Doesn't darwinian theory fall apart on ontological grounds?

[jeeprs]

I am very skeptical about this abiogenesis theory. It seems simple in principle, give us enough time, we will work out the sequence and the conditions, then we will know. It is like AI - we understand the principles, give us enough time, we can map it all out. Deeply skeptical. But then, it's science, isn't it, and that is not the usual target of skepticism.

Perhaps this is a reason why. There is a Sanskrit word 'svabhava' which literally means, 'self-born' or 'self-created'. In Buddhist philosophy, it is held that no being can be self-born: everthing that exists, owes its existence to another. The existence of all beings is derived from their relationship to other beings, both in the sense that their existence is imputed by a subject, and also in the sense that they arise in accordance with conditions and subsequent to previous actions which caused them to be able to exist.

So at one time, according to the abiogenesis theory, there must have been a being, to which all subsequent beings owe their existence. This was the primordial cell, the origin of all life. So the question is, how did this being come into existence? If it did not owe its existence to another being, what made it exist? How did it pass from non-existence into existence?

I don't have an answer at this point - only a question. I don't even know if it is a real question but let's see.

[Aedes]

By mechanical I was not referring to machines. I meant only that assembly of cellular components happened without any central genetic program, and solely because of chemical and physical conditions that potentiated them.

me⋅chan⋅i⋅cal

–adjective
1.having to do with machinery: a mechanical failure.
2.being a machine; operated by machinery: a mechanical toy.
3.caused by or derived from machinery: mechanical propulsion.
4.using machine parts only.
5.brought about by friction, abrasion, etc.: a mechanical bond between stones; mechanical erosion.
6.pertaining to the design, use, understanding, etc., of tools and machinery: the mechanical trades; mechanical ability.
7.acting or performed without spontaneity, spirit, individuality, etc.: a mechanical performance.
8.habitual; routine; automatic: Practice that step until it becomes mechanical.
9.belonging or pertaining to the subject matter of mechanics.
10.pertaining to, or controlled or effected by, physical forces.
11.(of a philosopher or philosophical theory) explaining phenomena as due to mechanical action or the material forces of the universe.

You haven't addressed the rest of my post concerning mutation (a misused word unto itself in this conversation, but I'll take the colloquial use of "mutation" to mean genetic change or allelic polymorphism).

---------- Post added 11-27-2009 at 09:19 AM ----------

Originally Posted by jeeprs

I am very skeptical about this abiogenesis theory. It seems simple in principle, give us enough time, we will work out the sequence and the conditions, then we will know.

Maybe we'll know, maybe we won't. But unlike evolutionary biology (or like anthropology, history, geology, or any other science that reconstructs the past), we do not have preserved signatures (i.e. fossils) of the primordial soup that will give us the answer. The only way to build on this theory is to try to recreate early earth conditions in a laboratory setting and see what happens prospectively. Given the size of the early earth and the length of time, it's not likely possible to do this in a lab, certainly not witness the spontaneous generation of life. But the question is will we see the spontaneous generation of organic macromolecules and polymers, i.e. the generation of fundamental molecular constituents of cells.

There's nothing really to be skeptical of in the abiogenesis theory, unless you're inclined to invoke non-physical contributions (i.e. God). What abiogenesis comes down to is the notion that life is a natural phenomenon, and it therefore came into being as a result of natural materials, natural conditions, and natural forces. The next step is to make inferences to how that MIGHT have been possible in the early earth and to see what happens when you model those conditions.

Originally Posted by jeeprs

But then, it's science, isn't it, and that is not the usual target of skepticism.

Of course it is. Science targets itself with skepticism because its growth demands evidence. Science develops in part by overturning or embellishing past science.

Originally Posted by jeeprs

So at one time, according to the abiogenesis theory, there must have been a being, to which all subsequent beings owe their existence.

No, that's evolution -- the notion that all life is derived from ancestral populations. Abiogenesis is the notion that this ancestral population came into being via natural phenomena. The word "being" is metaphysical, so I'd leave it out of a scientific discussion.

