The editor of a new journal that published a paper that has been met with disbelief by many in the blogoshpere — and those are the polite reactions — has posted a narrative about how the paper came to appear in his journal. Retraction Watch readers may recall that Case Western, home to the paper’s author, Erik Andrulis, retracted its press release about the work. Several of the journal’s editorial board members have resigned over it.
Life’s editor, Shu-Kun Lin, writes that there was a switch in editors:
So that our readership has as much information as I can divulge without violating the confidentiality of the review process, what follows is the background of these events. Professor Bassez had previously guest-edited a successful special issue titled “The Origin of Life” in another MDPI journal [2]. Although Professor Bassez [3] had also planned to be the Guest Editor of the special issue “Origin of Life – Feature Papers” for Life [4], she was, for personal reasons, unable to do so. I therefore volunteered to take this responsibility on her behalf and to guest edit this special issue and supervise the editorial procedure for the papers. I made the decision of acceptance based on the peer review reports we received and their recommendation in support of publication.
Later he gives details of those reports:
the two reviewers were both faculty members of reputable universities different than the author’s and both went to considerable trouble presenting lengthy review reports. Dr. Andrulis revised his manuscript as requested, and the paper was subsequently published.
Derek Lowe of In the Pipeline, where we found news of the explanation, wasn’t very impressed with it. Neither were we, although we should say that we welcome any efforts to pull back the veil of peer review and increase transparency. This line sort of says it all:
I feel obliged to stress that although we will strive to guarantee the scientific standard of the papers published in this journal, all the responsibility for the ideas contained in the published articles rests entirely on their authors.
So, um, what value is the journal adding, exactly?
There’s one line in particular that we think is worthy of extra attention:
All papers are peer-reviewed, although it is often difficult to obtain expert reviewers for some of the interdisciplinary topics covered by this journal.
To us, that suggests an obvious question: Shouldn’t journals check whether there are really enough qualified peer reviewers before they launch a journal that promises quality peer review?
It’s one thing if publishers launch journals whose criteria for publication are a “sanity test,” as F1000 has done with F1000 Research. (Some have wondered whether this Life paper would have passed that test, but more literally than F1000 means it.) Such papers would be marked as unreviewed. But if there aren’t enough peer reviewers out there to staff peer-reviewed journals, should we really support publishers who launch endless numbers of them?
Interesting that this article mentions F1000 and its “sanity check” as well as discussing the Andrulis Life paper and the problem over peer review. These seem to link into the fundamental problem with the recent proliferation of journals, which is a dilution of quality. This may not matter too much to the progression of science (apart from the waste of productive time), but it ‘s a problem at a time when there are considerable efforts to politicise areas of science that have important societal impacts. Loads of low quality journals with low scientific standards makes it much easier to publish some of the self-serving rubbish that is used to construct pretences of “scientific” validity to bolster political agendas (we could give examples), and “sanity checks” would likely not catch these [Rebecca Lawrence of F1000 responded to my comment on this on another thread, but I’m not convinced this isn’t a problem: http://www.retractionwatch.com/2012/01/30/an-arxiv-for-all-of-science-f1000-launches-new-immediate-publication-journal/#comment-9582 ].
I work in molecular biology/biophysics reviewing around 10 papers a year on average. However already this year I’ve had 6 requests to review, 4 of these from journals I’ve never heard of (one asked me to return my review within a week). At least two of the manuscripts are truly dismal, but several are of the extreme dull but sound category (e.g. run of the mill experiments on systems/fields that were sorted out a decade ago). I’m convinced that most of these manuscripts wouldn’t have been submitted 10 or 20 years ago. In the past I’ve been happy to make the effort to improve weak manuscripts but I simply haven’t got the time to review all of this dispiriting stuff; I suspect these manuscripts will find their way into journals with rather little benefit to anyone but the authors (CV bolstered) and publisher (more cash).
Maybe it doesn’t matter, but I can’t see how it benefits science at all. Is this just an intermediate period of chaos as scientific publishing shifts from the traditional mode into some new model? Perhaps we’re sliding towards the post-modernist idyll whereby anything at all can be published as science, and thus everything has a scientific validity, and so whether smoking is bad for you health, or enhanced atmospheric CO2 makes the world warm, or making more people poor tends to have adverse effects on society and so on are matters that are not so much informed by science as by choice, since there’s plenty of “scientific” support in the literature for all points of view, and so “the science isn’t settled”…
I agree. I had a paper to review at the end of January, 2012 for PlosOne that had a manuscript number of 12-02800. I thought that this couldn’t be the 2800th manuscript submitted in a month? I then looked at the number of papers published in that journal – 253 in the last week alone and in the short time it had been in business (3 years, I think), they had published their 10,000th manuscript in June of 2011. Really? Over a thousand papers a month are published? How can every manuscript be subject to thorough peer review and editorial oversight?
Note that PLoS One has a LOT of Editors. It is also very broad, so thorough review should not be a problem.
PLOS one only judges whether the data are consistent with the conclusions. They do not weigh in on novelty or originality to a large degree. We need something like that somewhere.
There has to be a place to publish negative results as well. Otherwise, people waste their time repeating the same fruitless experiments.
Note that PlosOne is crap, essentially.
Andrulis has published a new paper on PLoS:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078105
Are his endeavors funded by taxpayers (like me) via grants?
Have you read old journals? If the standard for acceptance by a journal is that the submission “benefits science”, much of what has been published over the last hundred years would fail the test. And so would much of what has been published in Science and Nature. There have always been politically motivated agendas. There have always been dull rehashes. There is no shortage of papers that are examples of a scientist wandering confusedly in the intellectual forest or industriously chopping wood in the career forest. Quality has always been diluted. The digital age makes publishing cheaper, faster, easier, and therefore unrestrained by some of the limitations that formerly constrained journals. Unfortunately, the human brain has not kept pace with developments in technology. Nevertheless, everybody must publish. If everybody must, ways will be found that everybody can.
This same explosion has occurred in other kinds of publishing. Back when not everybody could afford a printing press, publishing houses had editors who tried to evaluate the merit (either intellectual or economic) of manuscripts. This did not always result in high-quality output. But it did eliminate most of the obvious dross and it supported some standards of spelling and punctuation. Now that anybody can publish merely by putting stuff up on the internet, a reader has access to gazillions of novels that never would have gotten past the gatekeepers of yore.
This is not necessarily a bad thing. Publishers have rejected good stuff, as attested to by numerous tales of authors having submitted the same manuscript to dozens of publishers before one agreed to take it and the rest was best-seller history. Publishers have printed bad stuff, especially if the client paid up front or was a bankable celebrity. So gatekeepers make mistakes in both directions, if the criterion is true worth. Expanding the channel to allow more good stuff through also allows more bad stuff through. As always, the consumer must exercise some judgment and should not believe everything the salesman says.
I wish that our society could judge based on worth rather than on numbers, but counting is so much easier than reading and understanding. When “evaluating the candidate’s contribution to science” becomes “counting the number of papers published”, it’s no surprise that scientists will figure out ways to increase the only statistic that matters, and no surprise that entrepreneurs will find ways to exploit the need.
Judy, I have looked at old journals and my experience is that the overall level of contribution was higher in the past because there were fewer scientists publishing fewer papers and the general ethos of scientific research was that one generally tackled important problems and only published a paper when one had something of significance to say. I didn’t say that every paper should “benefit science”! I questioned whether the massive proliferation of poorly referreed, little cited journals with poor standards of quality control benefit science.
I’ve done research in what are largely University Biochemistry/Mol Biol/Mol Biophys. departments over the last 25 years. If you look at papers from the 1970’s (say) onwards in the “core” journals of this field (Biochemistry, The Biochemical Journal, BBA, Journal of Biol. Chem., J. Mol. Biol.) the quality of contributions was high. You can inspect issues of the Biochemical J or J Mol Biol from the 1970’s or 80’s and find very high proportions of papers that directly contributed to their subjects – the working out of cellular metabolism and oxidative phosphorylation and the structures of metabolic enzymes in the Biochemical J.; great series of papers that lead to the development of NMR as a method for protein structure determination in J. Mol Biol; the extraordinary developments in molecular genetics and protein allostery in J. Mol. Biol. And so on.
Similarly ground-breaking research is still done nowadays but it certainly isn’t published in the vast outpouring of new weak journals, some of which are little more than vanity publishing exercises. But all this stuff has to be edited and “peer reviewed” and it’s a waste of time.
The old good biological journals were all Zeitschrift fur… and they published years of research in one paper. Who now can read and write in three languages, not me. But they had drawings that became the foundation of biology. The difference is huge.
Chris,
Thought I’d counter you here too. Hopefully, you won’t stray from a discussion of the paper.
“journals, which is a dilution of quality. This may not matter too much to the progression of science (apart from the waste of productive time), but it ‘s a problem at a time when there are considerable efforts to politicise areas of science that have important societal impacts. Loads of low quality journals with low scientific standards makes it much easier to publish some of the self-serving rubbish that is used to construct pretences of “scientific” validity to bolster political agendas (we could give examples), and “sanity checks” would likely not catch these”
Sure, so I do read these journals. I suppose you don’t too, this paper excepted.
“I work in molecular biology/biophysics”
I had forgotten. So, you /should/ recognize the science in Erik’s paper, he describes it in great detail. You don’t, I am guessing, because of the paper’s atypical illustrations and language. Your loss.
“I can’t see how it benefits science at all”
Clearly. I benefits science by unifying many systems that previously had no explanation for how they interrelated. It is to the detriment of many scientists because it solves the overarching problem of describing all these systems — and in a way alien to all scientists. They have every reason to fight for the status quo — and thus disparage this paper — despite grant rates being at 8%. At 8%, as two independent scientists told me, science is dead — and not because of this paper. The paper is a coup de grace, though.
“Perhaps we’re sliding towards the post-modernist idyll whereby anything at all can be published as science,”
Maybe so, but you don’t address the content of the paper or give specific criticisms to rebut. You then digress into material that is off topic.
Don’t pollute this thread with /your/ nonsense. Stay on a discussion, and criticize particular elements of the paper for me to rebut.
The paper is correct in its modeling
I doubt I can convince you in the foreseeable future. With regards to the paper, your lack of intellectual curiosity, mental tenacity, and open mind (a triquantum to use the lexicon of the paper) prevents your proper critical evaluation of any part of the paper. Others seem to be able to do so, albeit not here as far as I can tell.
10,000 manuscripts in 3 years with a 70% acceptance rate. No thank you.
It is hard to imagine the papers were rigorously reviewed with that acceptance rate.
Acceptance rates follow a round of review, so it isn’t “yes/no” it’s “yes/maybe if you do x, y, z/no” and many, many of those articles do that x,y,z. So you would need to know the accepted w/revision rate.
@Pinko Punko Yes, you are correct on that. Thanks for the clarification.
Since in academic circles one’s income depends predominantly on the number of publications, some academics try to achieve it by self-plagiarism as already mentioned here http://www.retractionwatch.com/2012/02/01/no-small-matter-acs-nano-journal-growing-alarmed-by-self-plagiarism/. Others are more inventive – they set up new journals where they publish each other. They form alliances (new constellations) where person (or group) A cites person (or group) B, and of course, person/group B consequently cites person/group A. Please note that A and B are from different institutions, preferably even in different countries for ensuring “impartiality/objectiveness”. In the end both groups achieve the number of published papers which is needed for getting more grants and promotions. That’s how you get over a thousand papers published per month! In most cases such papers never ever will be used for anything else except to be cited from the allied group. Remember that the main goal is not the public usefulness of the papers, but ensuring future income from more tax payers grants.
Conspiracies everywhere!
Um. You do know this phenomenon has been documented, almost-exactly as described by YouKnowBestOfAll, in mathematics? A conspiracy to defraud the scientific research community, yes.
http://www.ams.org/notices/201103/rtx110300434p.pdf
In Adrulis’s own words:
“Publishing in science is fundamental to demonstrating one’s productivity, aptitude, and vision. Without papers, one can’t get grant funding. And without money, one can’t be productive. A catch-22. And without papers and money, one certainly won’t hold a position in academia.”
http://erikandrulis.wordpress.com/2013/09/10/manuscript-accepted/
“Let’s hope funding agencies think our work is important….”
http://erikandrulis.wordpress.com/2013/10/23/manuscript-published/
chris is right…this stuff is logically no good. another reason to read this blog is that there are some really informed comments that explain everything. On the long discussion to the previous entry on the Andrulis paper are two people who wrote in with personal knowledge of Andrulis, who gave telling testimony.
