proximity1

(Terms for the reader: "stochastic" refers to randomness in events) I believe Kupiec's theory is a bit more nuanced than the summarization offered here by Arete. For instance, the stochastic character of activity as described by Kupiec's theory pervades not simply what is termed above "gene regulation" (which in itself is something of a misnomer as interpreted in the theory), but, all molecular processes of an organism; and that this character is an inescapable feature of the fact that molecular behaviors observed in living tissue, just as in "inanimate" matter/energy, are themselves the product of the molecules' more basic quantum characterists in their components. What, in fact, as I understand it, is argued is something much more routinely accepted in the realms of quantum physics, namely, that all physical behavior of matter/energy is fundamentally stochastic in nature, that this factor necessarily redounds in the behavior of the dependent physical structures of "living organisms" and that, to properly take account of such a quantum foundation, the theoretical understanding of biological processes, like all other matter/energy behavior, must recognize and assume this aspect of basic physics. (certain terms are presented in quotation marks because their actual nature is in some respects open to question; as in "animate" versus "inanimate"; for the same reason, I refer not to "matter" or "energy" as distinct, but rather to "matter/energy". These are my own conventions, not those of Professor Kupiec. And, in general, all opinions and interpretations I present here including their errors, are my own, and they do not necessarily reflect the views of J-J Kupiec, who has neither reviewed or provided counsel in the presentations here.)

This thread springs from a discussion which began in "The Lounge," by Hypercube who posed the question: "Why Are Scientists Seemingly Reluctant to Accept New Ideas? (in some cases at least)" I proposed in that thread, as an example of such reluctance, the case of the French biologist and researcher, Jean-Jacques KUPIEC, Ph.D. , of France's INSERM, the national institute of health and medical research, and the Centre Cavaillès of the Ecole Normale Supérieure of Paris, whose work in molecular biology since 1983, conducted both independently and in conjuction with other researchers as well as other similarly oriented work by other researchers which can reasonably be interpreted to lend supplemental support to the hypotheses advanced by Kupiec et al, has, over thirty years, fostered a body of theory and experimental research which presents a credible theoretical challenge to the still-prevalent paradigm which encompasses what may be called Neodarwinian evolutionary biology. This thread is a split-off from that in the Lounge mentioned above and is intended to offer a venue for the extended consideration of the merits, current or potential, of Kupiec's theories which go by the term he coined, "Ontophylogenesis", or, as some view it, "Cellular Darwinism." Kupiec, besides having published results of his research in peer-reviewed scientific journals, has the following texts to his credit: L'origine des individus (2008, Fayard (Le Temps des Sciences), Paris; isbn: 978 2 213 62924 7) published in an English translation, The Origin of Individuals, (2009, World Scientific Publishers, Singapore). L'ontoohylogenèse: Evolution des espèces et développement de l'individu, (2012, éditions Quae, Versailles) Ni Dieu ni gène: Pour une autre théorie de l'hérédité (with Pierre Sonigo), ( Neither God Nor Gene: For Another Theory of Heredity) (2000, Editions du Seuil, Paris) A review of The Origin of Individuals was published in the journal Nature, 460, 35-36 (2 July 2009) | doi:10.1038/460035a; Published online 1 July 2009. For further reading (directly or indirectly) supporting the current paradigm in evolutionary molecular biology, see, for example, publications by such past or present leading scholars as: Ernst Mayr (1904-2005), Paul Oppenheim (1885-1977), Hilary Putnam(1926- ), Hans Dreisch (1867-1941), Jacques E. Dumont and others cited in the bibliographical references of The Origin of Individuals. This thread is opened for all further general discussion of the topics in and related to issues concerning Ontophylogenesis or Cellular Darwinism, pro or contra. I take a view supporting the central theses developed by J-J Kupiec in his texts cited above. Some related links for background on the theory presented by J-J Kupiec: Slides for an oral presentation : http://www2.mfo.ac.u...d%20Lamarck.pdf Scientific progress specific to biology: An epistemological overview Title page, Foreword, and contents pages from The Origin of Individuals, 2009, World Scientific Publishers, Singapore. Pure variation and organic stratification , by Jérôme Rosanvallon (Université Paris 7, Diderot, France) Progress in Biophysics and Molecular Biology (impact factor: 3.99). 07/2012; DOI:10.1016/j.pbiomolbio.2012.06.002 ) ; at www.researchgate.net

by Bertrand Russell: A History of Western Philosophy The Basic Writings of Bertrand Russell My Philosophical Development by Neil Postman: Technopoly: The Surrender of Culture to Technology ( a philosophical treatise on technology, science and culture) and, my musings of last evening, found already-written brilliantly in this essay's exposition by Stephen Maitzen: Stop Asking Why There's Anything, (2011, Springer+Business Media ) .pdf link: http://philosophy.ac...itzen_SAWTA.pdf

