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Retraction Watch

Tracking retractions as a window into the scientific process

Case Western explains why it withdrew press release about Andrulis origin of life paper

with 143 comments

The wild and woolly saga of the paper that claims to solve “the puzzle of the origin and evolution of cellular life in the universe” continues.

Yesterday, Ivan wrote on his Tumblr about Case Western’s Erik D. Andrulis‘ paper, “Theory of the Origin, Evolution, and Nature of Life:”

The paper is 105 pages, which includes a whopping 800 references. It depends heavily on the gyre:

In the theory proposed herein, I use the heterodox yet simple gyre—a spiral, vortex, whorl, or similar circular pattern—as a core model for understanding life. Because many elements of the gyre model (gyromodel) are alien, I introduce neologisms and important terms in bold italics to identify them; a theoretical lexicon is presented in Table 1. The central idea of this theory is that all physical reality, stretching from the so-called inanimate into the animate realm and from micro- to meso- to macrocosmic scales, can be interpreted and modeled as manifestations of a single geometric entity, the gyre.

Andrulis concludes:

…this catholic theory provides an innovative and elegant solution to the origin, evolution, and nature of life in the cosmos. I humbly proffer my theory as a viable system for knowing life.

Our humble author also includes paragraphs like this, which led some on Twitter to wonder if the paper was for real:

The philosopher Bachelard claimed that scientific history is replete with unconsciously constructed or immanent “epistemological obstacles,” that are eventually broken through and shed during “epistemological rupture [796].” I conclude that my theoretical work elicits a Bachelardian rupture of intradisciplinary noöspheres and interdisciplinary boundaries. Kuhn proposed a related concept of “paradigm shift” to explain the process surrounding worldview conversion during a scientific revolution [797]. Whether the advent of this theory elicits a Kuhnian gestalt switch is debatable, though such an iconoclastic event has been foretold [798-800].

On Thursday, Case Western had put out a press release about the study. That release is still available on ScienceDaily and other sites, but the medical school removed it from their own site. Today, Liz Lear, senior director, School of Medicine Marketing and Communications, tells us:

The School of Medicine’s public affairs office promotes all faculty research as possible. We have been evaluating our processes regarding media outreach and elected to remove the release from our website while we assess our policies surrounding promotional communications.

We’ll continue to update this story as we find out more. In the meantime, you can read PZ Myers’ take, in which he suggests that “the comparison to jabberwocky” is inevitable, and John Timmer’s, in which he wonders “How the craziest f#@!ing “theory of everything” got published and promoted.”

Update, 5:45 p.m. Eastern, 1/31/12: Carl Zimmer reports that a number of the journal’s editors have resigned.

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Written by ivanoransky

January 28, 2012 at 2:01 pm

143 Responses

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  1. “Explains”?

    “Back-pedals and temporizes with bureaucratic boilerplate” would be more appropriate, I think.

    Blake Stacey

    January 28, 2012 at 2:10 pm

  2. Sounds like they had no policy and realized how wacky this paper really sounds. So now, they pulled the press release to give time to build some policy which is defensible to promote all the papers by all the staff and yet not make the PR office look like mere megaphones.

    Martin Badke

    January 28, 2012 at 2:35 pm

  3. Here’s a chucke – from the paper: “Received: 15 November 2011; in revised form: 10 December 2011 / Accepted: 13 December 2011 / Published: 23 December 2011″

    So, a 105 page paper with 800 references is reviewed and resubmitted in 25 day, accepted 3 days later, and published 10 days after that.

    Rapid review is important, no question. However, it is equally important that, if a paper seems bizarre, to sit on it and cogitate. I downloaded the paper, and briefly glanced through it. The paper starts sort of OK, but when you get to the definitions page, in which he defines about 60 new terms, where the first definition reads: ”
    Alternagyre A gyrosystem whose gyrapex is not triquantal
    Dextragyre A right-handed gyre or gyromodel
    Focagyre A gyre that is the focal point of analysis or discussion
    Gyradaptor The gyre singularity—a quantum—that exerts all forces on the gyrosystem
    Gyrapex The relativistically high potential, excited, unstable, learning state of a particle
    Gyraxiom A fact, condition, principle, or rule that constrains and defines the theoretical framework
    Gyre The spacetime shape or path of a particle or group of particles; a quantum”

    Enough to make you gyrate, eh?

    Here’s from p. 5: “2.1.2. Gyre Qualities There are several characteristics of a gyre that make it theoretically appealing. Most notably, gyres are organic, that is, they have qualities identical to those found in living systems: they adapt their shape, size, position, rate, strength, and direction. Furthermore, gyres follow a life cycle of emergence (birth), development (aging), and dissolution (death). Gyres spontaneously self-organize when the pressure, temperature, energy, and matter conditions are appropriate.”

    As a scientist, I can only say that the last sentence is certainly true, and is also certainly false, and is certainly also untestable.

    Here is a paragraph from p. 41: “R corresponds to the grouped nucleotide sugar and nitrogenous base and gyradaptive P/Ⓟ is the particle/quantum orthophosphoric acid, the phosphon—the mIEM and singularity of the ribogyre. Given the protean quality of gyromodel symbolism, the gyrapical R3P and gyrobasal R2P can represent any one or all NTPs (adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)) and NDPs, respectively.”

    I am not a biologist or chemist, but all of that gyromodel stuff??

    I think it’s a Sokal.

    Paul Thompson

    January 28, 2012 at 4:21 pm

    • It seems that the kinds of definitions used make a confusion that was defined by Schopenhauer in the “Quadruple Root of the Principle of Sufficient Reason”, that is, between reason in the ontological domain and reason in the epystemological one. I do not think the paper is a Sokal, by no means (I know Alan and his paper was a hoax), the idea of gyres may be good. The only thing we need, besides a very difficult paper to understand, is at least one good experimental fact, foreseen by this new theory. Science, and certainly such a broad one, that takes on all scales, should give us some results!

      Saint Clair Cemin

      February 6, 2012 at 7:41 pm

    • Paul Thompson,
      “I think it’s a Sokal.”
      Think as you please. You are wrong. The paper is genuine and true, save for at least one mistake.

      “Here’s a chucke – from the paper: “Received: 15 November 2011; in revised form: 10 December 2011 / Accepted: 13 December 2011 / Published: 23 December 2011″

      So, a 105 page paper with 800 references is reviewed and resubmitted in 25 day, accepted 3 days later, and published 10 days after that.

      Rapid review is important, no question. However, it is equally important that, if a paper seems bizarre, to sit on it and cogitate.”
      I couldn’t agree more.

      “Enough to make you gyrate, eh?”
      Certainly. You already are gyrating. Eat, do daily activities, sleep. Also, eat, metabolise, excrete. Deficate, urinate, exhale. Note the grouping of threes. /You/ are the trimergent form. The paper describes you.
      Important to note, that science coins new words all the time. If you mock the new jargon in the paper, you must mock the new terms in science (all the ‘omes e.g.) to be consistent. Otherwise, you spout hypocrisy.

      “As a scientist, I can only say that the last sentence is certainly true, and is also certainly false, and is certainly also untestable.”
      As a scientist you do not know what a theory should be. Shocking. How can we test string “theory.” Shouldn’t we call it string /hypothesis/ until we can test it? If not, why not. Moreover, Erik provides 800 references of experiments for you with experiments supporting his gyre theory.
      As a scientist you have a mind that is freakishly closed when it comes to the new ideas in the paper.
      Scientists are /supposed/ to be interested in the new and the strange. Where did you go astray?

      “I am not a biologist or chemist”
      So, you have /no/ friggin’ way to understand the paper save for the overarching principle that Erik has explained how the photon relates to the electron and interactions all the way up to the cell. Oddly, you ignore that. I guess you are comfortable with your ad hoc theories that do not interelate. Right? How water relate to RNA? How does DNA relate to the phospholipid bilayer? How does the electron relate to the emergence of the cell? All these questions were unanswered — until the paper.

      I could explain the paper if you were interested, but I think you lack the intellectual curiosity and mental tenacity to understand even what I write (as have others here), and aren’t interested in a radically new theory that unites so many systems.

      nettle

      February 21, 2012 at 5:13 pm

  4. Whoever reviewed this paper after submission needed a lot more than three days to even try to understand it (if it is indeed possible to understand.) More like three months.

    Conrad T Seitz MD

    January 28, 2012 at 4:51 pm

  5. Every so often scientists are forced, by their own minds, to grapple with the incongruity of very limited methods and the ‘big questions’ that frequently is used to justify the research. Often enough, I find, a researcher wanders off and writes a crazy few pages about the solution to the ‘big problem’ using some funky idea and a bunch of references. Usually, he gets stuck, edits or completely rewrites it a few times, and gives up in the realization that the big question hasn’t really been solved yet, not even in a framework fashion. Then it is back to our regularly scheduled programming – reductive, typically; practical and sensible, often enough.

    It sounds as if this paper just got out of control; and was somehow finished before being completely scrapped. Then, perhaps, he decided to put it out there, to see what would happen.

    Ben

    January 28, 2012 at 4:56 pm

    • For the sake of his health, his family, and his career, I hope you are right on the reason, and that it is not mental illness. Unfortunately, I have a good friend with bipolar disorder, and this reads a lot like the way my friend describes going through pre-mania and mania.

      Whatever the reason, it has a rich, sci-fi feel to it. I’d bet a nickel that this will gather a small cult following, and that we may see movies and games that use its idea in the coming years. It may even irritate some of the more thin-skinned string theorists, which I find perversely amusing to watch.

      Part of me is just simply enthralled by the dedication that the author had to this work: 105 pages and 800 references! I wish I currently felt that excited by my own work.

      sfs

      January 29, 2012 at 4:33 pm

  6. Very odd indeed. Surely this is just a joke. His faculty profile page is not all that wacky and he has published some solid basic research in very nice journals, including NAR etc. He does seem overly wordy in my opinion, even in his description of his research, but either he has totally lost his mind recently, or he is having a laugh with this. A lot of work for just a giggle though………..

    Dave

    January 28, 2012 at 5:18 pm

  7. Guys,

    It is not a joke. It is a sad case of what appears to be mental illness. Just very sad.

    He was quite successful as both a graduate student and a post-doctoral fellow. He has become obsessed with this idea and this will be the end of his career. He is ill, in my opinion.

    Editor’s note: Last sentence changed to make it clear this is the commenter’s opinion.

    Pinko Punko

    January 28, 2012 at 9:50 pm

    • - the schizophrenia of “A Beautiful Mind”.

      DuD

      January 29, 2012 at 12:03 am

  8. Sokalism applied to evolutionary theory?

    Karen Shashok

    January 29, 2012 at 3:24 am

  9. Hello, I am a psychiatrist who also does research. There is a long history of scientists (brilliant and otherwise) who become mentally ill at various points in time. There is also a long, documented history of great discoveries and/or masterworks being produced by individuals during periods of manic-depressive illness and/or schizophrenia. See here for some unusually ill geniuses:
    http://www.cracked.com/article_16559_7-eccentric-geniuses-who-were-clearly-just-insane.html

    I do not know the details of this particular case, but my initial reading of some of the quotes in this paper, as cited above, along with the post from Pinko Punko, make me suspect that this particular individual has likely entered into a period of mania or psychoses. This is a sad, unfortunate occurrence that can happen to anyone, for many reasons, both genetic and/or environmental. I hope that this individual can return to both a good life and a productive scientific career. We need such people to advance science, medicine and humanity.

    Gholson Lyon

    January 29, 2012 at 3:54 am

    • Fascinating comments Gholson and I agree that this could turn out to be a very sad incident. From what I know about psychoses/mental illness, which is obviously very little, it would be unusual for an individual of his age to SUDDENLY slip into some kind of psycosis. It would also be very unusual for him to develop genuine schizophrenia at his age. Surely this recent development would instead reflect some underlying issues that have been around for some time and/or a manic phase of a long-standing manic-depressive disorder (as you suggest). Would this be accurate?

      Dave

      January 29, 2012 at 5:05 pm

      • Makes perfect sense to me, and why can’t we be open about the ravages of mental illness? Why is there still such stigma?

        From a mental health advocate.

        Bella Pazza

        January 31, 2012 at 2:12 am

      • Just to be clear, I am NOT in any way diagnosing this individual. But, if he needs help, I hope he gets it.

        As detailed in the link from above and in MANY other links on the web, many brilliant people can get into periods of severe mental illness. This includes fixed, false beliefs, which are called delusions. Peer review is meant to slow down the torrential downpour of people trying to get shoddy, poor quality, fraudulent, or non-falsifiable papers published, but as is the case here, post-publication peer review is also very useful, particularly if and when the pre-publication peer review process breaks down.

        Gholson Lyon

        February 2, 2012 at 10:44 am

    • Gholson Lyon,
      Your comments are dangerously ignorant because they are ex cathedra for anyone who believes your claim to being a psychiatrist. This imprimatur makes you more credible to the gullible who can not think for themselves — and who put their trust in you. All the while, you demonstrate you can not think for yourself on matters regarding Erik or, oh yeah remember, his paper. I am talking about folks like Dave who follow your comment. How irresponsible of you.

      “There is a long history of scientists (brilliant and otherwise) who become mentally ill at various points in time.”
      Ok. So what?

      You are either a make-believe psychiatrist or have bizarre gaps in your ability to reason. Einstein, Planck, Schroedinger… The list goes on and on and /on and on./ At least some (if not the large proportion) of those scientists were not mentally ill outside of the common cold of psychiatry, depression. Why don’t you acknowledge them?

      Correlation does not imply causation. How come I have to say this to you, a claimed psychiatrist?

      You have not met Erik, have not read any of his papers carefully, and did not let your ignorance of Erik’s ongoing productive scientific career stop you from a veiled attack on the Erik. I am a longtime, very close friend of his. I am not a psychiatrist and have only studied psychology for one year. My ignorance stops /me/ from judging Erik’s mental health. I can say in layman’s terms that he seems fully functional and healthy to me and those around him. I can also say that his reasoning skills are at a level demonstrably beyond yours.

      The paper is hard to understand, but that won’t stop you from not trying. Yeah. Not trying. Easy.

      By the way, how does a scientist have a productive career when the funding rate of grants is 8% of applications? Answer, theoretically: through dedication, intellect, and political nous to convince the benefactor. How does a scientist continue to have a productive career? Answer, /in practice/: at a 8% grant approval rate most likely he or she does not. Where does mental health apply in this funding problem? Hint: don’t look too hard.

      1. “I do not know the details of this particular case”
      Your ignorance on the details does not stop you from strongly implying that Erik is insane. You should have your license to practice medicine revoked if you practice medicine the way you treat Erik. Your comments are flippant and counterproductive.
      2. “but my initial reading of some of the quotes in this paper, as cited above”
      Your initial reading is unworthy of a child. A child would at least ask questions. Only an adult would have a mind as prejudiced and closed as yours when faced with the ideas in the paper. You do not understand them, you have not tried, and you may not have the capability to understand.
      3. “along with the post from Pinko Punko”
      You jump to a conclusion based on stale information. Good God what have You done to Gholson’s mind? Gholson, you claim to be trained in psychiatry yet rely on third-party, non-contemporary information (claims) from a stranger to come to your conclusions? If you act this way with your patients you are a quack who is a menace to integrity in the field of psychiatry.

      I am very good friends with a psychiatrist. He visited me recently. When I showed him this page and described the paper and its supporting work, he was thrilled by the ideas (I had shared the big picture with him before) and almost begged me for the original work from which this paper is derived. He also asked questions. Why are you not able to be so intellectually curious, open-minded, and inquisitive?

      Three comments you make are particularly outrageous. They follow.

      I fear for your patients treatment as much as you hope Erik “can return to both a good life and a productive scientific career.”
      You can’t return to what you already have. Moreover, with an 8% funding rate, scientists can not remain productive.

      “We need such people to advance science, medicine and humanity.”
      If you believed what you said, you would be up in arms over the mere 8% approval rate of grants for reseach. But you don’t. So, you aren’t.

      In a later post you say,
      “Just to be clear, I am NOT in any way diagnosing this individual. But, if he needs help, I hope he gets it.”
      You fail to realize that you have already poisoned the well with your ignorant comments backed by your ` I-am-a-psychistrist -and-I-think-this` stamp of expert approval. If you were a solidier, you would say,”ready fire!, aim.
      You then tack on a sentence that you know or /should know/ leads the layman into believing that you /do/ think Erik likely has mental problem. You hope he “gets it,” “advances science, and “return[s] to a good life and a productive scientific career” so badly that immediately after the post you /forgot/ Erik — neglecting even to called him at CWRU to offer /any/ assistance. You had your chance to prove your psychiatric and altruistic credentials, and boy, did you.

      Your credibility is zilch.

      You are a liar — and a bad one at that, save when it comes to deceiving yourself and the gullible.

      You care as much for Erik as you care for a thorough, studious, tenacious reading of his paper.

      In case that last sentence went over your head, let me be clear. /You don’t care./

      Your hypocritical comments, falsehoods, and mental laziness demand harsh reproach from every open-minded person.

      nettle

      February 25, 2012 at 8:35 pm

      • errata in previous post (grammar and spelling):

        at an 8%
        soldier
        call him

        I suppose there are others. I post too quickly.

        nettle

        February 26, 2012 at 12:56 pm

  10. I very much doubt it’s a joke… No-one would write a 100 page, 800 reference joke. Well, if they did, they would deserve a medal for dedication to their art.

