On Ontophylogenesis or "Cellular Darwinism"

proximity1 · September 3, 2012

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

Edited September 3, 2012 by proximity1

Arete · September 3, 2012

Kupiec's theory (for those reading along, the fundamental premise is that gene regulation is purely stochastic and local environmental pressures cause selection amongst cells in an embryo, ultimately leading to phenotypic differentiation in the resultant individual) has some fundamental flaws/gaps:

A) There's an extraordinary body of evidence that regulatory genes constrain embryonic development: 668, 000 hits on Google Scholar, representing thousands of individual experiments empirically confirming that unlike as Kupiec claims, the expression of regulatory genes is not stochastic. e.g. http://www.nature.co...bs/nrg2781.html http://www.plantcell...12/8/1491.short http://www.jimmunol....46/6/1914.short etc.

B) If, as Kupiec claims, regulatory genes are purely stochastic and the local enviroment is wholly responsible for embryonic development, what evolutionary purpose do the regulatory genes whose existence is experimentally confirmed (e.g. HOX genes: http://en.wikipedia.org/wiki/Hox_gene) serve?

C) If the local enviroment drives diversification, why do all embryos pass through the same developmental stages? If the local enviroment is driving cellular selection, surely there would be variation in the process of embryonic development, in association with variation in selection pressure. This is not observed, even in widespread species living in vastly different environments. Differences in embryonic development appear to be related to divergent evolutionary history, not differences in environmental pressures. http://en.wikipedia....i/Embryogenesis

D) If the genome is, as Kupiec assumes, purely a generator of proteins without regulatory functionality, how do organisms with very similar protein coding structures existing in very similar environments wind up being very different organisms? http://nook.cs.ucdav...ehl_COSB_01.pdf

proximity1 · September 3, 2012

Kupiec's theory (for those reading along, the fundamental premise is that gene regulation is purely stochastic and local environmental pressures cause selection amongst cells in an embryo, ultimately leading to phenotypic differentiation in the resultant individual) has some fundamental flaws/gaps:

A) There's an extraordinary body of evidence that regulatory genes constrain embryonic development: 668, 000 hits on Google Scholar, representing thousands of individual experiments empirically confirming that unlike as Kupiec claims, the expression of regulatory genes is not stochastic. e.g. http://www.nature.co...bs/nrg2781.html http://www.plantcell...12/8/1491.short http://www.jimmunol....46/6/1914.short etc.

B) If, as Kupiec claims, regulatory genes are purely stochastic and the local enviroment is wholly responsible for embryonic development, what evolutionary purpose do the regulatory genes whose existence is experimentally confirmed (e.g. HOX genes: http://en.wikipedia.org/wiki/Hox_gene) serve?

C) If the local enviroment drives diversification, why do all embryos pass through the same developmental stages? If the local enviroment is driving cellular selection, surely there would be variation in the process of embryonic development, in association with variation in selection pressure. This is not observed, even in widespread species living in vastly different environments. Differences in embryonic development appear to be related to divergent evolutionary history, not differences in environmental pressures. http://en.wikipedia....i/Embryogenesis

D) If the genome is, as Kupiec assumes, purely a generator of proteins without regulatory functionality, how do organisms with very similar protein coding structures existing in very similar environments wind up being very different organisms? http://nook.cs.ucdav...ehl_COSB_01.pdf

(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.)

Edited September 3, 2012 by proximity1

proximity1 · September 4, 2012

CAVEAT:

It's a pity that the opening post is no longer subject to editing. If it were, I'd remove the reference/link to

Pure variation and organic stratification , by Jérôme Rosanvallon (Université Paris 7, Diderot, France)

which, on further examination, has no place in a consideration of Kupiec's work as I see it.

While, I hope, there shall be much more to come in this thread, here are other amendments I'd make to the opening post.

In the following, I intend to refer to Kupiec's theory by the term he has coined for it, "ontophylogenesis" and drop any further use of "cellular Darwinism" in my posts. Even though "cellular Darwinism" as a phrase figures in the English translation of his L'origine des individus (2009, Fayard, Paris) I don't see in it any advantages over the term "ontophylogenesis" and think that "cellular Darwinism" may prompt misconceptions, so varied are popular notions of just what "Darwinism" denotes.

I add the following two citations for a prefatory "flavor" to the thread:

"I am in no degree ashamed of having changed my opinions. What physicist who was active in 1900 would dream of boasting that his opinions had not changed?" -- Bertrand Russell, (cited in the introduction to The Basic Writings of Bertrand Russell, ( 1961, George Allen & Unwin, London, )

"In order to avoid the reproach of having failed to do what I have not pretended to have done, in order to prevent, if that may be done, misunderstandings which, once produced, are nearly impossible to clear away, I shall try to define unambiguously the object of the present work." -- Lucien Lévy-Bruhl from the preface to the fourth edition of La mythologie primitive (1935)

(my translation) Edited September 4, 2012 by proximity1

**imatfaal** · September 4, 2012

proximity1

we tend to think that after a period of time they should stay as they are to allow a linear readability; personally I think that once posts have received a response they should become uneditable. Your message above is more than enough to show that you have revisited your initial ideas. No one expects posts to be fully formed and flawless logical entities - and the progress from initial idea to final thoughts is very interesting (synth-/antith-/thesis dialectic etc)

proximity1 · September 5, 2012

Previous recommended reading, courtesy of Arete

from the "Lounge" discussion : Why are scientists seemingly reluctant to accept new ideas? In some cases, at least

Ernst Mayr and the modern concept of species by Kevin de Queiroz (Smithsonian Institution, Washington, D.C.)

Species Concepts and Species Delimitation (from the Oxford University journal Systematic Biology ) by Kevin de Queiroz (Smithsonian Institution, Washington, D.C.)

Genetics and the Origin of Species (1951) (excerpt) by Theodosius Dobzhansky (1900-1975) (from the Unofficial Stephen J. Gould Archive

"DARWIN ON SPECIES DEFINITIONS AND SPECIATION" (selected citations)

On the Non-Existence of Human Races by Frank B. Livingstone and Theodosius Dobzhansky

Counterpoint recommended reading, ( suggested by proximity1) :

Speciation: From Darwin to Mayr and back again by Dr. Diethard Tautz, Director at the Max Planck Institute for Evolutionary Biology in Plön (Germany); in Lab Times , January 2009, pp. 24-27 (with references for further reading)

As support for the view that scientists frequently "lag" in their readiness to give serious, fair consideration to new and challenging theories, this article makes for an interesting entry in that discussion.

E.G.

(page 24-25) "The theory of population genetics was developed in the 1930s, based on the principles of Mendelian
genetics. One of the non-intuitive, and in fact surprising, outcomes of this theory is that only a small amount of gene flow is

sufficient to homogenize allele frequencies within a gene pool. Mayr´s species concept essentially defines a gene pool, and population genetics seemed to imply that only

very powerful forces could disrupt it. To the biologists at the time, this strongly suggested that only geographic separation could cause such disruption. This was the origin

of the allopatric paradigm of speciation. It was most forcefully advocated by Theodosius Dobzhansky and Ernst Mayr, who integrated this paradigm into their “synthetic

theory of evolution”. It is still the paradigm most prominently presented in almost every textbook. Although it may be a little too early to conclude a historical analysis of recent

decades, it may well be that, one day, this period of uncompromising dogma will be seen as the Dark Ages of speciation research. The allopatric paradigm was based

on a few facts, a lot of faith, and on paradigmatic despots ruling the field. And we haven’t yet reached the speciation Enlightenment. Anyone who tries to publish alternative

speciation scenarios will, sooner or later, be confronted by medieval referees. Personally, I have a good collection of dismissive comments from such colleagues."