RE: ... " worth a thread split if you wish to discuss this specific example further" ... I don't know, what do you think about it? A thread-split implies creating a new thread and, unless I'm mistaken, that's "above my pay-grade" at the moment. I'm a very "newbie"--not even 30 posts to my credit/discredit. RE: ..." have a read through the first link in the post you quoted" .... I shall do that. Thank you. (BTW, it doesn't include the letter to Hooker, unless I missed it.) And, I'll read the hyper-link to Nature you posted. Thank you, too, for that. (EDITED TO ADD: A brilliant recommendation, that one. I very much appreciate your pointing to it. I'll get it later in the week, when I'm at a library with free, direct access to Nature 's archive. The same holds for the other two main links you present, the PNAS and the one to an article by Stephen J. Gould.) I don't know it for an absolute fact, but, if I had a farm, I'd bet it on the proposition that Kupiec has not only read but pored over every word ever published by Darwin. For a clear appreciation of Darwin's work and importance, though it's only my amateur's opinion, I believe Kupiec has no living peer. I'm the first to admit my limitations on knowledge in this area. I think that now it's time that you do some of that because, unless you've read in some form (English or French are the two currently published editions) The Origin of Individuals (2009, World Scientific Publishers, Singapore), then I think you go too far in this assertion: "yet his theory proposes the overthrow of many fundamental aspects of these fields without really offering an alternative explanation for much of the observed phenomena supporting current paradigms". In fact, he does indeed propose detailed alternative explanations for the observed phenomena which supposedly support (only) current paradigms (and he's aware that he must, in doing so, take account of Mayr's arguments, among others, which he describes and critiques). In a word, his alternative explanation he calls "ontophylogenesis", but, in deference to your point about splitting the thread, which I agree is better than persuing these points here, I refrain from going on in any descrîption of the details of his alternatives. BTW, I sent Kupiec an e-mail with a link to this discussion thread. Apparently, he has more pressing things to do than read or participate here. That doesn't really surprise me. He's now written a major work setting out his views in the non-specialist press, that would be his The Origin of Individuals (2009, World Scientific Publishers, Singapore) and is co-author, with Pierre Sonigo, of Ni Dieu ni gène , (Editions du Seuil, Paris, 2000). So, if in his opinion, anyone really interested in his work could read these rather than impose on him to defend it here, I can't really blame him for that. The Darwin citation, by the way, is in another text, (footnote, page 12) of L'ontophylogenèse: Evolution des espèces et développement de l'individu (April, 2012, Editions Quae, Versailles) a transcript of an oral presentation from 2011. If you care to, please open a thread. I cannot do that. If you prefer not to, "no salesman will call", I won't take it amiss in the least. You're an expert in the field. I'm a complete (?) amateur.

( deleted (by the posting member), upon noticing the moderator's note above.) Update: Sheesh. I just can't keep up with the movements here! ;^) In a science forum, a (general) discussion of censorship should have some place and, as I see it, that place should be important---better, for example, than what's offered by real world "free speech zones". That is not intended as any criticism of this site or its administration. I haven't been here long enough to know much about those. But I did leave the public discussion fora at the U.K.'s The Guardian in disgust over the blatant censorship practiced by what they are pleased to call "moderators"---some of the least moderate people I have ever encountered (but steeping in Political Correctness will do that to people).