The problem is as weird as the paper itself. My opinion: and only my opinion: This man has what my psychiatry instructor (lo so many yr ago) called a “psychotic lacuna.” Only it’s big enough to drive a truck through. A “psychotic lacuna” is an area or topic (or person) on which the individual has impaired reality testing and/or is delusional. Everything else is fine with the individual. No bipolar disease. No schizophrenia. Just a huge hole in their reality filled with craziness, mistaken but firmly held ideas, delusions, you name it.
Only in this fashion could a respected scientist produce a 105 page paper with 800 references that makes no sense at all, then submit it to twelve publishers.
Once you get the concept of “psychotic lacuna” you can start applying it everywhere. Instances of this phenomenon will just jump out at you. Unfortunately, gyres won’t give you this effect.
This is a nice hypothesis. I think the psychotic lacuna hypothesis should be tested using fMRI, and the results may reveal new ideas about brain function. Once somebody tests the hypothesis, the results could be published in let’s say PLOS One (Ms No 2012-one zillion).
I think I know several people who suffer from psychotic lacuna, perhaps I should recommend them for your fMRI clinical trial……
To my mind the two elements of a publishing model that supports top class scientific research are “good faith” and “quality”. If either of these is bypassed in any particular case the result can be publication of rubbish.
The vast majority of scientists working in decent scientific institutions prepare manuscripts for good journals when they consider they have something valuable to communicate. Manuscripts are submitted in good faith and reviewers review the papers with the presumption of good faith. All the examples of fraudulent behaviour on RetractionWatch are cases where the presumption by editors/reviewers of good faith on the part of the author was misplaced.
It’s much rarer to find examples of bad faith both on the part of the author and the editor, but this creepy occurrence does happen where misguided individuals consider their political views trump real world evidence. Climate science seems particularly susceptible to this (see e.g. the retraction of a paper by Edward Wegman written as part of a campaign to smear a climate scientist http://www.retractionwatch.com/2011/05/17/controversial-paper-critiquing-climate-change-science-set-to-be-retracted-because-of-plagiarism/#more-2628 ).
In several of these cases, and also the Andrulis one, publishers have apologized and editorial board members have resigned. I actually don’t have a problem with Andrulis’s paper – I don’t believe it was submitted in bad faith nor that it was accepted due to underhand behaviour by editors. In this case the resignations relate to standards of quality on the part of members of the editorial board.
Quality in science should pervade the entire system. Scientists should have standards that are reflected in the quality of their manuscripts (a most important element of peer review is “self peer review”). Reviewers and editors should have standards of quality with respect to their journal. My concern is that several of the new publishing models significantly dilute quality in scientific publishing and make it easier for those that attempt to publish stuff in “bad faith” (e.g. to support creepy agendas).
Perhaps this doesn’t matter, since good quality science will continue to be done by scientists with high standards of quality and good faith, and will continue to be published in decent journals. I’m genuinely curious about how all this will play out (i.e. the realignment of the models of scientific publishing, if that’s what we are observing!). Whatever publishing models we have in 10, 20 or 30 years, they should promote quality and minimize bad faith efforts to publish self-serving rubbish (which I reemphasise doesn’t apply to Andrulis’s paper since I’m sure it was written in good faith.)
Well said, sir.
Ditto
OhMyGod–fMRI of psychotic lacunae! Believe you me, my professor never anticipated that. The lacuna is a description of a phenomenon; I can’t get my head around it as a hypothesis. But I knew you were being sarcastic right away. Sure I did.
The lacuna “hypothesis” would validate the estimate chris makes of Andrulis’ good faith: he really, really believes in what he’s writing. Since fMRI is supposed to detect lies (supposed to, anyway) I think the scan would show “truth.”
More importantly, Andrulis doesn’t make any testable predictions (unfortunately, this prompts a comparison to string theory) or produce any better explanations of anything (although he claims to.)
I tried to read the paper, really tried; but the first sentence struck me as inaccurate: there is, to me, no mystery as to how life abides by the second law of thermodynamics while becoming more complex over time. Life only develops in open systems; if stuck in a closed system, life eventually ebbs away. The fate of a closed system is death: the goldfish winds up floating upside down. Right? Pretty basic stuff, but Andrulis calls it a “mystery.”
The more I tried to read the paper, the stupider I felt.
On another subject, as I loosely associate my way across the universe:
I just got through a web site that touts a “petition” against global warming; it presents a 12 page paper that supposedly refutes global warming claims. It looks good, superficially, but I noticed it was published in a medical journal (Journal of American Physicians and Surgeons) and I thought, if it’s about climate change, what’s it doing in a journal about medicine (which, as far as I know, has no direct relationship to meteorology or atmosphere science)?? Perhaps the editors of the journal could explain how they reviewed the paper with their special expertise (sarcasm intended.)
Conrad, I think a quick perusal of the wikipedia page on the Journal of American Physicians and Surgeons will explain a lot:
http://en.wikipedia.org/wiki/Association_of_American_Physicians_and_Surgeons#Journal_of_American_Physicians_and_Surgeons
Yes that’s interesting Conrad (i.e. the J. Am. Phys. Surg. and it’s nonsense on climate change). But JAPS isn’t a science journal; it seems to be a mouthpiece for right wing opinionating (I’ve listed the book review titles from one of its issues below which is quite enlightening I think!).
Unfortunately that’s part of the problem with respect to “bad faith” of the extreme form, that attempts to insinuate “sciencey-sounding” stuff into either what sound like “science journals” or (even better) into science journals themselves. The stuff, of course, being rubbish that supports particular political viewpoints.
Another example I came across a few years ago is the “Regent University Law Review”. Just the place to find “papers” attempting to trash the science that informs us on the genetic contribution to homosexuality (which is quite significant it seems)! It’s odd that a “University” “Law Review” journal would have papers on this, but it turns out that “Regent University” is a fundamentalist pseudochristian organizations, one of the pillers of the “faith” being that homosexuality is a sin and therefore must be a “choice”, and so it’s convenient to construct a pretence of “sciency-sounding” stuff.that seems to oppose the science on this rather interesting subject.
Sadly science is very dangerous to many creepy vested interests since it does attempt to find out what is true, even if its truths are often rather proximal rather than profound. So quite a lot of effort goes into attempting to trash the science on topics of sociopolitical relevance. Up until quite recently this was mostly done (I think) through the efforts of right wing “think tanks” and corporate lobbyists, but nowadays considerable efforts are made to sneak self-serving junk into the lower echelons of the scientific literature to bolster weak ideas with a veneer of “scientific respectability”.
Here’s the book reviews of one of the issues of JAPS (not very “medical” in most cases!):
Book Review:
Sapira’s Art & Science Of Bedside Diagnosis, 4th ed.
(Jane M. Orient, M.D.)#
Reviewed by Shafeek Shamsudeen, M.B.B.S.
ARGUING WITH IDIOTS: How To Stop Small Minds And Big
Government (Glenn Beck)
Reviewed Chester C. Danehower, M.D.
Never Enough: America’s Limitless Welfare State
(William Voegeli)
Reviewed by Sally Christman
Guilty: Liberal “Victims” And Their Assault On America
(Ann Coulter)
Reviewed by Jerome C. Arnett, Jr., M.D.
United In Hate: The Left’s Romance With Tyranny And Terror
(Jamie Glazov)
Reviewed by Jerome C. Arnett, Jr., M.D.
Callous Disregard: Autism and Vaccines – the Truth Behind a
Tradgedy (Andrew J.Wakefield)
Reviewed by Jane M. Orient, M.D.
I work with surgeons, don’t expect logical thinking from them:)
Talk about ways to waste your time. I have found the ultimate. Try, just try to read this paper by Andrulis.
It has been three hours and I’ve gotten to page 30. So far, I find such remarkable items as the assertion that water has memory, the Earth formed by expansion rather than accretion, and solar output is related to earthquake activity. I have had to look up words such as “quale” only to find that they added nothing to the sentence Andrulis used them in.
Then there are the assertions that his “theory” explains the particle-wave duality, the nature of leptons (they are slowed-down photons), the existence of water, the presence of oxygen and carbon dioxide in the atmosphere(with a shout-out to Keeling), the origin of the Solar System, and so on up to and including man, I suspect, I just haven’t gotten that far. The “theory” is, literally, some hand-waving with mostly chemically-derived equations and a series of assertions that are either so elementary as to be useless or highly improbable. I kid you not.
This is junk of the worst sort, I do honestly believe.
I’ve only read a third of it, yet I am already convinced that this guy dropped acid, saw the fact that there are spirals everywhere in nature, and went, “ooh, pretty…” Then when he recovered, two days later, all he could remember was that he had had this transcendental experience and that somehow it was related to spirals. This is a perfect example of Conrad’s first maxum: “Obsessive-compulsive individuals should not take LSD.”
I would like to extend a grateful word of thanks to the commenters who pointed me back to the indispensable W*k*p*d*. The stated reason on the denier website for publishing in JAPS was that they were generous with the copyright and allowed them to republish the paper without limits in its original, really authentic looking, journal-like appearance format. Which really had me fooled, because it looks just like the NEJM. Even the graphs look real.
The assertion that water has memory is the “explanation” used by practitioners of homeopathy. Allegedly water “remembers” what was dissolved in it, so you can dilute the solution until there are none of the original solute particles left, and it will still have the same medicinal properties as the original solution.
Even better, they believe that the MORE you dilute the solution, the more effective it is!
This second point was easily refuted by a group of people in the UK who took “overdoses” of homeopathic remedies two years ago, e.g. http://www.quackometer.net/blog/2010/01/1023-my-personal-homeopathic-overdose.html
Anyway… my congratulations and commiserations for getting as far as page 63 (you poor thing), and I hope your brain has not fallen out of your head.
That’s maxim, not “maxum”, which has been bothering me since yesterday.
And of course, “denier” means “one who denies”, not the weight of a fabric, nor an obsolete coin of France.
This morning I am again entertaining the possibility of a “Sokal” based on the unnecessarily dense and obfuscating nature of the text; common phrases have been replaced with obscure equivalents in many places.
For example, “throughout the cosmic and tellurian realms.” instead of “everywhere.”
In addition, there is the paragraph which states: “The gyromodel is incommensurable with prior and existing theories.”, “this theory challenges…patience.”, and “this manuscript is dense.” (Why does he have to wait until page eight to tell us that it is “dense”? If you’ve made it this far, you know it’s denser than depleted uranium already.)
The same paragraph redefines Ockham’s (Occam’s) Razor in a somewhat idiosyncratic fashion that separates it from its essential test: “Ockham’s Razor[52]–the scientific principle that things behave or are connected in the simplest and most economical fashion” followed by, he says, a separate criterion: “…the ability to explain the available scientific data.” I thought that Occam’s Razor says, “the simplest theory that connects all the facts is the most likely to the the correct one.” Silly me.
(Sokal, A. 1996. “Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity”, Social Text, 46/47: 217-52.) (By coincidence, I discovered the exact reference in the latest issue of “Skeptical Inquirer” which came in the mail yesterday.)
No, I never did(to the best of my knowledge)(though I did have some curious experiences during services at the local Unitarian Church), but some of my friends (who never graduated) did. A sad waste of human potential.
“Twas brillig, and the slithey toves
Did gyre and gymbal in the wabes;
All mimsy were the borogroves,
And the mome raths outgrabe.”
It’s a Sokal.
From page 63: “This theory proves that the gyre is the long-sought invisible and inevitable metaphysical element of the universe, fulfilling a philosophical goal that dates to ancient Greece [795].”
The paper is genuine. I know because I have read it and previous versions — plus and enormity of additional, related material
The paper is heterodox and VERY dense, so naturally most people will take the intellectually lazy route and just mock it.
I have spent several YEARS in conversations with Erik about the paper (and related material). He has made corrections and revisions and has made coherent arguments.
I have advanced degrees in science, and those, coupled with my many discussions with Erik give me a distinct advantage in understanding this paper.