(some notes on this suggested reading: as I noted above, in the opening post here, though most everything I contribute on this topic is based primarily on my reading of Kupiec, I do not pretend to necessarily represent his own views in my comments or suggested reading. Here, for example, while I find the article by Dr. Tautz an excellent reply to the arguments (as I've read them so far) in the links above recommended by Arete, Kupiec, who knows the literature thoroughly as I do not, will know whether and in what respects his own work and views diverge from those of Dr. Tautz. Other non-specialists like myself should bear this factor in mind throughout this thread's progress.)

Edited September 5, 2012 by proximity1

proximity1 · September 8, 2012

Here' a little «status report »

Currently, I'm reading through Arete's recommended reading. So this is a kind of « intermission » time for me.

Still to read, or currently reading:

de Queiroz, K. « Ernst Mayr and the modern concept of species » journal PNAS, 3 May 2005

de Queiroz, K. « Species Concepts and Species Delimitation » from the journal Systematic Biology, 56(6):879-886, 2007

Mayr, E.; One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought , Harvard University Press (fFrench translation)

Arete · September 8, 2012

I find the article by Dr. Tautz an excellent reply to the arguments (as I've read them so far) in the links above recommended by Arete,

Only it's a few decades behind the current state of the field, which has moved beyond strict allopatric models of speciation:

see ecological/sympatric speciation:

http://en.wikipedia.org/wiki/Sympatric_speciation

http://www.pnas.org/content/early/2009/06/15/0901264106

http://www.sciencemag.org/content/323/5915/737.full

http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02392.x/abstract;jsessionid=E288FCD88EAECA86B2EF9D2D534B1E47.d03t02

and hybrid speciation:

http://en.wikipedia.org/wiki/Hybrid_speciation

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002274

http://www.nature.com/nature/journal/v446/n7133/full/nature05706.html

as examples.

proximity1 · September 9, 2012

Only it's a few decades behind the current state of the field*, which has moved beyond strict allopatric models of speciation:

see ecological/sympatric speciation:

http://en.wikipedia....tric_speciation

http://www.pnas.org/...6/15/0901264106 (dated June, 2009)

http://www.sciencema...3/5915/737.full (dated February, 2009)

http://onlinelibrary...534B1E47.d03t02 (Publication History: Received 13 January 2011; revised 19 August 2011; accepted 19 August 2011 ) Hence, written in 2010 at the latest.

and hybrid speciation:

http://en.wikipedia....brid_speciation (Wikipedia, dating from 2009? (last revised in Feb. 2012 has no probative value.) As a "source" for rebuttal of Tautz's article in Lab Times of 2009? )

http://www.plosgenet...al.pgen.1002274 (Received: April 7, 2011)

http://www.nature.co...ature05706.html (dated 15 March 2007)

as examples.

(* emphasis added)

Let's review: you are reproaching as outdated by "a few decades" an article written in 2009 by a professional scholar in the specialty concerned here and offering, as "evidence" of more recent work, articles which are dated, respectively, 2009; 2009; January 2011; 2009 (with unspecified revisions in 2012); April 2011 and, finally, March 2007.

In addition, your rejection of Tautz's arguments comes completely without comment. At no point do you indicate any specific defect in the claims, reasoning and conclusions of Diethard Tautz. Instead, the reader is offered a flat unsupported assertion that Tautz's article is not receivable here because, by your claim, it is "...a few decades behind the current state of the field...."

As I understand it, then, you are authorized to cite at will whatever you please as presumed valid scholarship while my citations in reply, despite their devastating cogency, are ruled out of order without review or comment on your part.

I believe that the picture emerging does not serve you or your case well; on the contrary, nothing I've read so far of your cited articles has made the slightest impression on me for their pertinence to the issues concerned here.

At this point, I have nearly finished reading all the previously cited articles you presented---with the exceptions of, first, the supposedly more up-to-date work of Kevin de Queiroz in "Species Concepts and Species Delimitation," which was submitted to the journal, Systematic Biology, in November of 2006 and, secondly, of Mayr's One Long Argument, published in 1992, and which I won't obtain until tomorrow at the earliest, from a library.

But, even before I can finish these and write a comment on their merits or the lack of them, you present fresh reading recommendations with your observation that the state of the art has moved on, leaving Diethard Tautz's views lagging behind by a few decades.

Let me conclude this by the observation that, having arrived within one and a half pages of finishing Kevin de Queiroz's article, "Ernst Mayr and the modern concept of species" my heart sinks at the prospects of having to read stilll another of his articles. For a picture of someone conceptually totally "at sea" and desperately flailing about for something which will float, I am very hard-pressed to imagine anything more compelling than what the author offers us there. Indeed, I cannot recommend strongly enough that readers examine this article--and, can it be doubted? his other one you recommend--for a vivid picture of a discipline in full conceptual disarray. By contrast, Kupiec's work and reasonings are models of everything that one could wish for in your champions' offerings, but does not find there.

My next step is to invite Professor Tautz to have a look at what we have here so far as a discussion.

Please excuse me, as I have more painfully dreary, plodding, text of tortured circular reasoning to return to and to read at your recommendation before I can comment further with examples in support.

Edited September 9, 2012 by proximity1

Arete · September 9, 2012

Let's review: you are reproaching as outdated by "a few decades" an article written in 2009 by a professional scholar in the specialty concerned here and offering, as "evidence" of more recent work, articles which are dated, respectively, 2009; 2009; January 2011; 2009 (with unspecified revisions in 2012); April 2011 and, finally, March 2007.

Err I'm not sure you're understanding - To quote Tautz:

"This was the origin of the allopatric paradigm of speciation. It was most forcefully advocated by Theodosius Dobzhansky and Ernst Mayr..."

What I'm saying is that the "allopatric paradigm of speciation" is no longer a central paradigm in evolutionary biology, and providing references to support the acceptance of sympatric speciation models in the literature - including a couple of review papers. There are a few stalwart academics who oppose the idea that speciation can occur in sympatry (like Jerry Coyne) but most biologists do not subscribe to purely allopatric mechanisms of speciation, so Tautz's article is arguing against an outdated point of view.

The reason I linked to wikipedia articlesis because they are written in plain English. As a layperson, I though these might be more tractable as background reading than specialist scientific papers. Systematic Biology is a methodologically angled journal which is usually heavy going even by scientific journal standards.

I'm sorry that's what you took away from the (page and a half you read) De Querioz article. The intent of the article is to present the various conceptual approaches which scientists have tried to reconcile the fact that organismal diversification is a dynamic, continuous process and as logically follows, organisms don't always fit into neat little categories the way we'd like them to. Nevertheless the process of diversification results in differentiated organisms, and to conduct studies and convey meaningful information we need categories. The Evolutionary Species concept he outlines in his 2007 paper is probably the closest there is to a universally recognized species concept as science currently has.

Tautz's assertion that the allopatric model of speciation is "It is still the paradigm most prominently presented in almost every textbook." Is not very well supported by actual examinations of texts. Take Schluter's "The Ecology of Adaptive Speciation (2000)" or Frankham et al.'s and "Introduction to Conservation Genetics (2002)" as contradictory examples of texts which discuss sympatric speciation which I know of off the top of my head.

The central issue with Kupiec's work I outlined in my first post in this thread. He's not offering a new concept of species, he's offering an entirely new mechanism of organismal diversification, which, in the view of extremely large quantities of contradictory evidence (i.e. that regulatory genes regulate embryonic development), is poorly supported. Attacking current species concepts and using their shortcomings as somehow supporting his hypothesis is a strawman argument - even if all concepts of species are invalidated, it does not support cellular Darwinism one bit until it is shown that the local enviroment rather than regulatory genes govern embryonic development.

