crickets.
And what is this 'it' anyway? What are you trying to explain?
You are not making any sense.
Why bother about the cell shape when we're talking about the origin of tens of thousands of protein families?EDIT: What are your 'thermophenes'. The only Google hits on the entire internet are your posts here!!
Ill clean this up later if at interest. Thermophenes were introduced in to the genetics literature by a Case Western researcher whos name escapes me as to qutifiying the effect of temperature on wing formation in drosophila. Ask again I will find the reprint. I wont be home for another week or so so I need that much about time.
[This message has been edited by Tranquility Base, 07-11-2002][/B][/QUOTE]
I ll try answer more later. JD Murray of Oxford, invited me to graduate work in Math Bio Dept there in UK but I declined becuase he said both that I would be able to see what I would be doing at Ox FORD (he had just showd me his latest zebra stripe model) and insisted that it was ok to use these equations with snakes with out being able to tell me why this was justified. After reading Feynmans QED I knew that Murray may have just been inviting me to 10 yrs of thesis that would be false 20yrs down the road. I went my own way and the result is quite unique to me but Gottlieb (and I do not drop names, they are short cuts for long senentences for me that would prevent me from getting to point) as used experience with "coactions" to say the same but without all the physical possibilites being parralled at most.
[This message has been edited by Brad McFall, 07-11-2002]

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[This message has been edited by Brad McFall, 07-11-2002]

Z i will have to spend some more time with the thread. So forgive me for being even shorter. As it became clear with talking with TB I need to work even more on seperating out the within generation effects of any given transduction way and the cross generational ones in ecological time. It may be that I would need to criticize a lot of ecology before I could return but now I have not the time nor brain cells to think of it. Later. Brad.