Posted on 07/19/2009 7:46:56 PM PDT by djf
Research by a group of Montreal scientists calls into question one of the most basic assumptions of human genetics: that when it comes to DNA, every cell in the body is essentially identical to every other cell. Their results appear in the July issue of the journal Human Mutation.
This discovery may undercut the rationale behind numerous large-scale genetic studies conducted over the last 15 years, studies which were supposed to isolate the causes of scores of human diseases.
(Excerpt) Read more at sciencedaily.com ...
Just thinking of the idea (debugging, sensitivity analysis for the parameters) gives me the willies.
Then the cells into an organ...
Then the organs into an organism.
Then tweak various "objects" to mimic faulty genes or disease processes.
We'd need "Deep Thought" (Hitchhiker's Guide to the Galaxy) to begin to model it.
Cheers!
You are speaking of powerful mathematical tools here, dear grey_whiskers. As such, they are "indifferent" as to whether they are used by physicists or biologists. What does a tool per se have to say about biological behavior, or how does a Fourier transform answer the question "What is life?"
Rosen is dealing with a higher-order problem than mere tool using.
What Rosen is essentially saying is that physics is a "special case" (i.e., non-generic) because it deals only with simple material systems, which are themselves nongeneric and even relatively rare in nature; while biology is the realm of the generic, that is, of complex material systems, which comprise the majority of systems in nature. Since biology is inherently complex, it is more generic than physics. That's what reverses the normative view that biology is a "special case" of physics. Biology is simply much more general than physics is, and includes physics within itself.
That is my understanding of Rosen's argument. I can illustrate it further if you like. He himself adverted to David Hilbert's attempts to formalize Number Theory as a good illustration of the problem.
Ultimately, all of Rosen's arguments are premised in mathematics, especially set theory and category theory.
Sorry, Betty. As usual I wasn't very clear.
All I meant was that physics exists *independently* of biology -- I used the F.T. as an example of a construct which would "exist" (but *that* bit of philosophy is another can of worms entirely) even if there were never any living things.
Since biology is inherently complex, it is more generic than physics. That's what reverses the normative view that biology is a "special case" of physics. Biology is simply much more general than physics is, and includes physics within itself.
I beg to differ: biological laws hold for living systems, the laws of physics are *universal* (as far as we know, within any single Universe out of all the hypothesized multiverses, and for the nonce neglecting the supernatural).
In other words, there is no special "animal magnetism" (except when my wife & I are alone on a Saturday night...) -- all of the physical interactions which go into making up an organism, apply equally as well in the lab, or in non-living systems.
Biological entities act different for several reasons, including:
a) Complexity. We need distributed supercomputers to model protein folding, but the body does it on the fly in real time.
b) Complexity leading to chaotic/turbulent behaviour -- aside from the probabilistic intromission of quantum effects, both the physical *layout* of the body (e.g. blood flow) and the large number of interactions (DNA replication, genes being turned on and off by interacting with the environment, etc. etc.) make it hard to quantify reproducibly.
c) Any questions of a "soul" or "life force" (I prefer Dave Barry's definition of life as "anything that dies when you stomp on it") which are outside the scope of peaceful discussion on a thread such as this: most people can't even agree on a definition, let alone the presence or absence of such things. Sigh.
Thanks for putting up with the rant betty. In return I'll regale you with one of my favorite related jokes:
A rich man takes a fancy for thoroughbred horseracing. Not being accustomed to failure, he contracts out with several experts, to make sure he maximizes his chances of starting a successful stable. He hires a biologist, an engineer, and a physicist, gives each a goodly sum of money, and asks them to report back in a year.
A year goes by. He calls the biologist first.
"Well, I have discovered through genealogical histories that of all horses, brown ones are the fastest. You would have thought it would be the dappled grey ones, but you should stick with brown."
The rich man thanks him, and goes on to the engineer.
"I have studied films of the final leg of many horse races, and I have found that you can learn a lot by stroboscopic examination: the horses with the smallest, whiplike legs do surprisingly well, rather than the bulkier, more muscled horses."
The rich man makes his notes -- "O.K. Brown horses, thin legs." He turns to the physicist. "And what do you have for me?"
The physicist says, "If we consider (without loss of generality) the case of a spherical horse in simple harmonic motion..."
Cheers! Cheers!
"Complex systems — which Rosen says are the generic or "typical" case in nature, and simple systems the nongeneric — are simply not computable; they do not reduce to algorithms. They have the beastly habit of spawning what Bertrand Russell called impredicativities, or "vicious circles" involving self-reference and semantic meaning which cannot be reduced to syntax/algorithms/computability. Worse, they seem to invoke the Aristotelian "final cause" — which has been utterly banished from science for the past three hundred and more years because final cause in some sense seems to put the "cause" of something in the present in the future, and this the Newtonian formalism absolutely forbids. Though biologists working on what are generically called "anticipatory systems" evidently are trying to put it back into the scientific mix."
to this thread.