    Neuroskeptic

    January 29, 2012 at 5:17 am

  11. Fascinating.

    Jon Beckmann

    January 29, 2012 at 6:07 am

    • Live long and prosper.

      µ

      January 29, 2012 at 4:06 pm

  12. This has got to be a joke about poor quality fluff getting pushed through to publication by lazy editors and reviewers.

    Honclbrif

    January 29, 2012 at 1:42 pm

    • The editor and reviewer would have to be incapacitated in this case…….

      Dave

      January 29, 2012 at 5:06 pm

    • Let’s keep in mind that the editor has ultimate authority over publication; we have no idea what the reviewers thought of the paper. The piece is clearly controversial, but, unlike papers by HiV-deniers like Duesberg, there is no harm in publishing it. No lives will be harmed by the publication of this piece; it’s an online journal, so no trees were killed in its distribution, either.

      The article is definitely relevant to the journal: http://www.mdpi.com/journal/life/about/

      It’s a theoretical paper that the author has clearly put some time into. The journal is relevant, and in fact states “manuscripts regarding research proposals and research ideas will be particularly welcomed.” The work could easily be argued to be and extended research idea. For that reason, I can see an editor deciding to publishing it simply to put the ideas out there. What, exactly, is wrong with that?

      Rip into the ideas all you want; I don’t know why anyone finds the actual *publication* offensive. It’s a low-impact, specialized journal that invites articles discussing research ideas/proposals. There’s a place for that.

      sfs

      January 29, 2012 at 5:39 pm

      • I have not read that anyone finds it “offensive”. I certainly don’t and could not care less about the article to be honest. It is not my idea of science, but each to their own. I just find it very odd indeed.

        Otherwise, great post and you make some nice points.

        Dave

        January 30, 2012 at 11:46 am

  13. I’ve emailed with the editor on this “special edition” of the journal, someone who also happens to be the journal publisher. He informs me that this paper was sent for review to “more than two” potential reviewers. Two reviewers ultimately submitted comments, both of them from the US, and both of them ranking it as “accept with minor revision.”

  14. Let’s not rush to dismiss something we do not
    understand. Who knows, he may be up to
    something. It is definitely more exciting than
    crystallography.

    MT Orr

    January 29, 2012 at 7:13 pm

  15. This reminds me of a guy who used to be a constant feature in my neighborhood. He would stand on a street corner and hand out leaflets to passers-by. The leaflet described his very short proof of Fermat’s Last Theorem.

    chirality

    January 30, 2012 at 9:27 am

  16. ah yes, let’s lean back and watch the smear campaigns…

    i really wonder who of that mob has actually read (not to say understood) the paper…

    asdf

    January 30, 2012 at 9:40 am

    • Well, we are waiting for your explication of the paper. It is available for download. Read it and get back to us on some of the points raised here. The paper is very odd, and is either an extremely elaborate hoax that took hundreds of hours of preparation, or is the product of a disordered process, in my opinion. The paper is not science in the way that I understand it. It is philosophical musings, possibly, and is speculative in it’s intent. But before calling questions a smear campaign you should do research.

      Paul Thompson

      January 30, 2012 at 9:55 am

    • Who said anything about smear campaigns? My god this blog is ridiculous at times. It is perfectly reasonable to express some confusion over this publication and the institutions behavior contributed to this. Remember that it would not even be on this website were it not for the “retraction” of the press release in the first place, which is quite an unusual move I’m sure you will agree. So let us not take this to a whole different level and start an argument about smears etc etc. It’s not helpful.

      I have read parts of it and have absolutely no idea what he is on about. Literally, zero. Perhaps that is my fault, but perhaps the author has a responsibility to make it understandable if the article is genuine. I think that if you are making up new words and have to define them at the beginning of the article, you are facing an uphill battle with the readers. Just my $0.02 as usual.

      Dave

      January 30, 2012 at 11:43 am

  17. I’ve actually met the person in real life, at the Origin of Life Gordon Research Conference earlier this month. He’s a great guy with a deep, rich mind; he runs mental circles around the majority of academic professors. He’s sociable, has a great sense of humor, relaxed, and very passionate about science and trying to discern the truth, like we all are. I really like the guy. I definitely DO NOT think he is psychotic, manic-depressive, or schizophrenic, as has been mentioned above – and I believe it is quite rude to even mention the fact, especially on a PUBLIC FORUM BOARD.

    Unfortunately, at some point in his life, he got some very strange meta-scientific notions in his head (based, he says, on previous Real Science he performed – published in the journal Science) and expounded on these ideas until he came up with this… unprovable theorem that no one can understand, or comprehend. I’ve had hours of conversation with him, trying to get to the “nature of gyres”, how they came to be, how we can study them, how they create everything, etc., etc., but it is to no avail; he is unfortunately not amenable to debate or discussion about the existence of gyres.

    It reminds me very much of trying to have a conversation about the nature of religion with someone who is wholly faithful in that religion – steadfast, dogmatic, and unmoving. He certainly does have the mental capacity to defend himself, and does so quite well, and if you do not have the knowledge of quantum mechanics, nucleic acids, polymers, etc., he will fill in those gaps and shame you – but you will never be able to convince him that his theory is bogus – just like you’ll never be able to convince any “true believer” that their faith is bogus, either. He will even admit to this if you ask him.

    That all being said, as long as you didn’t talk to him about HIS science, he was a great person to converse with. He actually gave me some pointers for my own research that I found helpful, and he was, overall, a really interesting person to talk to.

    Does his science deserve high-impact publication? Of course not – he said that he sent this publication into 12 journals before it was accepted – but that is the nature of our current publication system. If you have an idea, or a theory, submit it – and if the audience thinks it is bogus, we will debate it. These debates will help us raise important questions and issues that typically lay assumed, untouched – and though this debate, the publication process becomes stronger and better than before.

    David

    January 30, 2012 at 3:00 pm

    • Goodness gracious, an informed opinion. Thank you thank you thank you, I’d almost forgotten what they are.

      Very helpful background information to an interesting article.

      BoDuke

      January 30, 2012 at 7:29 pm

    • You can decipher most of these things from reading his paper- he is clearly quite functional, and deeply intelligent. Examine is vocabulary and phrasing. He is a really smart guy. Becoming obsessed with an inexplicable theory comprising an entirely new and inexplicable grammar, and basing this theory on the observation that the exosome has pleiotropic effects when mutated, and that different processes in the cell have evolved to use different nucleotides for control/regulation of different processes indicates a gigantic, irrational gap in his assumptions. It is not inappropriate to recognize that something deeply unscientific is occurring in an otherwise rational and intelligent package. That is where I am coming from. This idea of his appears to be a symptom of something else and not the something else being a symptom of his following this idea.

      Pinko Punko

      January 31, 2012 at 9:22 am

      • I have no way of measuring his intelligence from the manuscript. Anyone can write complex-sounding stuff. What he’s written about quantum gravity appears to be largely hand-waving. He claims that a gyre-model of some kind can unite quantum mechanics with general relativity, producing a long-sought model for quantum gravity.

        However, if you read what’s written, it reads very much like: “see, here’s this thing that I’ve defined, and based on my definitions, it kind of obeys some properties of subatomic particles.” It’s proof by metaphor.

        You cannot substitute metaphors for carefully-done theoretical work. To make this kind of claim, you need *derivations* that show how the gyre-model reduces to current theory under the appropriate conditions. I see none of that.

        sfs

        January 31, 2012 at 10:17 am

        • Yep. You’ve nailed it. I have a theory, and it says that if you have anything useful to say, say it in a way that others can understand. And since I can’t understand his stuff – I assume its rubbish. I could be wrong, but then other people would understand it, and they would write about it in a way that was accessible.

          John Brookes

          September 5, 2013 at 11:06 am

    • The issue is not his intelligence or the depth of the theory. The issue is “Is this science?” and the answer is not clear. It is a large piece, which I have glanced at briefly.

      From P 5: “Gyres spontaneously self-organize when the pressure, temperature, energy, and matter conditions are appropriate.”

      This is not a scientific statement. It is a tautology. It is certainly true, 100% of the time.

      For this paper to become science, the testable implications of the statement must be defined.

      Paul Thompson

      January 31, 2012 at 10:28 am

    • While it is certainly true that he is a smart guy and did some very nice work as a junior researchers (when his mind was restrained by a supervisor and corresponding author), it is also true that his recent papers in the field of RNA degradation have become more and more strange and are largely ignored by the community. There is of course the possibility that he is the only one who truly understands matters but I doubt it. When reading his papers (the real ones on RNA decay) it is very clear that he selectively blows findings out of proportion that fits to his theories and completely ignores work that doesnt fit into his framework. That is not a very scientific approach, I guess his latest 105 page paper wont help him re-establish his reputation. But I guess he probably doesnt really care about that either…

      Exosome

      February 6, 2012 at 9:56 am

  18. I taught this guy when he was a graduate student. As I recall, he struck me as bright and inquisitive and I think he ended up doing his dissertation research in a productive lab with a very well regarded mentor.

    I don’t know how promotion and tenure works at CWRU but in thinking about when I knew him it seems to me that Dr Andrulis must have been there for a while and might be coming up for tenure.

    Perhaps writing a potentially contentious “cult” paper is a way to bring up issues of “academic freedom” that might work to his advantage if he is otherwise struggling to make the grade.

    scotus

    January 30, 2012 at 4:16 pm

  19. This is troubling in so many ways, but I
    am concerned if this young scientist might be mentally ill. This reminds me of John Nash’s brilliance and psychosis.

    This is an inexcusable oversight.

    Shame on more individuals than I can count.

    Bella Pazza

    January 31, 2012 at 2:05 am

  20. It seems to me he is trying to unite science & what we used to call “metaphysics” without resorting to traditional religions. Let him, if it’s how he wants to spend his time. It would be more conducive to a coffee table book with an artist’s illustrations than publication in a peer-reviewed scientific journal, but at least he isn’t hurting anybody. He wouldn’t be the first person to have speculated about a continuum from non-living things to living ones. Every time we think we define “life” something comes along that challenges the boundaries – viruses, then retroviruses, then prions. Efforts, however unsuccessful, in things like cryogenics, and the very real possibility of cloning a woolly mammoth from ancient DNA stretch the definition of life in the opposite direction, pushing back the boundaries of death or extinction. I like to think that life is, In Freeman Dyson’s phrase, “infinite in all directions.” If I ever go looking for a religion to replace the ones I lost (plural), I probably won’t turn to the theory of gyres, which sounds too inelegant for science and too esoteric for religion. But, honestly, there are brilliant minds that do not stick to the scientific method. I’m reading some of Philip K. Dick’s published notebooks, and I think he and this guy seem to share the kind of exhilaration you get out of the window of an airplane when the big picture is just so clear. There’s a place for that, but also a need to view that in its place, which it sounds like the press release did not.

    AnnaX

    January 31, 2012 at 2:47 am

  21. I’m going to have to give this paper some time when I have the time. It seems to be a rather psychedelic work. I can’t speak for the author’s influences, but it certainly reminds me of some thoughts and connections I have made while taking acid or mushrooms, such as the feelings of everything being alive (or understanding how it is potentially so), the interconnectedness of all things, and the similarities in formation and motion between the animate, inanimate, microscopic, and galactic.

    Nettles

    January 31, 2012 at 3:52 am

    • I’ve never had acid or mushrooms- but I get these feelings as well.
      I consider myself well grounded (not mentally ill).
      I believe that I’ve had the opportunity to experience many things and take all the experiences into account.
      I believe his theory is fascinating and not to be disregarded as “insane”.
      History repeats itself in certain ways- and like many great theories they are discarded as “insane” right away.
      Take what you will from his writings and apply it to your own experiences and see how they relate.

      If you spend your life dedicated to one area of study or belief system, it becomes difficult to consider any other area— to me that is insanity.

      Derek

      January 31, 2012 at 3:23 pm

  22. The obsession with spirals reminds me of this movie:
    http://en.wikipedia.org/wiki/Uzumaki_(film)

    shac

    January 31, 2012 at 8:54 am

  23. Have none of you read Viktor Schauberger’s work on the LIFE of water?? Claim: “Water is a living substance!” There are numerous ways to look at Nature, to understand the workings of energy. Now you want to stamp this writer with ‘mental illness’? Why? Because you cannot understand what he has written? Because it is easier to dismiss him if he is ‘not in his right mind’? If the review was flawed, so be it. But try to open up your minds and widen your vision. Life energy is not anal, like science and religion.

    Sarah Ruth

    January 31, 2012 at 11:03 am

    • The PC Humanities contingent is out in full force. No wonder Presidents from most Unis want to shut down their Departments!

      Terry Sejn

      January 31, 2012 at 6:14 pm

      • Yes, the cranks are cranking. Oh the humanity….

        Paul Thompson

        January 31, 2012 at 6:54 pm

      • Background in Human Phys and Biology, thank you very much. Unscrewed from religion and open to the possibilities.

        Sarah Ruth

        February 1, 2012 at 11:51 am

  24. I read the paper, and understand it. He is either the Albert Einstein of “life”, or when the “boys” in the “Ivory Tower” acccept his work, he will reply “GOTCHA!” (followed by hysterical laughter). for comparison, see: http://www.wingmakers.com

    Meijin

    January 31, 2012 at 3:11 pm

    • Wow, how deeply impressive. So, you now understand the whole thing. What’s the most testable claim?

      I read the first couple pages, and it’s either true or false.

      Paul Thompson

      January 31, 2012 at 5:18 pm

  25. I speculation about mania may be correct. But two things bother me:
    1) That people are suggesting that this means his career is over. This is absurd. Many brilliant people suffer from mood disorders. Some even say hypo-mania aids them in creative thought. Mood disorders are not a 100% bad thing, although the benefits are not as pronounced as the costs (also – it is not unheard of for people to go undiagnosed for years before moving from hypo to all out mania, and doing something odd).
    2) That people think just because he is manic that he is “crazy” and/or this paper is COMPLETE nonsense. The paper could be filled with some very good ideas, or perhaps conclusions that make sense given absurd assumptions. To an outsider, mania seems like complete nonsense. But it has it’s own sort of structure. And it’s built on some normal thinking as well. So when you are very intelligent, you can get these very odd ideas that you’ve built up over such a long period of time that to someone who hasn’t followed your reasoning (and what you’ve read), they seem “crazy”. Yes, they may be incorrect, but they aren’t without their own structure.

    thepatlibstat

    January 31, 2012 at 10:57 pm

    • You’ve gotten the order wrong. We aren’t diagnosing him as crazy and then dismissing the paper, and no one has said that the work had no structure. We’re finding the paper to be a bit crazy, and wondering about the author.

      The paper is very very odd, and apparently incongruous with his previous publication record. It makes some pretty sweeping claims. Some of these claims are not supported in any kind of rigorous way, and others appear to be completely untestable. This is not how science works, or how scientists are trained to think.

      sfs

      January 31, 2012 at 11:58 pm

  26. @sfs. You are right. My second point is more about how people typically view others who suffer from mental illness. It’s not, per se, a reaction to prior posts. But were his mania to become public (i.e. the order reversed), I would guess that this would be the reaction (I have seen it in other cases). No doubt, the paper is very very odd. I’m definitely not trying to argue it is scientific, rigorous, testable, etc. And it seems like mania, in my opinion. But it bothers me that some posts have suggested mental illness is a death sentence for his career. I think this is a hasty conclusion, and an unfair one.

    thepatlibstat

    February 1, 2012 at 12:13 am

  27. The real question is: does such a scientist deserve tenure? It’s not like there haven’t been crackpot professors before. Just think, we could have our very own Brian Josephson!

    D^2

    February 1, 2012 at 3:24 am

  28. I browsed the paper you linked to and found that Andrulis cites Manfred Eigen and Winkler as reference 13., but found no such reference in the text. This strikes me as odd since, Eigen’s concept of hypercycle naturally comes to mind as inspiring Andrulis’s gyres.

    Joachim

    February 1, 2012 at 8:37 am

  29. Only need to read the first few paragraphs to identify a bunch of illogic and poor argumentation especially of the “damning by false précis” sort which Andrulis applies to sweep away all theories of origin of life to leave a clean slate for his own!

    e.g first sentence:

    ”How life abides by the second law of thermodynamics yet evolutionarily complexifies and maintains its intrinsic order is a fundamental mystery in physics, chemistry, and biology.”

    Are these “fundamental mysteries”? The evidence is overwhelming that increased complexity (“complexifies”?!) through evolutionary time arises from rather well understood gene/genome duplication events and there’s no reason why this should be puzzling in the context of the Second Law. Likewise living things maintain their intrinsic order (until they die at which point they begin to lose it) since they’re open systems that feed off energy in their surrounds using metabolic systems evolved to maintain homeostasis. Life is certainly wonderfully mysterious, but supposed incompatibilities with the Second Law are passe and actually pretty boring.

    He then goes on to pooh-pooh by a sort of minimilist précis, some of the theories for the nature of development of early life, as if these theories (in the two sentence précis he accords them) are useless since they don’t answer EVERYTHING. Thus:

    ”Finally, the RNA (ribonucleic acid) world hypothesis posits that ribonucleotide-based genetic systems evolved prior to protein and deoxyribonucleic acid (DNA). This hypothesis does not fit well with the central dogma and is unable to resolve precisely how the translation apparatus, genetic code, and biometabolic pathways evolved [7-9].”