Edited September 9, 2012 by Arete

proximity1 · September 10, 2012

Err I'm not sure you're understanding - To quote Tautz:

I'm sorry that's what you took away from the (page and a half you read) De Querioz article.

That is what you understood by this?:

"Let me conclude this by the observation that, having arrived within one and a half pages of finishing Kevin de Queiroz's article, "Ernst Mayr and the modern concept of species" my heart sinks at the prospects of having to read stilll another of his articles. "

(emphasis added)

Allow me to corrcect your faulty reading, understanding: I didn't read merely one and a half pages of de Queiroz's articles, I read (and have now read) ALL of them---those you referenced. And, let's stop on this point and think a moment: you've just insinuated, erroneously, that I read only one and a half pages of the article mentioned. (And to do that, you had to miss the clear import of what I actually wrote.)

Now, on the other hand, in a thread I opened with the object of discussing another text, The Origin of Individuals, by Jean-Jacques Kupiec, as far as I know at this writing, you have read little or even nothing at all of it. You'll correct me, I'm sure, if I'm mistaken about that.

To continue, your style of argument is interesting: you offer for support, certain texts; then, faced with cogent rebuttals of the text you yourself cited, you allege that the rebuttals are outdated because the state of current knowledge has moved on.

The central issue with Kupiec's work I outlined in my first post in this thread. He's not offering a new concept of species, he's offering an entirely new mechanism of organismal diversification, which, in the view of extremely large quantities of contradictory evidence (i.e. that regulatory genes regulate embryonic development), is poorly supported. Attacking current species concepts and using their shortcomings as somehow supporting his hypothesis is a strawman argument - even if all concepts of species are invalidated, it does not support cellular Darwinism one bit until it is shown that the local enviroment rather than regulatory genes govern embryonic development.

But, if we are discussing species concepts at all, it is not because I made them a part of the discussion but, rather, because they are one of the central topics of the articles you cited. (for support? If not, why, then, did you cite them if species concepts are not really germane to this discussion?)

Should I expect more of that from you? And, just out of curiosity, when, in a discussion, your interlocuteur points out an error on your part, do you ever acknowledge it, even implicitly, by, for example, changing tack and correcting course?

Edited September 10, 2012 by proximity1

Arete · September 10, 2012

Apologies for misinterpreting your post. It did read to me like you'd gotten 1.5 pages into the De Queiroz paper and written it off. Syst Biol is a very dense journal format, aimed at methodological development in phylogentics and allied fields and thus written for an audience working in that arena. Thus articles there are often a bit inaccessible for the layperson. I chose the De Queiroz articles not because he's some kind of "champion" in the field, but because he'd written a review paper. Here's another good one by Jody Hey's group in Evolution which is a broader scoped journal -

http://onlinelibrary...11.01542.x/full

There's some scary maths behind it (I mean scary for biologists, not as a personal judgement of you ) , but some more nitty gritty methodological papers which tackle species delimitation from various angles are out there too, and there's a sizeable body of capable people tackling the problem of how we define, and then delimit species in a biologically relevant, but useful and tractable manner:

http://sysbio.oxford...t/59/1/59.short

http://www.pnas.org/...7/20/9264.short

and some interesting/topical applications thereof:

http://sysbio.oxford...3.full.pdf+html

http://www.amjbot.or...5.full.pdf+html

You'll correct me, I'm sure, if I'm mistaken about that.

I prefer to stick with what Kupiec's gotten through peer review, than his popular science texts.

i.e.

http://www.sciencedi...079610709000790

http://www.springerl...t18e9d1hmlp4tt/

To continue, your style of argument is interesting: you offer for support, certain texts; then, faced with cogent rebuttals of the text you yourself cited, you allege that the rebuttals are outdated because the state of current knowledge has moved on.

To recap (since it happened in the other thread). I stated, as a criticism of Kupiec's supposed call to reject the concept of species and that Darwin himself had scoffed at the concept - that a significant body of work had been done on the species problem since Darwin, citing work by Mayr and Dobzhansky as significant contributions. These guys and their colleagues at the time made considerable advances on our understanding of organismal diversification in light of the emergent field of genetics at the time, and to neglect to mention their contributions when launching straight from Darwin -> now overlooks the significant advances which have been made in the field over the last ~150 years. This was my initial criticism of Kupiec's supposed call.

The Tautz article cited by you, criticized the point of view of particularly Ernst Mayr, that speciation could only occur in allopatry. Taut'z point is very relevant to such exclusively allopatric models of speciation - and sure, has been leveled at this model before - such that most scientists in the field accept that allopatry is not necessary for speciation to occur. It's not terribly surprising that, as new information has become available, the concept of species and our understanding of the processes which generate species have been refined in the last 60-70 years.

The big however - which I was trying to point out is that the Tautz article, while quite rightly criticizing strictly allopatric models of speciation, is not a criticism which can be applied to current state of the field, which has progressed beyond the model critiqued by Tautz. If you've read some of the De Quieroz papers, you might have a bit of an understanding of how the field has progressed (though it seems as though you've dismissed it as fundamentally flawed - a view which most biologists would disagree with). It's tough trying to disseminate 150 years worth of work by hundreds of scientists in the context of a forum discussion, so I think some level of miscommunication is inevitable - sorry if I lost you along the way through omissions or lack of clarification.

TBut, if we are discussing species concepts at all, it is not because I made them a part of the discussion but, rather, because they are one of the central topics of the articles you cited. (for support? If not, why, then, did you cite them if species concepts are not really germane to this discussion?)

The criticism arose when you stated that Kupiec proposed the rejection of the concept of species outright - using the claim that "Darwin himself scoffed at it". One of my criticisms was that the concept of species has undergone a lot of advancement since then - followed by an attempt to give you a picture of the field's progression and current state. I felt that Kupiec's supposed statement neglected the body of work since Darwin and the current state of the field.

As further clarification - it's unsuprising that he would call for the rejection the modern synthesis, as acceptance of his hypothesis requires a fundamentally changed view of organismal biology altogether. The problem is that the modern evolutionary synthesis has come about as the refinement and culmination of centuries of great thinkers, and countless thousands of independent pieces of empirical evidence.

I'm certainly not saying Kupiec's work is entirely without merit - intercellular competition probably has a role in biological development, it's a fascinating topic of research and he is a very astute written communicator. Does it merit the overthrow of everything we currently accept about speciation? Certainly not.

The evidence for the currently accepted (though still under refinement) understanding of organismal diversification vastly outweighs the evidence for "ontophylogenesis" as the dominant mechanism in diversification. Again, Kupiec's work is interesting and valuable, but hugely overstated as a replacement for the modern synthesis.

We could test the validity of his concept as an overarching architecture with a relatively easily contrived experiment - many organisms produce vast numbers of clonal (i.e. genetically identical) embryos. We could take a homosporous plant - in which each embryo has identical protein coding and regulatory genes, and raise them in different local environments. We would expect, under Kupiec's premise that we would, due to diverse selection conditions, end up with a phenotypically diverse arrangement of organisms. Observational evidence of geographically widespread homosporous plants shows that both fundamental phenotype and the process of embryonic development are largely the same.

Conversely, if we raise spores from individuals with different regulatory genes in the same local environment, we should see similar phenotypes. Again, observational evidence contradicts this.

Should I expect more of that from you? And, just out of curiosity, when, in a discussion, your interlocuteur points out an error on your part, do you ever acknowledge it, even implicitly, by, for example, changing tack and correcting course?

