Re: What's more important, self-organzation or evolution?

dkomo wrote:

John Harshman wrote:


dkomo wrote:



sheldongb@xxxxxxx wrote:



On Jul 29, 5:42 pm, dkomo <dkomo...@xxxxxxxxxxx> wrote:




John Harshman wrote:




dkomo wrote:

John Harshman wrote:

Perplexed in Peoria wrote:

<sheldo...@xxxxxxx> wrote in messagenews:1185661229.854287.98150@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

On Jul 28, 1:40 am, j.wilki...@xxxxxxxxx (John Wilkins) wrote:

dkomo <dkomo...@xxxxxxxxxxx> wrote:

John Harshman wrote:

dkomo wrote:

This was one of the questions I wanted to get answered when I first
poked my head into this n.g. a number of years ago. I must say, I have
been major big time disappointed. Discussions of evolution have been
endless and endlessly repetitive. The received view in biology has been
recycled over and over again. Discussions of self-organization in
biology have been virtually nil.

Yet, I think there is a way to resolve this question, and the answer
IMHO is that self-organization is *way* more important than evolution in
producing the phenomenon of life, as can be seen by examining one
particular aspect of organisms. What do you think that is?

No idea. Why not stop being coy and tell us all what you mean?

An organism's structure and function is vastly *underdetermined* by its
genome. Its DNA governs how protein and RNA molecules are built, when
and how much. It doesn't direct where those molecules are to go inside
a cell and what they are to do. The cell's self-organizational
processes take care of that. In fact, the existence of DNA itself is a
result of those processes

Development of a multicellular organism from a single cell to complete
adult is an excellent example of self-organization. DNA has a
ralatively minor part to play in that. Another example is how brains
wire themselves up automatically. The trillions of synaptic connections
are not mapped at all in DNA.

All selection can do is pick the most effective self-organized forms,
but it does not have detailed control over the tremendous complexity of
that organization.

The problem arises from thinking of DNA as a recipe for an organism and
its phenotype. It ain't. It's part of the evolving causal process by
which chemicals self-organise themselves into organisms from prior
organisms.

What are you talking about? The DNA *is* a recipe for an organism and
it's phenotype, Darwinian wise. That it "evolves" does not detract

from being true for "an organism". Any consideration of "self-

organization" must consider heritability or waver from Darwinian
concepts; DNA is regarded as what is inherited and determines
phenotype. Sure, the way I brush my hair or develop as a result of
environmental variables will cause individual traits to occur in a
population, but these are not heritable, and therefore not relevant to
evolution. Dkomo provides "brain wiring" to be an example of "self-
organization", yet that is a profoundly trivial assumption not
relevant to "life", even were he right that DNA only plays a minor
part in brain wiring. And "relatively minor part" is an unproven
assumption at that. He suggests that selection chooses from these
"self-organized forms" but that DNA doesn't have "detailed" control
over phenotypic complexity. That's plain hogwash; you grow four limbs,
one pecker and a big schnose whether you were raised in AU or the US.
If you were born with less or more, Darwinism dictates the reason is
because of DNA, and nothing but DNA.

Bravo! And out of the mouth of Glenn Sheldon, yet.

And the most remarkable thing is that our resident philosopher, who takes
Rick Norman and I to task for suggesting that there is emergence in
biology, is here claiming that DNA is "part of the evolving causal process
by which chemicals self-organise themselves into organisms from prior
organisms." And why does he adopt this tortured way of speaking? Because
he sees this as the only alternative to saying "DNA is a recipe"!

I don't care much about emergence, but I wouldn't say that DNA is a
recipe. That may be a little better or a little worse than the computer
program analogy, but that's because both are more or less useless. DNA
isn't much like anything else I can think of. I like Wilkins'
formulation much better than "DNA is a recipe".

DNA is a part of a complex system of interactions that also include
proteins, RNAs, various signalling molecules (some of which are proteins
and some of which aren't), other physical signals, and the properties of
materials.

Huh? The information in DNA is composed of nucleotides. It is only
those that get transcribed. So the only molecules it can code for are
proteins and RNAs. It couldn't, for example, code for ATP or for
carbohydrates. So I'm not sure what you mean by "various signalling
molecules (some of which are proteins and some of which aren't), other
physical signals, and the properties of materials."

Several points:

DNA doesn't code for ATP or carbohyrdates, but it does code for all the
proteins that act to synthesize them.