    But there’s no reason why the RNA world hypothesis (which is a description of a development of living things through an early evolutionary age), should “fit well with” the central dogma, which is a description of how (mostly) information in the genome is unidirectly transferred into protein in living things on a 4 billion year old Earth. In fact Crick’s original formulation of the Central Dogma (”It states that such information cannot be transferred back from protein to either protein or nucleic acid.”) is fully in accord with an early “RNA world” especially if “nucleic acid” is taken to mean deoxyribonucleic acid and ribonucleic acid.

    And why should the RNA world theory “resolve precisely how the translation apparatus” etc. evolved. Andrulis’ “theory” doesn’t!

    The thing that confers the status of science on all of the theories that Andrulis dismisses is that these are all well defined and testable even if their testing is difficult and annoyingly incremental. Neither of the latter apply to Andrulis’s “theory”.

    chris

    February 1, 2012 at 2:49 pm

  30. Seriously, are none of you familiar with the work of Viktor Schauberger ???

    Living Energies: Viktor Schauberger’s Brilliant Work With Natural Energy Explained, by Callum Coats.

    There are bigger pictures, if you would just open up and explore. Not every new idea or possibility needs to be crammed into a square box where it can be analyzed and dissected to fit the present understanding.
    Consider Galileo and Bruno.

    Sarah Ruth

    February 2, 2012 at 10:34 am

    • @Sarah Ruth:

      “There are bigger pictures, if you would just open up and explore.”

      We are all open to bigger pictures, but not so open that our brains fall out. This blog is about *science*, and science is, roughly, the business of understanding the physical world (not the metaphysical world) to such a level that we can predict what will happen. What we may lose in the warm and fuzzies, we make up for in raw predictive power. The paper by Andrulis, in its current form, provides no clear predictions.

      If you’re actually serious about being open to possibilities, I would suggest that you spend some time understanding what came before Viktor Schauberger. You use the term “energy,” but you don’t seem to understand what it is, the laws that govern it, how these laws were developed, and the vast body of evidence that supports them.

      So, if you’re actually open to possibilities, perhaps you should read Callen’s _Thermodynamics and an Introduction to Thermostatistics_, Fermi’s _Thermodynamics_, or even just a decent p-chem text (_Physical Chemistry_ by McQuarrie and Simon does an okay job). Okay, they’re not fuzzy, cuddly books. In fact, they require real work to understand, but the payoff is worth it: you see the depth, consistency, and clarity of thought that gives thermodynamics its beauty and its predictive capabilities.

      sfs

      February 5, 2012 at 8:33 pm

  31. Nope I haven’t heard of Viktor Schauberger before now Sarah…

    Not sure what the connection with Galileo (firmly in the domain of science) nor Bruno (many of ideas were straightforwardly scientific in the sense that they were evidence-based). No one is persecuting Dr. Andrulis. I personally am never happy to see fruitful scientific theories damned with faint praise or false precis in order to raise the status of one’s own ideas. If Andrulis is simply philosophising then he might just as well leave those useful theories of origins of life alone. If his ideas are supposed to be scientific, then he should present them as such (e.g. with communicable evidence).

    So I don’t have a problem with Andrulis producing this stuff (it will live or die according to its usefulness), but amn’t happy about his trashing of other theories to “manufacture” a space for his own..

    chris

    February 2, 2012 at 12:55 pm

  32. Seems like Life has another problematic article written by D. Abel. See PZ Myers’ take on it:
    http://freethoughtblogs.com/pharyngula/2012/02/02/more-bad-science-in-the-literature/

    sparc

    February 3, 2012 at 12:20 am

  33. Erik D. Andrulis do not hear about ROMANIAN unified theory, is published and copyrighted from 3 years!
    His theory is included …there!?…and experienced from …3 years?!

    See download section of free project …
    http://www.thefundamentaluniverse.ro/

    DAN PREDA

    February 3, 2012 at 4:42 am

  34. This seems like a very interesting paper, anyone know where a html version is available? I’ve only been able to read snippets as not letting me download the pdf.
    It did immediately strike me that it wasn’t explaining anything it was claiming to. It seemed to be applying the theory loosely to different scenarios and claiming a precise fit. Maybe that is the point that this gyre can be applied to everything . The author obviously appears to have seen this connection.
    Think the talk of mental illness is a bit harsh and presumptuous.
    Did for a moment think it was a pisstake on the sort of mealy mouthed incomprehensible papers that get published. Read a genuine paper recently that smelt like bull was about using. Ultra high power magnetic fields to make a more efficient type of solar electric generator.

    Ben Wilson

    February 3, 2012 at 7:30 pm

  35. CWRU is being cowardly.

    A radically new idea is necessarily controversial. Come on guys.

    I am very familiar with this paper. Indeed, I have reviewed versions of it for YEARS along with an enormity of additional, related material. I have been in constant contact with Erik over these years and given him constructive criticism. He has adapted and expanded his material accordingly.

    When given a chance to explain the paper, Erik is very thoughtful and logical. He is clearly in full control of his mental faculties, and those who believe otherwise are simply freaked out by the outre nature of his work.

    If you reject his ideas, you simply have not taken the laborious task of trying to understand it. Learning the radically new is tough. For instance, you don’t understand Mandarin with a week’s study.

    If you attack Erik, or question his sanity, you are being intellectually lazy.

    If you are not both a psychiatrist AND a scientist, then you have no business judging Erik’s mental capacities. As someone who has known Erik for decades, I am well aware of the coherence of his thinking.

    I have advanced degrees in science and am knowledgeable in varied fields such as economics and politics. This paper is a work of genius — and a mere slice of what Erik has to offer.

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

    nettle

    February 11, 2012 at 9:39 am

    • My considered opinion of Mathis- Eric.pdf, after reading it, is that whatever Mathis has to say is not worth the effort of reading. He displays an appalling misapprehension of mathematics and physics, both in that document and on his website where he promotes his nonsense. His pages are a bane to students and anathema to teachers. The social convention of “Freedom of Speech”, when applied to information presented as factual, entails the responsibility of ensuring that the information is both meaningfull and true; it does not include the license to promote nonsense as truth.

      DuD

      February 17, 2012 at 1:57 am

      • “The social convention of “Freedom of Speech”, when applied to information presented as factual, entails the responsibility of ensuring that the information is both meaningfull and true; it does not include the license to promote nonsense as truth.”

        You clearly (and strangely) don’t even understand the first amendment, which protects both your criticism of the mathis pdf, and the publication of nonsense in general.

        Your ignorance of the darned simple First Amendment to the US Constitution (and other countries laws about free speech) calls into question your claims about mathis if not your critical thinking in general.

        You may not know this, but speech is only restricted in the US for slander, libel, criminal mischief, like shouting fire in a crowded theater, death threats, etc. As another example, Germans add a ban on promoting Nazi propaganda or views.

        People otherwise have the right to express their opinion and ideas, right or wrong.

        The entire point of this right of allowiing incorrect views to be expressed (geez, propaganda is the lifeblood of Fox News), is to 1. see if perhaps there aren’t incorrect, 2. see if they are at least partially correct, and 3. prevent correct views from becoming a religion. Reasoned debate is critical to prevent dysfunction in society.

        You don’t mention the paper, so I presume that you either haven’t read it or have and are still considering whether it is valid or not. If you have an open mind and are doing the latter, good for you.

        If you don’t want to take the effort to read Erik’s paper. That’s fine too.

        nettle

        February 17, 2012 at 10:05 am

      • The US Constitution only restricts government. “Freedom of speech” does not apply to journals. Otherwise, editors would be prohibited from exercising even basic good sense. Resorting to the US Constitution to shelter a crackpot scheme only makes it look even less scientific.

        Bryan Maloney

        February 17, 2012 at 12:07 pm

      • Bryan,

        Sure it does. You can publish a disreputable journal if you want.

        “The social convention of “Freedom of Speech”, when applied to information presented as factual, entails the responsibility of ensuring that the information is both meaningfull and true”
        Right.

        “it does not include the license to promote nonsense as truth.”
        Wrong. This “social convention” is broken all the time.

        Come on dude.

        Freaky new religious forms (formerly known as cults) publish nonsense and claim it to be true all the time.

        “Scientology” is, to my knowledge and in my opinion one big fraud.

        As for science see my comment about “Intellectual dishonesty is rampant in science.” below.

        Also see my comment about “the hypothetico-deductive approach has failed” below too.

        nettle

        February 17, 2012 at 12:35 pm

      • Bryan,
        I am not “Resorting to the US Constitution to shelter a crackpot scheme only makes it look even less scientific.”

        I am defending a paper which you clearly have not read, or if you have read it, even in part, you did not understand.

        Your statement’s context is wrong too, because I was responding to DuD’s comment about Mathis.

        Anyway, if you wish to remain ignorant of the paper’s contents, I support you.

        When you foolishly call it a “crackpot scheme” you are just making a stupid, under-informed remark.

        If presented with the math supporting General Relativity (without being told what it is), I suspect you would either give it a hard read (if you were a curious physicist) or pass over it in silence.

        When you see the radically new, though, with loads of science and 800 references, you result to mocking it.

        Yours is a fatuous choice.

        To each his own.

        nettle

        February 17, 2012 at 1:21 pm

        • I will lay down the matter explicitly: Propose specific experiments to test this alleged “theory”. That is the only valid scientific justification of a proposal. Anything else is the behavior of a religious cultist.

          If you understand science, it should be a very simple matter to propose specific experiments. The mark of a scientific theory vs. a pile of mumbo-jumbo is that the theory is potentially falsifiable. If one cannot propose specific experiments to test a proposal, one is disqualified from defending it, except as a fanboy, making arguments with all the scientific weight of Batman vs. Daredevil.

          It is not the responsibility of those who do not blindly accept a new proposal to propose experiments. It is the responsibility of the proponents to propose the experiments. That is how science works.

          Bryan Maloney

          February 17, 2012 at 2:17 pm

      • Bryan,
        “Propose specific experiments to test this alleged “theory”. That is the only valid scientific justification of a proposal. Anything else is the behavior of a religious cultist.”

        Praytell, what motivation do I have to someone who won’t take the time to critically read the paper?
        Answer: none.

        “If you understand science, it should be a very simple matter to propose specific experiments.”
        Right. So, if you are a scientist, /you/ propose the experiments.
        I am not going to do your homework for you — especially when you refuse to read the paper.

        “If one cannot propose specific experiments to test a proposal, one is disqualified from defending it, except as a fanboy, making arguments with all the scientific weight of Batman vs. Daredevil.”

        If one can not take the time and care to carefully read a paper — and decides to mock it instead — he is disqualified from making comments about it except as someone who wants to make himself as foolish as Donald Duck or Bozo the clown.
        Just playing fair here and keeping you honest.

        “It is not the responsibility of those who do not blindly accept a new proposal to propose experiments. It is the responsibility of the proponents to propose the experiments. That is how science works.”

        That is /not/ how science works.The cold fusion was disproved /not/ by Pons and Fleischmann, the original proponents, but by /other/ scientists who could not reproduce your work.

        How come you do not know this fact?

        Your comment reflects an ignorance of science.

        nettle

        February 17, 2012 at 2:41 pm

  36. Chris,

    This is a detailed reply to your comment above. It is the same as I posted to your direct query elsewhere, and I include it here for those who miss the other post.

    Nice, you and I both have similar experience, as I have worked in chemistry, biochemistry in molecular biology laboratories in Cambridge and Southern California. I didn’t mean it as a “ploy.” I meant it to be genuine. But I digress.

    Frankly, I don’t see the illogic nor do I see the non-sequitur nature of that quote you gave. Perhaps that’s because 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.

    nettle

    February 13, 2012 at 2:09 pm

  37. Wow! You asked one specific question. I answered it. And you didn’t respond to the substance of my answer! Amazingly, you don’t even /acknowledge/ that I responded to your question.

    You response is very visceral — not thoughtful — and very biased as to what a theory /should/ be.

    You don’t raise prior explanations about the genetic code like those from Jukes and Osawa or more modern explanation by Paul Higgs (no relation to Higgs boson).

    You didn’t notice that Erik in the paper says systems “tend” to emerge in units of threes — and then proceeds to focus on the available evidence proving the existence of these units of threes in all of those systems.

    You bizarrely (but conveniently) ignore “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).”

    Um, dude, a quarternary complex is /not/ a unit of three. Why did you not acknowledge that statement but go off on a list of things that organize as other numerical oligomers? Perhaps, you didn’t because to do so would be to admit that Erik DOES show an example here of a unit of four, and for some strange reason you want to trash the entire paper instead of doing the hard mental labor of trying to understand a radical new way of viewing present science. The paper fully acknowledges present science, but you knew that, because you read the paper, right?

    Continuing: In summarily rejecting the tri-quantal concept, you dismiss the blatantly obvious organization of units of threes creating high energy systems, to wit, ATP!

    Also, you didn’t acknowledge the theoretical profiling of oxaloacetic acid (a tetra-quantal system) in the paper (pp. 36-37, and in figure 3)

    You are clearly hard set on the idea of the status quo of ad hoc theories that to a large degree do not interlink and that have nothing to do with each other. Consider these “illogical and non-sequitur” questions that must be addressed when modeling life: What does the mitochondrion have to do with phospholipid bilayers? How did phospholipid bilayers come about? What drove their initial formation? WHY did they form? And what about the golgi body? WHY and HOW did that come about? What does a golgi body have to do with the initial formation of the ribosome? Why do the two have that relationship?

    You have no overarching explanation as to how all the organelles came about.

    Your response proves that you are very comfortable having no overarching explanation about how or WHY all biological processes and systems came to exist. And please, please don’t embarrass yourself by saying, “natural selection.”

    You are fixed on the idea that what we have “just works.” Yet, as an informed scientist, you should know our present understanding of biochemistry /alone/ is shot full of holes.

    I am not going to do your homework for you. I already did enough in giving you a studious response that you appear to have barely glossed over. Read the present literature to find the anomalies yourself. You do read other papers more carefully, I hope.

    Another point: You reject Erik’s neologisms when you know that science is full of them — and creates more of them all the time!

    Pick up any copy of Nature or Science. When you see that a new protein is discovered, it gets a new name! How is this naming of proteins (with associated alphabet soup acronyms) not obscurantist? Have you ever looked at the names of Drosophila proteins? How about “Mothers against decapentaplegic?” “Bicoid?” “Cheap date?” all of which have graced these and other scientific journals. Oh yea, sure those names explain /precisely/ what those proteins do to a layperson. Go ahead, tell yourself they’re not “obscurant gibberish, protected by claims of priviliged insight.”

    Here’s another question for ya: What is the inherent meaning of Neuropeptide Y? Neuro means we “know” (really should be “suspect”) that the protein has something to do with neurons or neurological activity, but what does it do? And how did it emerge in the evolution of multicellular eukaryotes? And why the “Y?”

    Also, the words purine and pyrimidine have no inherent meaning to a layperson. They are part of the cryptic (!) language of science. Obscurantist!

    Do you think you could chit-chat about nucleotides and their functions in a bar over beer with a stranger? Only if she or he was privy to science’s weird language — which largely bears as much resemblance to English as to Finnish.

    All the names for organelles I mentioned meant nothing until someone decided to make them up.
    All subatomic particles are made up words. All new pharmaceutical products have made up names. If you are consistent, I suppose you dismiss these neologisms, too.

    Tell me: Do you believe the meaning of finesteride to be obvious to any trained scientist because semantically it makes inherent sense? You don’t because it doesn’t.

    And, hey, while we’re at it, why should we have the word “finesteride?” We could just have the more explanatory (albeit prosaic) hyphenated word, “drug-that-restricts-and-shrinks-an-overgrown-prostate-with-the-positive-side-effect-of-inducing-the-growth-of-scalp-hair.”

    Using your phraseology and logic, that hyphenated name “can be explained in very simple terms in a way that allows the transmission of understanding from one individual to another. It doesn’t rest of obscurant gibberish, protected by claims of priviliged insight.”

    Summing up this part: What knuckle-dragging contradictory rubbish: defending the use of pharmacological, medical, and scientific obscurant-ish neologisms but attacking the use of theoretical neologisms.

    CONCLUSIONS:
    I conclude that you did not studiously read the paper or did not read the paper at all. Based upon our exchange, it appears you are unable or unwilling to do so. You like to argue talking points.

    The fact that you did not acknowledge or respond to my accurate, thorough, and sincere response to your question is clear indication that you did not read or understand what I wrote. This fact bespeaks to a greater intellectually laziness that one can intuit: you do not have the intellectual capacity that is beyond your little knowledge box.

    I conclude that you are unable to carry on conversations in a scholarly and respectable manner. This casts doubt on the scientific experience that you claim to have.

    You are welcome to respond. I have nothing further to say to you.

    Nonetheless, I wish you well.

    nettle

    February 14, 2012 at 10:57 am

    • In addition to mRNA, rRNA, and tRNA, miRNA is very important to the formation of peptides, not part of any sort of “tri-quantal” arrangement. You’re at least a decade behind the times.

      Bryan Maloney

      February 14, 2012 at 8:47 pm

    • nettle, since Andrulis states that “RNA world” theory is deficient because it doesn’t explain “precisely how the translation apparatus, genetic code, and biometabolic pathways evolved.”, I asked you to summarize how Andrulis’s “theory” “precisely” explains these things.

      You’re answer is a non-answer. The first sentence is patently incorrect since “systems” don’t “organize in units of three” (some do of course). Otherwise your explanation comprises simplistic descriptions of things already known interspersed with vague references to “gyres” and “tri-quantal states”.

