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  Topic: Carl Woese review article, Please synthesize this for relevance< Next Oldest | Next Newest >  
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Feb. 14 2008,17:40   

This article, A New Biology for a New CenturyHere

Edit, damn thing submitted on its own I swear.
...
Quote
Let's stop looking at the organism purely as a molecular machine. The machine metaphor certainly provides insights, but these come at the price of overlooking much of what biology is. Machines are not made of parts that continually turn over, renew. The organism is. Machines are stable and accurate because they are designed and built to be so. The stability of an organism lies in resilience, the homeostatic capacity to reestablish itself. While a machine is a mere collection of parts, some sort of "sense of the whole" inheres in the organism, a quality that becomes particularly apparent in phenomena such as regeneration in amphibians and certain invertebrates and in the homeorhesis exhibited by developing embryos.

If they are not machines, then what are organisms? A metaphor far more to my liking is this. Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow. A simple flow metaphor, of course, fails to capture much of what the organism is. None of our representations of organism capture it in its entirety. But the flow metaphor does begin to show us the organism's (and biology's) essence. And it is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not materialistically, as machines, but as (stable) complex, dynamic organization.


And I think he is attempting to create a broader blur between the organism, the population and the biosphere in general.

Quote
Enter the "era of the genetic code," when theoreticians and experimentalists alike were racing to see who would be first to "crack the code of life" (16, 22, 24, 30, 43). As we all know, once cracked, that code did not lead to a fundamental explanation of gene expression (translation). The code seemed to be merely an arbitrary correspondence table between the amino acids and corresponding trinucleotides. There seemed to be no simple physical-chemical interactions underlying the mechanism of gene expression (or that suggested the mode of its evolution). Could it be just another one of evolution's many "historical accidents"? Could there be nothing fundamental about it? That's how the molecularists saw it: outside of its structure, the only fundamental aspect of "the gene" was its mode of replication. Needless to say, classically trained biologists did not see it this way: in that translation (the heart of gene expression) was not yet understood, "the problem of the gene" could not possibly be completely (not to mention fundamentally) solved. No other single issue has exposed the difference between the molecular and classical perspectives more clearly than this one. Should the problem of translation be treated as just another (idiosyncratic) molecular mechanism (as it now is), or is that problem central, and thus fundamental, to the nature of the cell. As we shall see, biology today continues to live with this unresolved problem.

The genetic code became for me the looking glass through which I entered the world of real biology. Like many molecularists of the day, I was taken by the code, and at first I emulated their cryptographic approach to the problem (55). But that approach didn't have a biological "feel" to it. Wasn't it wrong to consider the codon assignments in cryptographic isolation? Weren't they just a superficial but important manifestation of something deeper and more interesting, i.e., how translation evolved? Here was the real problem of the gene, how the genotype-phenotype relationship had come to be. Translation, far from being just another relatively uninteresting study in biological idiosyncrasy, actually represented one of a new class of deep evolutionary questions, all of which had to be formulated and addressed on the molecular level.

Universal evolutionary problems of this kind can be approached only in the context of a universal phylogenetic framework, and in the mid-1960s, when I set out to study the evolution of translation, no such framework existed. Animal and plant phylogenies were reasonably fleshed out, but the huge and overwhelming bacterial world was effectively virgin phylogenetic territory. A massive job lay ahead merely to establish a framework within which to begin operating.


And here is where I need to defer to someone elses expertise:
Quote
A heavy price was paid for molecular biology's obsession with metaphysical reductionism. It stripped the organism from its environment; separated it from its history, from the evolutionary flow; and shredded it into parts to the extent that a sense of the whole—the whole cell, the whole multicellular organism, the biosphere—was effectively gone. Darwin saw biology as a "tangled bank" (12), with all its aspects interconnected. Our task now is to resynthesize biology; put the organism back into its environment; connect it again to its evolutionary past; and let us feel that complex flow that is organism, evolution, and environment united. The time has come for biology to enter the nonlinear world.