Can you address any of the points made in post #2?

proximity1 · September 10, 2012

In repsonse to RE: "Padren" @ post N° 63 , posted in "Why are scientists seemingly"...

proximity1, on 31 August 2012 - 03:30 PM, said:

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.

This is an example of an idea that - as an absolute amateur myself - I would be exceptionally reluctant to read up on, because frankly the sheer amount of ridiculousness in the idea suggests that "Either A) you are misrepresenting Kupiec B) Kupiec's contention is poorly articulated yet somehow carries a hidden grain of genius or C) Kupiec's contention is poorly articulated because it's idiotic drivel"

I say this because the claim that cells, tissue and organs "rather exactly mirror" external environmental relationships is dead wrong - I do not have wild livers breeding, competing and killing each other within my body, nor can any cellular mutation that leads to a momentary improvement in function actually pass those improvements on - mutations in liver cells don't migrate down into the reproductive genes of the host.

Now, I'm not a scientist, but I would generally give a person making that claim about 30 seconds to see if they can say something that would clarify the statement in a manner that is coherent, but not longer if the initial claim is already that inarticulate. I hear enough incoherent theories in a day (and I'm a laymen) that more than 30 seconds would become debilitating after a while. If there is scientific genius in the idea, then someone else will eventually discover it who is capable of articulating it, and if not then there's no loss.

[ Editorial note about citing texts: Because, for practical reasons, I don't have access to the translated English edition of Kupiec's text, I am persenting my own translations of his original French whenever I cite his work--except of course where he may use English in the original.

And in this thread and, in general, as I can read either English or French with equal facility, I choose, whenever practical, to read a work in either the author's original English or original French. But, where a text is either very difficult (or, of course, impossible) to obtain or obtaining it is for me too expensive, then I resort to whichever between French or English, is the cheaper, more easily obtained version. In the case of Mayr's texts (originally in English) I am using such of them as are easily available in French translations from libraries (but very hard to find in English other than by ordering them). So, since Kupiec's book is both very expensive and hard to come by as well as being no advantage to me in its English translation (except as I would like to cite the English translation's version), I have to, instead, offer my own translations, which might vary slightly from what a reader of the published translation finds on the page.]

My response:

Yes, that point of his text was, for me, too, one of the most startling, fascinating and interesting. But, by the time I arrived there, I'd already read and understood his theoretical arguments and their bases. However, though it surprises laymen such as we are, I suspect that this idea that I expressed as "Our bodies' organs are not "in the service of" our body as a whole. Instead, it is the other way around,' is, for some nuimber of scientists in biology, not really a great revelation. In fact, Kupiec gives full credit for this point to Claude Bernard, M.D., who, in Leçons sur les phénomènes de la vie communs aux animaux et aux végétaux at pages 357-359, writes, (in part ; this is an excerpt of Kupiec's excerpt of Bernard's text; elipses below show where I have skipped over Kupiec's citation)

Nous avons dit que l'organisme vivant est une association de cellules ou d'éléments plus ou moins modifiés et groupés en tissus, organes, appareils ou systèmes. C'est donc un vaste mécanisme qui résulte de l'assemblage de mécanismes secondaires. Depuis l'être cellule jusqu'à l'homme, on rencontre tous les degrés de complication dans ces groupements; les organes s'ajoutent aux organes, et l'animal le plus perfetionné en possède un grand nombre qui forment le système circulatoire, le système respiratoire, le système nerveux, etc.

Longtemps on a cru que ces rouages surajoutés avaient en eux-mêmes leur raison d'être ou qu'ils étaient le résultat du caprice d'une nature artiste. Aujourd'hui nous devons y voir une complication croissante régie par une loi. L'anatomie s'en tenant à l'observation des formes n'avait pas réussi à la dégager. C'est la physiologie seule qui peut en rendre compte.

Les organes, les systèmes, n'existe pas pour eux-mêmes; ils existent pour les cellules, pour les éléments anatomiques innombrables qui forment l'édifice organique. ...

Ainsi, la loi de la construction des organismes et du perfectionnement organique se confond avec les lois de la vie cellulaire. C'est pour permettre et régler plus rigoureusement la vie cellulaire que les organes s'ajoutent aux organes et les appareils aux systèmes. La tâche qui leur est imposée est de réunir qualitativement et quantitativement les conditions de la vie cellulaire. (LPV, p. 357-359)

-------------------

There, you have Bernard in the original, so that, if you please to do so, you can check my understanding of it as I translate it, in the following,

" We have said that the living organism is an association of cells or elements more or less modified and grouped in tissue, organs, devices or systems. It's thus a vast mechanism which results from the assembly of secondary mechanisms. From the (level of a) cell on up to that of man, we encounter all degrees of complication in these groupings; organs are added to organs, and the most perfected animal possesses a great number which form the circulatory system, the respiratory system, the nervous system, etc.

For a long time we have believed that these additive inner-works had in themselves their purpose or that they were the result of the caprice of artistic nature. Today, we must see in them an increasing complication regulated by a law. Anatomy, being focused on the observation of forms, did not succeed in discovering this. It is physiology alone which can take account of it.

The organs, the systems, do not exist for themselves; they exist for cells, for the innumerable anatomical elements which form the organic structure." ...

Thus, the law of the construction of organisms and of organic perfectionment are compounded with the laws of cellular life. It is to allow and to regulate cellular life more rigorously that the organs come to be added to organs and their combinations into systems. The task which is set for them is to bring together qualitatively and quantitatively the conditions of cellular life." (p. 357-359)

Kupiec then writes, following this citation of Bernard,

"L'organisation n'a pas pour but d'assurer le fonctionnement de l'organisme en tant que totalité. Elle crée le milieu intérieur qui apporte aux cellules ce dont elles ont besoin pour vivre."

"The (or "Such organic...) organisation does not have for its purpose the maintenance of the functioning of the organism in its totality. It creates the interior environment which provides cells with what they need to live."

At this point, I want to leave citations of Claude Bernard and return to Kupiec's own views, expressed a little earlier in the text to the portions just cited.

At page 170, he writes, (in his text's organisation, (section) 6.1.3 :

Le rapport entre l'organisme et ses parties est une autre question essentielle qui prête souvent à confusion. Dans l'ontophylogenèse, les cellules sont prises dans une contradiction: d'un côté elles sont individuelistes, chacune optilmisant sa propre multiplication, mais, d'un autre côté, elles ont besoin les unes des autres, chacune utilisant les produits du métabolisme de ses voisines. Chaque cellule, bien que travaillant pour son propre compte, est subordonnée à l'ensemble. Elle ne jouit pas d'une liberté totale mais d'une liberté surveillée, parce qu'elle est contrainte de se différencier d'une manière appropriée à la place qu'elle occupe dans la société cellulaire. L'organisme est construit à cause de cette contradiction, qui ne fait que refléter sa propre relation à l'environnement. Il existe en tant que'individu parce qu'il y a une unité fonctionnelle correspondant à l'ensemble des relations d'échange entre cellules. Mais, dans le même temps, l'organisation qui se met en place n'a pas pour finalité de créer l'organisme pour lui-même en tant qu'unité. Celui-ci est la conséquence d'un processus qui assure au mieux la vie des cellules. Cela est illustré par l'exemple du tas de cellules individuelles. Les cellules de la couche sombre nourrissent les cellules de la couche claire. Mais elles ne réalisent pas cette fonction de manière finalisée. Au contraire, elles ne fonctionnent que pour elle-mêmes. La fonction qu'elles acquièrent est une conséquence de leur activité métabolique et des relations internes qui s'établissent dans la population cellulaire. Ces relations n'existent elles-mêmes qu'à cause de la relation à l'environnement qui polarise les échanges de nutriments.