      Unfortunately, if one can’t explain something in simple terms (e.g. at the level of a first year Biochemistry undergraduate in this case), it probably means you don’t understand it. All of the outstanding discoveries/theories in molecular biology/biochem/biol chem of the last 100 years can be described very simply (e.g. it’s easy to explain in a paragraph the molecular level description of the double helix and the significance with respect to DNA replication/DNA as the repository of genetic information/molecular evolution). It’s unfortunate that you aren’t able to do this with a simple example that Andrulis himself raises with respect to his “theory”; unfortunately I suspect that his theory simply isn’t amenable to the sort of explanations that provides fundamental insights and allows wider dissemination of knowledge.

      Otherwise your posts don’t address the salient points, and are full of errors. You say, for example, “In summarily rejecting the tri-quantal concept, you dismiss the blatantly obvious organization of units of threes creating high energy systems, to wit, ATP!” But that can’t be right. ATP is produced by ATP-synthases linked to protonmotive force or by substrate level phosphorylation (e.g. glycolysis or adenylate kinase etc.). None of that has any relation to “units of three” (‘though part of the ATP synthase is a trimer!). High energy “systems” like pyrophosphate or NADH or phosphocreatine don’t have any relationship to “units of three” do they? …etc…

      chris

      February 15, 2012 at 6:03 am

  38. The preceding comment was a response to Chris’s comments on

    http://retractionwatch.wordpress.com/2012/02/03/editor-who-published-andrulis-paper-tries-to-explain-how-it-happened/#comment-10419

    and I include it here for completeness.

    nettle

    February 14, 2012 at 10:58 am

  39. Linus Pauling–a brilliant physical chemist who went far off the deep end with vitamin C. Great scientists are not omniscient.

    Bryan Maloney

    February 15, 2012 at 10:40 am

  40. Bryan,
    if you want to talk about miRNA, why not include guide RNAs, snRNA, or sRNAs,. What about ribozymes? Those are all important at a variety of levels of RNA biogeneisis, processing, and transport that occur before, during, or after the formation of a peptide?

    All of these are of course included in the Ribon which is infinite by necessity to account for all RNAs.

    This inclusion reflects the universality of the model in the paper.

    “Great scientists are not omniscient.” What an obnoxious comment — and a non-sequitur too.

    You haven’t read the paper carefully if at all.

    Get back to me when you have read it. Otherwise, we’ll talk past each other..

    nettle

    February 15, 2012 at 12:09 pm

    • I did not mention the other RNA functions or forms because it was claimed, quite falsely, that there was some kind of “triquantum” nature to RNA in and of itself, and it was likewise falsely claimed that the magical triad of mRNA/tRNA/rRNA somehow proved this. Therefore, all that was necessary to disprove such groundless fantasizing was to bring up a single counter-example. Throwing even more on the pile would have been unnecessary and excessive.

      My mention then provides ample opportunity to demonstrate that whether this alleged “theory” is merely pseudo-science in the vein of Velikovsky. Instead of proposing specific experiments, every concrete objection is met by an ad hoc reformulation and an insult against the objector. Thus, since the claim of a mystical “tri-quantum” nature to RNA, specifically embodied in a Trinity of mRNA/rRNA/tRNA, has been debunked, the goal posts are moved, an ad hoc response is given, stating that this alleged Trinity doesn’t really matter, since what now matters is the alleged unity of a “Ribon”. By your own acts, by your own refusal to discuss an alleged scientific matter in scientific terms, you have relegated your own article of faith to the pseudoscience heap.

      Therefore, get back to me when you can actually discuss science as science instead of religious doctrine. Where are the specific, testable predictions? Where are the proposed experiments? A “theory” with no proposals nor testable predictions is not a theory, it is fantasizing and idle speculation. An elegant lie is still a lie, no matter how elegant it might be. Defense of science amounts to proposing and carrying out specific, defined experiments. Defense of blind dogma consists of merely insisting that one has been “misunderstood”. Propose the specific experiments to test this alleged “theory”. The burden of experimental validation lies upon the proponents of a model, not its opponents. That is how science is done. Vain religious/political rhetoric, on the other hand, makes the opponents responsible for “disproof”.

      Finally, my mention of Pauling’s lunatic flights of fancy regarding vitamin C is not a non-sequitor. It is very much apropos. Pauling’s skill and scientific acumen in physical chemistry is unquestionable. However, when he stepped outside the narrow boundaries of his own specific field, he allowed himself to become just another quacksalver.

      Bryan Maloney

      February 15, 2012 at 1:20 pm

  41. Some general comments.

    The human mind is generally not capable of thinking outside of its own realm — defined by education and experience.

    People general want something new only if it fits what they expect, like, want, or need.

    What people say that expect, like, want, or need differs from what they truly expect, like, want, or need.

    The more experienced and educated a person is, the more that person will reject a new idea that does not agree with their preconceived notions.

    Science is as dogmatic as any religion, albeit the former changes a bit more quickly than the latter.

    Most analytic data in science comes from snapshots — like looking at a frozen river — despite the fact that we know that, like the river (when not frozen), we have flows — e.g. the biochemical shuttling of ATP to ADP and subsequent recycling of ADP to ATP.

    Scientists don’t really know what’s going on in, say, a flask full of chemicals. Instead, they put their faith in what they have been taught and what they have read. If that attitude sounds like religion that’s because it shares many of religion’s attributes.

    (Sure you can do such tests as carbon-13 labeling, but with the majority of reactions you can’t do that. Too costly. Also, I know of no human biological experiments in a living person involve carbon-13 labelling. I suspect that even if there have been some (which seems strange to me), there has not been a complete carbon-13 labeling of all human biological processes.)

    Just because the academy teaches something does not make it true.

    Just because the academy does not teach something does not make it false.

    In internet exchanges, people may occasionally change their minds, but they never admit they were wrong.

    nettle

    February 15, 2012 at 2:01 pm

    • in other words nettle, you really haven’t got anything of substance to say, and dump dreary and false platitudes.

      The biochemical shuttling of ATP to ADP and vice versa can be followed in real time (try NMR spectroscopy). Sometimes snapshots are perfectly adequate for the questions explored. Of course one can’t measure everything in real time so far, but clever, insightful and competent scientists continue to extend the methodologies….others sit on the sidelines spouting platitudes.

      …there are loads of “human biological experiments in a living person involving carbon-13 labelling” (infusion of 13C acetate to study TCA cycle in living human brain; 13-C labelled drug metabolism studies…hundreds of these)

      chris

      February 15, 2012 at 2:52 pm

  42. Chris,
    Thanks for your criticism.
    My previous post was so broad to the point of being erroneous. I apologize
    I will take you at your word on the studies, and state that I made a presumptious and ignorant comment.

    I will now correct and clarify.

    I am referring to a single NXP or the single C-13 atom.

    Could you point me to a study that involves a following a single NXP or the single C-13 atom?
    In the NMR studies and in the hundreds of the drug metabolism studies, can you find me one?

    I think that sort of study does not exist and can not exist (both to my knowledge, I am being more careful this time) because modern science is not suited to and does not have techniques to perform those studies.

    If there are hundreds of thousands of trees in a forest, you won’t know what the state of the individual tree is until you observe it.
    If you know that half of the trees in the forest have no leaves, you have no idea which tree in which location has no leaves until you go and look.

    The upshot is that you have no idea about the individual NXP or C-13 atom until you observe it.

    You might not think that this observation of the individual is important, but it is.

    You stand upon the assumption that by understanding how the pool of NXPs or C13 containing molecules work, you will understand how the components work. But this is not so. You know nothing about how the individual NXP or C13 atom works. You assume that you do.

    The goal of the paper is to show how the individual systems works.

    We have the schroedinger’s cat problem at every level.
    While physicists acknowledge this conundrum, biologists conveniently ignore it.
    There is no tool known to man that allows man to know a condition of something until he observes it.

    nettle

    February 15, 2012 at 7:40 pm

  43. Let me modify my last statement.
    I still believe my previous post was so broad or vague to the point of being erroneous – I did not specify that my focus was on the individual ATP or C13.

    I am ignorant of the C13 labeled studies of drug metabolism, but that was not what I was talking about, as I specified.

    “there has not been a complete carbon-13 labeling of all human biological processes.”

    Anyway, in a sense whether there has been or there hasn’t; I know of no studies that follow /one/ ATP molecule converting to ADP + P or /one/ C13 in a human biological pathway.

    If anyone could point me to such a study, I would be grateful.

    nettle

    February 16, 2012 at 7:23 am

  44. In present science, when a scientist gets a six results, and three make sense, one is a little off, and two are anomalous, scientists keep the three results that make sense and simply throw the other three away.

    Thus, science gains only a partial understanding of a system works.

    You can’t have data points that you don’t understand and throw away, and claim to have a complete understanding of a system, yet scientists do this /all. the. time./

    Intellectual dishonesty is rampant in science.

    It is not looked upon as intellectual dishonesty because of the imprimatur of the peer review system.

    nettle

    February 17, 2012 at 10:58 am

  45. Geez, I’m sloppy today. Second sentence corrected.

    In present science, when a scientist gets a six results, and three make sense, one is a little off, and two are anomalous, scientists keep the three results that make sense and simply throw the other three away.

    Thus, science gains only a partial understanding of how a system works.

    You can’t have data points that you don’t understand and throw away, and claim to have a complete understanding of a system, yet scientists do this /all. the. time./

    Intellectual dishonesty is rampant in science.

    It is not looked upon as intellectual dishonesty because of the imprimatur of the peer review system.

    nettle

    February 17, 2012 at 11:20 am

    • Rampant? Identify specific laboratories that routinely throw out HALF their readings. Go ahead, name some names. If it’s “rampant”, one should be able to easily come up with thousands of instances right off the top of your head. What percent of labs qualifies as “rampant”, anyway? 50%? 30%? 20%? Give a figure and back it up.

      Relativity wasn’t confirmed by claiming “rampant” fraud. It was confirmed by specific experiments. Germ theory of disease wasn’t confirmed by claiming “rampant” fraud. It was confirmed by specific experiments. The Central Dogma (DNA -> RNA -> protein as a one-way trip), the principle that pre-natal imprintation was the only form of epigenetic modification, and the principle of non-heritability of aquired characteristics other than DNA sequence primary mutation weren’t overturned by claiming “rampant” fraud. They were overturned by specific experiments.

      (Yes, some acquired characteristics can be inherited in addition to DNA mutation, if those characteristics take the form of certain post-natal epigenetic DNA modifications.)

      Bryan Maloney

      February 17, 2012 at 2:24 pm

      • Bryan.
        “What percent of labs qualifies as “rampant”, anyway? 50%? 30%? 20%? Give a figure and back it up.”
        No. You are being lazy and are undeserving of my help on this matter.
        Why don’t /you/ do some research and reading for a change?

        “Relativity wasn’t confirmed by claiming “rampant” fraud. It was confirmed by specific experiments”
        Drawing a conclusion on a handful of theories is a logical fallacy.

        Cold fusion was not a fraud, it was simply an error

        The NIH scandal about made-up data very much /was/ a fraud.

        You do know about the NIH scandal right?

        Science has its fair share of fraud, and if you cared on the matter you would already know, but you don’t seem to care.

        By the way, what is a DNA mutation? A random change?

        Get real.

        Randomness is a philosophical idea that science has absorbed to mask an acknowledgment of ignorance.

        If the proper scientific language was “by a process of which science is unaware,” then science would be more honest. But it isn’t. Such arrogance is breathtaking.

        nettle

        February 17, 2012 at 2:59 pm

        • Responsibility of proof lies on the accuser, except in the minds of lunatic conspiracy theorists, of course.

          Bryan Maloney

          February 18, 2012 at 4:02 pm

          • “Responsibility of proof lies on the accuser.”
            Right.
            But I’ve spent more than enough time with you and your closed mind.
            You mock what you don’t understand and perhaps can’t understand.

            nettle

            February 19, 2012 at 7:19 am

  46. When a scientist gets 6 results and three make sense, one is a little off and two are anomalous a good scientist goes back and does more experiments around the areas where the results are strange.

    In an ideal world we would only have good scientists.

    Even so, they may not find the answer.

    They may not necessarily have a good explanation for the two anomalies.

    They may have /one/ explanation but is it the right explanation? Hard to tell at least sometimes.

    Is their explanation the only answer?

    Could their explanation be a biased explanation that supports the purpose of their grant?

    Let’s be honest here, most scientists are simply defending their thesis.

    Also, the hypothetico-deductive approach has failed.

    We should see that a scientist is that a scientist is looking for data that falsifies their ideas, but the status quo is that a scientist is looking for data that supports their ideas.

    “The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ but ‘That’s funny…’–Isaac Asimov.”

    A famous quote by a privileged scientist with the status to defend a /really/ strange anomaly.

    That’s funny, but I don’t have time to address funny, I have to spend time defending my thesis project (e.g.), is more typical.

    For the typical scientist, that’s funny, but it challenges the major conclusions in the field, is not fun at all.

    Erik’s having providing a overarching “overscience” in his paper is no fun for him at all.

    nettle

    February 17, 2012 at 12:37 pm

  47. Shucks.
    Erik’s having provided a overarching “overscience” in his paper is no fun for him at all.

    No further corrections. Clearly, I am a bad proofreader today.

    nettle

    February 17, 2012 at 12:39 pm

  48. In reply to a response by nettle, on February 17, 2012 at 10:05 am, to my reply to his post on February 11, 2012 at 9:39 am—

    The internet is not US territory. The US constitution is irrelevant in this discussion.
    Nettle should read words properly : “Freedom of Speech” as a SOCIAL CONVENTION excludes consideration of any entrenchment of FoS in any country’s constitution.

    Many forums, comment pages, etc. prohibit flaming and troll-like behaviour. Many forums are topic specific and disallow irrelevant posts.

    In a physics lecture on the origin of the universe the commonly accepted interpretation of FoS, as a social convention, allows members of the audience to ask relevant questions at appropriate times but disallows them from mere recital of the opening passage of Genesis.

    Providing incorrect answers in an exam is exercising FoS, but it has deleterious consequences.

    Thus there are accepted limitations to FoS, as a social convention, imposed in various venues both on the internet and elsewhere.

    However with regard to the US constitution, in Roth v. United States – 354 U.S. 476 (1957) the court held that “the unconditional phrasing of the First Amendment was not intended to protect every utterance”. While it may be argued that as the case concerned obscene material then the pronouncement was in reference to such material, it can be counter argued that blatant nonsense promoted as factual, and blatant fallacies promoted as truth, are obscenities to the intellect.

    That Mathis does not understand the mathematics prerequisite to much of physics is a fact. It is not an opinion, irrespective of what the mathematical illiterati may think. That it is a fact is easily ascertained, by those who are mathematically competent, from the demonstrable fallacies in various statements Mathis made in his document (http://milesmathis.com/erik.pdf) and in various pages on his web-site (http://milesmathis.com/).

    I have indeed read a sufficient amount of Andrulis’s paper to make the following observations.

    He uses the word “triquantal” in his lexicon but does not well-define the term, even though some of his other words have meanings contingent on the meaning of that word. He identifies the concept of ‘quantum’ with that of ‘particle’, apparently oblivious to the meaning of ‘quantum’ as the smallest quantity of a PROPERTY that a physical system can possess.

    On page 5 he states that “(a)ny gyre is fractal” clearly oblivious of the non-fractal gyres that inhabit my bath-tub after the plug is removed. Also on page 5 is “…a radial axis that bisects the singularity…”, an expression that exposes his ignorance of the meaning of the word “bisect”.

    Page7 has “(g)yres are open thermodynamic entities that require energy and matter mobilization to establish and maintain themselves … gyres import energy and matter from their surroundings into themselves, ebb and flow energy and matter within themselves, and dissipate energy and matter from themselves into their surroundings”. But if a gyre is “the spacetime shape or path of a particle or group of particles; a quantum”, according to his lexicon, then one could conclude that the spacetime shape of a particle, like a photon, is an open thermodynamic entity that requires energy and matter mobilization to establish and maintain itself, imports energy and matter from its surroundings into itself, ebbs and flows energy and matter within itself, and dissipates energy and matter from itself into its surroundings. Such a conclusion requires a far more complex model of the photon than is currently used in physics. Moreover experimental proof of the acuity of such a model of a photon is impossible to obtain as such would require observation and measurement of the internal structure of a photon. But this is only one example among many where Andrulis keeps on changing the meanings of his terms apparently inorder to accommodate the exponential increase in the outlandishness of his ideas as they are developed in his paper.

    Andrulis does not understand physics and does not appreciate the necessity of providing mathematical justification for speculations in the subject.

    Section “3.1. Visible Matter” of his paper cannot even be classified as metaphysics; it is no more than pseudo-intellectual spiritualesque gibberish. Although at times he claims that his conceptualization has explanatory and predictive power and that his diagrams are evidence in support of his claims, nowhere in section 3.1 does he supply any proof of those claims.

    The section entitled ‘Lepton’ (p.19) contains:
    “As modeled here, the lepton is a visible energy particle (a photon,…) that step-decelerates below light speed due to the opposing, balancing forces and directionalities of the subgyre/subquantum,(… ). In other words, in reducing its vibrational, rotational, and translational rate, the photon particle literally manifests as the lepton particle.”
    His claim that electrons are slowed-down photons is a glaring example of ignorance. Electrons are spin-½ charged particles that have mass, photons are spin-1 uncharged massless particles. They are governed by quite different mathematics.: Electrons are not slowed down photons. The concepts of electrons and photons are mathematical constructs which yield the best-so-far models used to provide a mathematically consistent description of various physical phenomena. To identify them. as he does. is sheer fallacious sophistry.