From a theoretical point of view, one thing can be said about evolution with fair assurance: it is a complex, dynamic process. But it is only now, in the context of computer algorithms, fractals, and chaos mathematics, that we are beginning to get a useful feeling for what that means (33, 51), and it means that evolution is a bumpy road to who knows where. "Bumpy" implies that evolution, as a complex dynamic process, will encounter critical points in its course, junctures that result in phase transitions (drastic changes in the character of the system as a whole) (19, 26, 33, 51). "Who knows where" implies that the outcomes of these transitions, saltations, are not predictable a priori. Biologists now need to reformulate their view of evolution to study it in complex dynamic-systems terms.

When one starts looking for major evolutionary saltations, they are not all that hard to identify (48). It is immediately apparent that one of them is the development of language(s). Human language is a development that has set Homo sapiens worlds apart from its otherwise very close primate relatives, adding new dimensions to the phase space within which human evolution occurs. Another good critical-point candidate is the advent of (eucaryotic) multicellularity. Here too the saltation is accompanied by a qualitatively new world of possibilities.

Next comes the evolution of the eucaryotic cell itself. While biologists have traditionally seen this as a step (saltation) beyond the stage of bacterial cells, I do not. The idea that eucaryotic cell structure is the product of symbioses among bacteria, and so represents a higher stage than that of the bacterial cell, goes back a good century and a half, but there has been no effort to seriously rethink the matter in the light of modern biological knowledge. Nowhere in thinking about a symbiotic origin of the eucaryotic cell has consideration been given to the fact that the process as envisioned would involve radical change in the designs of the cells involved. You can't just tear cell designs apart and willy-nilly construct a new type of design from the parts. The cells we know are not just loosely coupled arrangements of quasi-independent modules. They are highly, intricately, and precisely integrated networks of entities and interactions. Any dismantling of a cell design would not reverse the evolution that brought it into existence; that is not possible. To think that a new cell design can be created more or less haphazardly from chunks of other modern cell designs is just another fallacy born of a mechanistic, reductionist view of the organism.

But what about the mitochondrion; isn't that a direct counterexample of what has just been said? No, it is not. Evolving the mitochondrion through (endo)symbiosis is fundamentally different from evolving the eucaryotic cell in this way. Whereas the latter process would involve a disruptive dismantling of the preexisting eucaryotic cellular design, acquisition of a mitochondrion does not significantly perturb the eucaryotic cell's basic organization, which is in essence the same with or without the mitochondrion's presence. I take it as a general rule in biology that the more complex, integrated, and specific a cell design becomes, the more intolerant of change that design is. For modern cells, the changes possible in their designs (other than degeneration) are all of a trivial, but not necessarily unimportant, nature. (Granted, the organization of the mitochondrial endosymbiont is radically changed during its evolution, but that change is a degeneration to a far simpler "cell-like" design, and the mitochondrial design could never evolve back to the level of complexity that its free-living [bacterial] ancestor had.)

In the remote evolutionary past lies the RNA world (18) or, as I call it, the era of nucleic acid life (57), an evolutionary stage whose existence is here taken for granted. The transition that gave rise to this era must have been one of the great evolutionary saltations, as was the transition(s) from that era ultimately to the world of the (proteinaceous) cells as we know them. Somewhere along the line there had to have occurred a saltation that we could call the "coding threshold," where the capacity to represent nucleic acid sequence symbolically in terms of a (colinear) amino acid sequence developed, a development that would generate a truly enormous new, totally unique evolutionary phase space.


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Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

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BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Feb. 14 2008,17:50   

Sorry. See edit above

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Feb. 14 2008,22:44   

I'm guessing that no one cares much about this? I just wondered if any one had anything to help me get the relevance of it.

Well, I'll check back later.

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
Kristine



Posts: 3061
Joined: Sep. 2006

(Permalink) Posted: Feb. 14 2008,23:08   

Quote (BWE @ Feb. 14 2008,21:44)
I'm guessing that no one cares much about this? I just wondered if any one had anything to help me get the relevance of it.

