http://retractionwatch.wordpress.com/2012/02/03/editor-who-published-andrulis-paper-tries-to-explain-how-it-happened/

http://retractionwatch.wordpress.com/2012/01/28/case-western-explains-why-it-withdrew-press-release-about-andrulis-origin-of-life-paper/

CWRU is being cowardly.

The deposition of the orthophosphate puts NXP into a high energy state.
The eviction of the orthophosphate put NXP into a low energy state.

So, just as the earth cycles around the sun with an aphelion and a perihelion, so does the NXP, a particle, oscillate around the orthophophate which it absorbs and ejects — with high energy states (e.g. ATP) and low energy state (e.g. ADP).

Thus, through the oscillation of these states we have a wave (or if you prefer, cycle) — the gyre.

The gyre maps the space-time path of the individual particle as it oscillates between the two states.

The quantum captures the entire phenomenon — i.e. the quantum is a shorthand notation for compressing the biological (or any) process — both the wave and the particle. Thus, the quantum is just a way of representing the two states and you know that a process that has already been described in the literature (NTP NDP+P), but you don’t know which state the NXP is in until you observe it.

This arrangement is exactly like Schroedingers’ cat. We don’t know if its dead or alive until we observe it.

As a wave, the NXP has a time period (wavelength) for the cycle, an amplitude (set by the high and low energy states), and it has a frequency (as wavelength and frequency are directly related).

As a particle, the NXP necessarily is moving through space and time, has a rotation (as does every molecule), and vibrates and stretches (just as every molecule).

By the way, the standard method for measuring the stretching and vibrating of bonds is IR (infrared spectrometers).

I can see quite clearly that the RNA world hypothesis says nothing about the flow of genetic information in an extant cell (central dogma) and the central dogma says nothing about the origin and evolution of RNA. The point Erik was trying to make is that current models/theories/hypotheses/ideas are ad hoc and thus should be considered provisional at best and wrong at worst. Could you point out the illogic there?

As for how theory treats those three problems (translation apparatus, genetic code, and biometabolic pathways), I would call your attention to where these problems are treated:

- p. 43 Origin of the genetic code

Erik’s core model shows that systems organize in units of threes, creating a system that has high potential energy but less exergy than the evolutionarily prior system. The tri-quantal system (as he calls it) is the tri-nucleotide, with each component of the system having a relative amount of energy (see section 2.4.5, pp. 13-14), “(i) a high energy (exergic), unstable, excited form; (ii) an intermediate energy, quasi-stable, transition form; and (iii) a low energy, stable, ground form.” My read of this is that the first nucleotide is the most stable, the second is the quasi-stable, and the third position of the codon is the least stable. His model echoes what I know about the wobble hypothesis and the variability of the genetic code. Is there a problem with the interpretation that I am missing?

Erik has proposed that the code evolved autocatalytically, from the metabolism of the orthophosphate bonds between the 2nd and/or 3rd nucleotides. Perhaps the reason why I don’t find Erik’s proposal so outlandish is that it is fully consistent with mainstream scientific ideas: both the Nobelist Eigen and complexity theorist Kauffmann argue that the origin of RNA involved autocatalytic systems. I assume you are familiar with their work.

- pp. 45-48 Specificity of genetic code; origin of translation apparatus.

Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide. Erik models these RNAs as being the tri-quantal state that drives the emergence of and exists in a quarternary complex with one or more amino acid(s). Again, points for Erik, as this is, in fact, what one observes in existing cells (in fact, to the best of my knowledge, RNA scientists have shown that the peptide bond can form sans accessory ribosomal proteins; more points). The cycling of one RNA (the rRNA) leaves a ternary complex of the amino acid (linked to the tRNA, Erik calls it aa-tRNA) and the mRNA. And, just as the rRNA can cycle in and out of the quarternary complex, Erik models the mRNA cycling in and out that previously mentioned ternary complex. Both cycling phenomena are depicted accurately by the gyre and the latter of the two reveals a co-adaptational relationship between the aa-tRNA and the mRNA.

