Life turned upside down

By Carl Zimmer | January 31, 2012 11:59 am

Thousands of papers get published every week, but every now and then a truly strange one pops up. On December 23, a new journal called Life published a paper by Case Western Reserve University biochemist Eric Andrulis called “Theory of the Origin, Evolution, and Nature of Life.”

At Ars Technica, John Timmer unpacks this 105-page paper and delves into the weirdness, in a post called “How the craziest f#@!ing paper got published and promoted.”

The basic idea is that everything, from subatomic particles to living systems, is based on helical systems the author calls “gyres,” which transform matter, energy, and information. These transformations then determine the properties of various natural systems, living and otherwise. What are these gyres? It’s really hard to say; even Andrulis admits that they’re just “a straightforward and non-mathematical core model” (although he seems to think that’s a good thing). Just about everything can be derived from this core model; the author cites “major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations.”

He’s serious about the “not limited to” part; one of the sections describes how gyres could cause the Moon to form.

Is this a viable theory of everything? The word “boson,” the particle that carries forces, isn’t in the text at all. “Quark” appears once—in the title of one of the 800 references. The only subatomic particle Andrulis describes is the electron; he skips from there straight up to oxygen. Enormous gaps exist everywhere one looks.

The theory is supposed to be testable, but the word “test” only shows up in the text twice. In both cases, Andrulis simply claims his theory is testable in specific areas of study. He does not indicate what those tests might be, nor what results would be predicted based on his gyres.

I could easily go into more specifics (very easily—I’ve got lots of notes), but it’s clear that there’s nothing in the paper that much resembles science.

Timmer goes on to look at how the paper glided smoothly into the science media machine, first with a press release from Case Western , and then with reprints of said press release at outlets like Science Daily and Physorg, without anyone wondering if it deserved this sort of attention.

I wondered how the paper got published and checked out the editorial board of Life. One name popped out at me: Stephen Mojzsis, a University of Colorado geochemist. I met Mojzsis while working on a story about the age of the Earth for National Geographic, and I’ve stayed in touch on and off ever since.  I dropped him a note Sunday to ask about the paper. To which he replied,

“You saw it before me!  I am pretty unhappy about it.  Have just contacted the Editor in Chief.”

The more Mojzsis looked into it, the less he liked the situation. Yesterday he tendered his resignation from the board. Today his name is gone from the journal’s web site, along with a number of other editors.

I have to scramble today to get ready for a talk at the University of Maryland tomorrow, so I won’t be digging deep into this story. I’d suggest you keep up with Timmer, as well as Ivan Oransky at Retraction Watch, to see how this drama unfolds.


Comments (21)

  1. Timmer does a lot of name calling and very little scientific (e.g., the frequency of word use like quark does not render a paper invalid) criticism.
    I am doubting the paper, but I doubt all papers equally and find the flaws myself. That is the scientific process, not name calling.
    On a good note, perhaps this will call attention to the fact that peer-review needs to be improved. I am not saying that it is flawed, but people review for free and are already over worked and underpaid.
    Also, it is important to remember that “crazy” ideas can transform science. Take the late Lynn Margulis having her paper rejected by over a dozen journals on endosymbiotic theory. This completely transformed the way we looked at all of biology.

  2. Eli

    I suspect this is another “Hermeneutics of Quantum Gravity”-type thing. There are a zillion new open access (read “cash cow”) journals popping up, and this reads like a test of the true “peer review” nature of the model.

  3. zackoz

    PZ Myers has already panned this:

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

  4. Another Kevin

    Wow. Gyres, eh? Sounds like Yeats’s The Second Coming: (Yeats actually had a theory of gyres, too: expostulated in his A Vision, which also purported to be a theory of everything.)

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

  5. David B. Benson

    Well, this year is 2012 so I suppose this kind of time wasting is to be expected.

  6. marcel

    DB Benson @7: Why? Because it’s a presidential election year in the US or because the world as we know it is coming to an end this year? Or do I repeat myself?

  7. Ken

    From the post title and my first glimpse of the figure, I was momentarily expecting something about the developmental differences among the bilateral animal phyla. Pity.

  8. David B. Benson

    marcel @8 — You not only peat yourself but you repeat yourself.

  9. sat

    Here’s more from the author:

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

  10. In my humble opinion, you guys, are practicing group selection, but, in a wrong way, it is group discrimination, against the course of Natural History. This guy, Andrulis, is a searcher. He has the brain hard-wired in a non-usual way, which makes to perceive or mistakenly imagining invisible forces in Nature as answer for those no yet answered mysteries around natural phenomenons. Which brain is the best hard-wired: yours, ours, or Andrulis’s brain? Scientifically nobody knows, only time has the answer.

    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.

  11. nettle

    Chris Moore and Louis Morelli,
    you guys are freethinkers. Good for you!
    (Louis, he is Dr. Erik Andrulis.)

    zackoz, here is a link to numerous crazy ideas that transformed science:
    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:

  12. nettle

    I would like to supplement my previous post with some lengthy defenses of Erik’s paper.

    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.

  13. nettle

    Contrast a NTP and a NDP. One NXP can’t be NTP and NDP at the same time.

    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).


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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.


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