Well, I'll check back later.

I read the beginning - I'll get to it, for whatever my contribution's worth. I think I just stunk at a quiz in my night class...  :(

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Which came first: the shimmy, or the hip?

AtBC Poet Laureate

"I happen to think that this prerequisite criterion of empirical evidence is itself not empirical." - Clive

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Henry J



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Joined: Mar. 2005

(Permalink) Posted: Feb. 14 2008,23:12   

I found it fascinating, but being an amateur I can't really judge relevance. That part about somebody thinking that bacteria merged to form eukaroytes, that surprised me, since everything I've read related to that indicated that mitochondrial eukaryotes were eukaryotes before they had mitochondria - so I didn't know that anybody ever thought otherwise to that.

Henry

  
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Feb. 14 2008,23:17   

Thanks Kristine, sorry to hear about the quiz.
Quote
When the great American Humorist, Robert Benchley, was at Harvard, he took a course in International Law.

The final exam consisted of one essay question:

     Discuss the arbitration of the international fisheries problem with respect to the catcheries protocol and dragnet and trawl procedures as it effects: the point of view of the USA, the point of view of Great Britain.

Benchley who had not spent a great deal of time studying for the exam desperately wrote:

     I know nothing about the point of view of Great Britain or the arbitration of the International Fisheries problem and nothing about the point of view of the USA therefore I shall discuss the question from the point of view of the fish.'


--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Feb. 14 2008,23:19   

Quote (Henry J @ Feb. 14 2008,23:12)
I found it fascinating, but being an amateur I can't really judge relevance. That part about somebody thinking that bacteria merged to form eukaroytes, that surprised me, since everything I've read related to that indicated that mitochondrial eukaryotes were eukaryotes before they had mitochondria - so I didn't know that anybody ever thought otherwise to that.

Henry

To say the least. I took a fair bit of Biology way back when and they didn't make that suggestion.

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
mitschlag



Posts: 236
Joined: Sep. 2006

(Permalink) Posted: Feb. 16 2008,17:26   

Hey, thanks for the link.  :)

Looks good.

It almost slipped under the radar.

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"You can establish any “rule” you like if you start with the rule and then interpret the evidence accordingly." - George Gaylord Simpson (1902-1984)

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: Feb. 17 2008,10:46   

This is a fascinating article, written by a seasoned, productive and influential scientist with unquestionable sci-cred.

Its not my field, so I mostly settled into a learning mode in attempting to digest this material. But I can make a few quick meta-comments, for now:

First, I'd suggest that Ftk and creationist ilk read this paper, absorb the historical material, then consider the article itself in the context of that history. A central creationist myth is that mainstream biology is locked into conspiratorial dogmas and unexamined hand-wavings from which no dissent is permitted - all to hide the emptiness of evolutionary explanations of the diversity of life. This article certainly does document the occurrence of dogmas and acceptance of unexamined assumptions that have constrained progress in biology. However, at the same time, it is itself a demonstration that courageous dissent and the formulation of new conceptual frames of reference can and do arise from those who are working from deep within those conventional contexts. Indeed, embeddedness within and mastery of the knowledge base and even the dogmas of a discipline are certainly prerequisites for engaging in this kind of dissent and constructive rethinking. It can't be meaningfully accomplished by philosophical amateurs working from the outside (e.g. Dembski and friends).

Secondly, Ftk should notice that it is the fact that Woese brings a very deep evolutionary perspective, and a knowledge of the evolutionary literature back to Darwin, that equips him to make the discoveries he has made, challenge the above noted dogmas (e.g. regarding the monophyly of the procaryotes), and propose a way forward. This article affirms Dobzhansky's dictum once again.  