    He demonstrates a lack of comprehension of electromagnetism. In the section of that name he delivers some meaningless statements and concludes: “Thus, electro-magnetism can be rewritten as gyral repulsion-attraction [91]“. His “reference” [91] is “(t)he frequently presented 2D lengthening wavelengths of the electromagnetic spectrum from gamma rays to radio rays are modeled as the 4D expansion or widening of the electrogyre from the photonic singularity”. This gobbledygook is just gibberish. Furthermore if electro-magnetism, a mathematical construct, could can be rewritten as “gyral repulsion-attraction” then his gyres must be amenable to mathematical analysis thereby contradictig his statements to the contrary in the last paragraph on page 5.

    He apparently fails to recognize fundamental requirements of writing an acceptable scientific paper:
    - the language employed must be understandable by others;
    - new terms, or old words with new meanings, must be well-defined;
    - any conclusions must be supported by unequivocal proof.

    The section headed “Planetary Orbit” (p.22) is utter drivel. He appears to have no comprehension of either Newtonian mechanics or Einstein/Hilbert general relativity.

    He provides no evidence that he understand quantum mechanics and appears to be not qualified to make the judgment that his “theory” is a viable framework for unification of QM and GR.

    His descriptive framework (if one can indeed be kind enough to him to call it that – it is not a theory in the strict scientific use of that word) misuses words that have well defined meanings. Eg the word “singularity” (commonly understood by the cognoscenti as meaning a region or point wherein some physically meaningful quantity becomes infinite) is not well-defined anywhere in his paper, but seems to be used therein to mean nothing more than the central region of rotation of his “gyre”. He seems oblivious to to the fact that in fluid mechanics, wherein gyres are amenable to mathematical analysis, such central regions are within surfaces or lines of discontinuity and are not regarded as singularities..

    By its very nature, Andrulis’s sophistry is not conducive to mathematical formulation. A fact which he not only recognises but seems to regard as a plus, whereas, according to Baez’s “Crackpot Index” (http://math.ucr.edu/home/baez/crackpot.html) , it is a big minus. Andrulis’s paper is non-science; it is nonsense. It has no place in scientific journals. It is a gargantuan gyre of guano. Possibly Andrulis is emulating Sokal, or maybe he is suffering from gyrephrenia. Reading his paper reminded me of The Muppets rendition of “Windmills of your mind”. Even though Disney’s Gyro Gearloose was an eccentric genius, the name does sound compellingly appropriate.

    Those who claim to understand his paper need to be prepared to counter the accusation that they are suffering “folie à deux” (http://en.wikipedia.org/wiki/Folie_à_deux).

    Nettle’s defence of the freedom to expound nonsense, or to promote falsehoods as truths, is revealing and raises questions about the veracity of his/her claims to acquaintance with Andrulis, claims to graduate status, and any other claims to any other credentials.

    DuD

    February 19, 2012 at 12:04 am

  49. DuD
    The internet is not US territory.
    Right. Iranian laws apply if you’re in Iran. Chinese laws apply if you’re in China. I am in the US, where, whaddya know, US laws apply.

    “Freedom of Speech” as a SOCIAL CONVENTION excludes consideration of any entrenchment of FoS in any country’s constitution.
    I agree.

    “However with regard to the US constitution, in Roth v. United States – 354 U.S. 476 (1957) the court held that “the unconditional phrasing of the First Amendment was not intended to protect every utterance””
    For you to make this statement is foolish and reflects the fact that you have not carefully read my comment(s).

    In my reply to you on February 17, I said, “…speech is only restricted in the US for slander, libel, criminal mischief, like shouting fire in a crowded theater, death threats, etc. As another example, Germans add a ban on promoting Nazi propaganda or views.”
    Oliver Wendell Holmes conclusion (The most stringent protection of free speech would not protect a man falsely shouting fire in a theater and causing a panic) was given in 1919, so this 1957 case is superfluous.

    Of course I agree with you!

    Come on, dude.

    “That Mathis does not understand the mathematics prerequisite to much of physics is a fact.”
    You may be right. I admit ignorance here.

    “Furthermore if electro-magnetism, a mathematical construct, could can be rewritten as “gyral repulsion-attraction” then his gyres must be amenable to mathematical analysis thereby contradictig his statements to the contrary in the last paragraph on page 5.”
    Can gyres be modeled mathematically? Yes. Can they be modeled accurately. No.

    Mathematicians and physicists know full well about the inability to fully capture nature using math.

    You attacking parts of the paper when you must understand it works as a whole. You can’t pick and choose.

    You just don’t like the fact that he is dealing with overarching concepts to describe electromagnetism.

    Erik sent me two emails he received from a theoretical physicist, one of which read (in part),
    “I have worked out the number circle, as opposed to the number line, where plus and minus infinity are joined.
    Also, new mathematical definitions are required which /strike fear / [my emphasis] in the hearts of
    scientists and mathematicians:

    1/∞ = 0, which implies that yes, 1/0 = ∞, and more interestingly, 0·∞ = 1.”

    He apparently fails to recognize fundamental requirements of writing an acceptable scientific paper:
    “- the language employed must be understandable by others;”
    Man, you couldn’t be more /wrong/.

    Science makes up new words all the time — and they often have /no/ intrinsic meaning. You know that, but you hypocritically say Erik can’t. Baloney.

    Moreover, as I said in my comment on February 14 (which you conveniently ignored),
    “Pick up any copy of Nature or Science. When you see that a new protein is discovered, it gets a new name! How is this naming of proteins (with associated alphabet soup acronyms) not obscurantist? Have you ever looked at the names of Drosophila proteins? How about “Mothers against decapentaplegic?” “Bicoid?” “Cheap date?” all of which have graced these and other scientific journals. Oh yea, sure those names explain /precisely/ what those proteins do to a layperson. Go ahead, tell yourself they’re not “obscurant gibberish, protected by claims of priviliged insight.””

    “- new terms, or old words with new meanings, must be well-defined;”
    I think they are. Other scientists do too. You don’t understand, but the paper is hard to understand, so your not understanding is understandable.

    “- any conclusions must be supported by unequivocal proof.”
    Erik provides such proof to the satisfaction of me and other scientists.
    If you are not satisfied by 800 references backing up a paper loaded with science — and a radically new way of viewing a variety of systems — you are just hard to please.

    You make some good critical comments, I don’t agree with them, and neither do the scientists that have called to support Erik.

    Criticism is healthy. Mockery isn’t. Papers can be wrong, but wrongness do not mean crackpot. It just means incorrect.

    “By its very nature, Andrulis’s sophistry is not conducive to mathematical formulation. A fact which he not only recognises but seems to regard as a plus, whereas, according to Baez’s “Crackpot Index” (http://math.ucr.edu/home/baez/crackpot.html) , it is a big minus.”
    According to me, it is neither a plus nor a minus. It just is.
    If you want to follow Baez in lockstep, so be it.

    “Those who claim to understand his paper need to be prepared to counter the accusation that they are suffering “folie à deux””
    According to Erik (I know because I just asked him), about thirty scientists and even non-scientists have called or emailed Erik to express their understanding (even if vague) of the paper and their appreciation of it. Thus, I can not be suffering from a “folie à deux.” I could be suffering from a folie à trente et un (31),” though.

    “Nettle’s defence of the freedom to expound nonsense, or to promote falsehoods as truths, is revealing”
    Let’s be clear here.
    1. The paper is not nonsense. Something you don’t understand but which others (not just me) do, at least in part, do, has meaning.
    2. My defense (US spelling) is revealing that I believe we need to allow nonsense because (a) it may not be nonsense, just very hard to understand (exactly the case with Erik’s paper), (b) it may be partly correct (but we may not see the partial correctness), and (c) we don’t want true ideas to be treated with a religious faith; we want to continually question, just as you have done.

    “raises questions about the veracity of his/her claims to acquaintance with Andrulis, claims to graduate status, and any other claims to any other credentials.”
    It sure does — but only in the minds of those who mock the content of the paper and clearly lack even the ability to understand the paper.
    An exception, though, is I see no reason why you question my acquaintance with Erik. I would have no motivation to expend so much effort into defending a paper were he not a close friend. Your statement is therefore, on this point, illogical.
    I have no idea why /you/ are putting so much effort into criticizing and mocking this paper.
    As for your questioning /any/ other credentials, you are being extreme in your skepticism.

    You are free to critique, to mock, and even to put forward falsehoods as truth, as you do with your criticism.

    You don’t understand the paper and that’s fine. You mock what you don’t understand and that’s not.

    nettle

    February 19, 2012 at 9:30 am

  50. For the purists and the petty,
    in my previous post I wrote “do” where I meant “does.”

    For general edification I reproduce the aforementioned two emails below.

    The first one reads,
    I am a theoretical physicist, and I have been working on a dynamic/fractal/living
    universe model. I found your new paper in life magazine very original and
    /exciting/ [emphasis mine]. I am sure that you have had /a thousand skeptics/ [emphasis mine] and quacks contact you. However, if you actually read this and are interested in useful collaboration,
    let me know.

    The second reads,
    Thanks for getting back to me. I was thinking about the historical development of
    science, and found it interesting that while, say, Galileo had only the church to
    anger, now it is possible to make angry the scientists also!

    I would be willing to share my ideas with you. Mainly they are all in my head, but
    some have made it onto paper. The nature of my work is a fractal model of the
    universe, where every system is composed of subsystems, and likewise every system is
    a subsystem of a larger system. These axioms allow for a universe that extends
    hierarchically from any level away from the observer into the micro and macro. A
    key feature of the model is interaction between adjacent levels, where smaller
    bodies are “bound” in a structure to a larger body: electrons to proton,
    hydrogens to oxygen, kids to adults, planets to sun, stars to galactic center. So
    we see that not only is there form to the “gyre” but there is a form to the
    grouping interactions.

    Most of my time has been spent on the mathematical framework of a fractal universe,
    pondering fractal calculus, and trying to create/solve a model (toy) problem that
    demonstrates the efficacy of the model. As such, I have worked out the number
    circle, as opposed to the number line, where plus and minus infinity are joined.
    Also, new mathematical definitions are required which /strike fear/ [emphasis mine] in the hearts of
    scientists and mathematicians:

    1/∞ = 0, which implies that yes, 1/0 = ∞, and more interestingly, 0·∞ = 1.

    nettle

    February 19, 2012 at 9:39 am

  51. Whoever is accusing Andrullis of being crazy, psychothic, manaic, etc. is wrong not because he suffers none of these afflictions, but because ad-ominen accusations should never, and I insist, never, be brought up either in philosophy or science. It is low, and the minimum of self discipline a thinker should have is to prevent him or herself from this form of bullying. Do not comment on the article, no one forces you to do this, but do not drag the entire discussion into the terrain of slander and contempt. Mr. Andrullis did not begin his article by qualifying the readers and their capacity to understand it, so now, you who read it, do not qualify the author, just stay on the level and comment the article alone.

    Saint Clair Cemin

    February 19, 2012 at 9:53 am

  52. I agree that Andrulis is not crazy. He’s just wrong, in much the same way that Josephson, Sheldrake, and Montagnier are wrong.

    D^2

    February 20, 2012 at 2:40 am

  53. Dear D^2

    I did not say that Andrulis is not crazy. What I’m saying is that how the man can be called, crazy or boring, is besides the point.
    We should discuss his argument, not his brain or the brand of his underwear. Also, why is he wrong “the same way” Josephson, Sheldrake and Montagnier? Is there any similitude between his paper and the theories of the men you mentioned? Because if there isn’t you could say that he is as wrong “the same way” a rabbit is wrong in trying to eat a dollar bill, which amounts to strictly nothing.

    Saint Clair Cemin

    February 20, 2012 at 3:13 am

  54. I said “in much the same way”, not “the same way”.

    D^2

    February 20, 2012 at 3:39 am

  55. Dialogue between a Lunatic and a Scientist
    A Farce in One Act

    Lunatic: Whaaaaargarble! Whaaaaargarble! Whaaaaargarble!
    Scientist: What?
    Lunatic: WhaaaaaaaaaaaaaaaaaaaaaaaaarGARBLE!
    Scientist: Do you have any experiments to test this? After all, scientific theories are tested by specific experiments based on hypotheses derived from the theories, that’s how science is distinguished from arguments among NASCAR fans and from theology. What are the experiments proposed in this case?
    Lunatic: You cannot understand the Whaaaaaaaaaaargarble! Science is dishonest! It is filled with rampant fraud!!!!
    Scientist: Really? Where? We need specifics.
    Lunatic: Whaaaaaargarble!!!!! I cannot be bothered to give evidence to back up my accusations. You are close-minded!!!! WhaaaaaaaaaaaaaaaaaaaaaaaaaaaaarGARBLEBARBLEYARBLE!!!!

    Bryan Maloney

    February 20, 2012 at 9:09 am

    • Bryan,

      You prove yourself not just intellectually lazy but also shamelessly /dishonest./

      I hope that the only person you are fooling is yourself.

      You have not read the paper.

      You lack the desire to read the paper.

      You lack the mental tenacity to study the paper.

      You mock the paper in your ignorance.

      You make up a foolish exchange which contributes negatively to an informed debate.

      “A Farce in One Act” is a misleading , as you have farcical content in up to (being generous here) six of your other posts. One gem worth another look is “It is not the responsibility of those who do not blindly accept a new proposal to propose experiments. It is the responsibility of the proponents to propose the experiments. That is how science works.”

      Beautifully absurd.

      “What are the experiments proposed in this case?” See my first line.

      You conveniently ignore the 800 references many of which refer to experiments and the resulting data. See my first line.

      You caterwaul about no data in the paper, but the entire paper is based upon the available data. See my first line.

      You are ignorant of or conveniently the fraud of Imanishi-Kari and the NIH. See my first line.

      By the way, Imanishi-Kari is now a tenured professor. That outcome does not reflect a scientist who proved herself disreputable. It sounds more like a reward despite (for?) the fraud.

      I could not find any information, save an association with the fraud for the whistleblower who called her out.

      Whistleblowers almost always take a hit. No one likes a snitch (with notable exceptions like Markopolous) or wants to hire a boss-killer.

      So, I would think twice about ratting someone out, and my hunch is that others do too.

      Thus, fraud persists.

      You didn’t even bother to /google/ for fraud in science. See my first line

      Here is the link (I suspect you to be too lazy too google, so I did this puny task for you. See my first line.): http://www.google.com/search?q=fraud+in+science
      And the first two hits follow
      http://www.aaronsw.com/weblog/001616
      http://www.economist.com/node/13776974

      I post two quotations below because, I suspect you are too lazy not just to click on the google link, but also to click on the other links I provided. Just maybe you at least read what is posted here. See my first line.

      From the first link, “It can’t happen here. That’s what most scientists will tell you about fraud in science. Science is magically self-correcting, fraudsters are isolated incidents, fraud is something that happens in those other professions. Well, they’re all wrong, as Horace Freeland Judson shows in his new book The Great Betrayal: Fraud in Science. While estimates of fraud — faking evidence, omitting or distorting evidence, and plagiarism — are naturally hard to come by, even very conservative studies place it as high as 10% — a staggering number to those who place their trust in Science.”

      From the second link (the Economist is a very reputable paper by the way — and don’t tell me it’s a magazine. It calls itself a paper.),
      “Lower-level fraud, however, is much harder to detect”

      Time to eat crow dude.

      If you were a plane’s inspector, you would fly on that plane that was, conservatively speaking, 10% broken, because you would be /willfully/ ignorant of the problem. See my first line.

      You are derelict in duty when it comes to studious analysis – even just of my posts. See my first line.

      Careful criticism even of the /true/ should be omnipresent and continual.

      If you want to look increasingly fatuous, just continue to post /your/ “Whaaaaargarble! ”

      You demonstrate with regard to the paper where the lunacy lies in this forum. Also, see my first line.

      nettle

      February 20, 2012 at 10:42 am

  56. Saint Clair Cemin
    Thanks for trying to keep the forum focused on the substance of the paper.

    “Do not comment on the article, no one forces you to do this, but do not drag the entire discussion into the terrain of slander and contempt.”
    Could you clarify your statement.

    I think you meant,
    Do not comment on the article, no one forces you to do this, /or if you do then/ do not drag the entire discussion into the terrain of slander and contempt.
    Am I wrong in this interpretation?

    D^2
    You may have read the paper, but you clearly don’t understand it.

    The paper is not wrong. You are — in your conclusions.

    The problem with the paper, and this point is critically important, is that the reader either needs to be a pan-sophist (as I have been told I am; I know a lot about many fields) or a /very/ diligent student of Erik’s work.

    Since I am both, and have had /years/ of exposure to the material, Erik being my good friend, I have had a huge advantage over others in understanding the paper.

    Were I not to know Erik, I would take passing interest at best in the paper. I would have a hard time understanding it, and I would lose interest in it quickly.

    I would at least have the wisdom (and despite my knowledge and experience, I don’t have that much wisdom in me, at least in my opinion) to say /nothing/ about that which I don’t comprehend.

    What we cannot speak of we must pass over in silence. ~ Ludwig Wittgenstein

    Erik has heard from about thirty others who express their appreciation of the material, though I suspect most of them only have inklings about the paper’s implications if even its contents. The paper relates science in a radically new way that is alien to the present paradigm.

    One conclusion that I draw from the paper is that life will necessarily emerge elsewhere under proper conditions (water must be liquid, e.g.) and in /exactly/ the same way as on Earth.