To those who think, “This is a perfect example of Conrad’s first maxum: “Obsessive-compulsive individuals should not take LSD.” You don’t know Erik. I do. He is in complete control of his mental faculties.
“chris is right…this stuff is logically no good” Wrong. You and he just lack the discipline to do the HARD mental labor of learning something radically new. You can’t learn Mandarin overnight, and you can’t understand this paper without VERY serious study and critical thinking.
If any serious reader wants to understand this paper, he or she will have to read it several times — if only to get a notion of what it is about.
The radically new can be extremely hard to understand, you see.
Far easier to dismiss something radically new then to try to understand it.
Also, for your consideration: http://milesmathis.com/erik.pdf
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.
nettle, my comments identifying very specific examples of illogic were described here:
http://www.retractionwatch.com/2012/01/28/case-western-explains-why-it-withdrew-press-release-about-andrulis-origin-of-life-paper/#comment-9679
perhaps you might want to address those specifically on that thread.
Otherwise you seem to be playing the “I can understand Andrulis’s paper because I have advanced degrees in science” ploy. But I (and lots of others too) have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.). Of course that doesn’t rule out the possibility that I can’t recognize paradigm-shifting brilliance when I see it, but it’s usually the case that remarkable insights in molecular life sciences are amenable to rather simple explanations (by far the hardest part of obtaining astonishing insight in molecular biology in its broadest sense is in overcoming experimental/technical issues).
So Andrulis’ states (using straw-man, and non-sequitur type illogic) in his introduction : “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].”
Yor task, nettle, (since you understand Andrulis’ paper very well), is to explain to us in simple terms how Andrulis’s hypothesis “resolves precisely how the translation apparatus, genetic code, and biometabolic pathways evolved”.
Chris,
Otherwise you seem to be playing the “I can understand Andrulis’s paper because I have advanced degrees in science” ploy. But I (and lots of others too) have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.). Of course that doesn’t rule out the possibility that I can’t recognize paradigm-shifting brilliance when I see it, but it’s usually the case that remarkable insights in molecular life sciences are amenable to rather simple explanations (by far the hardest part of obtaining astonishing insight in molecular biology in its broadest sense is in overcoming experimental/technical issues).
So Andrulis’ states (using straw-man, and non-sequitur type illogic) in his introduction : “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].”
Yor task, nettle, (since you understand Andrulis’ paper very well), is to explain to us in simple terms how Andrulis’s hypothesis “resolves precisely how the translation apparatus, genetic code, and biometabolic pathways evolved”.
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.
I can see that Andrulis has some supporters.
Let me add my two cents from the point of view of a relative layman:
I think that Andrulis obscures his meaning with his use of rare and difficult to recognize words and phrases. I think that his notation is even more obscure. I think that he makes many, many assertions without logically arguing for their validity.
I am especially unhappy with certain passages, such as the one in which he asserts that water has memory (this is an assumption of homeopathy advocates used to explain “how it works”.) Another passage (page eight, “caveats”) that I have trouble with is the one in which he states that his “theory” has to satisfy two criteria. The first criterion is “Ockham’s razor” (as he defines it: “the simplest theory”) and the second criterion is merely part of Occam’s razor as I define it (“that fits all the facts”). This doesn’t make sense to me and doesn’t fit with his apparent intelligence level.
There is nothing wrong with using “gyres” as allegories (not “models”) for the state of affairs in every physical system. I don’t see the logic or usefulness of his assertions that “gyres” “explain” everything better than current theories or speculations do.
Finally, I can see that my feeble attempts at humor have fallen flat. My mention of an “acid trip” was intended to speculate as to why Andrulis is obsessed with spirals, not claim that he has brain damage. Those of you who have not observed “acid trips” are not familiar with the intense anxiety experienced by those with highly ordered personalities.
There is no question in my mind that Andrulis is a brilliant man whose ability to reason is unimpaired by such mental disorders as schizophrenia, bipolar disorder, or drug use.
My problem is with the assertion that his “gyre” “model” goes anywhere, makes any testable predictions, or contributes to deepening our understanding of physical phenomena. I think that his supporters have the unenviable task of trying to show some way in which his assertions lead to new areas of research, make predictions, or clarify anything. Unfortunately, Andrulis’ paper obfuscates rather than clarifies.
You write: “My problem is with the assertion that his ‘gyre’ ‘model’… makes any testable predictions….”
Agreed, and the matter is that simple.
Andrulis dismisses your observation (which has been made by many) as nefarious, denying its relevance:
“Despite the personal attacks, condemnation, ridicule, rejection, and suppression, I’m still here, singing my song. And I’m still waiting for a single colleague to… discredit… or otherwise dismantle the theory.”
http://erikandrulis.wordpress.com/about/theory-of-life-2/controversy-and-suppression/
Of course, making predictions is what demarcates science from non-science; at least as the word ‘science’ is used by Karl Popper, by the U.S. Supreme Court (which defers to Popper in Daubert v. Merrell Dow Pharmaceuticals, 509 U.S. 579), and by institutions speaking the same language as Popper and the Supreme Court.
At times he promises that predictions are forthcoming, but he never delivers:
“As I have been made abundantly aware, I failed to give a substantial set of predictions in my paper. Let me just take this opportunity to say that I plan on offering specific predictions—deduced from that theory—in later posts.”
http://erikandrulis.wordpress.com/2013/09/30/science-and-religion-share-a-secret-the-provocative-meaning-of-theory/
At other times, he attempts to construe ‘falsifiability’ (i.e., testability; i.e., making predictions) as a weakness — one not suffered by his paper because his paper is supposedly “Truth”:
“Truth is, well, unfalsifiable.”
http://erikandrulis.wordpress.com/2013/10/15/mutiny-on-the-scientific-bounty/
The milesmathis link, to those who don’t click on links, is an admitted “hatchet job” of a “hatchet job.” It begins with the assertion that a “freelance” journalist who wrote a hatchet job on Andrulis is working for the government. It also claims that something Andrulis wrote is dangerous (to the gov’t or to some other vested interest.) I wasn’t able to discern anything remotely dangerous in the paper. There are no logical arguments in this link, and the author states that he hasn’t read the Andrulis paper. I’m afraid that nothing in this link adds anything to our understanding of this paper. You’ve got to read the paper, for starters.
Yes, it is hard to understand, and so is Mandarin. But Chinese is much easier to understand than this paper.
Conrad,.
“I think that Andrulis obscures his meaning with his use of rare and difficult to recognize words and phrases. I think that his notation is even more obscure. I think that he makes many, many assertions without logically arguing for their validity.”
I agree with your first point; Erik has a robust vocabulary and knowledge of esoteric concepts within and without of scientific borders. I guess that comes from reading over 1000 peer-reviewed papers and 500 non-fiction books as part of his theoretical research into the problem of life.
His notation is not so obscure to me, as I am trained in organic and physical chemistry. I feel your pain, though, as it took me a while to figure chemical notation out myself and hence flow diagrams may be obscure to he who is not a chemist.
As to your problem with his assertions: You say “many, many,” yet that there is no disclosure of what they are. Please identify one assertion you have a problem with and perhaps I can address it. Even without a response, I would say that his assertions are not validated by dint of “logically arguing.” Erik’s assertions are validated by economical fitting (his words) of the available data, defining the evolutionary relationships of phenomena and systems, and deducing modes of operation. He even says this on p. 17.
“I am especially unhappy with certain passages, such as the one in which he asserts that water has memory (this is an assumption of homeopathy advocates used to explain “how it works”.)”
Heh. Each person has preferences and pleasures; the world would be a boring place is everyone had the same ones. So, I respect and cotton to your displeasure; heck, I’m not too fond of Erik’s assertion about water memory either. However, a revolutionary theory is not about what is comfortable, pleasurable, fashionable, or what is acceptable to the mind. It is the exact opposite. By definition, a revolutionary challenges the status quo and shatters the intellectual hubris of man. And, I submit, no man enjoys such a shock; it’s like the Emperor being stripped of clothes that he was never wearing. Hence, the caterwauling and anger towards Erik. I believe that his core model provides as plausible an explanation for universal learning and memory that I have ever observed. Perhaps you are aware of other explanations for these unsolved features of living systems?
“Another passage (page eight, “caveats”) that I have trouble with is the one in which he states that his “theory” has to satisfy two criteria. The first criterion is “Ockham’s razor” (as he defines it: “the simplest theory”) and the second criterion is merely part of Occam’s razor as I define it (“that fits all the facts”). This doesn’t make sense to me and doesn’t fit with his apparent intelligence level.”
Well, you may be right here. But I think where you use the word “fit,” Erik uses the word “explain.” I think you would agree that just because a model “fits” facts (let’s say, that all organic matter is explained in one system model named the carbogyre), this does not necessarily mean that the carbogyre would necessarily “explain” how organic matter emerged during the evolution of the universe, exists on comets and asteroids and in Earth’s crust and mantle, and cycles through biogeochemical systems. I think equating fitting with explanation is a stretch, but, maybe it’s just a semantic argument.
“There is nothing wrong with using “gyres” as allegories (not “models”) for the state of affairs in every physical system.”
I’m confused. Why can a gyre not be a “model?” Call it “allegory,” “archetype,” “visual representation,” “exemplar,” “logical superfluidity,” “illicit attempt at explanation,” “convenient fiction,” call it what you will. I think “model” is concise, understandable, and definitionally consistent. Here’s the definition of model from my computer’s dictionary: “a three-dimensional representation of a person or thing or of a proposed structure, typically on a smaller scale than the original.” Seems to work quite well for me.
(I skipped over some parts of your response…)
“I don’t see the logic or usefulness of his assertions that “gyres” “explain” everything better than current theories or speculations do….My problem is with the assertion that his “gyre” “model” goes anywhere, makes any testable predictions, or contributes to deepening our understanding of physical phenomena. I think that his supporters have the unenviable task of trying to show some way in which his assertions lead to new areas of research, make predictions, or clarify anything. Unfortunately, Andrulis’ paper obfuscates rather than clarifies.”
Again, all current theories are ad hoc (see my response in the above post, I can give many more examples of the ad hoc nature of current theories). The goal of a theorist is to unify. Look at the last century of quantum mechanics and general relativity: the goal here is to unify, to find a theory of quantum gravity. Extending this into other realms, the theorist wants to unify all macrocosmic and microcosmic phenomena and to unify evolutionary and present-day phenomena.
Turning to your point re: new areas of research, predictions, clarifications. Here’s a curve ball for ya: Science had an evolutionary beginning, some argue with Galilei, some argue in ancient Greece. Does science have an end? That is, will science never reach a destination of knowledge, or is ever forced to create new areas of research? Will science ever find a theory that proves that natural systems have both predictable and unpredictable qualities? Finally, I am not sure how the paper obfuscates, because you never provide a specific example. How about one?
Even in the absence of such an example, isn’t a goal of science to arrive at the correct theory? And wouldn’t that theory, by definition, be the true depiction of how things work and are? Several philosophers and scientists have predicted the existence of such a theory — a theory that is complete and consistent, including an explanation of itself within itself. How would one know if Erik’s offering were or were not that final theory?
I’m not sure if you noticed, but one last thing I should point out. Erik’s theory models the movement of information, energy, and matter (what he calls “IEM” – I don’t like this acronym, to be honest, it’s too silly) through a cell mass. Since I am a mass of cells, DNA, protein, RNA, lipids, sugars, water, and elements, his theory models me. He is also modeling every and any other cell mass, with one unified theory of life. His theory models you. You are alive, aren’t you?
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)
Nettle, I explained the illogic of that quote in the post to which I linked above. Simply put, the “RNA world” theory is a theory that addresses the early stages of life evolution (i.e. that early RNA molecules played the role of both biological catalysts and carriers of genetic information). The central dogma is a (partial) description of the flow of genetic information in extant organisms in a 4.6 billion year old Earth. It’s a strawman argument and a non-sequitur to insinuate that the “RNA world” theory should explain observations pertaining after 4 billion years of evolution. That illogic ignores the entire contingent nature of evolution over virtually the entire history of the earth. The “RNA world” doesn’t explain the origin of the eukaryote (engulfing of primitive cells to produce mitochondria in extant animal cells), but that also doesn’t make it a deficient theory about life origins; you’d have to be a brutal and committed determinist to consider that everything we see in the natural world around us was effectively pre-determined in the early stages of life’s origins more than 4 billion years ago.