Une telle conception heurte à nouveau les croyacnes les plus ancrées en nous. À cause de notre anthropocentrisme sontané, nous avons une forte tendance à croire que nous sommes la finalité des processus naturels, que ce soit dans l'évolution ou dans l'embryogenèse. Dans le cas de l'évolution, la théorie de la sélection naturelle y a mis fin, malgré toutes les résistances religieuses qu'elle suscite. Dans le cas de l'embryogenèse, cette croyance se perpétue avec la théorie du programme génétique, où la cause finale a pris le nom de télénomie (Pittendrigh, 1958; Mayr, 1961; Hull, 1982). Le but du programme génétique serait de construire l'organisme selon les instructions présentes dans le génome, toutes ses parties, de la molécule aux organes, étant asservies à ce projet (voir figure 11A).

Nous avons du mal à accepter l'dée que nous sommes au service de nos cellules et non l'inverse. Poutant, elle est, comme précédement, inscrite dans la théorie du milieu intérieur."

-------------------------

The relationship between the organism and its parts is another central question which often leads to confusion. In ontophylogenesis, the cells are in the grips of a contradiction: from one point of view, they are individualists, each one optimising its own multiplication, but, from another point of view, they need each other, each one using the products of the metabolism of its neighbors. Each cell, even though working on its own account, is subordinated to the whole. The cell doesn't enjoy a total liberty but, instead, a supervised liberty, because it is constrained to differentiate itself in an appropriate way from the place it occupies in the cellular society. The organism is constructed as a result of this contradiction which merely reflects its own relationship to the environment. It exists as individual because there is a functional unity corresponding to the whole of the relations of exchange between the cells. But, at the same time, the organisation which comes into place does not have for its finality the creation of the organism for itself as a unity. This latter is the consequence of a process which optimally assures the life of the cells. That is illustrated by the example of the mass of individual cells (note: this references illustration figure N° 17 in the text). The cells of the dark layer nourish the cells of the lighter layer. But they do not effect this function as a final end. On the contrary, they are functioning for their own needs. The consequential function that they acquire (i.e., by secondary effect, their own cellular nourishment redounds to that of other, adjacent, layers' cells) is due to their metabolic activity and to the relations which come about in the cell population. These relations themselves only exist from the relation to the (local cellular) environment which polarizes the exchanges of nutriments.

Such a conception again runs against the most deep-seated of our beliefs. Because of our spontaneous anthropocentrism, we have a strong tendency to believe that we are the finality of the natural processes, whether they be in evolution or in embryogenesis. In the case of evolution, the theory of natural selection put an end to that depsite all the religious resistance it incites. In the case of embryogenesis, this belief perpetuates itself with the theory of a genetic program, where the final cause has taken the name of teleonomy (Pittendrigh, 1958; Mayr, 1961; Hull, 1982) The goal of the genetic program would be to construct the organism according to the instructions present in the genome, all its parts, from the molecule to the organs, being slaves to this project. (See figure 11a) (that is a reference to a diagramatic presentation of differing models, in this case, genetic determinism, shown hierarchicly as (lower to higher) : 1. genes, 2. proteins, 3. cells/organelles, 4. tissues/organs, 5. organisms)

"We are hard-pressed to accept the idea that we are at the service of our cells and not the other way around. However, that idea is, as previously, inscribed in the theory of the interior environment." (references a prior citation of Claude Bernard).

re-posted OR EDITED from a saved file, this is to partially replace the botched version of N° 13.

So, briefly, I wrote a long and a detailed reply to Arete which for some reason was either corrupted or lost in the writing and editing. Sorry about that. And, as I am now spent, used up, from sitting at this desk, I'm taking leave to read and relax.

Arete, I"ll get to your post N° 2 with comments on another day; and also later sometime I'll recompose what I'd written and lost in the response that didn't take.

Edited September 10, 2012 by proximity1

proximity1 · September 11, 2012

Kupiec's theory (for those reading along, the fundamental premise is that gene regulation is purely stochastic and local environmental pressures cause selection amongst cells in an embryo, ultimately leading to phenotypic differentiation in the resultant individual) has some fundamental flaws/gaps:

A) There's an extraordinary body of evidence that regulatory genes constrain embryonic development: 668, 000 hits on Google Scholar, representing thousands of individual experiments empirically confirming that unlike as Kupiec claims, the expression of regulatory genes is not stochastic. e.g. http://www.nature.co...bs/nrg2781.html http://www.plantcell...12/8/1491.short http://www.jimmunol....46/6/1914.short etc.

(Parenthetical terms or phrases below are mine, added for clarity in translation except where attributions to authors' research is indicated--e.g. "(Berg and von Hippel, 1985; Haalford and Marko, 2004)" ; numbered footnotes and all emphasis, except where noted otherwise, are those in the original text . )

From the heading summary introduction to Chapter 6, « Hetero-organization » :

[ « The organism is the result of a process of hetero-organization. The non-specificity of molecules introduces (a probabilistic) randomness in the interactions between proteins, which generate a great combination of potential structures. This combination is useful to the living. It produces the diversity of cells necessary in the formation of tissues in the organism. In the course of ontogenesis, it is controlled by a process of selection. Each cell adapts to its microenvironment, constituted by the other cells of the organism. This microenvironment is itself dependent on the exterior environment. In this way, natural selection is propagated in the interior environment (of the organism) and is the causal agent of the formation of the organism. » ]

From page 227 (section 6.5.3)

« DNA as random generator of proteins subject to natural selection:

« Two types of associated (« solidaires ») constraints act on the expression of genes during the embryonic development of an organism: those having their source in its immediate development (its ontogenesis) and those which have their source in its history (its phylogenesis). On one hand, the selective constraints of the microenvironment of cells arise in the embryo due its development itself. They induce the stabilization (or the destabilization) of the expression of genes (figures 16 and 22). On the other hand, the embryonic development is itself constrained by its initial conditions, that is, by the structure of the egg which is the product of its evoluative history (figure 15). In this phylogenetic constraint, the DNA plays a preponderant rôle because it possesses the property of being transmitted in a manner (relatively) invariant to each generation. By this invariance, it favors the reproductability of ontogenesis. Our theory does not, then, deny its (i.e. DNA's) importance in biological processes but it attributes to it a different rôle. For it, just as for the synthetic theory of evolution, DNA is the result of external selective constraints suffered by the organism which have been interiorized in its structure via mutations and genetic recombinations. But, in ontophylogenesis, it acts as a random (probabilistic) generator of proteins, and not as a genetic program. The important point to underline in this conception is that DNA, by its structure, by its position relative to genes, continues to influence cellular behavior. It is not reduced to a rôle of a simple passive furnisher of genetic components or RNA that the cell would employ at its discretion. At present, numerous researchers critique genetic determinism. They are sometimes the same ones who not so long ago were ferocious partisans of it. By a see-saw effect, they come to deny any and all active rôle to DNA. We believe that this is a mistake.

« The model of DNA as random generator of proteins (Kupiec, 1983, 1989, 1996) rests on two properties of the molecules of the chromatin: first, they move about by Brownian diffusion in finding their target sequences in the DNA (Berg and von Hippel, 1985; Haalford and Marko, 2004), and, second, their interactions are not specific. From these two properties, the structure of DNA molecules determines the probabilities of gene expression in the course of embryonic development. The model can be summarized in two general principles which explain at one and the same time the structuring of the chromatin and the expression of genes.