[QuinticNon]

Originally Posted by jeeprs

Able to replicate without outside assistance. Any cell can do this, and no machine can.

What makes you think there is no outside assistance?

---------- Post added 11-27-2009 at 09:05 AM ----------

Originally Posted by l0ck

But we can imagine a machine that can, and thus we can create it.
Nano-Molecular Assembly.

That's not free of outside assistance. It must be designed to self replicate. It must be programmed to do so. Any computer virus will confirm this.

[QuinticNon]

Only codified information may cause self-replication. That's one (of many) reasons for the designation of DNA as being a code... the Genetic Code. That's specifically why it's not called the Genetic Blueprint, or the Genetic Template. Blueprints and Templates do not replicate themselves. Code does.

Excerpts from "Information Theory, Evolution, and the origin of life" Hubert P. Yockey
Information theory, evolution, and ... - Google Books

Specifically note the role of Gamov.

"The genome is sometimes called a "blueprint" by people who have never seen a blueprint. Blueprints, no longer used, were two-dimensional, a poor metaphor indeed, for the linear and digital sequence of nucleotides in the genome. The linear structure of DNA and mRNA is often referred to as a template. A template is two-dimensional, it is not subject to mutations, nor can it reproduce itself. This is a poor metaphor as anyone who has used a jigsaw will be aware. One must be careful not to make a play on words."

Codes require authorship, even stand alone self-replicating codes. They must be programmed to do this from the very beginning.

[Aedes]

Originally Posted by QuinticNon

That's one (of many) reasons for the designation of DNA as being a code...

Codes require authorship, even stand alone self-replicating codes. They must be programmed to do this from the very beginning.

First, to call DNA a "code" is metaphorical, because everything else in the universe we call a code is designed by humans. DNA is unique. It does have properties of a template, which you would easily appreciate by thinking about reverse genetics (inferring the coding sequences of the source gene from the amino acid sequence of the consequent protein, an extremely common practice). DNA specifies the linear sequence determinants of a protein. It does not directly determine its 3-dimensional structure or its function. For this to happen, DNA needs to be extrinsically regulated. Even in an unfertilized egg, there are environmental determinants trafficked into the egg by the mother that allow for asymmetrical expression of genes in different cells of an eventual embryo. In other words, the physiology of DNA requires a regulatory environment; a cell's DNA is functioning as a template for structural and functional effectors of this environment, but it is not independently predetermining it (or encoding it).

Because there is nothing else in nature analagous to DNA (or RNA for RNA viruses), it's a nonsequitur to say that it must have been programmed from the beginning. Only human codes must have been programmed as such from the beginning.

Secondly, DNA is NOT self-replicating. DNA is replicated by the cell that contains it, not by itself.

DNA replication requires, among other things, a DNA-dependant DNA polymerase, nucleotide monomers, and certain electrolytes (particularly magnesium) to replicate in vivo. Now this can all come from that selfsame DNA's transcription of DNA polymerase, metabolic synthesis of nucleotides, and determination of its host cell's chemical milieux. But not necessarily -- many viruses use host cell enzymes for the replication of their genome. And you can take a little tube with Taq polymerase to amplify and replicate naked DNA sequences ex vivo, otherwise known as PCR.

[QuinticNon]

Originally Posted by Aedes

First, to call DNA a "code" is metaphorical,...

Your argument is with Yockey, not me.

"Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies."
(emphasis mine)
Hubert P. Yockey - Information Theory, Evolution, and the origin of life.


---------- Post added 11-27-2009 at 10:51 AM ----------

Originally Posted by Aedes

...because everything else in the universe we call a code is designed by humans.

The bee waggle dance is a code. Whale song and wolf howls as well. Dolphins too.

[Aedes]

It's a very loose application of the word code if you are using it in a way that includes everything from morse code to wolf howls, so you can't have it both ways -- either "code" is an imprecise word and does not inherently necessitate "authorship"; or "code" is a precise word and it is therefore metaphorical to use it for things that lack authorship. Just because you've defined code a certain way does not mean that DNA fits that definition, and the fact that you've used the word code does not abdicate you from justifying why you think DNA has an author. To say "because Yockey says it's a code" doesn't solve the problem.