"Single-term" service (as does, in the current circumstances, all electoral politics), inherently favors the class, the party, the interest group, which is the wealthiest and best-organized. Do you understand why that would be? RE: ..." but unless a way is found to contain politicians to a single term in office, this ka-ka will go on forever".... It won't go on forever, of course. But, in ending or metamorphizing into something else, the something else could easily be far, far worse. What would actually change the facts on the ground is a system by which people come into office by random lots---assuming that this could be done without completely rigging and manipulation. That way, newcomers would present two (albeit temporary) problems to the forces of organized money's (OM) strangle-hold on the political processes--- 1) they (OM) would have to meet, get to know and successfully corrupt (or suffer a decline in their interests' dominance) a new group of office-holders who are not already beholden to these same interests for the financial support that they required to run a successful election campaign, 2) ordinary mortals, rather than the rich (OM) or those annointed by them (OM surrogates), would come to hold office and have an opportunity to resist the efforts of OM to corrupt them. This prospect, that ordinary people ---in majority numbers--might one day come to control democratic processes and institutions is the summum of power's fears and the thing the prevention of which it takes as its foremost goal in its efforts to propagandize the public. So far, those efforts are so spectacularly successful that there remains simply no danger at all that such an outcome could occur in the foreseeable future. The public, at this, are completely disarmed before the power and effectiveness of OM. To alter that imbalance would presuppose a degree of political awareness and attention that the public show less and less liklihood to have any interest or capacity to acquire. If they did, there would be a very bloody and open fight, for at that point, a rich and privileged tiny minority would be faced for the first time with the prospect of having its dominance reduced to its numerical place in the political processes and their outcomes.

What, I ask, is your view of the import of this, from Darwin's letter to Joseph Hooker, 24 December, 1856, cited (in the English original from The Life and Letters of Charles Darwin, (Darwin, F., 1877, London, John Murray; at page 88 of volume 2) ?: "It is really laughable to see what different ideas are prominent in various naturalists' minds, when they speak of 'species'; in some, resemblance is everything and descent of little weight--in some, resemblance seems to go for nothing, and Creation the reigning idea--in some, sterility an unfailing test, with others it is not worth a farthing. It all comes, I believe, from trying to define the indefinable."

Let's talk about this "layman to layman". You're curious, and that's fine, but your questions belie a misunderstanding of evolutionary processes themselves. Why, for example, is it important that there be some case of 'extra-species' mutation in a so-called "documented" form and, "during the span of Human scientific observation"? That's a very narrow frame in which to operate. I ask: why should you, I or anyone else take these as the key bases for speculations, investigations, and observations concerning evidence or observation of biological evolutions? Why aren't extant living organisms "evidence" of evolution's operation? What would that evidence's being "documented" mean? What is this "beyond standard variation" ?---- as in your "a species mutating beyond standard variation" ? Is there such a thing as "standard variation" in nature? This is a vague and I think meaningless concept. How do you come by it? Agree or disagree, please indicate your views for each: Humans (Homo sapiens) and chimpanzees (Pan troglodytes) have a common ancestor. Their DNA profiles are almost 99% identical. Consequently, if they are not one and the same species, then how are we to account for this amazing nearly identical DNA profile? Once arrived at this common ancestor's existence, there needn't be billions of years in mutations in order for humans and modern chimpanzees to have diverged, right? So, where are we so far in this? Your comments?..... ______________________________________________________ For further reading (or viewing) : Scientific American, May, 2009 (cover story) "What Makes Us Human?" http://www.scientifi...-makes-us-human Video: http://fora.tv/2009/..._Makes_Us_Human Research site homepage: http://docpollard.com/index.html

To stay within the topic of this thread, rather than make it a general discussion of the merits of Kupiec's work, I'll just reply that IF his work is eventually accepted and replaces, where it is pertinent, now-standard theory, then his case does, indeed, present us with a prime example of scientists showing themselves remarkably resistant to new theory---experimentally tested and peer-reviewed---which seriously challenges and overturns some of the current theory just as the OP has remarked above. RE: " He's never offered as an overthrow to species concepts and pop-gen principles in peer review to my knowledge." He may never have done so in the way that you intend by that remark; I don't know. But his work is done at the Centre Cavalliès of the Ecole Normale Supérieure, Paris; and published in peer-reviewed science journals of the best quality. I haven't read them but I'd be very much interested to read Ernst Mayr's One Long Argument, The Growth of Biological Thought and What Evolution Is . So those are now on my reading list. By the way, Kupiec's publisher of L'origine des individus , Fayard (Series: "Le Temps des Sciences") also publishes Mayr's French edition of The Growth of Biological Thought, Diversity, Evolution and Inheritance and This is Biology. Interesting coincidence, that.

You've read some of Kupiec's papers or his The Origin of Individuals, then?