My only problem in understanding is how the genetic information of RNA is transferred to the link between the amino acids that make up the polypeptide chain. Erik points out that the formation of the amide bond is, first, a consequence of loss of mRNA and rRNA relationships with the aa-tRNA. (I think he means after the tRNA passes from the A site to the P site in the ribosome.) Next, the nitrogen link imports information from the tRNA into the amide bond as is subsequently cycled out, too. (I think he means after the tRNA passes from the P site to the E site in the ribosome.) He relies on an axiom (the tenth one) to take this position. Seeing as this axiom applies to all systems in his theory, and finding no experimental evidence to refute it, I cannot dismiss it outright as wrong.

- pp. 30-60 Biometabolic pathways

Other than page 35, Erik does not use the term “biometabolic pathways” (because he did raise it up front, points against Erik). Perhaps the reason for this oversight is that every single pathway in the cell is a biometabolic pathway? In this regard, these 30 cited pages contain a large amount of discussion of many distinct aspects of cellular metabolism. If there’s one particular example you wanna go over, lemme know.

zackoz, here is a link to numerous crazy ideas that transformed science:
http://amasci.com/weird/vindac.html
Humbling, hunh?

The paper is genuine. I know because I have read it and previous versions — plus and enormity of additional, related material. (Louis, yeah, there is a heck of a lot more.)

The paper is heterodox and VERY dense, so naturally most people will take the intellectually lazy route and just mock it.

CWRU acted in a cowardly fashion by taking down its press release. Its press office was bullied by two physicists who were embarassed (threatened really) that a non-physicist would dare to trespass in their sacred territory. Science is about defending the status quo — and getting grants that support pet theories.

I have spent several YEARS in conversations with Erik about the paper (and related material). He has made corrections and revisions and has made coherent arguments.

I have advanced degrees in science, and those, coupled with my many discussions with Erik give me a distinct advantage in understanding this paper.

If any serious reader wants to understand this paper, he or she will have to read it several times — if only to get a notion of what it is about.

The radically new can be extremely hard to understand, you see.

Also, for your consideration: http://milesmathis.com/erik.pdf

Everytime we want a new product, we mixes ingredients, and we use liquefactiors, centrifugatiors, etc. Andrulis’s is saying just that: Nature also, everytime that produces the emergence of something new applies these kinds of swirls, wich he calls “gyres”. Why not? It is a logical thinking.
A responsible criticism about his work needs to show every mistake he could did at every one of his 800 references. It is not a job for any biologist, physicist, mathematician: it is a job for a group that reunites all expertises.

The Andrulis thesis says: “In other words, this theory indicates that craters are not due to impact (from without to within) but rather from “expact” (a cratering force exerted from within to without)”. I never thought in this way. Like the people of millenias ago never thougt that the sun is the center of our system. It is food for thought, it makes sense, and maybe he is right. What kind of proof do you have against it? His whole thesis is insightful in this way.

The Andrulis’s mistake was to introduce his thesis in a scientific journal. He forgot that the kind of hard-wired brain that dominates the iniversities and scientific method today will change, of course, but is different from his brain. He is a uncomfortable threat for conservation of social status like Galileo was to the Church.

In my opinion, the gyres is a strong hypothesis, but not the whole answer, it is only 1/7 part of the whole answer. The gyres are the piece performed by Function 1 in the Matrix/DNA formula, another thesis made by another different unusual hard-wired brain. Andrulis, instead trying to get recognition by this brain’s fashion on course just now, should doing what the author of Matrix/DNA theory is doing: make a website only, work hard searching in Nature evidences for this thesis, search also any proved fact that could destroy this thesis, go registering everything in that website, even that nobody else is reading it. He will die one day, and if he is right, if he discovered a great aspect of Nature, his job is disponible in the Internet for those that has an open mind to see it. I am reading the Andrulis thesis, I will try to read the 800 references, it is a healthy and instructive exercise. Thanks, Mr. Eric Andrulis.

http://tinfoilpalace.eamped.com/members/ik/

Note the bit half way down announcing the release of the paper.) He appears not to have written it in jest. :-/

Turning and turning in the widening gyre,
The falcon cannot hear the falconer.
Things fall apart; the center cannot hold; [....]

http://freethoughtblogs.com/pharyngula/2012/01/27/the-comparison-to-jabberwocky-is-inevitable/

Yes, crazy ideas can (rarely) transform science. Alas, more often, they’re just crazy.