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Author Topic:   Transition from chemistry to biology
Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 36 of 415 (78451)
01-14-2004 3:29 PM
Reply to: Message 1 by sidelined
01-04-2004 5:19 PM


?
conceptually or evidentially?? If you say both I will have said that both Gould and I made the same scaling error or deviation from variation when thinking of Whitman's claim contra De Vries and Darwin on not how the Leopard but the Pigeon got it's spots that...if there IS NOT a cicularity in reasoning to the larger clade then evidence will show that Gould was mistaken in series what I would be in sequence. Gould did it conceptually in that case and me "if"NOTGOULD or either/or evidentarily. We all know how to spell super-natural...

[This message has been edited by Brad McFall, 01-14-2004]


This message is a reply to:
 Message 1 by sidelined, posted 01-04-2004 5:19 PM sidelined has taken no action

Replies to this message:
 Message 37 by DNAunion, posted 01-14-2004 9:21 PM Brad McFall has replied

Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 38 of 415 (78702)
01-15-2004 5:24 PM
Reply to: Message 37 by DNAunion
01-14-2004 9:21 PM


Re: ?
No, but I might be if I got cable. I asked the question and I hope that Sideline-d will answer it directly for then I will try to "discuss" rather than 'circle the wagons'. What it did recall was my first web posting that I made on Taxacom but I know this has not the precision that has subsequently been established here. The link is
<http://listserv.nhm.ku.edu/cgi-bin/wa.exe?A2=ind0102&L=TAXACOM&P=R5038&D=1&O=D> and I have about 24 posting there that show that even the professionals could only keep up with my Lamarkian style of speculative argumentation for so long but still as this is chemsitry to biology you will see that I have been trying to talk about biology (protenomics and genomics TO chemistry) and from basis I might be able to discuss a few things in this thread.

Here is a little bit of those "older" textual things:

"I propose to use the virial to solve the conundrum in the term 'biological informatics' whether or not it rotates genetics in a new revolution and takes nostalgia back to a time before the distinction of bio-informatics was taken for the metaphase plate of geneticists or not and only is of service in a routable computer network of biological information.

Every gene in it's Mendelian instantiation will have a virial. These virials will build partial pressure by pressure the relation of genomic and protenomic informatics to the level of chemisty. Biochemistry begins with some free path these gene-virials have spatially available that eventually are cast in GIS areally co-extensive sets logically setting the stage from recognition of Some hierarchy to the organismic tissue-organ-cell level where upon acoustic/image processing and pre-DNA style genetics begin to not object to morphometrics; multitasking up to the graphic anatomy of the systematist generally but because with the expanded taxonomy that visualizations have provided the taxa specialist and the best-guess-species-location algorithm(s) by combining GIS(species and habitat layers), the impetus socially providing for l-commerce spins up to a biodiversity object web that from conservation and alpha taxonomy creates the deductive biogeography irregardless of time as in the style of Euclid and Newton but as part of morphogeny with or without virtual reality that is psychologically needed to move beyond "

I would be able to talk about WAXweb in this external channel but I know others here like to keep the techic stuff to a minimum so if I know if it is not going to be an issue c v e for BOTH evidence and concept I could give it a try else I will be content to understand that that in CGI the environment variable is "inherited" and thus how P likely got C for E!


This message is a reply to:
 Message 37 by DNAunion, posted 01-14-2004 9:21 PM DNAunion has replied

Replies to this message:
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Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 40 of 415 (79554)
01-20-2004 11:17 AM
Reply to: Message 39 by DNAunion
01-15-2004 6:38 PM


Re: ?
will it? (will it transcend????). this doesnt look that sublime to me.

This message is a reply to:
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Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 48 of 415 (385668)
02-16-2007 6:36 PM
Reply to: Message 43 by sidelined
05-08-2004 3:51 PM


outside or inside?
I just noticed while reading "Gould" today, that he DID NOT make a clear context for his own claims of relative frequency with the difference of the environment and some particular salamander.

While RAZD has responded in the afirmative I will, in the negative.

I can agree with you that 'the fundamental' process need not come "from outside" (there is a difference between 'outside' and 'above') EXCEPT when it comes to pure standard Darwinism of individual selections dominating the interpretation of change. This exception however is no guarentor of a lack of supernaturalism it is only that some dynamics (that the chemical elements move WITHIN) is governed by differences in individual organisms. One can "dissect" these creatures into combinations of elements and their forces however and in this sense the "fundamental" process might not be OUTSIDE our current understanding.