In fact there’s a good bit of evidence in support of the “RNA world” and it’s also a testable theory. Together with the fact that the “RNA world” theory and its evidence can be stated and described very clearly in language that we all use to communicate with each other, the “RNA world” theory is an excellent theory, and it’s sad that Andrulis feels it appropriate to trash it so as to clear a little elbow room for his own effort.
As for your description of Andrulis’s “explanation” for the precise explanation for translation apparatus, genetic code, and biometabolic pathways :
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…...and etc.
That’s nonsense though isn’t it nettles? Systems don’t “organize” in units of three”. Some classes of systems (proteins) organize in units of: one (myoglobin); two (dimeric coiled-coil proteins; transcription factors; glycophorin); trimers (collagen); tetramers (hemoglobin; pyruvate kinase); hexamers (hsp90); heptamers (some chaperonins) and many other discrete states of organization.
The beauty of proper scientific description and theory is that one can understand these different levels of self-organization in terms of simple knowledge of molecular structure and ideas about shape, electrostatics, and hydrophobicity that governs intermolecular interactions. This very hard-won knowledge 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.
Set aside for the moment that the paper itself does appear to either be an attempt to “Sokal” the journal, or sad evidence of a deteriorating mind. The real crime for me is that Case allowed a release to be issued on this at all.
To begin with, the release was written by a med center PR staffer who, based on her bio, has agency experience but no science-writing experience, and therefore can’t expect to be able to evaluate the news potential of a research paper. This is in spite of the fact that they have a decent science writer on staff in the media office.
The fact that a paper is in a peer-reviewed journal is only the first hurdle that needs to be cleared in determining whether to do a release on a study. An institutional science writer needs to then evaluate whether a story would have broad interest and news value. If not, don’t do a release! In some shops, the writers are just told what to write — they have no role in review. Those are the shops that do releases on request, regardless of the quality of the science or the impact on the public. Those cases serve only to sooth egos or make the boss look good, they do nothing to support science or the public’s understanding of it!
Institutional science writers need to have both the skills and knowledge, as well as the guts and integrity, to look at such papers and tactfully refuse. Sadly, a good many media relations shops are set up to take orders but not to make decisions on quality control. This is what happens when science communications practices are dictated from above rather than evolve from the expertise of the staff science writer. The end result is that, in those cases, the university and the media relations staff are seen as naive at best, and incompetent at worst.
And the response from the senior director of marketing and communications is extremely lame. Clearly they had no evaluative process to determine which research warrants attention by their staff or coverage by the media, and never considered having one. Good communications shops know specifically why they’re doing what they do, what the expected outcome would be, and when to say “no” to proposed stories that shouldn’t be done. At an institution the size of Case, with its vast array of research underway, this should never have happened.
While we can all sympathize with the apparently sad possibility that the author has serious problems, the episode should allow no sympathy for the institution and its media operation.
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.
Earle,
clearly you have not only NOT read the paper but also NOT read my posts..
You didn’t post ANYTHING that shows you understand ANYTHING about either.
“While we can all sympathize with the apparently sad possibility that the author has serious problems”
I know the author and have for years. The only problem he has is that people like you and Chris have neither the intellectual curiosity nor the mental tenacity to try to learn a radically new theory. Instead you dismiss quickly that which you didn’t even read. What insipidness!
You show indifference toward Erik even though his paper, while dense, is clearly and coherently written on a matter of great relevance to modern science. Disrespect!
I challenge you to prove me wrong. Explain to me one fallacy in the paper. Just one.
Too tough for you?
Ok. I understand. The paper is hard to read.
Softball: show me one fallacy in my defenses of the paper.
My suspicion is that you won’t because you can’t. Just a hunch.
Instead, I think you will follow in Chris’s footsteps (well tread ground) and not address what I said at all.
Maybe you will throw out something totally unrelated to what is in the paper or in my responses.
I have already given generous defenses of Erik’s paper. If you are out of your depth in comprehendingjust my responses, then don’t bother to reply. You will just make yourself look like Chris, who has already spent enough effort making himself look foolish.
I sympathize. with the apparently sad possibility that that you have serious problems.
I sincerely wish you well.
Nettle:
Yes, I have read the paper. I find it filled with gibberish. Any time an author needs to provide a new vocabulary for readers to understand a paper, something is seriously wrong. That’s based on four decades of reading and translating scientific papers.
No, I haven’t read your posts. I tried to but found them ponderous and far from unemotional, as comments should be.
My point, in my comment, took issue, not with the content of the paper, but with the institution’s actions in first issuing a news release promoting the finding — a release that is embarrassingly devoid of understandable fact — and then removing that release when the reaction to the paper was hostile.
My observation was that the institution, in spite of its reputation as a strong research university, failed in its responsibility to provide the public with understandable information about the research in question, and clearly showed systematic errors in their decision-making process about which research they decide to communicate about.
When members of a journal’s board choose to resign over a paper’s publication, and when the editor offers what appears to be a substantially questionable explanation/excuse for why the paper was published, then something is wrong with the submitted paper.
Feel free to question my mental prowess if it will make you feel superior in your own mind. I could care less what your opinion could be, given the troll-like attacks you make on those with whom you disagree.
Earle,
“Any time an author needs to provide a new vocabulary for readers to understand a paper, something is seriously wrong.”
Based on that statement, I presume you would, upon reading papers on pharmceuticals (and not being in the pharmaceutical industry), figure something is seriously wrong about the pharmaceutical industry — because its vocabulary is almost entirely based on the generation of new words. For example, Celebrex. Hunh? Where did that word come from. Ask any physician about his repertoire of drugs and he will rattle off pure gibberish. Or do you disagree?
“That’s based on four decades of reading and translating scientific papers.”
And there is your problem. You have spend forty years of your life understanding and studying the present paradigm You have way too much invested in “what we have now” to put in the effort to what we could have that is radically different.
Einstein’s theory of general relativity met with a decade or so of resistance. Why? Because it was radically new and most scientists (with very notable exceptions) had far too much invested in the status quo to study and learn such “gibberish.” Is the theory of general relativity gibberish? It all depends on your point of view.
“No, I haven’t read your posts. I tried to but found them ponderous and far from unemotional, as comments should be.” Your statement is demonstrably false as my first two posts were indeed unemotional. I find strange tha you find my second comment ponderous, as I am largely dealing with pretty basic biochemistry — and not some arcana.
But, when people react with dismissiveness of something that has significance, I should not be frustrated but respond as an automaton? That seems silly, but ok.
After forty years you appear not to realize that ALL of science is ponderous. Pick up a copy of JACS and give an article from it to a undergrad chemistry major. There is no way they will understand it.
“My observation was that the institution, in spite of its reputation as a strong research university, failed in its responsibility to provide the public with understandable information about the research in question, and clearly showed systematic errors in their decision-making process about which research they decide to communicate about.”
Do you know WHY the retraction occurred? Did you think for a moment that if CWRU made an error in putting out the publicity, they may have made an error in retracting it? Possible?
Definite! CWRU was bullied by two physicists who were “embarrassed” (e.g. threatened) by the paper. Why the heck should they care? Well, for starters, they saw a molecular biologist not just trespassing on their sacred ground, but audaciously slaughtering one of their sacred cows.
For instance that the photon resides within the electron. But we KNOW this arrangement to be true. Heck, when an electron and a position “annihilate” they release, whaddya know, photons. Photons are not nothing, so this occurance is not annihilation. For a molecular biologist to be even mentioning the properties of the electron in a fashion alien to physicists is simply unacceptable in the ivory tower.
“I could care less what your opinion could be” It is apparent that my opinion is not the only idea about which you could care less. A radically new theory that is hard to grasp seems to be one two. Suspicion about political games at CWRU’s publicity office is another one.
“the troll-like attacks you make on those with whom you disagree.” Sorry if you feel that way. I have offered serious defenses with the sincere goal of explaining parts of the paper. If you feel I have just been rambling than 1. I have not made myself clear 2. you have not cared to studiously read what I say, or 3. both.
Anyway, I am the lonesome defender of a radically new theory, which, while full of neologisms, unifies all sorts of ad hoc theories (what does snRNA have to do with a vacuole?). Necessarily such a theory such be impenetrable to those who cling to our present hodgepodge of science “that just works” — until it doesn’t.
As I said before . . . tiresome and ponderous.
Wow. Oh Wow. I really did start reading the Andrulis paper again this morning. Trying to make sense out of it. Examples of unsupported assertions. Where do I begin. I’ll be right back.
OK. An example of an unsupported assertion:
“The gyromodel clarifies how a quantum has both wave and particle qualities: as one particle
oscillates between two extreme gyrostates, its gyratory path creates an undulating pattern that is
detected as a wave. When many particles oscillate around the same or different singularities, they
create constructive or destructive waveforms. When the gyromodel is considered as a gyre, it manifests
classical wave characteristics: wavelength, amplitude, and frequency. When considered as a quantum,
it exhibits particle characteristics: translational, rotational, and vibrational movement. The gyromodel
thus accounts for particle spin.”
Could you expand on this a little bit? It seems to me that this gyre quantum, although it can create an undulating pattern and you can consider it as a gyre or as a quantum with consequent wave and particle characteristics, is …uh…(system crashes)…
Contrast a NTP and a NDP. One NXP can’t be NTP and NDP at the same time.
The deposition of the orthophosphate puts NXP into a high energy state.
The eviction of the orthophosphate put NXP into a low energy state.
So, just as the earth cycles around the sun with an aphelion and a perihelion, so does the NXP, a particle, oscillate around the orthophophate which it absorbs and ejects — with high energy states (e.g. ATP) and low energy state (e.g. ADP).
Thus, through the oscillation of these states we have a wave (or if you prefer, cycle) — the gyre.
The gyre maps the space-time path of the individual particle as it oscillates between the two states.
The quantum captures the entire phenomenon — i.e. the quantum is a shorthand notation for compressing the biological (or any) process — both the wave and the particle. Thus, the quantum is just a way of representing the two states and you know that a process that has already been described in the literature (NTPNDP+P), but you don’t know which state the NXP is in until you observe it.
This arrangement is exactly like Schroedingers’ cat. We don’t know if its dead or alive until we observe it.
As a wave, the NXP has a time period (wavelength) for the cycle, an amplitude (set by the high and low energy states), and it has a frequency (as wavelength and frequency are directly related).
As a particle, the NXP necessarily is moving through space and time, has a rotation (as does every molecule), and vibrates and stretches (just as every molecule).
By the way, the standard method for measuring the stretching and vibrating of bonds is IR (infrared spectrometers).
more gibberish. ATP and ADP don’t “oscillate between two states”. It’s foolish and ignorant to consider this in any way akin to quantum uncertainty(Schroedinger’s cat). ATP and ADP are discrete molecules; you can buy them seperately as sodium salts from Sigma, and measure them in working living muscle using in vivo NMR.
as for “As a wave, the NXP has a time period (wavelength) for the cycle…”, I think you’ll find that the time period for a cycle is its frequency (or inverse frequency). Wavelength is a distance.
I do hope Dr. Andrulis’ style of incoherent postulation isn’t catching!
(NTPNDP+P) should read NTP goes to NDP+P and vice-versa.
I had a double headed arrow (which I try to produce below)
but for some reason it did not post.
Jeez…can’t you guys see that nettle and Andrulis are one in the same?
Physician Scientist,
though I am flattered by your comment. It’s not true.
I do know Erik well, and have for years, but I am not he.
I have had years to read previous versions of this paper — and an enormous amount of supporting material — hence my understanding and defense of the paper.
So, your mistake is understandable.
Believe what you will.
Perhaps you are Angela Merkel. I don’t know and I don’t intend to find out — because it doesn’t matter.
0. My system crashed because of a stack overflow, a result of a function calling itself too many times. So Andrulis’ style of postulation IS contagious.
