Tuesday, May 19, 2015

A Second Look At Quanta's "How Structure Arose In The Primordial Soup": What are evolving proteins?

I took a second look at an article in Quanta, "How structure arose in the primordial soup". I realized that they had ignored completely my questions, two of them, and never bothered to clarify what they meant by "evolving proteins" or for that matter "learning proteins?". Though the author, Emily Singer, who strikes me as somewhat technical, did answer three (3) OTHER commentators' technical questions. Perhaps I'm still reeling from getting blocked and then 'unblocked' from Quanta.
I'm sorry, is science now something that you can mold to your liking? Tailor it, so as to avoid obvious, relevant information or contradictory evidence at your leisure? Just because you're a writer of an article? They bother to mention some sort of triumvirate" of genomics and proteomics and something else, but fail completely to include the glaring fact that no one has ever made molecules "evolve." How will such a story differentiate itself from "bat-shit crazy" ideas? The stuff more appropriate to fiction. And I have nothing against fiction, mind you, but standards are standards and science is not a genre. In avoiding and cherry picking the science, they only open the door to such nonsense as "lightening bolts", why not? Anyone can go to the Quanta article and see that neither of my querries, are somehow deemed relevant to their strange, baffling chemistry of "evolving proteins." Who are we fooling? At the very least such "science" does a disservice to those who actually work with proteins in applied settings. But where is this 'evolution? so that others may duplicate such experiments.

"Most researchers believe that the code began simply with basic proteins made from a limited alphabet of amino acids. It then grew in complexity over time, as these proteins learned to make more sophisticated molecules."

 And again, I believe it is grossly distorting what science currently "knows" even theoretically, are the barriers to understanding the primordial life problem. Some red flags are the self-leaning title, which presumes to answer "how" the soup arose, not "if", as if to imply that we are now on to the finer details of that story. Furthermore, no one has demonstrated polymers that self-replicate, so to imply that's already a hurdle that's been passed is obviously wrong. And "evolution" is not a chemical process, these are proteins, they do not "learn". It would be akin to a title like "researchers are now delving into finer details of how perpetual energy works..." Stop the press?!
Is rationality, yet another victim of the instantaneous gratification demanded by such articles? There is significant if not overwhelming evidence that this pathway, which they all-out assume molecules can violate, is not feasible, which they have apparently ignored, but I discuss in my paper. One sign of a strong theory is its ability to discuss available evidence and findings. Signs of non-supportive theories are unfortunately, just the opposite, the avoidance of contradictory evidence.

 There are many researchers who assume certain paradigms, and thus commence with research, but I'm frankly dumbfounded by the unblinking assumptions of this article, and also its technical backing. References are cited as though again, the focus we're to understand, is not "if" but on "how" this is purported to work. Where's the feasibility? (I reference a 2013 Cambridge study indicating only "progress" towards a soup model, whatever that might mean).

It assumes that the informed public is largely ignorant, but slanting your article to imply that they are now examining finer details of an intractable problem, instead of the big picture questions, i.e. do we really know, even remotely, what the composition was? Does a disservice to scientific reporting. It also completely misleads the informed public about the basic problems of the theory, or theories, which I noted, are never even mentioned. Just because Haldane in 1929, worked diligently on primordial soup, doesn't mean that the chemical basis is worked out any more now, than it was then. And there were alternate theories of Boltzmann's atom model, i.e. a non-atom model, which were just as wrong then as they would be now. The "issue" about amino acid ratio is absurdly detailed, as are the so called "ancestral molecules", (again this points an arrow to a chemical theory) and it's not clear if the contributors to these theories, like Greg Fournier, and many others in this field, really understands that the proof of concept of his model is non-existent. I propose that no such proof exists, and give reasons why here (it has nothing to do with WHAT kinds of molecules you are starting with):

Thanks to a large degree on the misapprehension of laws such as constructal laws, it is currently a widely held belief that the earth acts as a kind of heat regulator, like a refrigerator or a heater, depending on what is apparently 'needed.'
Although I querried the scientists, who authored the paper about the issues relating to their self- selecting and evolving polymers, I did not get a response to these valid questions. Here is what I wrote to the authors, (below).. and I've since incorporated it into my new theory, which I'm giving folks a peek at here:

Though constructal law itself has been criticized, the concensus is that inanimate is a phenomena connected with the animate, or vice versa .. so this incorrect view is not only owing to "Constructal law", but also to MEP , so called maximum entropy production, among others.
Why else would the scientists use such fuzzy, non defined terms like "evolving" or selecting molecules,
I asked them to define what evolving might mean in terms of a molecule, in terms of chemistry, but there was no reply from the researchers themselves. Again it appears that researchers are going along with the flow, several theories combined to give the illusion of something real. Molecules select themselves based on some preference, and systems export entropy much like a refrigerator does. Look no further than the "work" of MEP theory, (Kleidon but also RC Dewar, 2005 ..) constructal law, or the combined *dissipation-natural selection theory recently from MIT. *Which has been advocated in different forms.
The earth is viewed as an engine, regulating the temperature of the atmosphere. Whereas it is true that our atmosphere does obviously cycle, these dissipations are in continuity , a "continuity principal" I'm introducing ("see Fig 2. Condition 1, B") but also here (#13), such that their normal forces are not opposed, these movements are in line with the packets of energy received from the sun. This means that the system will progress towards a least resistive path. I also propose in the paper, that only a normalized force, 
In reality, in the "Virtual Closed System" theory, there is no means for groups of molecules to export entropy. Despite their insistence that the earth's cycle can do so. Again thanks to the "myth" promulgated by these other theories. Discussion turns into 'they said it was so.."  in what amounts to a kind of conventional bait and switch routine, where only part of the story is known and knowledge of its greater workings of the theory, is deferred. Based on continuity of the forces involved, inanimate molecules are subject to the same dissipative phenomenon, as their surroundings. That principal is a thermodynamic Coda on their so called self redirecting or self improving primordial broths.
Again they simply refuse to reply to my big questions about feasibility of "self-assembly", the elephant in the room.. and it seems this kind of "research approach" in which smaller irrelevant questions are taken in stride, but big ticket items ignored, ones that obviously contradict the "findings" and befuddled "learned proteins" might help sell it in an article, but only muddy the very definition of science.

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