The problem comes in when one is trying to think if the kinematics underlaying the dynamics (now if you reject the Darwinian individual level then my response here after is not relevant for you...) are changing with the environment or against it and then what chemical properties this environment possess. Seeing that Gould rejected making it clear ABOVE the species level whether or not a guild of salamanders was involved or not indicates that he can think evolutionarily WITHOUT needing to descend to chemical combinations and yet he probably would not be against the idea of life from simple chemical combinations WITH THE ADDITION OF THE Darwinian algorithm.

Now Gould was ALSO unable to decide how to discuss a reference to "metabolic energy" in this ENVIRONMENTAL content however. And THIS notion which may or may not enable one to decide if there is still some idea "above" us on this topic (whether transcendental or not) needs to be decided IN THE SAME ENVIRONMENT if there is to be some real determination on/in this life"". Fundamental process as for instance understood by Freeman Dyson require a difference of metabolism and replication but this withinus need not energetically be reduced from the same macroperspetive of Gould necessarily, says me. I seem to think differently up the hierarchy than Gould does down it. So when you ask about "proper combinations and environment" in your next posting in this threaded series and responded to lately by RAZD it appeared literate to me that the tangential nature of responses in this thread is due to the latter word especially.


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Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 52 of 415 (385809)
02-17-2007 9:17 AM
Reply to: Message 49 by RAZD
02-16-2007 8:01 PM


Re: arbitrary or non-arbitrary?
Biologically speaking I can not say that the continuum of particle scaling properties applies. This is what distinguishes a thought of physics and one of biology for me. A physcist of the experience is free to scale from the absurdly small to the nair infinitely large but I do not accept that the forces of the smallest physical speculation apply in biology as I do not accept that there are Martins on Mars, unless it was shown so.

I know this is opinion. I am still trying to think through the different discrete particulate applications of heirarchical thermodynamics, which did apply to the subatomic according to Gladyshev and the macrothermodynamic that he tried to write amon ontogentic&phylogenetic differences. Earlier I was exposed to Kervran's ideas that weak forces are a part of form-making and translation in space. There is still no serious science of this. So, while there is no doubt that strong forces are responsible for "higher" units of combination that DO have causal influence in biology I do not find (via the 1st Law of thermo) that whatever fundamentally one is to make of the "aggregation" and said forces that this is 'the same' as a concept of 'replication.' I would sooner think that the periodic table of elements is actually infinite than that a physicists forces were conceptually equivalent to Dyson's differences.

When thinking biologically one needs to think about "gravitation" vs. "e-m" more often than a crumb of particles themselves or the protoplasm that was left behind on the microscope slide. Design still resides for me at the lower limit where the USE of atomic forces gives way to the purely physical forces in trajectory with nuceli. This may be an artifact of my present level knowledge and understanding but I can only use that which I do do.

I had noticed when DS Wilson was talking at Darwin Day that he considered organelles as "visually" integrated histories of different lineages within a modern cell. This he attributed to Margulis but there was no sense of biological history here, he simply accepted the visual picture as evidence of integration and expected the audinece to "see the same" way. I never have. There is a difference between level of organization and level of selection and so the notion of design has you presented it does not seem to keep these seperated. I do not say this acrimoniously. It seems to be THE common problem in theoretical biology. Gould did not do it either.


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 Message 49 by RAZD, posted 02-16-2007 8:01 PM RAZD has replied

Replies to this message:
 Message 53 by RAZD, posted 02-17-2007 12:12 PM Brad McFall has replied

Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 54 of 415 (385856)
02-17-2007 4:48 PM
Reply to: Message 53 by RAZD
02-17-2007 12:12 PM


Re:chemistry in the middle
Yes, that is all very interesting.

Crick simply assumed that Eigen hypercycles change WAS selection but I had in mind that to which population genetics is the pricipal suspect. The difficulty is to sustain a thought about a "population" of organisms and "population"/aggregate of particles as a "whole" I come closest to this thought when trying to unify my own reading of Gladyshev.

Being accepted in the Chemistry Major at Cornell I had hoped for a day to discuss protein folding with H. Scheraga
http://www.chem.cornell.edu/has5/
but that day never came. I tend to think that the shapes that matter are the result of non-worked out symmetry relations encoded between DNA and Proteins which may have extra-expressive targets. But these thoughts verge on fiction. Protein denaturation always seemed an issue to me too. And yes they would have existed sans life but as long as the likes of Crick have no problem confounding the before and after of chemical force since DNA with impunity and there are not biophysicists who try to show how supramolecular chemistry is downward causal onto what bonding patterns were or may have been around before life as we know it was is, I will continue to work out mathematical ideas rather than conceptual ones at this juncture.