1. I don’t see how the ADP/ATP system can be modeled as a gyre: orthophosphate doesn’t make a good center. It doesn’t attract ADP or ATP, it doesn’t impose any sort of regular cycle on the system, there is no definite periodicity to the transition from ADP to ATP, and ATP/ADP is much larger than orthophosphate. As chris points out, ADP is stable indefinitely, even if it is in solution with orthophosphate. It takes energy and a catalyst to make ATP at an appreciable rate.
If you want to make a general model that would include/fit/explain the ADP+PO=ATP system, you need something that represents the enzymes that catalyze the transformation and something that represents the energy input/output involved. A gyre doesn’t work for me.
A model is “a three dimensional representation of a person, building, or other thing that is smaller than the original but readily recognizable as what it represents.” In more general terms, a model represents a physical process in such a way that it captures the essentials of the process in an easily recognizable, abbreviated form.
Water going down the drain in a bathtub is a good model of matter falling into a black hole. It is not a good model of the ADP/ATP system. Unless you (nettle) can explain it more clearly.
2. The fact that the vast majority of people can’t understand the Andrulis paper doesn’t make everybody stupid. It indicates that Andrulis is having a hard time explaining what he is thinking.
3. I tentatively favor the hypothesis that nettle is Andrulis. Otherwise, how would he know that Andrulis has read 1,000 journal articles and 500 nonfiction books? And why hasn’t Andrulis in person come forward to defend himself?? As a corollary, would nettle please state just one or two of the scientific works that directly support Andrulis’ paper? (A particularly useful part of the “enormous amount of supporting material” that you mentioned, one that I can look up and read at least somewhat easily.)
4. I was trying not to talk about the assertion that water has memory, but I can’t help it. This assertion has been used by advocates of homeopathy to explain how it works. Unfortunately, homeopathy does NOT work, so the assertion is unnecessary. I know that this is trivial to those not in the field of medicine, but it is extremely annoying to those who are, especially when we see homeopathic remedies advertised as if they really worked. As far as I know, the assertion that water has memory has no other application, so mentioning it, even in passing, tends to impair my sense that the author has any sense.
Conrad,
1. Orthophosphate is the obvious center. It does attract ADP and repel from ATP. Good grief man. ATP and ADP are constantly cycling. For example, when I lift a heavy weight, I convert an enormous amount ATP to ADP + P. That ATP is regenerated when my cells break down glucose to reform the ATP. There we have a cycle. ADP is therefore not stable in a living organism.
A gyre may not work for you, but that does not make it an incorrect model. We most certainly have an oscillation, yes involving enzymes, but an oscillation nonetheless. For theoretical tidyness Erik has omitted the enzymes in the process but he is not denying their existence. The point is to focus on the molecules doing the oscillating. One could certainly include all sorts of additional details such as enzymes into the gyre model, but the paper is already 65 pages, not counting the references. You have to stop at some level of detail.
“Water going down the drain in a bathtub is a good model of matter falling into a black hole. It is not a good model of the ADP/ATP system. Unless you (nettle) can explain it more clearly.”
I will try. If you consider any oscillation between two states, you have a high energy state and a low energy state. A gyre has a high point and a low point, and oscillates between them. NXP has a high point and a low point, and oscillates between them. The focus of the oscillation with NXP is the orthophosphate which shuttles back and forth. You convert ATP to ADP + P. Then, you convert ADP + P back to ATP. Clearly, this behavior is a wave. I go to the gym, I convert mucho ATP to ADP + P. I rest, and eat, and convert ADP + P to ATP. This oscillation has a regularity based on the frequency of my visits to a gym. The combined gyres of all this conversion has a frequency and amplitude based on the frequency I go to the gym and the quantity of weight lifting that I do. Back and forth.
Theoretically, we can measure the quantity of ATP that I convert to ADP + P based on the amount of weight lifting that I did. Too, we can measure the quantity of ADP + P I converted back based on 1. knowing how much ADP + P I produced, 2. knowing that I have an adequate diet. We now know the amplitude of ATP/ADP+P wave.
Hence, for each AXP we have a gyre (or wave if you prefer), with a frequency and an amplitude. Where the AXP is depends on whether it is awaiting use (high energy state, pre-workout), is being used (transfering from high to low energy state, workout), or has been used (low energy state, post workout)..’
We also have a particle, as we can isolate ATP and ADP.
Thus AXP is both a wave and a particle. The gyre is a model of the both. The quantum is, somewhat confusingly, a combination of both. Just as in quantum mechanics, we don’t know what state a particular AXP is in until we go and look.
2. “The fact that the vast majority of people can’t understand the Andrulis paper doesn’t make everybody stupid. It indicates that Andrulis is having a hard time explaining what he is thinking.”
I agree. The fact that quantum mechanics or physical chemistry (honk if you passed physical chemistry was a bumper sticker at one time) is hard to learn doesn’t make everyone stupid either. They are strange, they use weird language and math, they are sometimes counterintuitive.
My problem with physical chemistry was not that the professor had a hard time explaining. In retrospect, he did a fabulous job. My problem with physical chemistry is that it bore no resemblance to anything I had previously learned — save for the math. But, and this is important, the math was used in a way that was /very different/ from what I had learned — and was related to what for me were arcane subject. Plus, it came with these laws which to me were not immediately obvious.
If my description of p-chem sounds like a description of Erik’s paper, that’s because it should.
My experience with Erik’s paper has been a bit easier than p-chem, thank goodness, because I have an enormous amount of additional supporting material from Erik that I had read before the paper.
3. “3. I tentatively favor the hypothesis that nettle is Andrulis. Otherwise, how would he know that Andrulis has read 1,000 journal articles and 500 nonfiction books?”
Perhaps, because I have known Erik for decades, and he told me so, and I saw him constantly reading, and I have seen his library of 500 or so books that he bought? Otherwise, I don’t know.
“And why hasn’t Andrulis in person come forward to defend himself??”
He has. He had a blog which he took down because it was largely ignored.
Furthermore, I just called Erik and he said the following.
What forum would you propose for him to use?
Think about how broad in scope his paper is. What needs to be defended?
How does one maintain a discussion forum that reaches across so many fields?
Certainly the scholars in each field should offering their critiques, but they have been completely silence
He received invitations from two different bloggers, but he declined.
This is not about politics, it’s about explaining it is about an idea that needs to move into the zeitgeist.
Also, Erik has previously told me that he feels the only way the paper will general be treated to sincere, studious scrutiny is if someone in a respected field took interest in the paper and stated so publicly.
There is a lot of hostility, plenty of dismissal, but aside from me and you, and a few people who have emailed Erik, there has been /no/ scholarly attempt at analyzing the paper.
4a. “I was trying not to talk about the assertion that water has memory, but I can’t help it. ”
When you look at Erik’s model, he is saying that learning and memory are core features of the model itself.
Erik posits that learning and memory applies at all levels, though we may not recognize such as happening. He is not playing favorites.
For this very broad idea of learning and memory, Erik invokes gyronosis and gyromnemsis.
When you talk about memory, the tendency of the mind is to form cognitive (mental) meanings.
Erik is trying to provide non-cogntive meanings for learning and memory.
For example, when someone talks about genetic information aren’t they talking about the integration, transfer, storage and retrieval of information? Aren’t those processes learning and memory? One doesn’t think this way, but that manner of thought does not logically mean that we don’t have learning and memory.
Further thoughts:
Single cells clearly take in information relative to their surroundings.
Where is that information stored? How is it stored? Where and how is it retrieved?
Within a single cell how do biological pathways adapt (learn) and how does they store (remember) that information that it has taken in?
How does a cell maintain homeostasis?
How does a cell maintain its structure?
Too, keep in mind:
There is no explanation as to why life is 70% water.
There is no theory that unifies the modern day nature or the evolution of water.
4b. “As a corollary, would nettle please state just one or two of the scientific works that directly support Andrulis’ paper?”
This query seems to be a common one. I find it truly perplexing when the paper has 800 references.
On a different (and clearly disreputatable) forum, I am mocked for not providing scientific references. Why should I when the paper is chock full of them?
Anyway, check out some of the 800 references. Pick one or two. There you go.
I have put such detail into my explanations because you are the /only/ person I have found on the internet who has taken the paper as one that merits careful analysis.
As a side note, as of Feb 13, the paper has been downloaded 29,918 times.
Conrad,
to clarify, think of a horizontal gyre. It has high points and low points. If viewed in two dimensions, it can be a sine wave, but it does not have to be. Oscillations can be irregular — just as my trips to the gym are.
In regards to references, that is supporting material, the references in the paper (unless I missed one) are all highly tangential to the basic issue of gyre-ism. Some make me wonder why Andrulis bothered to include them, as they merely obscure the issue. I’m referring to the page where he quotes a paper: “shamefacedly…”, etc. It turns out that paper was written in 1987, long before the notion of an impactor on early proto-earth forming the moon became current. That is, the author had no idea that this extremely popular and highly probable theory would become current, so he could say that then current theories really didn’t fit the newest data. So what does all this have to do with gyres? Nothing. So why include it in this “dense” paper when it merely serves to fill up space that could be better used in explaining the gyre? I don’t know. That’s what makes me think of a Sokal, or some variation on that theme (publicity is great for many purposes.)
That’s really all I can think of this evening. I certainly reserve judgement (because I’m relatively stupid and an abject layman at everything except clinical medicine) but I am entertaining two possibilities: one, the author has a psychotic lacuna; and two, the paper is a Sokal. I am sorry to tell you that I am not seriously considering the possibility that this paper will EVER have a beneficial effect on the advancement of science. The Grand Unified Theory is as far away as ever.
You say that orthophosphate is the obvious center of a gyre modeling the cycling of ADP/ATP. I say you’re just trying to make a square peg fit into a round hole. I understand the cycling between low and high energy states, with an intermediate state of transitioning between them. But memory? There you’ve lost me. Especially when you talk about water having a memory. Memory can certainly be non-cognitive. But whatever it is, it’s got to be fixed in some way, and water is not fixed in any way.
I’m really tired of explaining why this paper explains nothing. I just go around in circles with you. The fact that the paper has been downloaded thirty thousand times just makes me more tired. It’s not impressive, especially after the publicity release and the subsequent notoriety. I downloaded it. That doesn’t make me a fan.
Conrad,
“It turns out that paper was written in 1987, long before the notion of an impactor on early proto-earth forming the moon became current.”
The point is that no one observed the impact. This conjecture may be true or maybe false. There is no way to test this idea. Show me an experiment that you can reproduce this There is no way to prove it with out is a consistent theory. Its all speculation. It’s a nice story.
You can say that there is the same material in the moon as in the Earth but that a correlation.
You are believing a story to be true because its been repeated and accepted by the academy, but that does not mean that it is true.
“I certainly reserve judgement”
Thus, I enjoy our exchanges.
“You say that orthophosphate is the obvious center of a gyre modeling the cycling of ADP/ATP. I say you’re just trying to make a square peg fit into a round hole”
I believe my explanation to be rock solid. We will have to agree to disagree.
“But memory? There you’ve lost me”
In 4a I tried to explain that memory is a broad concept.
I also said the following,
Single cells clearly take in information relative to their surroundings.
Where is that information stored? How is it stored? Where and how is it retrieved?
You did not address those questions, so I suppose you don’t have an answer.
“Memory can certainly be non-cognitive. But whatever it is, it’s got to be fixed in some way, and water is not fixed in any way.”
Ice is fixed. Shucks, it was fixed enough to sink the Titanic. This kind of fixed is /not/ how the paper limits the memory of water, though. I just point it out as an easy to understand example of water “remembering” its form. Ice does not morph unless melted.
More important, Erik is not talking about memory broadly — so as to include the homeostasis of the cell, and /all/ other matter.
The paper is /not/ talking about homeopathy, though the confusion is understandable.
From wikipedia:
“Homeopathy is a vitalist philosophy that interprets diseases and sickness as caused by disturbances in a hypothetical vital force or life force…However, Hahnemann rejected the notion of a disease as a separate thing or invading entity and insisted that it was always part of the “living whole”.[33] Hahnemann proposed homeopathy in reaction to the state of traditional western medicine at that time, which often was brutal and more harmful than helpful. ”
Read the rest of the page for further information.
Interestingly, according to the page,
“short-range order in water only persists for about 1 picosecond”
How does short-range order persist at all? And why 1 picosecond? Why not 1 attosecond?