« First principle : the non-specificity of interactions between molecules^* leads to a multiplicity of interactions between the molecules of the chromatin¹ and their sites of linkage. …

« Second principle: from the fact of the instability of interactions between molecules in the chromatin, the molecules may be redistributed in a random manner on their linkage sites. However, all redistributions are not equally probable. The probability of transition between two distributions depends on two principal parameters: one, the instability of interactions between the molecules of the chromatin and their sites of linkage in the DNA; second, the relative position of genes in the DNA molecule. These parameters determine the chronological sequences of expression of genes which have the highest probabilities to occur in a cell in the course of embryogenesis. These sequences correspond to different paths of cellular differentiation. » (pp. 227-229 of the French edition)

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*In a separate post elsewhere, I erroneously indicated that the operative level of stochastic influence in Kupiec's theory is found in atoms and their component particles when, in fact, this is not at all the case. His theory takes for the locale of stochastic influence the cellular molecules. (my note)

1This principle remains valid whatever the chemical nature of these molecules.

Arete · September 11, 2012

The model of DNA as random generator of proteins

I previously cited (post #2) the enormous body of evidence which demonstrates this is not the case. Regulatory genes have been overwhelmingly shown to regulate embryonic development. Is there ANY empirical evidence to suggest that they don't?

proximity1 · September 11, 2012

Kupiec's theory (for those reading along, the fundamental premise is that gene regulation is purely stochastic and local environmental pressures cause selection amongst cells in an embryo, ultimately leading to phenotypic differentiation in the resultant individual) has some fundamental flaws/gaps:

B) If, as Kupiec claims, regulatory genes are purely stochastic and the local enviroment is wholly responsible for embryonic development, what evolutionary purpose do the regulatory genes whose existence is experimentally confirmed (e.g. HOX genes: http://en.wikipedia.org/wiki/Hox_gene) serve?

From page 81-82 (Section 4.1.4)

« Non-specificity in the control of genetic expression

« The interactions between the proteins of the chromatin, which control the expression of genes and their sequences of linkage in DNA, are equally non-specific. These sequences are only six to twenty nucleotides in their lengths. Numerous copies of them are present in the genome, permitting multiple interactions.

« This situation is illustrated by Hox genes. These genes determine several steps of embryonic development. The transcription factors which they code activate numerous genes implicated in the differentiation of the early embryo or the limbs in vertebrates and insects. However, these proteins do not present specificity at the level of their linkage (« liason ») with DNA. The sequences which they recognize are only six nucleotides in length, thus, present in high frequency in the genome (Gehring et al., 1994). From this fact, in vitro, they are capable of connecting themselves with all genes¹ while, in vivo, they do this only for a restrained number of such (Carr and Biggin, 1999; Biggin, 2001).

« The transcription factors also recognize, by weaker interactions, sequences called degenerated, differing only by one or several nucleotides from the sequences with maximal affinity. These degenerated sequences are also repeated a great number of times in the genomes of multicellular organisms with the effect of increasing the possibilities of interaction. (Zhang et al., 2006; Bendall et al., 1993).

« We may cite cases still more spectacular. MeCP2 is a repressor of activity in genes. Its target in DNA is present forty million times in a mamalian genome while there are only one million molecules of MeCP2 (Nan et al., 1997).

« Thus, as in the cases of protein-to-protein interactions of the signal transduction, the multiplicity of potential protein-DNA interactions is very large. »

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1Or in the regulatory regions of these genes

I previously cited (post #2) the enormous body of evidence which demonstrates this is not the case. Regulatory genes have been overwhelmingly shown to regulate embryonic development. Is there ANY empirical evidence to suggest that they don't?

The point here is not « whether » but how genes operate their « regulatory » effects within organisms.

As Kupiec clearly explains, the genes' influences, in themselves stochastic in character, combine with the given embryonic environmentitself a varible condition of development in each individual-- and with the particulars of each embryo's heritage as given in the originating ovum. This presents us with a picture which conforms to the expected importance of environment and natural selection (found everywhere else) as factors in organisms' internal biological processes.

The consequences for the organism are a life-enhancing « plasticity » by the greatly increased potentials available in such a multiform set of processes, consequences which a deterministic programed operation of genetic regulation, an identical copy-to-copy process--except where mutations and other « accidents » may intervenecannot equal and is, therefore, selectively inferior from any evolutionary perspective in which random natural selection is the mode.

I prefer to stick with what Kupiec's gotten through peer review, than his popular science texts.

i.e.

http://www.sciencedi...079610709000790

http://www.springerl...t18e9d1hmlp4tt/

And, of course, that's your prerogative to prefer it.

I want to shift my focus here away from what may have become a too-personally-aimed discussion and, instead, write and reply as though I address any interested reader rather than you in particular.

So, in that vein, considering scientists, researchers, students of natural sciences as under-graduates or graduates or post -doctoral students generally, why should any of them rule out the consideration of a text such as The Origin of Individuals ? The same just-mentioned scholars would not hesitate to read The Origin of Species or any of Ernst Mayr's books,

Books

Mayr, Ernst (1999). Systematics and the Origin of Species, from the Viewpoint of a Zoologist. Cambridge: Harvard University Press. ISBN 0-674-86250-3.

Mayr, Ernst (1963). Animal Species and Evolution. Cambridge: Belknap Press of Harvard University Press. ISBN 0-674-03750-2.

Mayr, Ernst (1970). Populations, Species, and Evolution. Cambridge: Belknap Press of Harvard University Press. ISBN 0-674-69013-3.

Mayr, Ernst (1976). Evolution and the Diversity of Life. Cambridge: Belknap Press of Harvard University Press. ISBN 0-674-27105-X.

Mayr, Ernst. & William B. Provine, (eds) (1980). The Evolutionary Synthesis: Perspectives on the Unification of Biology, ISBN 0-674-27225-0

Mayr, Ernst (1982). The Growth of Biological Thought. Cambridge (Mass.): Belknap P. of Harvard U.P. ISBN 0-674-36446-5.

Mayr, Ernst (1988). Toward a New Philosophy of Biology. Cambridge: Harvard University Press. ISBN 0-674-89666-1.

Mayr, Ernst (1991). Principles of Systematic Zoology. New York: McGraw-Hill. ISBN 0-07-041144-1.

Mayr, Ernst (1991). One Long Argument. Cambridge: Harvard University Press. ISBN 0-674-63906-5.

Mayr, Ernst (1997). This Is Biology. Cambridge: Belknap Press of Harvard University Press. ISBN 0-674-88469-8.

Mayr, Ernst (2001). The Birds of Northern Melanesia. Oxford Oxfordshire: Oxford University Press. ISBN 0-19-514170-9.

Mayr, Ernst (2001). What Evolution Is. New York: Basic Books. ISBN 0-465-04426-3.

Mayr, Ernst (2004). What Makes Biology Unique?. Cambridge: Cambridge University Press. ISBN 0-521-84114-3.

or Dobzhansky's, or any number of other scientist-researchers who, for centuries, have written and published their scientific work in forms that reach--because they are addressed to these---the wider interested public beyond the confines of an expert community.

No competent and self-respecting scholar-researcher in the natural sciences would offer to the non-specialist reading public a text which was in any serious way a departure from the same theoretical rigors applied in his or her writing for peer-reviewed journals.

So for any reader to eschew on such a basis regarding as fit for consideration a text which comes from a general publisher of non-fiction strikes me as a habit of a curiously uncurious kind for any person of scientific bent.