    The degree to and manner in which it evolves depends, naturally, on its environment — just as it does on Earth.

    nettle

    February 20, 2012 at 9:38 am

    • Dear Nettle,

      I’m glad to read your last entry. Yes, i’m sorry for the imprecision, but I meant that no one is forced to comment on the work of this man. There are so many things one can talk about, but to speculate about the sanity of the author is not constructive. On the other hand, I find that to come up with a theory that could potentially unify different fields and at very different scales, is fascinating. If you, personally see truth in the work of Erik,( which I do not quite understand) then it is encouraging. Intuitively I always felt that there must be a continuity from the inorganic to the organic, and that life is not an accident. I also believe that at this time it is important to keep alive interesting ideas, no matter how strange they may seem, and, most of all to do research on areas that are not the fashion of the moment and are not lavishly funded.
      I’m interested in many fields of enquiry, being in contact with philosophers, artists (I’m an artist myself) and cosmologists. I will be glad to share with you your views on Erik’s work and on other subjects.

      Saint Clair Cemin

      February 20, 2012 at 10:19 am

      • Dear Saint Clair Cemin,

        Thanks for calling me dear. I return the favor. I wrote with spaces for Bryan because I recognized his difficulty with reasoning and wanted to make my reply to him easy to read and understand. You show no such difficulty, so I will write more normally.

        Your fascination with the outre is admirable. Yours is a precious mind. To say you don’t understand the paper is a necessary outcome. Unless you are a pansophist /and/ have an open mind, you can not understand the paper without it being explained to you. Heck, I am a pansophist (I know a lot about a lot), and trained in and have practiced science, and /I/ don’t fully understand the paper. The oxygyre was a particular boggle for me. Erik took about an hour explaining it to me, and though I “got it” (much but not all) at the time, I need to revist the oxygyre. Geez. I need to revisit all the gyres.

        As you suspect, necessarily we must have an interlinking of /all/ systems somehow. Otherwise, they could not function as the magnificent concert known, tellingly, as the /uni/verse. The vortex is an ancient concept. In fact, Erik is only the first person to understand and /know/ the gyre systems; he is /not/ the first person to believe in them. Ancient Greece had at least one philosopher (whose name escapes me) who held that the vortex was the fundamental element of life (not earth, wind, fire, and water as Aristotle taught, simplistically but to a degree accurately). I remember that others held such a belief, but I did not commit their names to memory.

        The logical outcome of the (much bigger) work on which the paper is based is, in my opinion but not in Erik’s,. beyond the capability of human understanding — except for Erik. Even he keeps himself in the present paradigm (he pays his bills with fiat currency). He started to put his foot a bit too firmly in The Paradigm — i.e. this is /It/, the Eschaton, The Great End of Science, at least as we know it — and proceeded to bother people. I have urged him to pull back and stick in the present paradigm, and he has.

        As to The Great End of Science, I am /not/ making too strong a claim here. Science can not persist — even in the present paradigm — when only 8% (!) of proposals get grant money. Think of how you would function if your transportation worked 8% of the time — and you didn’t know when either. I asked two scientists what 8% funding meant. Neither knew the other. They both replied that it meant, “the death of science.” Same exact words. Either my thoughts influenced theirs some way, or the blunt conclusion is inescapable.

        Erik has about thirty known supporters, well thirty-two including you and me, both scientists and people like you. I hope you can get the gist of the paper, because that’s really all that anyone needs. You don’t really need to know the mechanisms if you know the relationships and most important, the outcome, which you already have started to consider. So, you’re thinking about the most important part: do these systems really interact in this way? I have managed to go many steps further, but I have no idea if I will reach full understanding. Perhaps you can help me here.

        If you would like to have an exchange here about each and every gyre, I would be pleased to go through the effort. This will be tough for me, but I have taught a lot to a lot, and thus I became very knowledgeable about the subjects I taught. In helping you, I will be helping me.

        Not coincidentally this gyre is the necessary (and humorous, wonderful, and absurd) point of Erik’s grand work — further discussion of which is not on the table right now. I will say, that our exchange is a gyre. We have the high energy learning state (man, this is hard) and the low energy memory state (oh, now I get it). Just as our posts oscillate and interlink (comment-reply—reply to reply—reply to reply to reply—…), so do our minds. I am in the low energy memory state of the gyre (having read your reply completed mine, and you are too, as you await (knowingly or not) this post. As you read it you will be in a high energy state of a gyre, but as you understand it, your mind will move to the low energy state of the gyre. Importantly, many (most, all?) gyres collapse, as I suspect my and Bryan’s gyre will soon after he tires of making himself look foolish. Gyres become unstable and collapse, you see, /exactly/ as a tornado dissipates.

        By the way, congratulations on your canonization. To my knowledge, I’ve never had an exchange with a saint before.

        nettle

        February 20, 2012 at 11:48 am

    • nettle: Are you a member of the Natural Philosophy Alliance by any chance? If not, you might consider joining.

      D^2

      February 20, 2012 at 11:16 am

      • D^2
        No thank you.

        I would commend to you a club that encourages traits like having an open mind and skills like critical, analytical reading, but I don’t find it strange that I don’t know of one.

        nettle

        February 20, 2012 at 11:51 am

        • Are you saying the Natural Philosophy Alliance isn’t open-minded? I think they would have some issue with that assessment.

          D^2

          February 20, 2012 at 11:54 am

          • D^2
            I am saying that /you/ aren’t open-minded.

            nettle

            February 20, 2012 at 1:26 pm

            • Are you open-minded to the possibility that the kinematics equation, “v = v_0 + at”, is correct for one-dimensional motion under constant acceleration? You don’t appear to be on your website.

              D^2

              February 20, 2012 at 1:32 pm

              • D^2
                “Are you open-minded to the possibility that the kinematics equation, “v = v_0 + at”, is correct for one-dimensional motion under constant acceleration?”
                I am ignorant of kinematics, and too preoccupied with other matters, alas. So, I am in no position for /any/ judgment or consideration.

                “You don’t appear to be on your website.”
                Uhm, I don’t have one, and I can’t be on what I don’t have.

                nettle

                February 20, 2012 at 2:11 pm

                • My mistake. I thought http://http://milesmathis.com/ was your website. Outsider scientists tend to be relentless self-promoters.

                  D^2

                  February 20, 2012 at 2:27 pm

                  • D^2
                    Yeah. We all make mistakes. I’ve found one in the paper that should not have gone past a thoughtful editor. See if you can find it without hints.

                    nettle

                    February 20, 2012 at 2:40 pm

    • Well, I thought that might happen. It seems Andrulis’s work is of a religious/philosophical nature (rather than science), and in order to get it one needs to have some sort of privileged “character” (e.g. to be a “pan-sophist”). That must be why nettle is unable to communicate any simple ideas or observations (the formation and nature of ATP, ADP and their interconversion; the nature of the hydrogen bond) in terms of Andrulis’ theory since these are (apparently) inexplicable in simple terms in the context of Andrulis’ theory….and that’s despite a virtual avalanche of nettle posting on these threads

      That’s fine. If one doesn’t have a clue about rather basic biochemistry (ATP, its formation and structure and interconversions, or the beautiful insight of the hydrogen bond from decades of hard-won, Nobel-prize-winning knowledge), that’s O.K. because one can simply assert that this is all contained (if not communicable) in terms of Andrulis’ theory (even if one is unable to explain how) and in one fell swoop one can raise oneself above all that trivial knowledge….after all a “pan-sophist” doesn’t really have to know anything since he’s attained the state of privilege. According to nettles exhausting posts here nothing needs to be explained…only asserted or claimed…a bit priest-y in fact.

      Simply put, if one can’t explain ideas in biology in simple terms it ain’t science. I think we knew that from the outset, but it’s good to have nettle confirm it so completely!

      chris

      February 20, 2012 at 11:50 am

      • Chris,
        “religious/philosophical nature (rather than science)”
        The paper is loaded with science; it just describes the science in a format beyond your comprehension.

        “in order to get it one needs to have some sort of privileged “character” (e.g. to be a “pan-sophist””
        Right. I don’t pretend to “get” Relativity. I am not a privileged character who understands that sort of math.

        “That must be why nettle is unable to communicate any simple ideas or observations (the formation and nature of ATP, ADP and their interconversion; the nature of the hydrogen bond) in terms of Andrulis’ theory since these are (apparently) inexplicable in simple terms in the context of Andrulis’ theory”
        Another reason may be that you are simply unable to understand the basic biochemistry that I posted on February 14, 2012. What is your education or training in biochemistry? Do you have extensive education of how DNA replicates and is used to produce RNA which produces proteins which then run the cell’s day to day operations?

        If you don’t you won’t be able to understand me, I understand. If you do, you’ve forgotten basic stuff. Either way, don’t say “nettle is unable to communicate,” say I just don’t have the ability to understand.

        “If one doesn’t have a clue about rather basic biochemistry”
        You are the one demonstrating such. My lengthy post on February 14, 2012 showed that indeed I have more than a clue about basic biochem.

        “one can simply assert that this is all contained (if not communicable) in terms of Andrulis’ theory (even if one is unable to explain how”
        Right on both points.
        I think you mean that I am unable to explain. I readily concede that I am unable to explain anything to those who do not want to read what I write, or who misread what I write, as you have with my February 14, 2012 post, which I commend to you to read.

        “after all a “pan-sophist” doesn’t really have to know anything since he’s attained the state of privilege. ”
        Uh, pan-sophist means one very knowledgeable in all fields. The paper does not include all fields, anyway. It only included physics, chemistry, biochemistry/molecular biology and cellular biology.

        “Simply put, if one can’t explain ideas in biology in simple terms it ain’t science.”
        Wrong. Silly too.
        If you put “how DNA replicates and is used to produce RNA which produces proteins which then run the cell’s day to day operations” in simple terms you will leave out the preponderance of what’s going on. Thus, you will under inform. For instance, you will have to leave out the workings of the golgi bodies, the chemistry occurring in the mitochondria, and of course mitosis and meiosis.

        How are the universe of ‘omes (ribosome, e.g) explainable in simple terms?

        “According to nettles exhausting posts here nothing needs to be explained…only asserted or claimed…a bit priest-y in fact. ”
        Life is tough, ain’t it? If you find my posts exhausting, you must have been a wreck in school what with those textbooks and all.
        I have explained a lot. You have been unable or unwilling to understand.
        I so indeed assert that the paper is correct. I do claim to be Erik’s friend. Correct on two of three counts.
        Nothing “priest-y” about it, save in the closed mind of a person who doesn’t understand the paper (and, let’s be honest here) is more interested in debating (not merely arguing, though, I’ll grant you that) something that he clearly has not taken the time to understand.

        The paper is tough. I understand that you would not understand. I do not understand how you can’t understand my posts, though. Oh well. I have limits of understanding too.

        “but it’s good to have nettle confirm it so completely!”
        What I have confirmed is your willful ignorance of the paper, your lack of desire to take it seriously, and your misunderstanding of this subject in general.

        Ignorance is not a shameful thing, save when it is willful.

        nettle

        February 20, 2012 at 2:06 pm

  57. Response to nettle’s post on February 19, 2012 at 9:30
    > “Oliver Wendell Holmes conclusion (The most stringent protection of free speech would not protect a man falsely shouting fire in a theater and causing a panic) was given in 1919, so this 1957 case is superfluous.”

    Causing a panic and possibly consequent loss of life is a completely different category to dissemination of obscene material, therefore the 1957 case is NOT superfluous. Being able to discern between categories is essential to clear thinking.

    > “You attacking parts of the paper when you must understand it works as a whole. You can’t pick and choose.”

    That is the same attitude espoused by religious nutters and victims entrapped by various cultic “philosophies”. Within the scientific/mathematical domain, one rotten idea within a paper can spoil the whole damn paper, especially if that idea is one of those upon which others are based. Those who have valid claims to scientific credentials should know this. Trying to “understand” the “truth of the whole” when major parts are obviously incorrect or are just plain gibberish, is to court insanity. Attempting to achieve such “understanding” is tantamount to brainwashing oneself by suspending the faculties of critical analysis and rationality, thereby inducing a state akin to that of a mental breakdown.

    > “You just don’t like the fact that he is dealing with overarching concepts to describe electromagnetism.”

    Accusing me of being prejudicial is an impertinent, presumptuous projection (psychological meaning). It is not “a FACT that he is dealing with overarching concepts to describe electromagnetism”. It is a fact that he has used the word ‘electromagnetism’ in a paragraph of gibberish and given a reference to further gibberish in what appears to be a vain attempt at justification. He has NOT described Electromagnetism; he misuses the word ‘electricity’; he coins the term “photonic singularity” without giving any definition of it; he does not supply any descriptions of the electric or magnetic fields, and their how their field-strengths vary in space-time; there is no mention of static or dynamic fields , dielectric permittivity, magnetic permeability, Maxwell’s equations, Poynting vector, speed of propagation, retarded or advanced potentials, or amplitude of waves, to name but a few omissions. The information content of reference 91 is zero; it IS nonsense. Within the subject of Electromagnetism there is nothing that could be regarded as a “photonic singularity”, and use of the word “photonic” shows confusion over the difference between Electromagnetism and Quantum mechanics. Within the paper no indication is given of any understanding of Electromagnetism, and the claim that “he is dealing with overarching concepts to describe electromagnetism” unequivocally shows that the person who made that claim also does not understand the subject. Any claim to understanding of what the paper says about the subject is invalid.

    > “1/∞ = 0, which implies that yes, 1/0 = ∞, and more interestingly, 0·∞ = 1.”

    That argument can be extended:
    For any number real number X :
    X/∞ = 0, which implies that X/0 = ∞, and therefore 0·∞ = X.
    But, from the quote immediately above, 0·∞ = 1 therefore X=1; i.e. all real numbers are equal to 1.
    This result is clearly absurd therefore the statement “1/∞ = 0, which implies that yes, 1/0 = ∞, and more interestingly, 0·∞ = 1″ is absurd. The lack of sufficient knowledge to recognise such absurdity indicates that the above quote came from a member of the mathematical illiterati. No theoretical physicist, in their right mind, would write such nonsense to an author of such a paper (assuming that the story is true, which, given the tenor of previous comments, is highly dubious) unless they were trying to indicate to the author that one his statements was logically reducible to absurdity. Given the wording of the email (nettle February 19, 2012 at 9:39) containing the quote above, the astute would likely be correct in assuming that the person who wrote the email had no valid claim to being a theoretical physicist.

    > “Science makes up new words all the time — and they often have /no/ intrinsic meaning. You know that, but you hypocritically say Erik can’t. Baloney.”

    Any author of worth well-defines any neologisms he/she presents, and gives references to relevant papers when employing relatively new words coined by others. There was no hypocrisy in any of my comments about Andrulis. The standards I use to evaluate the works of others are the same standards I use for self-evaluation. Making such a wanton and unsupportable accusation may well result in readers concluding that the accuser may be a flaming troll.

    > “Pick up any copy of Nature or Science. When you see that a new protein is discovered, it gets a new name! How is this naming of proteins (with associated alphabet soup acronyms) not obscurantist?”

    The naming of a new protein is quite different to Andrulis’s use of ill-defined and undefined neologisms. The incapacity to discern the difference is further evidence to the lack of veracity of the claim to scientific credentials. More effort must be exerted to understand the need to WELL-DEFINE any neologisms presented in a scientific paper.

    > ““- new terms, or old words with new meanings, must be well-defined;” I think they are. Other scientists do too. You don’t understand, but the paper is hard to understand, so your not understanding is understandable.”

    A claim to ‘think they are’ is not relevant to whether they actually are or not. As I said in my previous post the word “triquantal” is not defined anywhere in the paper, and as other words have meanings contingent on the meaning of “triquantal” then they also ARE NOT well-defined. The meaning of ‘well-definition’ needs to be properly understood, and the need for it must be appreciated. What other scientists?. Names and institutions?

    > ““- any conclusions must be supported by unequivocal proof.” Erik provides such proof to the satisfaction of me and other scientists.”

    Apparently there is little or no comprehension of what constitutes “unequivocal proof”, which is not surprising. Again the claim of “other scientists” necessitates the question: what other scientists?

    > “If you are not satisfied by 800 references backing up a paper loaded with science — and a radically new way of viewing a variety of systems — you are just hard to please.”

    That an author of a paper may refer to another paper for some purpose, does not mean that that other paper “backs up” the author’s paper. As has been pointed out by others, at least one of those 800 references is irrelevant to the thesis presented in the paper, and as I mentioned in my previous post, reference 91 is not another paper, it is just more gobbledygook. Use of the expression “loaded with science” to describe a paper loaded with a gobbledygook that has all the hallmarks of gibberish, shows that the actual nature of science is not understood. Use of the expression “a radically new way” displays ignorance of the sophistry of other authors who have tried to explain ‘the meaning of life, the universe, and everything’ using ‘vortexes’ – another name for gyres.

    > “According to Erik (I know because I just asked him), about thirty scientists and even non-scientists have called or emailed Erik to express their understanding (even if vague) of the paper and their appreciation of it.”

    Given that one of those “scientists” claimed to be a theoretical physicist but demonstrated that they do not have the mathematical where-with-all to justify such a title, one is left wondering about the calibre of the other 29.