And lastly, Ftk and ilk should take note of the unanswered questions, warring conceptual frameworks, genuine debates, periods of deep disorientation (and even hopelessness and resignation), cumulative empirical progress, and soaring open inquiry - not repetitions of dogma - that characterize progress in biology. Contrast this with the despicable caricatures she and ilk deploy in an effort to sustain willful ignorance of the state of knowledge within 21st century biological and evolutionary science.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
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Bob O'H



Posts: 2132
Joined: Oct. 2005

(Permalink) Posted: Feb. 17 2008,11:28   

Dammit, RB, you know they'kk just quote-mine instead.  e.g.
Quote
Machines are stable and accurate because they are designed and built to be so.

Look!  Look!  He wrote "designed"!  He must be a closet supporter of ID, who's too scared to come out.

Personally, I rather like this one:
Quote
A society that permits biology to become an engineering discipline...is a danger to itself.


Bob

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It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Feb. 18 2008,08:31   

I've been trying to get through it but it's really just hanging out, open, on my desktop.  It's a topic I'm really interested in though.
Quote
A heavy price was paid for molecular biology's obsession with metaphysical reductionism. It stripped the organism from its environment; separated it from its history, from the evolutionary flow; and shredded it into parts to the extent that a sense of the whole—the whole cell, the whole multicellular organism, the biosphere—was effectively gone.


I have seen this charge from others.  most memorably levins and lewontin but i believe Gould touched on this too.  essentially something along the lines of marxism (read 'dialectical materialism') was the most appropriate known philosophy of knowledge gathering and that somewhere at some point in the biological and/or technologcial revolution, the organism lost it's focal point, shattered into a million weakly interdependent traits, none of which are the perfect crystals for working with.  It's really easy to blame this on anything, from the ANOVA approach to agriculture and mathematical economic theories to cartesian coordinate systems.

And always somebody somewhere takes umbrage at the surficial comment 'biologists ignore the organism' and they say 'bloody hell, you might ignore it but i sure don't'.  then they go back to their models and attempt to reduce the number of parameters to increase the precision of their estimates.  

it can't be helped, as others have said, OK we are all now dialectical biologists.  Now what?  what does this mean?  don't we still have to determine good summary statistics, or find more-or-less natural groups that behave in more-or-less determined fashion, in order to refine our observational power and use it for the most statistical leverage?  

I'm not sure.  I think somewhere in this debate lies a valid dichotomy between those who are interested in the noise (or perhaps committed to ontologies of particulars) and those are quite willing to make abstract generalizations about broad swaths of reality and attempt to eliminate noise.

In other words,  we study what nature does, not what it is.

Edward Abbey reportedly once had this conversation with a visitor to the little backcountry hick desert park he was a-rangering,

She (pointing to a bird hopping around in the parking lot):  What is that?
He (tired of such exchange):  Ma'am, what it is no man knows, but some call it a raven.

Not finished with woese, so I haven't seen his alternative to synthetic holist reductionism (the ideal, if rarely implemented, method of science).  can't wait to get back to it.


Edited to add:  Kudos for finding the darwin quote!

Quote
(we may infer) that all the organic beings which have ever lived on this earth may be descended from some one primordial form. But this inference is chiefly grounded on analogy and it is immaterial whether or not it be accepted. No doubt it is possible, as Mr. G. H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so we may conclude that only a very few have left modified descendants.


single or multiple origins is really a metaphysical position at this point.  it likely will always be.  i'm just saying it's trivial.

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You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Reciprocating Bill



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Joined: Oct. 2006

(Permalink) Posted: Feb. 18 2008,20:04   

Quote (Erasmus @ FCD,Feb. 18 2008,09:31)
I've been trying to get through it but it's really just hanging out, open, on my desktop.  It's a topic I'm really interested in though.
 
Quote
A heavy price was paid for molecular biology's obsession with metaphysical reductionism. It stripped the organism from its environment; separated it from its history, from the evolutionary flow; and shredded it into parts to the extent that a sense of the whole—the whole cell, the whole multicellular organism, the biosphere—was effectively gone.