Edited September 11, 2012 by proximity1

Arete · September 11, 2012

As Kupiec clearly explains, the genes' influences, in themselves stochastic in character

This is specifically what I am taking issue with. A huge body of evidence shows gene expression is NOT stochastic in nature. Claims that regulatory genes target small, specific but common nucleotide sequences is not compelling evidence that they are stochastically expressed in the weight of empirical evidence showing they are not. Experimental studies of HOX genes show that they determine whether leg become antennae or antennae become legs in Drosophilia, under environmentally controlled conditions (i.e. the genes are certainly not stochastic sources of proteins to be simply regulated by the enviroment, and do play an active role in developmental regulation) :

"In Drosophila melanogaster, antennae and legs are homologous structures that differ from each other as a result of the Hox gene Antennapedia (Antp), which promotes leg identities by repressing unknown antennal-determining genes."

http://www.nature.co...s/392723a0.html

I am yet to see any contrary empirical evidence to counter the weight of available empirical evidence supporting the non stochastic role of regulatory genes in embryonic development, and as such there's absolutely no reason to accept the alternative hypothesis presented.

So for any reader to eschew on such a basis regarding as fit for consideration a text which comes from a general publisher of non-fiction strikes me as a habit of a curiously uncurious kind for any person of scientific bent.

Kupiec is presenting novel hypotheses, not a generalized text. As such, what he says about it should be vetted by peer review. If as you say, the content of his books and his papers are similar why does it matter?

You should probably cite wikipedia when you cut and paste from it.

Edited September 11, 2012 by Arete

proximity1 · September 11, 2012

Kupiec's theory (for those reading along, the fundamental premise is that gene regulation is purely stochastic and local environmental pressures cause selection amongst cells in an embryo, ultimately leading to phenotypic differentiation in the resultant individual) has some fundamental flaws/gaps:

C) If the local enviroment drives diversification, why do all embryos pass through the same developmental stages? If the local enviroment is driving cellular selection, surely there would be variation in the process of embryonic development, in association with variation in selection pressure. This is not observed, even in widespread species living in vastly different environments. Differences in embryonic development appear to be related to divergent evolutionary history, not differences in environmental pressures. http://en.wikipedia....i/Embryogenesis

« (5.3.1) The Holism neovitalist of Hans Dreisch

« Hans Dreisch (1867-1941), one of the pioneers of experimental embryologie, had supported a vitalist theory (Driesch, 1908, 1914). Wilhelm Roux, another pioneer of embryology, had destroyed, in the course of an experiment on a frog, one of two cells of the embryo after the first (cell) division. He had thus succeeded in provoking the development of a half (« demi »)-embryo. This seemed to confirm the theory of August Weismann (1834-1914), the precursor of genetic determinism. This latter postulated the existence in the germ cells of a highly organized microscopic material structure which he called the germinative plasma. This structure, which prefigured DNA, was supposed to control the embryonic develpment in a very precise manner, each one of its parts determining a part of the adult organism. Weismann supposed, in addition, that the germinative plasma was severed with each cellular division. Each embryonic cell, receiving only a part, could form only a specific region of the adult organism¹ correspnding to the fraction of germinative plasma which the cell had received. Thanks to this theory, Roux's experiment was easily explained. The (i.e. Roux's) surviving cell would have contained only half of the germinative plasma corresponding to half of the organism.

« Driesch then performed an experiment similar to that of Roux on a sea urchin. But he obtained results completely different. The destruction of one of the two cells of the embryo, rather than provoking the formation of a half-embryo, resulted in the formation of a complete individual, though one of a reduced size. Dreisch repeated his experiment on embryos having reached the stage of four cells, and he was able to show that one single cell or three taken together were capable of forming complete embryos. In the same fashion, half an older embryo composed of a thousand cells could generate a normal organism. These results contradicted Weismann's theory. If the cells resulting from several successive divisions could form complete organisms, they must possess the totality of the germinative plasma rather than a fraction.

« Dreisch drew a supplementary conclusion from these experiments. They showed that one embryonic cell, up to an advanced stage, could spawn all the cellular lines of an organism; it possessed, then, a potential for differentiation greater than that of its own actual destiny in the course of the embryogenesis. In multiplying the experiments on embryos taken at different stages of development in varied experimental conditions, Dreisch was able to confirm this conclusion and demonstrate that the cells possess a very great plasticity which permits them to adapt to these varied situations. The question then posed was to know how this immense potential for development might be reduced during embryogenesis in such a way that it expressed only a single potentiality.

« To answer this, Dreisch conducted experiments which led him to elaborate two supplemental concepts. First, the potential development of all the cells of a region of the embryo seemed constant. The embryo would then be « an equipotential system of development. » Second, we may, in to a certain extent, alter a region of the embryo without disturbing the development of other regions. The development of very different regions seem causally independent, yet results in an organism harmoniously forming an organized whole. »

« (6.2.1) Embryonic induction

« The experiments of Dreisch demonstrate that the differentiation of cells cannot be only the expression of their internal determinants (see chapter 5, Sec. 5.3.1 above). A supplementary mechanism which permits the restraint of the potential development is therefore necessary. Even if we reject the vitalism of Dreisch and of Elsasser, we must take this into account. It is the work of Hans Spemann (1869-1941) which shed light on this question. He conducted tissue grafts on the interior of embryos which showed the primordial rôle of interactions between cells. In the course of development of the embryo, the cells mutually influence each other. What becomes of each depends on the influences it receives from the others. This phenomenon was called embryonic induction (Spemann, 1938; Bouwmeester, 2001).

« Spemann's experiments do not by themselves give an indication of the nature of the inductive mechanism, but this latter was immediately conceived as a deterministic phenomenon. We supposed that the embryonic cells produce inducing molecules which act on their neighbors and determine the manner in which they differentiate themselves (Saha, 1991). »

1As opposed to DNA which is present in its entirety in each cell of the organism.

Kupiec is presenting novel hypotheses, not a generalized text. As such, what he says about it should be vetted by peer review. If as you say, the content of his books and his papers are similar why does it matter?

You should probably cite wikipedia when you cut and paste from it.

To place Kupiec as a scholar and researcher on a par with Wikipedia's level of scholarship is a degrading remark. It degrades you, not the scholarship or person of Kupiec.

With regard to novel hypotheses and their fitness for consideration by scientists and in what circumstances, etc., Darwin's main hypotheses concerning natural selection, too, when On the Origin of Species was first published, were extraordinarily novel :

" The opposition to natural selection continued without respite for nearly eighty years after the publication of The Origin of Species. Outside a few naturalists, there was hardly a biologist, and certainly no experimental researcher, who adopted natural selection as exclusive cause of adaptation. " (Mayr, 1991) ---Chapter 9, One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought ; Harvard Univ. Press. (this citation is my own re-translation from the French edition (translated by René Lambert) published by Odile Jacob.)

Edited September 11, 2012 by proximity1

Arete · September 11, 2012

To place Kupiec as a scholar and researcher on a par with Wikipedia's level of scholarship is a degrading remark. It degrades you, not the scholarship or person of Kupiec.

What are you talking about?

You cut and paste directly from the Wikipedia article about Ernst Mayr without citing it. My point was that you should probably cite sources you cut and paste directly from to avoid plagiarism. I'd appreciate you not taking offense when none is meant.

Do you have empirical evidence showing the stochasticity of regulatory genes? In its absence, I feel this thread is largely done.

Edited September 11, 2012 by Arete

proximity1 · September 12, 2012

What are you talking about?

You cut and paste directly from the Wikipedia article about Ernst Mayr without citing it. My point was that you should probably cite sources you cut and paste directly from to avoid plagiarism. I'd appreciate you not taking offense when none is meant.

Do you have empirical evidence showing the stochasticity of regulatory genes? In its absence, I feel this thread is largely done.