If some stability of the molecule is the guide to the notion of selection rather than the effect of this-whatever- ON the population of individuals that plurifact (Gould's term)(

quote:
The simple observation of plurifaction. – the relative increase an individual’s representation in the heredity of subsequent ...
quote:
www.linguistics.ucla.edu/people/stabler/4.pdf
&
quote:
The Structure of Evolutionary Theory - Google Books Resultby Stephen Jay Gould - 2002 - 1433 pages
But the contributions themselves can be wholes or parts, faithful replicates or disaggregated bits of functional heredity. Selection demands plurifaction ...
books.google.com/books?isbn=0674006135...

)then I tend to fear this is just an example of over eager molecular biology since Crick's force became reality.

As a teenager I had the wild idea that gravitational waves might interact with proteins as they come off ribosomes such that collective masses of biological activity of the same clade but in a different geographic region might affect shape(two shapes for one protein) via an "out of body" 'experience.' Gladyshev's phenomenological thermodynamics has disabused me of this youthful speculation that appears at worst to be a niave synthetic apriori as best I can recollect.

As for my physics ideas well, they probably just seem fanciful. They are not as intricate as my biological ones.

Edited by Brad McFall, : was is


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Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 60 of 415 (467475)
05-21-2008 7:38 PM
Reply to: Message 59 by AshsZ
05-21-2008 9:16 AM


back onto the track
Well, if you were asking what I was writing on-about, I started in 2004 to speak of orthogensis and I continued this past year with posts. I could direct my comments directly back to the OP again if that is desired but A-Z you could approach "divine creation" if you were able to say what the difference of the combination and enviroment is.

I doubt we can get here on this thread.

Chemical combinations would be a larger material realm than potential past biological environments but distinguishing comprehnsibly to any material combinations the difference of abiotic and biotic contributions to the continued process represented by evolution is enumerably even larger. There would be a need to specify the geometry of such a continuum. Accepting that Darwin did away with seperate creation then there still can be an issue within the original interval that spelled the first word in the op, "transition". Idont see entropy as an exception here but part of the transdimensional solution. That does not in itself open up the supernatural per say.


This message is a reply to:
 Message 59 by AshsZ, posted 05-21-2008 9:16 AM AshsZ has replied

Replies to this message:
 Message 61 by AshsZ, posted 05-22-2008 4:36 AM Brad McFall has replied

Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 62 of 415 (467605)
05-22-2008 7:46 PM
Reply to: Message 61 by AshsZ
05-22-2008 4:36 AM


Re:Gaia
Gaia is interesting but one would have to have some idea of what the “organism” as an organization is. When Margulis spoke of this I did not get a sense of what this is. One needs to posses what Kant called an “organon” which contains ‘instructions’. Penrose’s notion of microtubule information seemed to contain the same generality of thought , for me and that is nothing other than simply straight biophysics, if it is really of any use towards opening one’s intuition in the concept.

This turtle named “gaia”


Click to enlarge

was designed from a couple of books on reptiles I supplied, but the organization you suggested, prior, was that which is in the stars. Feynmann has mentioned “double stars” in this regard. I do not know how to think about this as of yet. The notion in this thread however IS NOT one of “reptile design” , to quote Gould, with or without any Gaia down to Earth. The eye was made from a Billard Ball.
quote:
Do you think it would be a reasonable statement to say that the earth itself was born into life at the time its mass coalesced and direct interaction of its matter began (prior to the existence of the "life" stuff we are talking about - the point in time where there existed the conditions that could lead to the "life" stuff we are talking about)? OR perhaps the planet came to life some time down the road from there.

The answer to this depends on if one is serious about leaving open the possibility of "bacterial" or other life off Earth. I dont discount this so sans the "geometry" I mentioned last post I can not say that the conversation 'must' reside before or after this 'road' as you put it.

The whole thing about DNA or RNA "life" is about oxygen. Do we really have a good idea bout changes in atmospheric O2 relative to "life"?

To use the word "evolution" here I would constrict it for sure to the continuum suggested even if one wants to disagree with Darwin on seperated creations which are rife in bariminology etc.

The fusion of physical "force" into biological factors has been seperate in biology as is evidenced in Carter's 100 years of evolution and is part of the warp and theme of Gould's structure of evolutionary theory. Direct imposition of force is not the billard ball as the center piece as much as I would like it to be.

So while I am in some hope that a better biophysics of life can be communicated among educated people as you suggest the amalgam that you present is more of a warm fuzzy than a rough truth without the commonly attached scruples that nonetheless often pass in popular discourse.

Edited by Brad McFall, : No reason given.

Edited by Brad McFall, : No reason given.