Science conjures up explanations, with loads of math, about the binding energy of hydrogen bonds, but science has never directly observed an /individual/ hydrogen bond. No one has observed the /individual/ hydrogen bond with its purported electron sharing. So, all this math and all these explanations may describe how a pool of water molecules work, but they ignore how the /individual/ water molecule behaves. Science glosses over or ignores what it lacks the tools to study.
Is water memory important to homeopathy. Not necessarily. But homeopathy has invoked that water retains effectiveness in diluted form. This conclusion is not logical but /very/ convenient — as homeopathy is largely incoherent in my limited understanding of it. I don’t believe that water has the sort of memory some homeopaths claim, nor should any reasonable person.
As an aside, science speculates with untestable theories all the time, but because it is /science/, even with untestable hypotheses, people fall in line. Take string “theory.” How do we look at an /individual/ string? Heck, how do we observe strings at all?
Good grief, we can observe Einstein’s relativity, so that’s a fine theory. Tested. Shown to be useful. Why not strings? If we have observed strings, then I am ignorant of such. I suspect we have not observed a /singular/ string, though. The math may work, but if it is based on false assumptions, it is wrong. Are the assumptions for string theory correct? How do we know? Furthermore, we know that measuring a system alters it — in however small a way. How do we measure the alteration? I’m not saying the secondary measurement is impossible, though I suspect it is. I am asking a general question.
More important, were a western doctor to accept /some/ of the principles of alternative medicine (not just homeopathy) then they would be makeing a concession to alternative forms of medicine — some of which actually work. We already know that modern medicine has serious problems. Examples include physicians’ inability to address — and cure — metastatized cancer, various neurological diseases (PD , Alzheimer’s, etc.), and (possibly, I may be wrong here), lower back pain.
Water is required for life, but it is not alive.Geez, what are we if not, if I recall correctly, 70% water.
How does water retain its form? Hydrogen bonds? What /exactly/ is an /individual/ hydrogen bond? (See my comment above.) Gravity? What is gravity? A warp in space time? What is space? What is time? Where did they come from? Why is space mostly nothing? What /exactly/ is a vacuum? How can a vacuum even exist if “Nature abhors a vacuum?” Why does time only move in one direction?
These questions are boggles of present science — explained away with hypotheses that can not be tested.
In sum, If this idea of memory perplexes or vexes you, I understand. It is a tough idea to grasp, as it is generally not intuitive. On the other hand, it does explain the behavior of a broad variety of systems, as the paper indicates.
I greatly admire the critical attention you have given to this paper. You have an inquisitive and open mind.
Also, for general consideration, here is an except from a supportive email Erik forwarded to me,
I am broadminded and intuitive. These are the characteristics that led me to your paper. At first I thought that it was a clever and carefully orchestrated joke, the sort of satire a bored professor might come up with as he approaches retirement and has nothing to lose. But I soon realised that you are in fact a young man employed in a prestigious American University with everything to lose(including tenure) by kicking the can. So I figured that it was worth spending some time reading and one way or the other digesting what it is you have to say. I found it perplexing profound and very exciting. My intuitive response is that what you write is true.
The point I was making about the “shamefaced” quote was that it is irrelevant and obsolete. The author of the “shamefaced” article did not know that the impactor theory would become the best available theory; he might not even have known about the impactor theory at all. Thus, his statement was overtaken by events and became irrelevant and obsolete. Lunar geologists are no longer “shamefaced” because they have something elegant and convincing to hang their hats on. So why use the quote or reference the article at all? Maybe because the quote looks shocking, and if you don’t notice that it is obsolete, you might think that lunar geologists still don’t have a theory that they’re happy with. I call this misleading at best. Otherwise, why waste any space on it at all? Your arguments against the impactor theory are trivial and irrelevant.
The same applies to your most recent response (if not to all of your very long responses.)
Another assertion which bothers me: “science has never directly observed an /individual/ hydrogen bond.” No one has “directly” observed an individual hydrogen bond. But we accept that they exist, because of a long line of evidence. What more proof do we need? To actually “look” at one? That’s impossible anyway. So what’s the big deal? Oh: “So, all this math and all these explanations may describe how a pool of water molecules work, but they ignore how the /individual/ water molecule behaves. Science glosses over or ignores what it lacks the tools to study.” Now, you’re talking. “Science” “glosses over or ignores” individual water molecules because they can’t see them directly. Who is this monolithic “science”? What are they “glossing over or ignoring”? Don’t answer that. Those are rhetorical questions.
Another assertion: “More important, were a western doctor to accept /some/ of the principles of alternative medicine (not just homeopathy) then they would be makeing[sic] a concession to alternative forms of medicine — some of which actually work.” By definition, alternative medicine does not work. When an “alternative” remedy actually works, it is accepted into “western” medicine and becomes part of the doctor’s armamentarium. We are not so hide-bound as you think. “We already know that modern medicine has serious problems. Examples include physicians’ inability to address — and cure — …” “Modern” medicine has problems but not so many problems as it did 200 years ago (when homeopathy was born) and, we hope, more problems than we will have 200 years from now. I don’t know why you include this rather banal point (as if I didn’t already know that “modern” medicine was a cesspool of corrupt doctors, me-too drugs, and unnecessary surgical procedures abetted by a venal and brutal insurance industry.) We were talking about the gyre model, not medicine.
Another assertion: “Single cells clearly take in information relative to their surroundings. Where is that information stored? How is it stored? Where and how is it retrieved? You did not address those questions, so I suppose you don’t have an answer.” No, I did not address those questions. I don’t have an answer. It’s irrelevant anyway. But there is a recent article about prions in yeast that might provide an answer. You should check it out.
Then there is your assertion “You are believing a story to be true because its[sic] been repeated and accepted by the academy, but that does not mean that it is true.” I did NOT say I believed the impactor theory. I said that it is very popular and highly probable. There is a difference, and any scientist would immediately see the yawning gulf between “believing” and “accepting a theory.” Therefore, I wonder about your scientific background or at least your scientific reasoning abilities, not to mention your spelling and grammar. I’m sorry to be making such a harsh statement but I am more and more beginning to tire of this exchange between us as it lacks scientific rigor and too much of what you say is either irrelevant or misleading.
Since you make this long digression into homeopathy: Homeopathy, regardless of what lies behind it historically and epistemologically (I think I used that word right) is not useful. The fact that it doesn’t work can easily be ascertained, not by testing it against other remedies or placebo, but simply by following the process through which a homeopathic preparation is made. Put simply, an “active ingredient” (usually a plant extract) is serially diluted until there is not one molecule left of the extract in what is essentially pure water. At the time Hahnemann lived, the theory of atoms was not widely accepted or even considered much, so this oversight might have been forgiven.
In recent times, some have claimed that homeopathy does work, and have used the notion that “water has memory” in an attempt to explain how it “works.” This is also prima facie absurd, and cannot be forgiven because it is a modern idea and can be refuted with already known facts. Water, in its fluid state, has no lasting bonds; the hydrogen bond only lasts a short time (whether it’s a picosecond or attosecond or even a millisecond is irrelevant) and is quickly replaced by another hydrogen bond. Ice certainly has “memory”–in its crudest form, one could write a thesis with a stylus on a piece of ice and it would last years as long as the ice didn’t melt. But homeopathy doesn’t use ice.
There is more, but I’m already tired of this subject. Your “information” about homeopathy is, sadly, very well known to me (since I was a doctor, I had occasion to study the issue along with many other “alternative” forms of medicine.) I don’t know why you insist on recapitulating all this in your response, as it is not only irrelevant but tiresome to me. Besides, this is not a medicine blog.
I will close with an ad hoc attempt to fit the ADP/ATP cycle to the gyre model. Let us say that ADP/ATP is in orbit around the enyme that converts them; orthophosphate is also orbiting. An energy input is required to drive the conversion of ADP to ATP, and conversely, energy is released when ATP goes to ADP. This is mediated by the enzyme. No, that doesn’t work. ATP attaches to an enzyme that requires energy to do another chemical reaction, and when ATP is cleaved, the enzyme morphs to a higher energy shape which allows it to then use that energy to run another reaction, after which the enzyme morphs back to a lower energy shape. This is a more general statement, as ATP is used by many different enzymes in the same way. I could go on, but gyring just doesn’t help any.
Your support of Andrulis and his paper has, sadly, reduced my ability to consider it useful. The more I look at it, the less I see. Your long, “tiresome and ponderous” posts display a superficial familiarity with scientific concepts but not an ability to synthesize them in a meaningful way: for example, your invocation of Schroedinger’s cat in your attempt to explain how “gyre quanta” model the NTP/NDP+P cycle. I wish you were Schroedinger’s cat. I would never open the box.
I would suggest that you tell Andrulis to start another blog. I’m sure that, due to the publicity attend on the publicity release and its retraction, he’ll get many more readers and commenters. Not that I think that will help, just that I think this particular blog has pretty much shot its bolt.
I give up. I really have to move on, or I’ll be stuck in this discussion forever. I can’t justify spending any more time (although I have “all the time in the world”) on the Andrulis paper. I could be wrong, but I’m willing to be wrong because I’m just too tired to care.
Conrad,
” I really have to move on, or I’ll be stuck in this discussion forever. I can’t justify spending any more time (although I have “all the time in the world”) on the Andrulis paper. I could be wrong, but I’m willing to be wrong because I’m just too tired to care”
I agree and totally understand.
You miss many of my points, so we are simply talking past each other. I won’t bother to provide examples.
“No one has “directly” observed an individual hydrogen bond. But we accept that they exist, because of a long line of evidence. What more proof do we need? To actually “look” at one?”
If we can not look at one then we only have observed how they work en mass.
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.
“By definition, alternative medicine does not work. ”
A statement by a western doctor. Come on. I am not a student of alternative medicine, so I can only provide one example: medical marijuana. That is not standard medicine. There has got to be at least /one/ other herb out there that modern medicine does not know but that is medicinally effective in some fashion.
‘“Single cells clearly take in information relative to their surroundings. Where is that information stored? How is it stored? Where and how is it retrieved? You did not address those questions, so I suppose you don’t have an answer.” No, I did not address those questions. I don’t have an answer. It’s irrelevant anyway”‘
If its irrelevant then we have wasted billions of dollars researching cell biology. After all, what cell biology is really about is how a cell takes in information (a variety of ways including but not limited to receptors) stores information (DNA), retrieves information (DNA transcriptase makes RNA which is read to make proteins). By the way, the parenthetical comments are only examples.
‘“You are believing a story to be true because its[sic] been repeated and accepted by the academy, but that does not mean that it is true.” I did NOT say I believed the impactor theory. I said that it is very popular and highly probable. There is a difference, and any scientist would immediately see the yawning gulf between “believing” and “accepting a theory.”’
If you say something is highly probable and reject my points on correlation, no reproducability, etc., then, you are believing — at least partly — the impactor /hypothesis/ As to contrasting “believing” and “accepting a theory,” I have no idea why you bring that up, unless you meant that I was wrong to state you believed in something and that you really meant you accepted the impactor hypothesis as theory.
Moreover, your earlier statement was
“Lunar geologists are no longer “shamefaced” because they have something elegant and convincing to hang their hats on. ”
You can’t call something “elegant and convincing” and then, when I say you believe it, disagree. No way.
“I wonder about your scientific background or at least your scientific reasoning abilities, not to mention your spelling and grammar.”
Ditto. I made two typos. You then call both my spelling /and/ my grammar into question.
I am disappointed in you.
You are being petty.
You do yourself a disservice to stoop to that level of reasoning.
Good grief, man, this is not some publication for broad consumption. This is a mere forum. Too, I fail to see my grammatical errors. I am not saying I did not make any, but I wish you had pointed them out, as I do try to use standard grammar. In fact, I strongly believe that I do most of the time. I admit to making mistakes, though.
“Since you make this long digression into homeopathy”
Uhm. Fifteen lines is not a long digression. The middle ten lines are dedicated to the properties of water.
Also, you ignored my statement,
“… as homeopathy is largely incoherent in my limited understanding of it. I don’t believe that water has the sort of memory some homeopaths claim, nor should any reasonable person.”
Heck, you ignored a lot of what I wrote. Oh well.