Cheers!
To illustrate, take a watch. This is a simple mechanical system. You can take it apart and study the parts to draw inferences about how it works; and then you can in principle reassemble it (provided you know how the parts originally fit together, which in a reversible process is fairly easy to do — just "backtrack").
But with a biological system, this does not work. You can't reduce it to its parts (analysis) and then put it back together again (synthesis), nor can you build it up from parts. The above situation of the watch in the biological case would be analogous to taking the watch and smashing it with a hammer. There's no hope of reconstituting it; for all you now have are artifacts, with no prayer of finding out how the whole system was "organized," or causally entailed, in the first place. That information is irretrievably lost.
So Rosen suggests that, rather than "fractionating" systems down to their material parts, and throwing out the organization (i.e., its system of causal entailment, which can be mathematically modelled), it's better to keep the organization, and throw out the material parts.
He thinks this is what must be done, if we want to get anywhere with biology, and perhaps answer the question, "What is life?"
Well, it doesn't look like a whole lot of "modeling" is going on here, just some excellent observations and a gift for asking the right questions.
Again, Brent and Brucks' (2006) comment comes to mind: "“Today, by contrast with descriptions of the physical world, the understanding of biological systems is most often represented by natural-language stories codified in natural-language papers and textbooks…. But insofar as biologists wish to attain deeper understanding (for example, to predict the quantitative behavior of biological systems), they will need to produce biological knowledge."
Thank you grey_whiskers for the very, very interesting article!
The only problem with such an approach is that you need to know at what level of detail or of granularity, the "root cause" of whatever disease process starts going wrong.
In otherwords, for cardio events, it does no good to treat the heart as an object with no interior: you need to consider the valves, the ability of coronary arteries to get blocked, the effects of cell weakening / death on the efficiency of the pump, etc.
It's a fascinating idea, I just wish I had been born sooner to have gotten in on the whole shebang.
Cheers!
Good grief man, don't you realize that with this statement, you have crossed into the forbidden realm of ontology? "Existence" isn't even in the lexicon of the Newtonian Paradigm. It is absolutely banned!
Plus if "F.T. [is] an example of a construct which would 'exist' even if there were never any living things," who'd be around to notice or verify this — or even care?
You wrote: "I beg to differ: biological laws hold for living systems, the laws of physics are *universal*." Okay, then please tell me: What are the biological laws? On what basis do you insist that the laws of physics are more universal than biology, if we don't even know what the laws of biology are yet (as I contend is the case)?
I am not arguing in favor of any kind of "vitalism" as a biological "law" here. It is not necessary.
You wrote: "all of the physical interactions which go into making up an organism, apply equally as well in the lab, or in non-living systems." The point is biological systems are "more than" their physical interactions: they are systems of causal entailment; i.e., they realize a plan of organization that typically features properties that are simply not seen in simple (e.g., nonliving) material systems — e.g., their impredicativities, that is their self-referential closed causal loops that cannot be reduced to computability because they are ultimately semantic — they deal with "meaning" (i.e., semantics, which demand external referents from outside the system itself) — and thus are not purely syntactical. The Newtonian Paradigm is a pure context-independent formalism that relentlessly expunges all consideration of "meaning" from its methods on the grounds that "meaning" implies subjectivity and/or "context-dependence." This is not allowed!
You wrote [and since we're "ranting," please indulge me cause I feel like ranting too, dear grey_whiskers!]:
Biological entities act different for several reasons, including:Thank you so very much for the most enjoyable "rant" grey_whiskers! These are such fascinating issues, and I thank you for your interest. And also thanks for the little "joke!" LOLOL!a) Complexity. We need distributed supercomputers to model protein folding, but the body does it on the fly in real time.
My guess is that if it's the supercomputers doing the modelling, such models cannot in principle reach to the problem of protein folding. The computer would need to "understand" HOW "the body does it on the fly." But this is the great unknown which the simple piling up of more and more syntactic elements cannot reach to. Computers only "do" syntax, ya know (syntax here defined as program and data). Semantics is strictly out of reach. In short, that's why computers can't spontaneously, meaningfully answer "Why?" questions.b) Complexity leading to chaotic/turbulent behaviour — aside from the probabilistic intromission of quantum effects, both the physical *layout* of the body (e.g. blood flow) and the large number of interactions (DNA replication, genes being turned on and off by interacting with the environment, etc. etc.) make it hard to quantify reproducibly.