I have seen this charge from others.  most memorably levins and lewontin but i believe Gould touched on this too.  essentially something along the lines of marxism (read 'dialectical materialism') was the most appropriate known philosophy of knowledge gathering and that somewhere at some point in the biological and/or technologcial revolution, the organism lost it's focal point, shattered into a million weakly interdependent traits, none of which are the perfect crystals for working with.  It's really easy to blame this on anything, from the ANOVA approach to agriculture and mathematical economic theories to cartesian coordinate systems.

And always somebody somewhere takes umbrage at the surficial comment 'biologists ignore the organism' and they say 'bloody hell, you might ignore it but i sure don't'.  then they go back to their models and attempt to reduce the number of parameters to increase the precision of their estimates.  

Seems to me that general systems theory (as in L. Bertalanffy etc.), writers such as the late Gregory Bateson, and even Whitehead's "process theology" have always argued that organisms can only be understood as dynamic, open, interacting, homeostatic wholes operating within contexts that themselves are also open systems (e.g. ecologies) - and that to ignore that dimension is to pass over the central defining characteristic of organism.  So some of these ideas are not novel - although few as biologically well informed as Woese have addressed them.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Feb. 18 2008,21:56   

RB that is heavier than i was prepared for.  

I suppose what interests me is that many biologists have claimed that they have never viewed organisms as anything but what the view you outline demands.  This, in spite of the fact that we may only view a trait or suite of traits at a time.  It is, as Abbey said about the raven, a reification of the blindly powerful nature of statistical investigation.

Literature citation bias has the tendency to uncritically report the results of prior authors, and most of the time we consider this to be valuable or at least unimportantly biased.  After all, the referential nature of theories is a property that we consider important.  We are interested in carving homogenous categories or even natural groupings from the panoply of variation in the world, and it helps to use the torches lit by our forebears.

Given this, I'm not sure that redefining organism to include the stochastic and contingent isn't an exercise in the same species of futility that includes all other hasty generalizations.  Relax the stranglehold on Dame Empiricus and immediately the rabble might say "well this still doesn't explain how the dog knows I'm coming home" or "Why do I love my baby more than the others in the nursery" or "If I'm just an organism pushed and pulled by forces out of my control, how come I can still beat Halo 3?"  And so on.  

and these questions are difficult to overcome, IMV, even if one grants the holistic proposition.  Now, I'd say this is because such questions are not formulated in such a manner that they be treated as legitimate questions, but there is very likely some hidden common ground that I'd be willing to concede.  Ye Olde Is-Ought.  And it's a tough nut.

* Edited to subtract uno extraneoso 'legitimate'

**  I'd add that I really don't know what the heck bacteria-world is all about, but I am fairly convinced that it is an altogether different ball game than the organismal biology in which i am trained.  that makes this issue a bit more difficult, unless one surrenders the categorical notions surrounding how we delimit the boundaries of the packets of biodiversity that occur at the microbial level.

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You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
keiths



Posts: 2041
Joined: Jan. 2006

(Permalink) Posted: Feb. 19 2008,06:11   

In the following passage, Woese attacks what he calls "fundamentalist reductionism":
Quote
Fundamentalist reductionism (the reductionism of 19th century classical physics), on the other hand, is in essence metaphysical.  It is ipso facto a statement about the nature of the world: living systems (like all else) can be completely understood in terms of the properties of their constituent parts.  This is a view that flies in the face of what classically trained biologists tended to take for granted, the notion of emergent properties.  Whereas emergence seems to be required to explain numerous biological phenomena, fundamentalist reductionism flatly denies its existence: in all cases the whole is no more than the sum of its parts.

Depending on what he means by "the sum of its parts", Woese is either attacking a straw man, or else making a very questionable claim of his own.

A pile of airplane parts and a fully assembled airplane can both be considered "sums of their parts", but even if equal, part for part, we'd still be surprised to see both of them accelerate down the runway and take off.  In that trivial sense, an airplane is more than the sum of its parts.  Knowing all of the parts, and all of their properties, is insufficient to predict the behavior of the aggregate; you also need to know how the parts are put together, and the nature of the environment the aggregation operates in.  