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Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 77 of 415 (472469)
06-22-2008 3:37 PM
Reply to: Message 76 by AshsZ
06-08-2008 4:55 PM


Re: Living organisms and their origin
I tend to have the opinion indeed that a futher "quantification" is possible. I think we do not have it because of the mathematical difference in applied intutions of counting verses equation creation.

I do not think that is any longer possible to imagine that counting and independent insertion of parameters into expanded versions of Hardy-Weinberg equilibria equations is purely extant.

Alfred J Lotka's book, "Elements of Physical Biology" later renamed
"Elements of Mathematical Biology"
expressed a desire to adapt chemical and biological(populational) equilibria.

quote:
(page 285 "But it is important to note that principle of the survival of the fittest is avowedly statistical in character, and is to be applied to organisms in the gross. This is true, also, of the principle of Le Chatelier in physcio-chemical systems; its field of application is to aggregates of molecules, not to the individual. But the applications that have been essayed in biology have been made to the individual; such applications can at the best yield a judgment of probabilities. In physical chemistry we deal for the most part with stable equilibria. But in biology, as has already been pointed out, though the races that come under our observation possess stability as races(else they would not have survived to be our contemporaries), it does not follow at all, that each and every individual is at all times in a state of stable equilibrium.

I think it is possible to go further than this WITHOUT necessiting constant dissipation of energy (in any relation of chemistry and biology, no matter the physics) as I suggest here
http://aexion.org/monohierarchy.aspx

There is certainly a place for "life" after matter but one needs to have a clear sense of the "direction" of the sequence. Evolutionary theory has tended to move away from popular notions of "progress" but this is not to say that the relation of chemsitry to biology has to be more than mere orbits made chaotic/dissipative. It could be quite a bit more organized. I fear we simply do not have the proper training of biologists on the maths. I am still one of those.

The key is in the "spontenity"/irreversibility of rxns as opposed to changes in the rates merely.

I think it will be very fruitful to consider new mutations, however counted or put into equations to offer increased entropy but this does not mean necessarily energy dissipation per say per change over time.


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Brad McFall
Member (Idle past 4265 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 259 of 415 (504988)
04-06-2009 9:20 AM
Reply to: Message 249 by traste
03-23-2009 11:41 PM


Reasteur limited impact on Mole bio
Hello traste,

It is not easy to bring the work of Pasteur into current bio-chemical discussions even though this is a clear connection for some creationists.

The reason that this conversation has not proceeded seems to me to be due to the changed reception of "evolution" following the De Vries' contribution and Mendel's rediscovery followed by the work of "Morganists" to say absoultely nothing about the changes in current thought since "Watson and Crick."

In 1926 Houghton Mifflin Company published "Darwin" by Gamaliel Bradford. The context of this book provides a way to see that Pasteur's work towards "a grand asymmetry" in life *might* be relevant but one would need to get past the cover's quote above a picture of Darwin's hat saying "He made hell a laughing-stock and heaven a dream." By the 70s and after "Rachael Carson" etc, reformed theologians began to analyze GRACE in ways that put MAN IN this world that this book attempted to exposit was the state of culture before/around "Scopes" making humanities' dream IN this world a veritable heaven rather than a state of perpetual humor. This was the post60s life and during this time molecular biology advanced.

There are ways to bring these two differnt times together but it is not a simple thing to expect different generations to agree by simple ocular evidence of writings just as I was able as a child to notice that my Grandparents DID think differently than my PARENTS.

So from a more extended examination of the difference between individual horizons of people's perspecitves either relying on concepts or intuitions and concepts combined one may proceed generally.

Particularly you may read in Bradford's "Darwin"(page 83)

"The natural hypothesis of earlier thinkers was that divien creative power, in whatever shape, had established the different forms of life on the earth pretty much as they exist today. But those who looked more deeply, were inclined to surmise, in view of the close and evident bonds of kinship between all living things, that variety had developed from comparative unity and that the vital impulse, having first appeared in elementary forms, became gradually elaborated into more and more complicated organisms."

The tranisition from chemistry to biology is about whatever these "elementary forms" might be. That Pascal showed some kind of asymetry only shows that whatever is imagined as NOT AN ARBITRARY powered shaping process, the description of the forms should not necessaruly be symmetrical but rather transtive and asymmetrical. That does not seem to be quite enough information to address the complicated associations among bonds developed since Watson and Crick.

But this does not preclude a modern man in the world and God from existing. It may be that the monomorphic ancestor vision that this social view of Darwinism held is simply false but what that assymetry is logically and in detail is as intricate and varigated as Darwin's "entagled bank."


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