“I will close with an ad hoc attempt to fit the ADP/ATP cycle to the gyre model. Let us say that ADP/ATP is in orbit around the enyme that converts them; orthophosphate is also orbiting. An energy input is required to drive the conversion of ADP to ATP, and conversely, energy is released when ATP goes to ADP. This is mediated by the enzyme. No, that doesn’t work.”
You miss my point and the point of the paper on the subject. Alas.
‘Your long, “tiresome and ponderous” posts display a superficial familiarity with scientific concepts but not an ability to synthesize them in a meaningful way’
Again, I understand, but I am disappointed that you feel that I have a superficial familiarity with scientific concepts as I have taught organic chemistry and biochemistry for several years.
Let’s be honest here.
My posts are as “tiresome and ponderous” as our yours.
Thanks for your playful and clever put down, “I wish you were Schroedinger’s cat. I would never open the box.” It made me laugh.
I have greatly enjoyed our exchange.
You debate in a very level-headed fashion, even when you miss my points or the points of the paper
I wish you well.
“No one has “directly” observed an individual hydrogen bond. But we accept that they exist, because of a long line of evidence. What more proof do we need? To actually “look” at one?”
If we can not look at one then we only have observed how they work en mass.
Download any high resolution X-ray, neutron diffraction or NMR structure from the protein data base (http://www.rcsb.org/pdb/home/home.do) and inspect the structure in an appropriate graphics programme. You will see dozens, hundreds, thousands of “individual hydrogen bonds”, beautifully defined in all their glory.
One of the wonderful things about real science and real and useful theories is the nature of prediction. The hydrogen bond was first predicted in the early part of the 20th century and its implication for molecular structure and organization well understood by the middle of the century (see Paulings “Nature of the Chemical Bond”). 40 and more years later when high resolution protein structures became available, there they are before our very eyes and exactly as predicted “indiidual hydrogen bonds”.
How silly to pretend that “one had “directly” observed an individual hydrogen bond”, when we can very easily observe individual hydrogen bonds to our heart’s content.
Clarification:
‘“No one has “directly” observed an individual hydrogen bond. But we accept that they exist, because of a long line of evidence. What more proof do we need? To actually “look” at one?”
If we can not look at one then we only have observed how they work en mass.’
I am referring to an individual /isolated/ hydrogen bond between two, and only two, water molecules over time.
I am well aware that we have observed them en mass and /in concert/.
That last point is /very/ important.
A concert is totally different then the functioning of, say, a lone violinist. It masks small mistakes, for instance.
We don’t know if, say, a violinist is playing to perfection until we listen to him or her alone.
It may very well be that he or she plays differently alone then when in concert.
Therefore, we can not know the qualities of the violinist — as they may vary.
He or she may be in a state of perfection and imperfection at the same time. Same violinist, but change the environment, and his or her quality changes from perfection to imperfection.
In fact, just studying the violinist may affect the status of his or her perfection. We have the Schroedinger’s Cat problem.
We have a serious conundrum, insoluble with our present understanding.
Ha. I embarrass myself. I mean to say I will provide some examples. I make mistakes.
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 datapoints 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 not look upon as intellectual dishonesty because of the imprimatur of the peer review system.
In my haste I made a grammatical mistake in the last sentence which I correct for the purists. Sorry about my mistake.
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 datapoints 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.
Geez, I’m sloppy today. Second and third 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.
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 provided a overarching “overscience” in his paper is no fun for him at all.
My final word on the issue: (I’m not ignoring anything nettle wrote, just trying to forget it.)
If nettle does not understand the difference between “belief” and “conditional acceptance” yet claims to understand Andrulis, then nettle is tergiversating.
“Belief” is a religious concept. Belief requires faith and “faith is the evidence of things unseen.” That is, you only believe in things for which you have no evidence.
You “accept” a theory because it satisfies Occam’s razor. In the future, new facts will be discovered which will require a new theory. You will no longer accept the old theory, which would be a problem if you “believed” in it.
That is the philosophy of a scientist. If one ignores the anomalies, then one is no longer a scientist.
Nettle is pointing out the errors of individuals and using them to paint the entire field as bad.
Nettle is not explaining anything, he’s just confusing the issue further.
I am cancelling my subscription to this thread.
L’ esprit de l’ escalier:
I forgot to mention that my psychiatry professor said that “psychotic lacunae” are contagious and are frequently shared between two or more people. My final theory is that nettle and Andrulis are sharing a psychotic lacuna.
No more time for theorizing. I’m dead meat on a stick.
puzzled monkey
Apparently, yours is an apt nick.
The wit of the staircase — is not necessarily correct, though you may think so. (I know esprit means spirit, but I speak French and spirit is not an appropriate translation here.)
“my psychiatry professor said that “psychotic lacunae” are contagious and are frequently shared between two or more people.”
Fine. How do you diagnose “psychotic lacunae” based on an internet exchange? Why do you not need to at least talk to a person, hear the tone of his voice, hear (with your ears) a discussion of the beliefs on the paper.
If you are a psychiatrist, then say so. If not, you are not qualified to judge me, and you just look silly.
If you are, then you are foolish to “diagnose” me based on my commentary on one paper and related subjects on an internet forum.
You do not know me, have not met me in person, and have not discussed other subjects with me.
Good grief man, if we had, in person, /sincerely/ debated the paper (i.e. your were interested in it and had studied it), with the paper and other supporting materialin front of use, then and only then could you come to a conclusion about my mental state.
A good friend of mine, who is a psychiatrist, says that I am fine. I have my idiosyncrasies but so does everyone. His patients on the other hand have some serious mental issues.
“No more time for theorizing. I’m dead meat on a stick.”
Well said.
Conrad
‘“Belief” is a religious concept.’
My belief that you are unable to understand is not a religious concept.
“That is the philosophy of a scientist. If one ignores the anomalies, then one is no longer a scientist.”
Spoken by a the good doctor — who not coincidentally is not a scientist.
If you /ask/ honest scientists, they will readily admit that they toss anomalies. I know because they have told me. No, I will not say who they are. I will protect them because they are playing by the rules of the game — which say ignore anomalies when necessary, among other things.
“Nettle is not explaining anything, he’s just confusing the issue further.”
Not understanding what I say does not mean I am not explaining anything.
If you are confused by what I say, that /may/ be my fault but it may be yours. It all depends on you point of view.
Also, blaming me for being “tiresome and ponderous” as Earle did just reflects intellectual laziness.
Learning physical chemistry was the tiresome and ponderous experience of my life, yet the field has great merit and predictive power.
“Nettle is pointing out the errors of individuals and using them to paint the entire field as bad.”
The entire field /is/ bad. Just because you have some people, even a majority of people, in a field playing by the rules, does not mean the field is level.
The outliers, the black swans, the hurricane Katrinas are the ones that /really/ matter — and corrupt the /entire/ field.
“I am cancelling my subscription to this thread”
Anyone who says he is leaving a thread is most likely a liar.
Anyone who invests time and effort into something has strong motivation to continue to follow — if not comment on — a thread.
If you are too proud to admit as much, so be it.
I should add an observation.
In my scientific experience , I have not seen anomalies.
Just luck, I guess.
I have seen unreproducible results, but they are usually just a reflection of sloppy science, faked data, or information intentionally withheld by the researcher.
Yes, scientists will withhold critical information sometimes.
Furthermore, I always get a second opinion from someone at least as qualified as me.
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.
Here are two emails for your consideration.
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.
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.
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.
I made this reply on the retraction watch for Case Western. I repeat it here for completeness.
“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.
So, is anyone here capable of offering one?
Just read through the paper myself. Although I am not a biochemist, my own work is much involved with formal representation and complex systems, and so I feel I am qualified to judge the underlying gyre theory.
Unfortunately, there appears to be nothing new in the paper. It begins with some fairly loose observations on common emergent patterns, though it does not seem aware of the fundamental distinctions in mechanism and dynamics that lie beneath the superficial similarities. This is not necessarily a fatal weakness: a unification based on a deeper abstraction would be quite interesting, and this is what the gyre theory apparently aims to offer.
Where the theory falls down is in the formal system established in Section 2; although the author provides an interesting collection of primitives, the operators for composition and evolution are underspecified. Formally, therefore, the model actually has a very limited breadth of expressivity. The author’s clear intent, however, was to produce a much more expressive model, and the remainder of Section 2 attaches semantics to the model that its syntax is not capable of representing.
This is the fundamental error that causes the rest of the paper to collapse. In essence, the inconsistency between syntax and semantics allows ill-defined conclusions to be derived by shuttling back and forth between the two perspectives. This is closely analogous to the well-known principle of classical logic that the acceptance of any contraction allows all conclusions to be drawn.
Thus, without a solid foundation the remainder of the work included in the paper is rendered simply ill-defined. In this case, experiments are actually beside the point, because the fundamental definitional flaw in the theory means that evidence cannot be related to the underlying ideas at all.
You are claiming that there is a lingusitic statement in the beginning of the paper that renders the entire paper wrong.
1. What is this error?
2. What logic do you use to dismiss the rest of the paper> and
3. What gives a non-biochemist the skills to understand a field he has not studied — in a format he has not been taught?
–nettle
P.S. When can we return to the discussion of one fact in the paper?
Nettle wrote:
> You are claiming that there is a lingusitic statement in the beginning of the paper that renders the entire paper wrong.
> 1. What is this error?
> 2. What logic do you use to dismiss the rest of the paper> and
> 3. What gives a non-biochemist the skills to understand a field he has not studied — in a format he has not been taught?
Let me explain the error to you. This is not a matter of linguistics,
it is a matter of elementary logic. When you boil away all the
metaphors and semantic attachments, the model presented in Section 2
is this (shown in modified EBNF):
(** Gyromodel syntax **)
gyre = (chirality, gyration)
chirality = “LH” | “RH”
quantum = “(*)” | gyre
particle = A | A{BB} | A{BBB}
(* where A and B are distinct quantums *)
[particle] = particle | particle[particle]
(* gyrapex gyrobase + gyradaptor *)
gyration =
A{BBB} A{BB} + B |
A{BBB} [A{B}] + BB |
A{BBB} [A] + BBB |
A{BB} [A{B}] + B |
A{BB} [A] + BB |
[A{B}] [A] + B |
(gyration)n
(* where A and B are distinct quantums *)
(** Gyromodel evolution rules **)
B + A{BB} -> A{BBBo}
A{BBBo} -> A{BBoB} | A{BoBB} | A{oBBB} | B + A{BBo}
A{BBoB} -> A{BBBo} | A{BoBB} | A{oBBB}
A{BoBB} -> A{BBBo} | A{BBoB} | A{oBBB}
A{oBBB} -> A{BBBo} | A{BBoB} | A{BoBB}
(* where A and B are distinct quantums *)
Although there are a number of physical concepts mentioned in
connection with the model (e.g. thermodynamics, forces, flow rates),
they are not formally represented in either the syntax or the
evolution rules for the model. Nor is there an equivalence relation
for quantums, although in several places there is a requirement that
quantums be non-equivalent.
So what we have is a model for a stack of objects, grounded in the
primitive object “(*)”. If any of those objects happens to be A{BBB},
A{BB} + B, [A{B}] + BB, or [A] + BBB, then it can evolve to A{BBBo},
juggle the o around, and stop at B + A{BBo}.
That is all that is formally permitted by the model, as defined. All
the rest of the things hoped for by the author simply are not formally
represented at present.
This is a fundamental error because it means that nearly everything
that the author wishes to discuss cannot be discussed using the
model that the author has presented.
Let me give you an equivalent example. Consider a collection of
cards, which are either red, blue, or green. We can build hands by
collecting sets of cards. Formally, the syntax of our model is this:
card = red | blue | green
hand = card | card,hand
Now we’d like to show that the odds of getting a hand with a mixture
of colors is more likely than of getting a hand that is all the same color.
This may seem intuitive if you have ever played card games: after all,
flushes are rare, right? But there is a fatal flaw: we have not
specified anything about the process for generating hands. Is it
random? Is it deterministic? Are the cards coming from a limited
source? How is the number of cards in the hand decided? Unless we
have a model that resolves these questions, it is simply meaningless
to talk about the odds of getting certain types of hands.