By "various signalling molecules" I mean any molecule that participates
in determining which genes are switched on or off. Some of these are
proteins, like the various transcription factors. Others are not, and
perhaps the most famous of these is cyclic adenosine monophosphate
(cAMP), which you might like to look up.

"Cyclic AMP and Ca++ often behave as second messengers, intracellular
substances that relay messages from [cell] receptors to target proteins"

--Raven & Johnson, Biology, 5th ed., p. 135





By "other physical signals" I mean the various means other than
molecules that help to determine which genes get turned on or off. This
includes physical forces like tension and compression, which are
communicated to sensors on cell surfaces and interiors, and thence by
signalling molecules (again) to the nucleus.

By "properties of materials", I refer to the physical features of cells
and extracellular matrices that are important in epigenesis.

All these things you're describing here are what I'm calling
"self-organizing" processes. I draw a boundary between DNA and the rest
of the biomachinery in the cell. DNA is simply a template for building
proteins and RNAs. It doesn't *do* anything! Rather, everything is
done to it. DNA is completely passive. It is not some kind of master
control module for everything that goes on in the cell. Nothing you've
described here contradicts that viewpoint. All the cell signaling,
protein transport and metabolism is done by the biochemical networks
outside of DNA, without any *direct* control by DNA.


You're probably wrong about DNA, but it doesn't support your viewpoint
either way. A cell is a system, DNA being a necessary part of that
system. If you think it could be otherwise, then any support you could
provide for that may support your view. As it stands your argument is
dependent upon what "do" means.



My argument is that there are different points of view regarding what
"do" means. My pov has the "doing" distributed throughout the cell, and
when development takes place, the "doing" is distributed across all the
cells of the developing embryo.

The guardians of the received view here on the n.g. prefer a genecentric
pov, with the "doing" centered on DNA. You are agreeing with that,
hence getting a lot of "attaboy's" from them.




In your OP you said: "It doesn't direct where those molecules are to
go inside a cell and what they are to do. The cell's self-
organizational processes take care of that. In fact, the existence of
DNA itself is a result of those processes"

What are the mechanisms of these processes, or the causal agent(s)? In
other words, why do they "do" what they "do"?



Good lord, I don't have the time to describe the details of embryo
development here. It's a highly complex and detailed process. Why
don't you read about it in a good biology textbook like Campbell and Reece?

However, as far as the DNA vs. distributed self-organization pov is
concerned, let me quote a paragraph from that textbook:

"One important source of information that operates early in development
is the cytoplasm of the unfertilized egg cell, which contains both RNA
and protein molecules encoded by the mother's DNA. The cytoplasm of an
egg cell and even its cytoplastic fluid are not homogeneous. Messenger
RNA, proteins, other substances, and organelles are distributed unevenly
in the unfertilized egg, and this heterogeneity has a profound impact on
the development of the future embryo in many species. After
fertilization, the cell nuclei resulting from mitotic division of the
zygote are exposed to different cytoplasmic environments. The maternal
substances in the egg that influence the course of early development,
called cytoplasmic determinanats, regulate the expression of genes that
affect the developmental fate of the cells."

Campbell and Reece, _Biology, 6th Ed._, p. 412

Note the words "cytoplasmic *determinants*" and "regulate the
expression". Different cells will express different genes depending on
their locations. Does this sound like DNA is in charge of the "doing"
or is it more accurate to say that the DNA is having something *done* to
it? In other words, I'm implying that DNA is a passive agent and that
the actual process of development is distributed across the embryo.
This is a holistic point of view as contrasted to the reductionistic
DNA-centric point of view.

Actually, you seem to have gone from the gene-centric view to the
cytoplasm-centric view without passing through any sort of balanced
assessment of the roles of all the parts of the system. DNA is no more
"passive" -- or active for that matter -- than anything else in the
cell. Which part of a circle is the beginning?

Now you're saying something I can agree with.

All is one. The problem is when you start applying reductionism and
getting into questions of "what does what to what?" I inadvertently
fell into a bit of reductionism myself above.

Unlike you, I don't consider "reductionism" to be a pejorative term.
"All is one" is a fine little mantra, but it doesn't get you anywhere.
Development is a complex system. The genome occupies what I would
consider a central role in that system, though certainly not the only
role. But everything that happens does follow causally from the genome
and a few maternal proteins and transcripts that are distributed
asymmetrically in the egg. (And sometimes a paternal contribution of
some kind, and sometimes a few gross physical features of egg anatomy,
and an environmental influence or two.)

.

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