But this is obvious even to the most ardent of reductionists, so surely Woese has something else in mind when he claims that the whole is greater than the sum of its parts.  Otherwise he is attacking a position that nobody in the scientific community takes seriously to begin with.

If not the straw man, what else could he possibly mean when he says that the whole is greater than the sum of its parts?  The only possibility I see is that he thinks the whole has some kind of downward causal power that overrides the properties that the parts would otherwise exhibit.  In other words, a simulation of the whole could not be created by linking together, in an appropriate fashion, simulations of the individual parts.  Such a simulation would be missing the element of downward causation.

This makes no sense to me.  

Suppose we have a system composed of multiple parts, each of which we are able to simulate accurately in terms of basic physics (and perhaps even quantum mechanics).  If some sort of downward causation were operative, by which the system as a whole overrides the properties of its constituent parts, then our simulations would be inaccurate when hooked together to model the whole system.  But that would mean that the laws of physics had changed for the parts, because otherwise the original models, being based on the laws of physics, would remain accurate.

Surely Woese doesn't think that the system is "reaching down" and altering the laws of physics, does he?

Do any of you folks see another possibility?  What is Woese trying to say, if it's not one of the two possibilities I've outlined here?

I hate to say it, but on this particular point, Woese sounds a bit like Granville Sewell.  In a recent essay, Sewell describes
Quote
a gigantic computer model which starts with the initial conditions on Earth 4 billion years ago and tries to simulate the effects that the four known forces of physics (the gravitational and electromagnetic forces and the strong and weak nuclear forces) would have on every atom and every subatomic particle on our planet. If we ran such a simulation out to the present day, I asked, would it predict that the basic forces of Nature would reorganize the basic particles of Nature into libraries full of encyclopedias, science texts and novels, nuclear power plants, aircraft carriers with supersonic jets parked on deck, and computers connected to laser printers, CRTs and keyboards?

Sewell, bafflingly, concludes that natural selection could not arise in such a simulation:
Quote
My friend looked at the new graphs and tried to mask his disappointment. Well, he said, of course the problem is you haven't taken into account the one natural force in the universe which can violate the second law of thermodynamics and create order out of disorder -- natural selection. You mean there is a fifth force -- why didn't you say so? Just give me the equations for this force and I will add it to my model. He said, I can't give you the equations, because it isn't actually a physical force, it doesn't actually move particles.  ...when he finished, I still didn't know how to incorporate natural selection -- or intelligence -- into my model, so I never did get the simulation to work. I decided the model was still missing a force or two -- or a smarter random number generator.

Of course, Granville being Granville, we know Who at least one of his "missing forces" is.  Woese is not suggesting divine intervention, but like Granville, he seems to be suggesting that the laws of physics are inadequate, in principle, to account for certain higher-level phenomena, biological or otherwise.

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And the set of natural numbers is also the set that starts at 0 and goes to the largest number.  -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

  
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Feb. 19 2008,13:19   

keiths,

That's the way I read it too. I don't think he specifically means that it defies physics so much as that the bacterial world is fundamentally a single organism that operates on different principles than eukaryotes. Sorry I've been out all weekend. I'll get back to this later today. And, right or wrong,

RBill caught the same thing I did in that Woese has established credibility. If he makes a wild claim, the claim will be subject to review the same as any other but he earned the right to make it. He certainly has the background and the understanding to know what he's talking about. The only problem for me is that I don't.
:(

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
keiths



Posts: 2041
Joined: Jan. 2006

(Permalink) Posted: Feb. 19 2008,14:51   

I agree that someone of Woese's stature is worthy of our attention.  It's just that his position seems to be either outlandish or trivial, depending on the interpretation, with no reasonable alternatives in sight.