    A comprehensive comprehension of Electromagnetism, Newtonian Mechanics, Quantum Mechanics and General Relativity is an essential prerequisite to making a valid claim of understanding a paper that purports to provide a reformulation of the first two aforementioned topics, and a unifying framework for the last two. The absence of such prerequisite knowledge prevents proper critical evaluation of the relevant parts of the paper, with the result that any claim to being able to understand the paper has no real substance and may well be no more than dishonesty or delusion. The presence of such prerequisite knowledge enables proper critical evaluation of the relevant passages of the paper, and enables the conclusion that those passages indicate the author lacks a working knowledge of the aforementioned areas of physics to a level sufficient for rigorous troubleshooting of the relevant ideas presented.

    DuD

    February 20, 2012 at 11:45 am

    • One of the real howlers in the paper is his attempt to justify his many neologisms by citing Phil Anderson’s classic essay, “More is Different”.

      D^2

      February 20, 2012 at 1:08 pm

      • D^2
        The paper contains much that is risible and even absurd — and correct.
        I am glad to see that you take as much amusement as I do with some of the paper’s claims.
        Humor, intentional or not, can be very enlightening, but I suspect you do not understand, and thus have not been enlightened.

        nettle

        February 20, 2012 at 1:21 pm

    • DuD,
      “Causing a panic and possibly consequent loss of life is a completely different category to dissemination of obscene material, therefore the 1957 case is NOT superfluous.”
      Your inability to understand is shocking. It /is/ superfluous when the matter in question are there limits in speech. The 1919 case demonstrated such. Case closed. The 1957 case just was an elaboration on the point.

      “That is the same attitude espoused by religious nutters and victims entrapped by various cultic “philosophies””
      It may very well be, but being so, does not make the paper wrong.

      “Trying to “understand” the “truth of the whole” when major parts are obviously incorrect or are just plain gibberish, is to court insanity.”
      I understand, dude. The paper is too hard for you to understand, as is gestalt theory, I suppose. I agree the paper is frustrating in its language. Keeping you consistent, you must consider fineteride, lorazapam, and methotrexate gibberish?

      You conveniently ignore my earlier comment which I repeat here.
      Have you ever looked at the names of Drosophila proteins? How about “Mothers against decapentaplegic?” “Bicoid?” “Cheap date?” all of which have graced these and other scientific journals. Oh yea, sure those names explain /precisely/ what those proteins do to a layperson. In the context, those names, including cheap date, inherently make no sense.

      “Accusing me of being prejudicial is an impertinent, presumptuous projection (psychological meaning).”
      No. It’s descriptive. You are in denial because you don’t understand the paper.

      It is not “a FACT that he is dealing with overarching concepts to describe electromagnetism”.”
      Sure it is. You just lack the mental tenacity and open mind even to begin to understand.

      “he coins the term “photonic singularity” without giving any definition of it”
      It has inherent meaning to me This comment and preceding ones just reflect that you don’t understand the paper.

      “therefore the statement “1/∞ = 0, which implies that yes, 1/0 = ∞, and more interestingly, 0·∞ = 1″ is absurd.”
      Couldn’t agree more, but the absurd can be true. Quantum entanglement is absurd. Schroedinger’s Cat is absurd. They both appear to be true, though.

      ##################################################################################
      Importantly, just as random is a cowardly euphemism for science when it lacks understanding (There is something there, but I don’t know how to go further), so absurd is for philosophy (There is something there, but I refuse to go further) and faith and hope are for religion (There is something there, but I want to go further.)
      ##################################################################################

      “The lack of sufficient knowledge to recognize such absurdity”
      Your statement is silly — and illogical.

      “Any author of worth well-defines any neologisms he/she presents, and gives references to relevant papers when employing relatively new words coined by others.”
      Dude, every word was new at some point. Science is pumping out new words all the time. Your comment is therefore illogical.

      “the word “triquantal” is not defined anywhere in the paper”
      You again just don’t get it. In the context of the paper the meaning is almost obvious. We have three quanta; three of the smallest elements in the gyre in question or any three units. For you to miss this easy idea shows you lack the ability to understand even the easy. I will /try/ to help you. Consider; science, philosophy, and religion; attraction, repulsion, immutabily; good, better, best.

      “That an author of a paper may refer to another paper for some purpose, does not mean that that other paper “backs up” the author’s paper. As has been pointed out by others, at least one of those 800 references is irrelevant”
      Wrong.

      “reference 91 is not another paper, it is just more gobbledygook”
      Sorry, it’s a footnote. It is not “gobbledygook.”
      An electron is known to oscillate. An electron that has more energy oscillates faster; less energy, slower. It thus moves through space-time (4D) as a wave. Erik is modeling this wave as a gyre which can be viewed as a spiral through space and time. Boy, that understanding was easy. I have no idea why you didn’t get it.

      “Use of the expression “a radically new way” displays ignorance of the sophistry”
      No it doesn’t. Relavity was a radically new way and it’s not sophistry, at least in my opinion.

      “Given that one of those “scientists” claimed to be a theoretical physicist but demonstrated that they do not have the mathematical where-with-all to justify such a title”
      How are you able to make this conclusion? If you are a mathematician or theoretical physicist then say so.

      “…one is left wondering about the calibre of the other 29″
      Correction, /you/ are left wondering. Their “calibre” doesn’t matter. They understand the paper and you don’t. In fact, you don’t understand at even my posts.

      “A comprehensive comprehension of Electromagnetism, Newtonian Mechanics, Quantum Mechanics and General Relativity is an essential prerequisite to making a valid claim of understanding a paper that purports to provide a reformulation of the first two aforementioned topics, and a unifying framework for the last two.”
      Because you say “this is how things have to be?” Please. You are too stuck in the present paradigm to even consider that there must be /some/ overarching final paradigm that links ever system together — and though it has to include the present paradigm, it need only descibe it sufficient;y enough to give the general idea. Those familiar with quantum mechanics can fill in the blancks just as modern science and engineering filled in the blancks with some of Gallileo’s and Da Vinci’s ideas.

      The absence of such prerequisite knowledge prevents proper critical evaluation of the relevant parts of the paper”
      Wrong. Your lack of intellectual curiosity, mental tenacity, and open mind (a triquantum) prevents /your/ proper critical evaluation of the relevant parts of the paper. Others seem to be able to do so.

      “any claim to being able to understand the paper has no real substance and may well be no more than dishonesty or delusion.”
      Or correct. Once again we have a triquantum. I hope you at least understand that word by now.

      “the conclusion that those passages indicate the author lacks a working knowledge of the aforementioned areas of physics to a level sufficient for rigorous troubleshooting of the relevant ideas presented.”
      Whether the author has this knowledge is irrelevant. You miss the entire point of the paper. If you got the point, you would understand that one need not have profound knowledge of a subject to describe it as a whole. Erik’s paper is not stuck in the minutiae. It is /over/ all these systems and unifies them.

      As an illustration, if you are in a airplane over part of a small village with a camera in your phone, you can’t can’t take street-level pictures (well, unless you have an insane pilot). You can take big pictures and as a mosaic put them all together to describe the big picture of the entire small village.

      The big picture is what the paper is all about.

      nettle

      February 20, 2012 at 1:18 pm

    • This thread seems to have been wrestled away from the RetractionWatch theme of highlighting and discussing papers that shouldn’t be in the scientific literature! However it does illustrate perfectly one of the consequences of deficient peer-review in the lower echelons of the publishing world where pretty much anything can be published.

      The thread has been hijacked by a troll. It’s quite similar to threads on other websites that discuss science related to, for example, global warming or evolution. There is an effort by creationists to get papers that seem to support creationist ideas into the scientific literature, and several papers that support non-scientific interpretations of global warming have been sneaked into publication. This allows a veneer of “respectability” to deficient ideas, and these are “protected” by the trollish behaviour that indicates a delight in the possibility that one doesn’t have to have any evidence in support of ideas, that ignorance can be a virtue, and that people that don’t know very much at all can argue dogmatically and aggressively with those that do.

      Imagine a world in which everyone could get anything published and everything in the literature had equivalent “value”. This thread illustrates what happens. The bullies and agenda-lead take over. It would be a little like the Cultural Revolution in China where academics and other people with talent were shunted off to the country to shovel pig manure by privileged thugs… nice!

      chris

      February 20, 2012 at 1:52 pm

      • Chris,
        “This thread seems to have been wrestled away from the RetractionWatch theme of highlighting and discussing papers that shouldn’t be in the scientific literature!”
        I am trying real hard to stick to those points. You are the one wrestling the thread away from a discussion of the paper and the paper only.

        You are digressing with unnecessary comments as,
        “”There is an effort by creationists to get papers that seem to support creationist ideas into the scientific literature, and several papers that support non-scientific interpretations of global warming have been sneaked into publication.”
        Tell me how this effort relates to the paper. You can’t, because it doesn’t. You may say it was an illustation but it is an unnecessary one as you could have chosen to stay on topic and just used the paper as an example.

        But you didn’t. Your choice. Not mine.

        Just keeping you honest.

        The following sentence does relate, though, so you only swerved off topic for one sentence, I will grant you.

        “This allows a veneer of “respectability” to deficient ideas, and these are “protected” by the trollish behaviour that indicates a delight in the possibility that one doesn’t have to have any evidence in support of ideas, that ignorance can be a virtue, and that people that don’t know very much at all can argue dogmatically and aggressively with those that do.””
        I agree. However, this has nothing to do with a discussion of the contents of a paper that you clearly do not understand, don’t want to understand, and lack the capability of understanding — right now at least.

        I hope you will change your mind.

        Mark my words, the game will change. Erik has already been contacted by other professors curious about his paper. (I am staying on topic.)

        “it does illustrate perfectly one of the consequences of deficient peer-review in the lower echelons of the publishing world where pretty much anything can be published.”
        No. Though other papers do. The imprimatur of peer review hides bad science. Aye, there’s deficiency.

        “The thread has been hijacked by a troll.”
        You couldn’t possibly be referring to someone who has given examples from the paper and defended the paper. I am performing a valuable and needed service in balancing the ignorance of those attacking a paper that they don’t understand one bit. In fact, you are referring to yourself.

        “Imagine a world in which everyone could get anything published and everything in the literature had equivalent “value”.
        You describe yourself. Complaining about the thread being wrestled away

        “This thread illustrates what happens. The bullies and agenda-lead take over.”
        You are the bully. You clearly want to strong arm ignorance over my attempts of addressing points within the paper. Our exchange would be much more productive if /you/ stayed on topic and picked sections of the paper to discuss. Why is such a task so hard for you?

        I (now with Saint Clair Cemin possibly) are the sole defenders of the paper.

        I throw down the gauntlet to see if you have /any/ sincere interest in “highlighting and discussing” this paper instead of dismissing it. Pick any section. I will explain it to you.

        I defend and explain the paper because I am longtime close friends with Erik.

        What is your motivation for your carrying on?

        nettle

        February 20, 2012 at 2:37 pm

  58. Chris
    My reply to you has an omission which I correct here.

    “Imagine a world in which everyone could get anything published and everything in the literature had equivalent “value”.
    You describe yourself. Complaining about the thread being wrestled away while hypocritically wrestling it away himself. How very odd.

    nettle

    February 20, 2012 at 2:43 pm

  59. Chris,
    Another clarification. Quotation marks were missing. Make fun of me if that makes you happy.

    “That must be why nettle is unable to communicate any simple ideas or observations (the formation and nature of ATP, ADP and their interconversion; the nature of the hydrogen bond) in terms of Andrulis’ theory since these are (apparently) inexplicable in simple terms in the context of Andrulis’ theory”
    Another reason may be that you are simply unable to understand the basic biochemistry that I posted on February 14, 2012. What is your education or training in biochemistry? Do you have extensive education of how DNA replicates and is used to produce RNA which produces proteins which then run the cell’s day to day operations?

    If you don’t you won’t be able to understand me, I understand. If you do, you’ve forgotten basic stuff. Either way, don’t say “nettle is unable to communicate,” say “I just don’t have the ability to understand.”

    nettle

    February 20, 2012 at 2:47 pm

  60. Nettle

    You are really engaged with Andruli’s paper. I would suggest that you write a book explaining it to the best of your abilities, with the help of Andruilis himself, hopefully, and anyone who would be willing to do it.
    It would be useful, it would be really good. Try to contact John Brockman from the Edge.org (great science literary agent) with a proposal.
    I will disconnect from this forum that I find of little interest.

    thanks for all
    good buy

    Saint Clair Cemin

    February 21, 2012 at 6:33 pm

    • And still not a single proposed experiment. One can write entire encyclopedias “explaining” purely fictional constructions that have no grounding in reality. Verbosity is not evidence. Victimology is not evidence. Whining about not being “understood” is not evidence. Experiments produce evidence. If it is science, then propose specific experiments. I have seen none, thus, the gyre is not science. It is a religion.

      Bryan Maloney

      February 21, 2012 at 7:43 pm

      • Bryan Maloney
        “And still not a single proposed experiment.”
        No need to propose experiments. You could find them within the 800 references if you were honestly interested.

        You aren’t. So, you won’t.

        “One can write entire encyclopedias “explaining” purely fictional constructions that have no grounding in reality.”
        Sure. Your statement only has bearing on the paper in that it shows you don’t understand the paper. Adjust.

        “Verbosity is not evidence.”
        As we see on this forum.

        Victimology is not evidence. Whining about not being “understood” is not evidence.
        Wrong. (I am presuming you mean Erik being a victim after the paper). Victimology is evidence that Erik has angered some in the academy, begging the question, why? No academic would persecute another unless the former was threatened in some was, as they are. I am not whining. I am describing /willfull/ ignorance, a lack of mental tenacity, and a lack of intellectual curiosity in folks like you.

        “Experiments produce evidence. If it is science, then propose specific experiments.”
        I am going to go out on a limb here and state that you are intelligent and motivated enough to check some of the 800 references for experiments — but clearly too lazy to do so.

        “I have seen none.”
        There are those who see; there are those who seen when they are shown; and there are those who can not see. The last of those three sentence describes you.

        “the gyre is not science. It is a religion.”
        The gyre has science on almost every, if not every page. You are incapable of seeing it because you are confined to a little box afforded by your closed mine. Sure, the gyre logically must subsume religion, but the paper sticks to science.

        You do not understand the paper, you lack the capability to understand the paper, and you lack the mental tenacity to read the paper.

        You don’t let your ignorance stop you from mocking what you don’t understand.

        nettle

        February 21, 2012 at 9:40 pm

  61. Saint Clair Cemin,
    Erik already has a book which is much more expansive in the topics it discusses.

    I guess I could write a book, but only after Erik publishes his. He was astonished to find absolutely no interest from publishers.

    Similarly I think I would have a hard time publishing a book just about the paper because of the controversial nature of its contents.

    “I will disconnect from this forum that I find of little interest.”
    You make me laugh.
    Ironically, you said,
    “On the other hand, I find that to come up with a theory that could potentially unify different fields and at very different scales, is fascinating.”

    So, you find it fascinating, but you turn down my offer to explain it to you further. Contradiction.

    Oh well.

    nettle

    February 21, 2012 at 7:34 pm

  62. Nettle,

    Please write to me directly. I feel dizzy with the forum, it is like being in the middle of a saloon brawl.

    Saint Clair Cemin

    February 21, 2012 at 7:41 pm

  63. Saint Clair Cemin
    My email (for this forum) is wiggles2012@hushmail.com.
    Either send your email there, or give me an alternative, please.

    nettle

    February 21, 2012 at 9:07 pm

  64. Someone on a different thread made a bizarre claim. For the open minded, I post my replies below.

    The first reply follows.

    “The fact that the theory ignores observations that the author doesn’t like is the single biggest weakness.”
    You are upset that a mere 65 page paper ignores observations? What are you expecting from a paper?
    It is not an encyclopedic discussion of gyres; it is a mere introduction, a survey.
    Please, give examples to the “observations that the author doesn’t like,” and I will offer elucidation.

    “I can have the most beautiful theory on paper and if I ignore evidence, it’s just a really advanced form of abstract art.”
    Wrong. You either are not a scientist or are intellectually dishonest.
    When a scientist finds six results, three of which fit the present theory, two of which are a little strange and one of which is way off the bell curve, he or she ignores the outlier (e.g. “I must have contaminated the sample under study”), and explains away the descrepancies of the other two, if he or she even includes them at all. The “funny” is often the foundation of a new realm of science — e.g. Relativity. More typical is “that’s funny, but I don’t have time for funny, I have to support my thesis — graduate or grant).

    More important, defending “that’s funny, but it goes against widely accepted theory” is no fun at all — as Erik is experiencing right now.

    Necessarily, the paper subsumes art — after all what is life if not a orchestra playing a beautiful, terrible, or neutral concert.
    A concert begs the question. Where is the conductor?
    The paper answers that question. The conductor is within, without and overarching the orchestra itself. The concert, let’s remember, involves the performers, the audience, and the location (music hall, half-shell, etc.) all at the same time. Take one out and you don’t have a concert.

    You should have backed /your/ opinion up with examples. How can you blame the author if you /yourself/ are remiss in this important duty. Don’t be hypocritical.
    You imply that claims require /all/ the facts that you deem relevant, then present no facts. Show me the money. Lay your cards on the table. Come clean.

    Until you offer one example, you opinion has no foundation whatsoever. By your own bizarre logic, if you ignore observations that you don’t like (e.g trimergence: RNA, DNA, protein; man, woman, child; good, better, best; etc.), “if [/you/ ] ignore evidence, it’s just a really advanced form of abstract art.” I take your words and show your folly.

    Buck up.

    Offer me /at least/ one purported weakness.

    nettle

    February 22, 2012 at 7:49 pm

    • Beauty and breadth are irrelevant. Propose one experiment that could falsify this theory.