Very well but, at the same time, that "it doesn't matter" why we are here can matter very, very much and in my opinion, it does matter that "it doesn't matter." I take it you mean ultimate meaning or purpose. And, in that sense, my answer is, "Fortunately, none that I have been able to discover." But, if meaning and purpose are relieved of the requirement that these be ultimate in scope, then my answer becomes, "Fortunately, as much meaning as one is able to devise to some noble end."

Fine, but, again, citing Kupiec as my "star-witness" example, his theories have a thirty year record of serious work behind them and, in his specialty, he is still regarded by many as a maverick--that is, his work remains very much the unorthodox view. (Bear in mind that in all that I post on this topic, I'm a layman relying on another's work as the basis of the positions I try to defend here. So, when you want to ask, "How do you know that?!" the answer is and most always will be, "I read it in a book by some very smart guy or woman.") To get an idea of just how unusual a theoretical approach is his, imagine that you changed your views on phylogenesis and phenotypes accordingly, "Species" is an abstraction that we must chuck out the window with "race" and other passé conceptions in biology. Darwin, Kupiec points out, scoffed at the attempts of his contemporaries to define "species" and, in the correspondence cited, wrote that it amused him to find these scientists trying to define what he saw as resistant to all definition. Our bodies' organs are not "in the service of" our body as a whole. Instead, it is the other way around. In general, each internal organ is a creature of evolution's work, and doesn't "exist to serve" some conception of the interests of the larger organism--if, for no other reason that there are no such "interests of the larger organism". Those are imported by people who impute a finalist view of biological processes. In the body, organs operate (well or not well) in the particular individual's "environment". Cells, tissue, and the organs they compose, work in ways that rather exactly mirror the interactive relationships of plant and animal life as it exists in an evolving natural environment, exterior to the human body. The same random (unpredictable) behavior at the quantum level of matter---the atomic protons, electrons, neutrons, etc.---which is assumed to operate in "inanimate matter" operates in the matter that composes living organisms. So, the compounds that compose genes, proteins, cells and all other living tissue are themselves composed of elemental particles which behave in a random fashion at their atomic level---with the result that a seeming deterministic operation of genes and DNA is instead the result of what are only probabalistic outcomes, over very great numbers of cells, etc. As strange ideas go, these are generally outside the mainstream views which students of biology learn--even as specialists, according to Kupiec. Is he wrong?

Permit me to add one, Jean-Jacques Kupiec though he's now a good deal less ignored than was once the case. (Note: I am not a scientist by training or profession. I've just developed---as though by accident--a sort of specialty interest in the very matter of unorthodox opinion facing intransigent orthodoxy--in science, in the arts, and other aspects. For example, not everyone believes that Shakespeare came from a modest and mainly illiterate family in Straford-Upon-Avon. Some see, instead, the the person of Edward de Vere, 17th Earl of Oxford, behind the name Shakespeare (and I am in that camp). But, if that is your view, too, then for a first-hand experience in the realities of bucking entrenched professional opinion, try getting a university position teaching Shakespeare and notice the consequences.) The fact is that the issue raised by the thread's opening post is indeed very, very common in science. In the case of Kupiec, while there is existing theory--indeed, lots of it---his version is quite revolutionary, even though he builds on important work from other predecessors and, most notably, Charles Darwin. Now, you've been warned that I'm not an expert on this or any other science, but here is my non-expert's assessment: Kupiec, not alone, of course, but together with his colleagues, is doing the work that I think Darwin would be doing if he were alive today and had the same benefit of the intervening years of scientific knowledge in molecular biology. My layman's view is that in his genius and in the importance of his work, Kupiec is every bit Darwin's peer and his L'origine des individus every bit the peer of The Origin of Species. And, yes, I know that that is a very great claim. But, if you haven't already read his work, read it and judge for yourself. His L'origine des individus will, I believe, one day have the status and importance of The Origin of Species.