Do you assume that chaos, "turbulent behavior," is characteristic of complex systems? Of biology in general? Well, I have heard of an ingenious hypothesis which states that chaos is "normative" for biology, and homeostasis the very kiss of death. It's interesting. But I don't happen to agree with it.c) Any questions of a "soul" or "life force" (I prefer Dave Barry's definition of life as "anything that dies when you stomp on it") which are outside the scope of peaceful discussion on a thread such as this: most people can't even agree on a definition, let alone the presence or absence of such things. Sigh.It is the very versatility of biological organisms — the plethora of functions that must be coordinated and executed for the benefit of the whole system — that makes its system of entailment, its causal organization, so critically important.
Well I certainly agree with you there, grey_whiskers! But such questions are not scientific questions to begin with. Notwithstanding, I sure admire Dave Barry's definition!
I just read an excellent paper that ventures five universal biological laws, and, wouldn’t you know it, the author concludes from these laws that materialist evolution is impossible :o)
PS I’ll be posting the article in the next couple of days, so be on the lookout for it!
All the best—GGG
Is that a riddle, or are you trying to be retarded?
One would think I’d be used to it by now ... but I never fail to be amazed by your posts. Thanks, Ms. Boop — you’re an absolute treasure.
Would it be too presumptuous to characterize the problem as follows?
We might consider the genome as a book; and the net effect of the HGP was that it transcribed the letters from the book into a computer database. And thus you have a bunch of computerized letters, collected in the order in which they appear, which is pretty swell -- an excellent resource.
The problem, of course, is that the letters aren't actually the point of the book at all; nor is the particular order in which they appear necessarily going to confer any deep knowledge to a reader who doesn't know the language, much less the ideas that the language is trying to express. The value of a book is that there's a meaning and a context to the book that far transcends the collection and pattern of those letters, that mere transcription cannot capture. We can't just look at the letters and understand the concepts, abstractions, the book contains -- much less the puns.
The analogy would seem to apply as well the compilation of DNA's letters. Merely having them confers no knowledge of what information they contain, nor what they mean when taken together as a system.
Moreover, a simple transcription of the letters and patterns does not address how the book is intended to be used ... the purpose of a phone book, for example, is different from that of the Bible or a text on topology. Even the chapters of a book have different applications.
Here I am drawing an analogy with respect to the interactions between the DNA code, and the mechanisms of the cell that actually operate on and with the DNA. Those cells provide a specific context for specific portions of the DNA -- in a very real sense the cellular mechanisms represent information that seems to me to be separate from, and perhaps even broader than, what the DNA itself holds.
If the HGP "failed," perhaps it failed by assuming that simply collecting letters would be enough...?
Absolutely outstanding, r9etb! I do believe you've captured the very problem in a nutshell, and have formulated beautiful conclusions.
In answer to your question above, I'd say: Yes, I do believe that. That's the very problem with it.
Thank you ever so much for your wonderfully insightful and incisive essay/post!
Jeepers, r9etb, that goes both ways. Thank you so very much for your kind words!
You bet I will GGG! May I have a ping?
And thank you all for this wonderful sidebar discussion!
I very strongly recommend Rosen's book "Life Itself" to everyone. His mathematical arguments are solid both in showing why the Newtonian mechanistic approach doesn't work for living systems and in his construction of a model that does work.
The root problems with the Newtonian paradigm are (a) that in living systems the whole is not equal to the sum of the parts and (b) that a mechanistic algorithm cannot anticipate what has not yet occurred (with a few notable exceptions such as the Fibonacci series.)
Another way to describe it is that the mechanistic approach can handle the syntax but it can't deal with the semantics.
r9etb's metaphor makes that point beautifully. What we have right now is a string of formatted letters (syntax.) But to read it, we must know the language (semantics.)
What a wonderful sidebar this has been!
This is not news. DNA polymerases, even though they have proofreading functions, have error rates around 1/ 10^6 bp. The human genome has about 3.4x10^9 bp, so about 1000 mutations happen per cell replication. Other proofreading enzymes probably bring it down to 10-100 mutations/ cell division.
Also, telomeres, like the aglets on shoelaces, stop the DNA from fraying. Since the DNA cannot replicate to the end of chromosome, some of the repeats at the ends are lost and the chromosome shortens. This puts a limit on the number of replications a cell can undergo before it dies.
As I said this has been known for a long time.
NOt that there is any reason to expect this going in, of course: but sometimes the most interesting science is found by picking up a rock everyone takes for granted and looking under it, so to speak.
Cheers!
No wonder all those convicted murderers are getting released years later due to DNA not matching...
Actually, it was supposed to be sarcasm.
EVOLUTION says that THINGS HAPPEN. Flatly stating that CHANGES occur - somehow - and they get passed on.
Always staing that various things COULD be the factor to facilitate change; but never showing just HOW they could occur.
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