I was referring, there, to the impression which I had that you were doing just that--putting Kupiec's work on a par with the stuff of Wikipedia. I came to that mistaken impression because of the close juxtaposition of the two remarks--one mentioning Kupiec, the other mentioning Wikipedia. With no mediating feature separating them, I mistook them as being related in your mind and in your reply.

"I'd appreciate you not taking offense when none is meant."

Yes, you're quite right, there. And, before even reading your reply here, my conscience had already recognized and pled your case successfully. So, I do indeed regret, apologize for and retract that accusation.

There is another thing on which we're agreed---at least in a sense. While this thread is not, in my opinion, at least, "largely done", I see and agree that your interest in it almost certainly is.

The evidence you claim to want for the stochastic character of gene expression is all evidence which you (apparently) refuse to read, or, if you read it, then, having read it, you refuse to recognize it. That is why I'm convinced your participation in this thread is probably at its end. For others who can and will read and recognize what you don't see, I think that the thread's interest can be or remain of interest.

Kupiec is presenting novel hypotheses, not a generalized text. As such, what he says about it should be vetted by peer review. If as you say, the content of his books and his papers are similar why does it matter?

The simple and short answer is that no one proceeds in that way. Of course, such writers do solicit the review and criticism of their own circle of professional friends--and some daring ones even go beyond the safety of their trusted friends for critical comment on a forthcoming text. But more than that is simply not done customarily in the case of such a text. It wasn't done by Darwin, or by anyone before or since, including Dobzhansky, Mayr and anyone else you'd care to cite when it comes to the publication of a text such as those listed above by Mayr or, in this case, that of Kupiec.

As for citing Wikipedia for attribution, credit, I wonder: is that really pertinent in the present example which concerns nothing other than a listing of publications---available from any number of non-exclusive, non-original sources? And, since the provenance of the list is entirely evident by launching any of the isbn hyper-links, isn't it also in effect "cited" in that implicit manner?

Edited September 12, 2012 by proximity1

illuusio · September 12, 2012

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)"

This is easy one! If you have invested many years of your life to current truth you won't accept new knowledge too easily. Scientists get funding more easily with main stream research areas, so research is biased.

It's hard for scientists who are swimming against the current

**imatfaal** · September 12, 2012

This is easy one! If you have invested many years of your life to current truth you won't accept new knowledge too easily. Scientists get funding more easily with main stream research areas, so research is biased.

It's hard for scientists who are swimming against the current

It's even harder for those theorists for whom observation, the scientific method, and mathematics show that their idea is incorrect. The immediate jump from i. you reject my idea to ii. you have rejected my idea due to bias, dogmatism, or short-sightedness is uncalled for, bigotted and cruel.

illuusio · September 12, 2012

It's even harder for those theorists for whom observation, the scientific method, and mathematics show that their idea is incorrect. The immediate jump from i. you reject my idea to ii. you have rejected my idea due to bias, dogmatism, or short-sightedness is uncalled for, bigotted and cruel.

Well, hard to say, I have no experience on that one

Edited September 12, 2012 by illuusio

Arete · September 12, 2012

The evidence you claim to want for the stochastic character of gene expression is all evidence which you (apparently) refuse to read, or, if you read it, then, having read it, you refuse to recognize it. That is why I'm convinced your participation in this thread is probably at its end. For others who can and will read and recognize what you don't see, I think that the thread's interest can be or remain of interest.

You haven't posted any empirical evidence. You've repeatedly posted Kupiec asserting that genes are expressed stochastically. We're yet to see any actual data supporting this, let alone anything compelling enough to overturn this:

There's an extraordinary body of evidence that regulatory genes constrain embryonic development: 668, 000 hits on Google Scholar, representing thousands of individual experiments empirically confirming that unlike as Kupiec claims, the expression of regulatory genes is not stochastic. e.g. http://www.nature.co...bs/nrg2781.html http://www.plantcell...12/8/1491.short http://www.jimmunol....46/6/1914.short etc.

The simple and short answer is that no one proceeds in that way. Of course, such writers do solicit the review and criticism of their own circle of professional friends--and some daring ones even go beyond the safety of their trusted friends for critical comment on a forthcoming text. But more than that is simply not done customarily in the case of such a text.

Are you trying to say scientists don't publish new scientific theories and concepts in peer reviewed journals?

proximity1 · September 20, 2012

When experts and non-experts discuss a theory, such as, for example, in this instance, the work of a reputable scientist doing work according to the accepted canons of scientific practice, and, in this case, a theory which challenges the currently prevailing paradigm in some significant way, I think it would be only wise and only fair of the experts in the discussion to consider the non-experts as presenting something for their consideration and that of the general readership; and, in the case of its expert complement, they should neither expect nor require of the non-expert more in explanation and defense of the theory than can be reasonably gained from a reading of the basic text(s) through which the original theorist makes his or her case.

Or, in other words, experts should neither expect nor require from the non-expert a point-by-point response to any and all criticisms that might be levelled by experts and a successful defense which presumes an expertise that only experts possess. Those questions, properly, should be directed to the original scientists behind the theory under discussion rather than the non-expert here.

I don't, for example, expect to convince each and every individual reader here of the validity of the theory I describe nor was that ever my intention or expectation. If that were possible, the scientist himself would have already accomplished this. Instead, a challenge to the prevailing paradigm is, by definition, one which has not gained the assent of the majority of the expert community. To expect a non-expert partisan to carry such a burden is, frankly, strange, to say the least. If such are the expectations here, then the site administration should dispense with any pretenses that this site welcomes opinion and participation from the lay public on science issues and frankly admit that such are not in fact really welcome here.

Kupiec's work and his theory do not reject or deny the general data amassed in molecular biology. Instead, his theory presents a radically different manner in which to interpret and understand that data. Therefore, arguments which contend that « numerous studies show.... » do not go to the point being presented, namely, the import and significance of these studies rather than the matter of whether the data collected is meaningful at all.

An effective rebuttal would show, rather, why such a reinterpretation is not tenable as an alternative to the prevailing interpretative view.

Kupiec is, I think, aware of the objections which I have seen raised thus far here and he answers them in a general way in the text on which my views draw and are based. But I'm simply not able or competent to respond to particular papers which are cited to show how on one or another specific point Kupiec's views are supposedly contradicted. Such have been offered here already and, as far as I have read them and can understand their points, they are not pertinent nor do they really demonstrate how and where the Kupiec's basic theory is false or untenable. But, again, even if this were the case, that is a matter to be addressed on the expert level between scientists—not a lay reader-participant here.

More astounding still, it seems to me, is that a critic here has levelled what are supposed to be expert criticisms which presume unanswered defects in Kupiec's theory while, the critic himself remains largely or entirely ignorant of the basic supporting text, and cannot even state that the criticisms have not been addressed already in that basic text.

post scriptum:

From the preface of Daniel C. Dennett's Darwin's Dangerous Idea (1995)

« Science is not done by quoting authorities, however eloquent and eminent, and then evaluating their arguments. Scientists do, however, quite properly persist in holding forth, in popular and not-so-popular books and essays, putting forward their interpretations of the work in the lab and the field, and trying to influence their fellow scientists. When I quote them, rhetoric and all, I am doing what they are doing: engaging in persuasion. There is no such thing as a sound Argument from Authority, but authorities can be persuasive, sometimes rightly and sometimes wrongly. I try to sort this all out, and I myself do not understand all the science that is relevant to the theories I discuss, but, then, neither do the scientists (with perhaps a few polymath exceptions). Interdisciplinary work has its risks. I have gone into the details of the various scientific issues far enough, I hope, to let the uninformed reader see just what the issues are, and why I put the interpretation on them that I do, and I have provided plenty of references. »

Edited September 20, 2012 by proximity1

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