I'm reminded of reading opinion poll results in the press which indicate what respondants have said concerning some controversial issue--without any idea of just how much, if anything, any of these respondants actually knows about the facts concerning the issue, its history, its variously contended aspects, etc. What difference does it, should it, make that X% of the respondants think Y or Z about topic "A" if, at the same time, some substantial portion of those respondants--and we don't know which ones among them all---are quite simply completely ignorant of the issue's basic facts? Imagine that you read an article presenting the results of people's opinions concerning topics in one of the natural sciences--physics, biology, chemistry, or another---and you had no idea which respondants replying one way or another had any familiarity with the facts about the topic about which the questions are posed: how much credit would you give to that poll's results? You write, above, "I've taken quite a bit of flack because of my inability to answer questions asked of me for statements or questions I myself have made or asked." I think that is rather fair criticism. It suggests, among other things, that you may not have even acquainted yourself on the issues sufficiently to respond with a demonstrated awareness of the already existing main opposing camps' views, an awareness of what these main camps hold as true or false and why, an awareness, in short, of the recent or not-so-recent history of the controversy over any given issue. And, if that is in fact the case, then why aren't your critics quite correct to fault you for having not-very-much to say as concerns what you'd propose to do about X, Y, or Z as a social or political problem? Indeed, the very definition of what's a problem and what isn't already tells us something important about a person's starting assumptions. In any question under consideration--- as I think would autoalmtically be the case concerning a topic in science--- the question of "Where do we begin concerning our readers' views about and knowledge of X ?" arises. We can read and gather a number of things about your views by interpreting the comments you've already posted. But, we still have little idea of the bases of these, even if we've interpreted the comments correctly. I'm much more interested in why you view some significant portion of Americans as being at or near the point of being fairly described as socialists or communists, much more interested in learning just what you may (or may not) know about what socialism or communism is (or is not) than in the fact itself that you consider some significant number of Americans to be rightly described as such. Am I making sense to you? I see I forgot to address the question at the end of your opening post: "So, if this Romney-Ryan is a winning ticket, will it bring us a better future or more heartache?" As I see it, the answer is: definitely more heartache as a nation as a whole. But that has to be put into perspective: in general, those who enjoy the very top-most privilege, wealth, power, will enjoy as much or more of these (for a while yet) under Romney and Ryan, than perhaps they do or would under Obama. For the rest, in increasing proportion as one descends the scale of wealth and privilege, the heartache increases until one reaches those with the least in material resources, in privilege and in power, where the heartache is proportionately the greatest. I wrote, "for a while yet" because the process of savaging the middle-class or, even more, the poorest, in order to transfer even greater wealth and privilege to those at the top of the pyramid can only go on for a certain limited time before the benefits to those at the top reach the limit of diminishing returns. Then things crash in an open and catastrophic way that seriously touches even the top of the pyramid.

I guess they are unable to converse in sign language and there's nothing mirror-like in which to see one's reflection. The dirty-faced sweep sees nothing amiss in his partner's appearance and so, suspecting no grime on his face, he doesn't wash up. The other, seeing the "opposite," a partner with a grimy face, assumes, for his part that his face, too, is probably grimy, so he washes his face though it doesn't need it. I thnk it's misleading to refer to "the people who use me" as being "users" of you. Strictly speaking, only those who buy "you" can be said to "use" you. The "user" you've referred to is a mistaken predicate in the sentence since, while there is an entity in that "role," this entity makes no "use" of anything in the proper sense. So, I think the riddle's statement is flawed.

Hello. As an introduction, I'm here, as I see it, as a refugee from the inanity of practically all other public internet discussion fora because it appears from experience that I'm either too smart or too stupid or both to be able to bear the, to me, amazing idiocy that is so common in other discussion fora. That, and the fact that I'm an amateur of sceince have led me to search for and join such a site as this. I'm not unmindful that science-"fans" are human, too, and that they can exhibit peculiar notions--some of mine would almost certainly strike some as peculiar--but I think that I have a better chance of finding interesting people and topics and discussions here than has been the case elsewhere. Because I prize science as a method, a way of approaching the world, there is really a very great deal about contemporary society which fills me with despair for the present and future. I am by nature not a particularly optimistic person. In other fora, my tendencies to speak frankly have found much resentment from other readers. The most recent unhappy experience was at the U.K. newspaper, The Guardian's discussion fora--which, though I haven't announced it there, I'fve left definitively. They would regard this as their gain and my loss; though I'm not inclined to see it that way. Some people who've been important influences on me by their lives, their careers, and, most of all, their writings, have been, to give you insight into my tastes and my politics, one of my other great intellectual interests-- Bertrand Russell, George Orwell, C. Wright Mills, Karl Popper, Benoît Mandelbrot, Konrad Lorenz, and, most recently and quite importantly, the person and work of Jean-Jacques Kupiec. Thanks for reading. Pleased to be here I hope.