The model in Andrulis’ paper is the same way. Because it is
under-specified, the rest of the paper is simply meaningless.
I can understand this, despite the unorthodox format, because creating
and interpreting new formats is my trade. I no more need to know
biochemistry to know this than I need to understand the rules of
bridge to understand the problem in the card example above.
HTML seems to have swallowed some of my formatting.
Here is the modified EBNF again with semicolons after each statement and ‘===’ in place of the bidirectional arrows.
(** Gyromodel syntax **)
gyre = (chirality, gyration) ;
chirality = “LH” | “RH” ;
quantum = “(*)” | gyre ;
particle = A | A{BB} | A{BBB} ;
(* where A and B are distinct quantums *)
[particle] = particle | particle[particle] ;
(* gyrapex === gyrobase + gyradaptor *)
gyration =
A{BBB} === A{BB} + B |
A{BBB} === [A{B}] + BB |
A{BBB} === [A] + BBB |
A{BB} === [A{B}] + B |
A{BB} === [A] + BB |
[A{B}] === [A] + B |
(gyration)n ;
(* where A and B are distinct quantums *)
(** Gyromodel evolution rules **)
B + A{BB} -> A{BBBo} ;
A{BBBo} -> A{BBoB} | A{BoBB} | A{oBBB} | B + A{BBo} ;
A{BBoB} -> A{BBBo} | A{BoBB} | A{oBBB} ;
A{BoBB} -> A{BBBo} | A{BBoB} | A{oBBB} ;
A{oBBB} -> A{BBBo} | A{BBoB} | A{BoBB} ;
(* where A and B are distinct quantums *)
Reviewer #3,
You need to have a basic understanding of physics, chemistry and cellular biology to undersand the basics of the paper.
Logic will not help you here just as it won’t help you understand hepatic surgery. Logic has not provided a concensus explanation of free will, emotions,. etc. No unification. FAILURE.
“Let me explain the error to you. This is not a matter of linguistics,
it is a matter of elementary logic. “
What do you mean by “error” in your context? Your usage is too protean for understanding. Or is it meant to be that way?
I do no purport to understand General Relativity; therefore I largely keep silent on the subject. Such ignorance would not stop you ,and I see, you are not so hindered.
If you are unwilling to engage with the substance of the objection,
then we are done here. “Unable to address major objection of
reviewer, paper rejected.”
If you are unable to do so (e.g. due to a lack of sufficient
background on your part), then I am happy to help you understand it
better so that you may. For a starting point, let us consider the
parallel example that I presented, of colored cards.
If you wish to engage, please state your understanding of the card
example, and we will begin from there. Any other reply I will take as
an unwillingness to engage in substantive discussion.
Google “erik andrulis” and “nettle” and you will see nettle has been posting pro-Andrulis messages on every single blog and website that publicized this story. It’s not hard to see that nettle is most likely Andrulis himself. Seriously, do you have any dignity?
I have repeatedly stated that I am a long time close friend of Erik. I have dignity for myself, my friends, and radical new ideas that fulfil multiple tests for veracity.
.
You, apparently, have dignity for gossip.
You conveniently ignore the strong possibility that if someone is defending an idea, he may /not/ be the originator of the idea. Or do you beleive all manic street preachers are Jesus Christ?
To each his own.
Hooray for Reviewer #3!
And one kudo to northwesternchemist for having the courage to google those two names together.
All it took was for someone sufficiently intelligent and well trained in the field Andrulis claims to be breaking into–whatever that is–to read it, then to point out and clearly describe the basic logical flaw(s) in this paper.
So the “fundamental error” is that there is an “inconsistency between semantics and syntax”
and, reversing the reviewer’s final thought, the “underlying ideas” cannot be used to make any physical predictions that might be tested. At least I think that’s what he meant.
OK, so I lied…I didn’t completely dis-associate myself from this thread.
My conclusions, ie those of the puzzled monkey, are that andrulis makes a lot of assertions about what he perceives as an ideal model. But the model doesn’t automatically support the assertions, and he doesn’t derive them (the assertions) in any way, much less a logical way. Also, all the things the reviewer said about underspecification, limited breadth, acceptance of a contraction, and a lot of other things I didn’t understand.
Conrad’s 0th maxim: Time spent in reconnaissance is never wasted. (attributed to Clausewitz.)
Here’s another one I picked up yesterday: “If you keep shooting at them, eventually they’re going to start shooting back.”
You’ve got the gist. Though apparently I typo’ed “contraction” instead of “contradiction”.
Yeah, I didn’t really understand that part. It makes a lot more sense if you insert “contradiction” for “contraction”. That is, “acceptance of any contradiction allows all conclusions to be drawn.” I still had to google it.
Logic is not my strong point, but I knew something was fishy when Andrulis started claiming that his model encompassed all these wonderful concepts like emergence, evolution, etc. without trying to derive the concepts logically from the model.
Actually, I was suspicious from the very first sentence. It is clear to me (and I’m only a monkey) that the emergence of life and its evolution are a logical consequence of the starting conditions specifying an open system, in light of the second law of thermodynamics (which everyone gets backwards: entropy does increase in a closed system, but Earth, the Solar System, the Milky Way, and even the Universe itself are all open systems. Therefore entropy will decrease in our local environment.) So for Andrulis to claim that there is some deep vacuum in our theoretical systems such that it fails to explain this situation is, like, ridiculous. To me.
Worse still, it reminded me unpleasantly of that paper that claimed that the random emergence of life on Earth is a contradiction of the second law of thermodynamics; therefore God must have done it. (That paper was retracted but it lives on in the creation-o-sphere.)
The last straw was when Andrulis mentioned in passing that water has a memory (a claim that I have only seen in one other place: an explanation of “why homeopathy works” (which is a false premise, so it goes nowhere.))
Then there is nettle, who has defended Andrulis with a torrent of irrelevant and sometimes insulting claims…and who fails to discuss the substantive issue at hand: his model doesn’t have any operators for composition, evolution, etc. so he can’t go anywhere with it.
It doesn’t matter who nettle is, nor whether he/she is physically distinct from Andrulis. What matters is that they share an unhealthy obsession with a model that goes nowhere. It’s like that Turing test, actually; they could be computers for all we know or care.
Long distance forensic psychiatry (my specialty): Andrulis is manic depressive, and during one of his manic episodes, he developed a delusional belief that he had a model that explained the origin of life (this is often called a “flight of fancy” or an “intuitive leap” and occurs frequently during a manic episode, particularly at the boundary between hypomania and full blown psychotic mania). This delusion (the “psychotic lacuna”) has taken over a significant part of his life, regardless of his current state of mania or depression.
I’m sorry to be the bearer of unpleasant conclusions, but I call them as I see them (which is one reason no one will hire me anymore.)
Luckily for us, Anon Rex has invited nettle away from this blog to his private email address. So we will be spared the continuing uncertainty over whether we are just too stupid to understand this ever so subtle theory. Frankly, I know I am stupid, but the beauty of Einstein was that he could explain this stuff even to people like me so that we could understand it. nettle: You’re no Einstein!
amazing responses from nettle. His/her comments can be published as a paper by itself!!
Ressci,
My amazing responses lay in the shadow of the open mind of your trying to understand.
–nettle
@nettle:
I’ve been reading through the paper and am extremely interested, but could definitely use some help understanding some of the nuts and bolts.
In particular, I could use a more thorough description of the very basic majorgyre with examples in different scopes, particularly in the cognitive, psychological, linguistic, and social realms since that’s my area of expertise.
I’m still unclear as to how to frame any given gyrosystem and how they develop over the course of several cycles. And I do understand that the recursive nature makes it hard to describe succinctly.
I’m sure this type of informal explanation outside of the super-dense manuscript could help everyone form more intelligent opinions about the framework.
Please get in touch by email if you’re willing to have an ongoing conversation about this, I’d love to understand the model better: [email protected]
Apropos the subject:
http://www.abyme.net/
EXCERPT:
“Part II: Experiments on Studying the Properties of Time, and Basic Findings ~
The experimental verification of the above-developed theoretical concepts was started as early as the winter of 1951-1952. From that time, these studies have been carried on continuously over the course of a number of years with the active participation by graduate student V.G. Labeysh. At the present time, they are underway at the laboratory of the Pulkovo Observatory with engineer V.V. Nasonov. The work performed by Nasonov imparted a high degree of reliability to the experiments. During the time of these investigations, we accumulated numerous and diversified data, permitting us to form a number of conclusions concerning the properties of time. We did not succeed in interpreting all of the material, and not all of the material has a uniform degree of reliability. Here we will discuss only those data which were subjected to a recurrent checking and which, from our viewpoint, are completely reliable. We will also strive to form conclusions from these data.
The theoretical concepts indicate that the tests on the study of causal relationships and the pattern of time need to be conducted with rotating bodies: namely, gyroscopes. The first tests were made in order to verify that the law of the conservation of a pulse is always fulfilled, and independently of the condition of rotation of bodies. These tests were conducted on lever—type weights [scales]. At a deceleration of the gyroscope, rotating by inertia, its moment of rotation should be imparted to the weights [scales], causing an inevitable torsion of the suspensions. In order to avert the suspension difficulties associate with this, the rotation of the gyroscope should be held constant. Therefore, we utilized gyroscopes from aviation automation, the velocity of which was controlled by a variable 3-phase current with a frequency of the order of 500 cps. The gyroscope’s rotor turned with this same frequency. It appeared possible, without decreasing significantly the suspension precision, to supply current to the gyroscope suspended on weights [scales] with the aid of three very thin uninsulated conductors. During the suspension the gyroscope was installed in a hermetically sealed box, which excluded completely the effect of air currents. The accuracy of this suspension was of the order of 0.1-0.2 mg. With a vertical arrangement of the axis and various rotation velocities, the readings of the weights [scales] remained unchanged. For example, proceeding from the data for one of the gyroscopes (average diameter D of rotor equals 4.2 cm: rotor weight Q equals 250 gr), we can conclude that with a linear rotational velocity u = 70 m/sec the effective force upon the weights [scales] will remain unchanged, with a precision higher than up to the sixth place. In these experiments, we also introduced the following interesting theoretical complication: The box with the gyroscope was suspended from an iron plate, which attracted the electromagnets fastened together with a certain mass. This entire system was suspended on weights [scales] by means of an elastic band. The current was supplied to the electromagnets with the aid of two very thin conductors. The system for breaking the current was accomplished separately from the weights [scales]. At the breaking of the circuit, the box with the gyroscope fell to a clipper fastened to the electromagnets. The amplitude of these drops and the subsequent rise could reach 2 mm. The test was conducted for various directions of suspension and rotation masses of the gyroscope, at different amplitudes, and at an oscillation frequency ranging from units to hundreds of cps. For a rotating gyroscope, just as for a stationary one, the readings of the weights [scales] remained unchanged. We can consider that the experiments described substantiate fairly well the theoretical conclusion concerning the conservation of a pulse in causal mechanics.
In spite of their theoretical interest, the previous experiments did not yield any new effects capable of confirming the role of causality in mechanics. However, in their fulfillment it was noted that in the transmission of the vibrations from the gyroscope to the support of the weights [scales} variations in the readings of the weights [scales] can appear, depending on the velocity and direction of rotation of the gyroscopes. When the vibrations of the weights [scales] themselves begin, the box with the gyroscope discontinues being strictly a closed system. However, the weights [scales} can go out o equilibrium if the additional effect of the gyroscope developing from rotation proves to be transferred from the shaft of the gyroscopes to the weights’ [scales’] support. From these observations, a series of tests with these gyroscopes developed.” – N. A. Kozyrev [Possibility of Experimental Study of the Properties of Time]
(continue reading in link for further explanation)
The editor wrote: “All papers are peer-reviewed, although it is often difficult to obtain expert reviewers for some of the interdisciplinary topics covered by this journal.”
The statement that it was difficult to find a reviewer does not fit to the incredible speed with which this 100-page article was accepted. The article states: “Received: 15 November 2011; in revised form: 10 December 2011 / Accepted: 13 December 2011 / Published: 23 December 2011”
Thus finding the reviewers, doing the reviews and revising the paper took less than a month. Then it is not possible that too much time was spend on finding reviewers. And this speed seems to be typical for this publisher, many articles are accepted within a month.