      Bryan Maloney

      February 22, 2012 at 8:16 pm

      • Bryan,

        You wrote, “Beauty and breadth are irrelevant.”

        I guess you like plain and perhaps ugly — as in the ugly truth. Too, I presume you like ad hoc theory, contradiction, and omission. Is there in truth no beauty? Do you not live in the /uni/verse? Would not one predict a /uni/fying theory of the /uni/verse?

        “Propose one experiment that could falsify this theory.”

        You can’t falsify what is true. Every experiment mya support the theory paper as true — or, alternatively may not prove the theory false. Science can only disprove; it can never prove. All you need is /one/ generally accepted physical theory to be not falsifiable to support the idea that a non-falsifiable theory can still be correct. We have at least one.

        To excerpt from the Miles mathis pdf posted earlier, he claims there to be many such physical theories, to wit,

        “Most of contemporary physics isn’t testable, and that includes much of the most feted theory of the past six decades. String theory isn’t testable, but that hasn’t stopped it from steady growth over the last thirty years. Most of QCD isn’t testable, since the quark and gluons and so on can’t be isolated. Symmetry breaking is not testable, virtual particles are not testable, quantum tunneling is not testable, black hole theory is not testable, inflation is not testable, and so on. Leonard Susskind, one of the top dogs of string theory, has told us (in defense of his own postulates) that physical theories don’t need to be falsifiable or testable. They are accepted because top physicists accept them. I don’t expect Susskind will include Andrulis in that defense. If you are at the center of the field, your pronouncements don’t need to be testable, but if you are at Case Western Reserve, they do.”

        I have no idea if he is correct on all of those theories. Again, all you need is one; Mathis shows us many.

        The paper makes no claim that the theory is not falsifiable, regardless. Perhaps it is, though.

        Still, being fair, I turn to your question about some experiments that test Erik’s theory. We can only test the electrogyre for falseness if we look at one individual electron, but we can’t. Similarly, we can not monitor the ejection of a single DNA molecule within or from the single cell. Therefore, the gyre model is unfalsifiable.

        Notice that once I discuss the phosphogyre onwards, the viewpoint is sometimes the reverse of how we presently describe the present systems. I acknowledge that enzymes apply in experiments from the phosphogyre onward, and omit them for explanatory clarity. Note, all the experiments beneath the cellulogyre have been observed only en masse — not singularly. We can only test the electrogyre for falseness if we look at one individual electron.

        Here are the experimental results from which you can find the experiments with a google search. No, I won’t do the searches for you.

        1. Electrogyre. Do electrons absorb photons when photons hit electrons? Yes. Do electrons emit photons when they fall to ground state? Yes. Emission of photon. Prediction, experiment, theory proven correct.

        2. Oxygyre. Do oxygens absorb (“share”) an electron if hydrogen is around and you add a spark (more electrons than simply the one on the hydrogens)? Yes Two experiments, two positives.

        3. Carbogyre. Does carbon attach to oxygen when you burn it? Yes. Is carbon cleaved from oxygen when living cells metabolize carbohydrates? Yes. Two experiments, two positives.

        4. Phosphogyre. Does a phosphate absorb a carbon in the formation of PEP (phosphoenol pyruvate)? Yes. When PEP catabolizes does it eject carbon? Yes, as formaldehyde. More experimental tests, more validation.

        5. Ribogyre. When the nucleotide polymerizes does RNA evict pyrophosphate? Yes, to form the link in the nucleotide polymer. When RNA breaks down to form a ribonucleotide does it the nucleotide reform high-energy phosphate bonds? Yes. You get the gist by now, right?

        6. Aminogyre. Is tRNA absorbed in the formation of polypeptides? Yes, though we tend to think of tRNA absorbing AA’s. Is the RNA ejected from the polypeptide at the end of its formation? Yes, though we tend to think of tRNA releasing the polypeptide. Moreover, sulfur-containing methionine is the first AA in most polypeptide chains — if not all – sometimes, Met gets cleaved off. People who mock the idea that Amino means sulfur along with amino acid and polypeptide conveniently ignore this prevalent, perhaps universal, fact. Shame on them.

        7. Deoxyribogyre. Does DNA absorb a polypeptide in the formation of chromatin? Yes. Does DNA eject the polypeptide when it unravels for the purposes of transcription, recombination, replication, repair? Yes. The consistent results here are pretty repetitive, hunh?

        8. Cellulogyre. Does a cell absorb DNA when a sperm juxtaposes an egg? Yes.  Does a cell eject DNA when it finishes mitosis (e.g. to form an a new cell at G0). Yes, yes it does.

        For each gyre, you now have two predictions, two experiments that have been performed and have come back positive. If you yourself would like to perform those experiments to test the falsity of the theory, be my guest.

        By the way, what brings a sperm and an egg together? What force prevents in humans (often, but not always), the absorption of a second sperm? We have an /overarching/ answer than includes both of these — and the next example too.

        We think we know how lipid fuse. We say van der Waals forces — but they are not generally applicable. They no known relationship to cells fusing — unless you consider the interlinking theory of gyres.

        How does Y universally know how to find X? How does X know how to find Y? I ask the latter question because they may well be looking for one another. How can we tell with present theories — aside from those in the paper?

        If we reject the theory of the paper, we are left with ad hoc theories, contradictory hypotheses, and ignorance.

        Summing up: You asked for one proposal. I exceeded your demand by more than an order of magnitude.

        If you are honest and fair, you will now offer /one/ experiment to the contrary of the sixteen I gave.

        nettleingenting

        February 23, 2012 at 3:16 pm

      • Omission in exaple #2 abobe
        Do oxygens release electrons (back to hydrogen) when a current is present and at least one free radical is available (typically more, HS experiments use a dose of hydrogen peroxide) and a current is applied? Yes, and thus hydrogen and oxygen gas form at opposite electrodes (to be captured by test tubes in HS experiements).

        nettle

        February 27, 2012 at 12:19 pm

  65. The complementing comment follows.

    “”I can have the most beautiful theory on paper and if I ignore evidence, it’s just a really advanced form of abstract art.”
    You are not just wrong, but possibly self-contradicting — or accidentally praising the paper. How can you have “the most beautiful theory” and ignore evidence?
    The theory is not an abstraction. An abstraction by its very nature is not concrete. Concrete is reified and concrete. The theory of gyres is concrete.
    A whirlpool exists. So does a tornado. On a greater scale does a hurricane.
    The symbols of representations but are depictions of what you can touch, see, and experience.

    I will play your game for a moment, even if it is abstract art, being abstract art is not “just” (i.e. merely) abstract art. It can represent something true and sublime.

    A cell, protein, DNA, etc. all all concrete — and modeled in the paper as interlinking gyres.

    Consider,
    “Science is nothing but trained and organized common sense, differing from the latter only as a veteran may differ from a raw recruit: and its methods differ from those of common sense only as far as the guardsman’s cut and thrust differ from the manner in which a savage wields his club.”
    T.H. Huxley

    “There is nothing so tragic as a beautiful theory destroyed by an ugly fact.”
    Sir Conan Doyle and/or T.H. Huxley

    Please, give me one fact that destroys the theory in this paper.

    If you can’t, then you are simply unwilling to accept the beauty and breadth of the theory contained with paper.

    nettle

    February 22, 2012 at 7:52 pm

    • Have you ever heard of Russell’s Teapot?

      You are doing nothing but presenting Invisible Pink Unicorn statements.

      “Beauty” and “breadth” are irrelevant to science. Falsifiability is a fundamental feature of science.

      Indeed, Huxley’s “ugly fact” statement was his own way of making fun of “beautiful” theories.

      Bryan Maloney

      February 27, 2012 at 1:21 pm

      • Bryan,

        You continue to clown around.

        Your are completely wrong with the idea of Russell’s Teapot.
        I am not claiming there is a teapot orbiting the Sun between Earth and Mars.
        This conjectural teapot has nothing to do with the results I gave.
        I am saying that experiments can be done and the results measured.

        You consider all sixteen experimental results to be “Invisible Pink Unicorn statements.”
        You bizarrely ignore commonly accepted science.

        ““Beauty” and “breadth” are irrelevant to science.”
        To you.
        Others find the beauty and breadth of e = mc^2 to be wondrous.

        “Huxley’s “ugly fact” statement was his own way of making fun of “beautiful” theories.”
        And my statements make fun of you.

        Give me a fact ugly or otherwise that refutes these experiments or the theory of the paper.

        In the absence of such a fact, if you can not recognize that these sixteen different experimental results are expermentally verifiable, then you reveal yourself as a chalatan.

        nettle

        February 28, 2012 at 10:17 am

  66. What do you want from a theory if not to know? What more are you looking for? All the data fits this paper’s theory.
    What is a theory and why must it be so?
    What is it that you want predict so badly that you must have a theory that describes it?
    What is it ultimately that you generally want?

    nettle

    February 23, 2012 at 3:20 pm

  67. It has become apparent that the self-appointed priest of the Church of the Gyre has no idea how science works, since he is offended by the term “falsify”. Falsifiability is the cornerstone of science. A “theory” that cannot be falsified by any means at all is a statement of religious dogma disguised as a theory.

    Bryan Maloney

    February 27, 2012 at 1:23 pm

  68. You can’t argue the points in the paper, so you create your own world of fantasy interpretation.

    I am not a priest but when you think of the paper (clearly you haven’t read it) you are a scientific apostate.

    I take no offense at the word falsify.

    From Webster: Theory
    A doctrine, or scheme of things, which terminates in
    speculation or contemplation, without a view to practice;
    hypothesis; speculation.

    You are imparting a new meaning on the word theory.

    Nothng anywhere in the word theory or in Erik’s paper has any mention or anything to do with dogma.

    “A “theory” that cannot be falsified by any means at all is a statement of religious dogma disguised as a theory.”
    Wrong.
    You’ve dug yourself into a hopelessly deep hole of ignorance from which you do not want to escape.

    Falsify General Relativity.

    Falsify Darwn’s Theory of Natural Selection.

    nettle

    February 28, 2012 at 10:29 am

    • nettle, it’s unfortunate that you are unable to provide a single example of a molecular/biological phenomenon that the Andrulis theory gives insight into in a way that’s not already understood, nor a single example of a prediction that follows from Andrulis theory, nor an example of an experiment that could be used to test the theory, nor an example of phenomena/observations that would falsify the theory. Andrulis theory is entirely deficient as a scientific theory if these criteria aren’t communicable in simple terms.

      But I think we all agree that Andrulis’s paper isn’t about science, nor describes a useful theory. I also find it unfortunate that you simply respond to posts here by a sort of inverse parroting of comments with semantically-flawed assertions.

      If you learn something about science you’ll discover that a scientific theory doesn’t have the same meaning as your Webster’s dictionary definition. A better description of a scientific theory can be found on the Wikipedia page (google “Wikipedia scientific theory”):

      “The defining characteristic of a scientific theory is that it makes falsifiable or testable predictions. The relevance and specificity of those predictions determine how potentially useful the theory is. A would-be theory that makes no predictions that can be observed is not a useful theory. Predictions not sufficiently specific to be tested are similarly not useful. In both cases, the term “theory” is hardly applicable.”

      By these criteria you’ve demonstrated that Andrulis’ notions don’t constitute a scientifc theory. If you read more carefully you might discover that the essential element of “falsifiability” isn’t that one can falsify the theory (e.g. your exhortions to “Falsify General Relativity” and “Falsify Darwn’s Theory of Natural Selection”). That’s just silly. The point is that these theories are falsifiable.

      Here’s your examples:

      General Relativity: This was an excellent theory from the outset since it explained several otherwise unexplained observations (e.g. the anomalous perhelion precession of mercury), and it made some specific predictions that could be tested by observations and experiment. Notice that if these predictions didn’t turn out to be observable the theory would be proven falsified at least in it’s essential form. Thus the theory predicts that light from a distant source should be “bent” by the gravitational field of intervening massive celestial bodies, that light from distant sources should be redshifted by the same phenomenon, that light should be unable to escape from black holes, and so on. There is a whole slew of observations/measurements that have been made to test General Relativity and the theory has always been falsifiable in the context of the failure of these observations/measurements to accord with predictions.

      Your task, nettle, is to give us equivalent examples of explanations afforded by Andrulis’ notions, and some of the predictions that can be used to test for falsifiability, and thus give us some reason to consider that Andrulis paper constitutes anything like a “theory” scientifically-speaking.

      Natural Selection: I’m sure if you think about this Natural Selection has massive explanatory power and is eminently falsifiable. For example natural selection would have been falsified if a completely validated fossil record showed a stratigraphy with jumbled progression of unrelated forms, or the demonstration of biomolecular mechanisms that eliminated the accumulation of mutations, or the observation of spontaneous generation of organisms, or the observation in the genomic databases of morphologically-related organisms that shared no similarity in the gene sequences, or the identification of phylogenies that didn’t show the progressive accumulation of changes in gene sequences according to the evolutionary distance of members of the phylogeny… and so on…

      In fact each of these theories contained within them a huge series of predictions that grew and were tested over more than 100 (Nat Sel) or nearly 100 (Gen Rel) years, and in the context of which they were continuously falsifiable. The fact that the theories have so far passed all of the tests devised to assess their predictive qualities means that each of these theories is afforded the status of being essentially true. In other words there is little doubt that General Relativity and Natural Selection are robust and reliable descriptions/mecanisms of their particular bit of the natural world, even if the might (like Newtonian Physics) turn out in future to be parts of some wider theory…

      chris

      March 1, 2012 at 1:22 pm

      • Chris,
        The paper shows how multiple systems work in concert — as do my comments, none of which you have read or have the capabablity to understand. Instead of being silent in you ignorance, you spread your lack of understadning. You clothe you answers in scholarly language, thus making your comments dangerous to the unimformed.

        In one answer I give sixteen examples and (1) the paper ties them all together as they have never been tied before! I go further to predict (2) unannotated RNA (more of it) and (3) the end of science as we know it. I know you are skeptical and impatient, so set this response aside for a while before reponding.
        -nettle

        nettle

        March 2, 2012 at 2:01 pm

  69. nettle says: “You clothe you answers in scholarly language, thus making your comments dangerous to the unimformed.”

    how sad..I pointed out earlier how your assertion of priviliged insight into an apparently unexplainable (by you) “theory” comes across as rather priestlike, and here you are castigating straightforward and completely standard descriptions of well characterized and real theories (natural selection and general relativity) and their falsifiability as “answers clothed in scholarly style” and “comments dangerous to the unimformed”. You sound just like the sort of theological inquisitors who persecuted Galileo.

    Unfortunately you seem unable to provide any insight whatsoever into Andrulis’ notions, nor to give any examples of predictions arising from these, or experiments/observations to address falsifiability. By these completely uncontroversial criteria you are reinforcing the conclusion that Andrulis’ notions don’t constitute a scientific theory.

    And your examples are moronic if I may say so. You “go further to predict unannotated RNA (more of it)……”. But how can you “predict” something that’s been known about for a decade? Since a whole slew of analyses on eukaryotic genomes indicates that as much as 50% of the genome might be transcribed, it doesn’t take a predictive genius to realize that more unannotated RNA is going to be discovered. Already in 2002 it was shown that the amount of transcription on two human chromosomes (21 and 22) was around 10-times that annotated in data banks. That basic biochemical and genetic science was done by people that understand how to do proper science and know how to call a shovel a shovel. It’s a little creepy for you to assert 10 years after its discovery that you “predict” unannotated RNA!

    Learn some biochemistry nettle…and take some elementary classes in philosophy of science. Don’t fall into the trap of thinking that you can bypass learning and knowledge by aligning yourself with gibberish over which you confer upon yourself the status of priviliged insight. That might be a clever strategy for internet trolling but it’s not going to take you very far in the real world…

    chris

    March 6, 2012 at 3:24 pm

  70. Life’s origin/nature without academEnglish verbiage

    Origin And Nature Of Earth Life, An Update…

    Liberate your mind from concepts dictated by religious trade-union AAAS.
    Life is just another mass format + re-comprehend natural selection + natural selection is ubiquitous, for all mass formats.

    Life Evolves by Naturally Selected Organic Matter

    I.
    Homegrown Organic Matter Found on Mars, But No Life
    http://news.sciencemag.org/sciencenow/2012/05/homegrown-organic-matter-found-o.html?ref=em

    II. EarthLife Genesis From Aromaticity/H-Bonding
    http://universe-life.com/2011/09/30/earthlife-genesis-from-aromaticityh-bonding/
    September 30, 2011

    A.
    Purines and pyrimidines are two of the building blocks of nucleic acids. Only two purines and three pyrimidines occur widely in nucleic acids.

    B.
    Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring.
    A purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature.
    Aromaticity ( Kekule, Loschmidt, Thiele) is essential for the Krebs Cycle for energy production.

    C.
    Natural selection is E (energy) temporarily constrained in an m (mass) format.

    Natural selection is a universal ubiquitous trait of ALL mass spin formats, inanimate and animate.

    Life began/evolved on Earth with the natural selection of inanimate RNA, then of some RNA nucleotides, then arriving at the ultimate mode of natural selection – self replication.

    Aromaticity enables good constraining of energy and good propensity to hydrogen bonding. The address of Earth Life Genesis, of phasing from inanimate to animate natural selection, is Aromaticity.Hydrogen Bonding.

    Dov Henis (comments from 22nd century)
    http://universe-life.com/2012/02/03/universe-energy-mass-life-compilation/

    tags: life genesis, natural selection, life mass format

    dovhenis

    November 20, 2012 at 5:22 am


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