It seems pretty clear that he believes that emergent phenomena permeate biology, but cannot be explained reductively:
Quote
Whereas emergence seems to be required to explain numerous biological phenomena, fundamentalist reductionism flatly denies its existence: in all cases the whole is no more than the sum of its parts.


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And the set of natural numbers is also the set that starts at 0 and goes to the largest number.  -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: Feb. 19 2008,15:45   

A form of reductionism that is missed in Woese's article is what Jerry Fodor called "intertheoretic reduction," which describes something different from both fundamentalist and empirical reduction. To assert that everything ultimately reduces ontologically to quantum physics is one thing; to assert that the theories we construct at various levels can or should ultimately be reduced to physical theory is quite another. Whether or not the former is true, it is unlikely to be be possible or necessarily desirable to accomplish the latter. Example: the mathematical description/modeling of biological phenemena at the level of quantum physics is neither possible nor helpful; biological phenomena are, for the most part, better described at more macro levels to which quantum physics ordinarily has little to contribute - even as we all understand that all biological phenomena are in some sense highly derived quantum-physical phenomena.

I take it that Woese (and, earlier, general systems theory) is arguing is that there are elements of biological phenomena that, however reducible in principle they are to a chemical and molecular level (and "below"), are better described in "cybernetic" terms (per Bateson): organismic functions that can be represented as loops of homeostasis and feedback, self-regulation, open interaction with the environment, etc. While ontologically reducible to molecular, chemical, and ultimately quantum physical levels, in practice the intertheoretic reduction to levels below these "whole system" levels of description would be unweildy and, most importantly, likely to distract us from attending to behavior and levels of organization best theoretically detected and modeled at a relatively high level of abstraction. Hence the general cybernetic phenomenon of homeostasis can be described at a theoretical level independent of any particular physical instantiation of homeostatic interaction. Pointedly, in terms of very complex biological phenomena that begin to take on the quality of Turing computation, such as human cognition in some instances, the physical substrate "hosting" the phenomenon becomes relatively unimportant to a description of the computational activity, and distracts from the essence of what is occurring at that level.

(I can assert these things because I have absolutely no credibility whatsoever.)

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(Permalink) Posted: Feb. 19 2008,19:15   

RB you said that a good deal better than I could.  I deleted a post I was working on about this that essentially made the argument that the issue that Woese is discussing is explanatory reduction which is a function of this intertheoretic business (got any good cites for that Fodor stuff?).  one could probably support an argument that if we grant the ontological reduction to physical process (some have called this global supervenience but i am aware that this term has an ambiguous history), then biology becomes 'unconstrained pattern hunting'.  this problem has been magnified in ecology where there are no perfect crystals for observation and even simple concepts such as species or community are not necessarily supported by data but given as priors (for example it's amazing how many field studies use morphospecies concepts).

So it's really easy to say this and not have an alternative, and for that reason I think that most authors treating the subject of reduction in biology have been forced to attack straw men.  there is room for an every-man common sense pragmatism wrt 'what is an organism' and on up the hierarchical scale to communities or clades or taxonomic entities or food web members.  it works.  if you want to dig ginseng you are wasting your time in a spruce-fir forest.  even so, it is difficult to rigorously demonstrate how to map these patterns and processes directly to the observed phenomena without opening up this thorny issue of the validity of higher order generalization in biology.

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(Permalink) Posted: Feb. 19 2008,20:14   

Quote (Erasmus @ FCD,Feb. 19 2008,20:15)
Got any good cites for that Fodor stuff?

Here is Fodor's review of E. O. Wilson's Consilience, reductionism's version of Girls gone wild. An amusing skewering of reductionism taken too far.

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keiths



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(Permalink) Posted: Feb. 20 2008,00:26   

Quote (Reciprocating Bill @ Feb. 19 2008,15:45)
I take it that Woese (and, earlier, general systems theory) is arguing is that there are elements of biological phenomena that, however reducible in principle they are to a chemical and molecular level (and "below"), are better described in "cybernetic" terms...

Quote (Erasmus @ FCD,Feb. 19 2008,19:15)
I deleted a post I was working on about this that essentially made the argument that the issue that Woese is discussing is explanatory reduction...

Woese would be wise to wimit himself to the position you both have ascribed to him.  I think we can all agree that although economics supervenes on physics, for example, an "explanation" of cost-push inflation in terms of the four fundamental forces would be useless at best (to humans, anyway).  The appropriate and practical level of explanation is much higher.

However, I think you're cutting Woese more slack than he deserves, reading your more sensible position into what Woese is saying, when his actual position is less defensible.  After all, he is adamant that the "fundamentalist reductionism" he is criticizing is a metaphysical position and not merely methodological or epistemological:
Quote
Empirical reductionism is in essence methodological; it is simply a mode of analysis, the dissection of a biological entity or system into its constituent parts in order better to understand it. Empirical reductionism makes no assumptions about the fundamental nature, an ultimate understanding, of living things. Fundamentalist reductionism (the reductionism of 19th century classical physics), on the other hand, is in essence metaphysical. It is ipso facto a statement about the nature of the world: living systems (like all else) can be completely understood in terms of the properties of their constituent parts. This is a view that flies in the face of what classically trained biologists tended to take for granted, the notion of emergent properties. Whereas emergence seems to be required to explain numerous biological phenomena, fundamentalist reductionism flatly denies its existence:in all cases the whole is no more than the sum of its parts. [Emphasis mine]

By contrast, Fodor is not criticizing metaphysical reductionism in the review that RB cited:
Quote
Consilience is an epistemological thesis: roughly, it says that all knowledge reduces to basic science. This would appear to be very different from the metaphysical thesis that all the facts supervene on the facts of basic science. In particular, it is by no means obvious that the epistemological kind of physicalism follows from the metaphysical kind. And if it doesn’t, then an enthusiast for the second might consistently – even plausibly – reject the first.


The position that we have all taken in this thread aligns with Fodor's.  Woese is the odd man out.

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(Permalink) Posted: Feb. 20 2008,16:30   

Quote
On the evolution of cells.

Woese CR.

Department of Microbiology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, B103 Chemical and Life Sciences Laboratory, Urbana, IL 61801-3709, USA. carl@phylo.life.uiuc.edu

A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.


link

Also a Panda's link:
link

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Henry J



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(Permalink) Posted: Feb. 20 2008,17:06   

DNA (or whatever they were using back then) swapping before there were real boundaries between species?

  
BWE



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(Permalink) Posted: Feb. 20 2008,17:13   

apparently.

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Louis



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(Permalink) Posted: Feb. 21 2008,03:26   

Quote (Reciprocating Bill @ Feb. 20 2008,02:14)
Quote (Erasmus @ FCD,Feb. 19 2008,20:15)
Got any good cites for that Fodor stuff?

Here is Fodor's review of E. O. Wilson's Consilience, reductionism's version of Girls gone wild. An amusing skewering of reductionism taken too far.

Bill and BWE and others,

I want to discuss this general topic but I'll have to take my time to do so for two reasons:

1) It's a technical subject with which I am only briefly familiar.

2) A decent discussion with intelligent, informed people like yourselves about a technical topic is best done (in my experience) with some degree of preparation.

I just thought I'd stick a placemarker in our minds that this is a subject I reckon we could have a fascintaing discussion about. YMMV ;-)

Cheers

Louis

P.S. When the moment comes I reckon I'll start a new thread to avoid derailing this Woese thread. Sound fair?

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BWE



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(Permalink) Posted: Feb. 21 2008,11:30   

Hi Louis,

I hoped you might pitch in your two cents. The only part of microbiology I remember clearly involved the professor's unusual smell. Please do start a new thread if you wish. The idea of a darwinian threshold struck me as fascinating for some reason.

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Lou FCD



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(Permalink) Posted: Feb. 28 2008,07:21   

This thread and the following one at ERV may bear on the topic at hand, in an oblique way.

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