[QuinticNon]

Originally Posted by Aedes

It's a very loose application of the word code if you are using it in a way that includes everything from morse code to wolf howls...

Not at all. All codes, any code, runs effortlessly through the protocols set forth by Claude Shannon in his book "A Mathematical Theory of Communication"
Shannon Model http://www.ctphotographx.com/clients...onComModel.jpg

Yockey did not "decide" that DNA was a code. Gamow discovered that it was a code and Yockey successfully mapped it to Claude Shannon's model confirming Gamow's discovery.
Yockey Model http://www.ctphotographx.com/clients...eyComModel.jpg

All codes run through the Shannon model. If they didn't, they wouldn't be codes. Nothing from the cause/reaction realm of chaos can run through the model. Their are very specific protocols for calling something a code.

Formal Definition of Code as adhered to in Yockey's book, defined by Perlwitz, Burks, and Waterman, as determined by Claude Shannon Information Theory. http://www.ctphotographx.com/clients...ry/CodeDef.jpg

Originally Posted by Aedes

...so you can't have it both ways -- either "code" is an imprecise word...

The precision is extreme. Refer to formal definition above.

Originally Posted by Aedes

...and does not inherently necessitate "authorship";...

Sentient authorship is the only known mechanism to explain the existence of code. SETI is not looking for life, or water. SETI is looking for a genuine codified signal that adheres to the principles of Information Theory.

Originally Posted by Aedes

...or "code" is a precise word and it is therefore metaphorical to use it for things that lack authorship.

See Yockey above. Or provide one example of code that does not arise from sentient authorship. I reject your assumption that "precise" and "metaphorical" may be conflated. And please don't claim that DNA is the example of non-sentient authorship. Doing so begs the question of demonstrating the non sentient mechanism.

There are many instances of anonymous authorship. But we cannot claim without reason that code can exist without sentient authorship. It is testable (as every comment on this forum confirms), it is repeatable (as future comments will confirm), and it is falsifiable (upon demonstrating a non-sentient model of code).

We must infer authorship to explain the existence of the genome. By every standard that we use to infer the existence of gravity, we must, in all good consciousness, infer the existence of sentient authorship.

I make no claims as to the nature of the required author. I only accept what science demands of me, and infer that there must indeed be one.

Originally Posted by Aedes

Just because you've defined code a certain way does not mean that DNA fits that definition...

I didn't define code. Perlwitz, Burks, Waterman, Yockey, Gamow and Shannon did. I did not make it fit the Shannon protocols either. Nobody made it fit the protocols. We simply discovered that it does fit, hence the designation of genetic code.

Certainly you don't believe that Gamow and Yockey made a tremendous blunder by not calling DNA the Genetic Template, or the Genetic Blueprint?

Repeating from Yockey:
"The genome is sometimes called a "blueprint" by people who have never seen a blueprint. Blueprints, no longer used, were two-dimensional, a poor metaphor indeed, for the linear and digital sequence of nucleotides in the genome. The linear structure of DNA and mRNA is often referred to as a template. A template is two-dimensional, it is not subject to mutations, nor can it reproduce itself. This is a poor metaphor as anyone who has used a jigsaw will be aware. One must be careful not to make a play on words."

Just read the book. The link is above, and it clearly demonstrates the close relationship of genetics to linguistics and information theory. Every Biologist adheres to Yockey's model for transcription. This shouldn't be such a shock.

Originally Posted by Aedes

...and the fact that you've used the word code does not abdicate you from justifying why you think DNA has an author.

I'm just acknowledging the very same protocols that we all use. I didn't call it a code. It was discovered to be a code... again, Yockey:
"The conceptual framework, for DNA coding thus proposed by Gamow, led to the correct solution of the question of how the sequences in DNA control heredity. Without Gamow's contribution, the work may well have gone to mechanism-reductionism and perhaps dialectical materialism".

Originally Posted by Aedes

To say "because Yockey says it's a code" doesn't solve the problem.

Sir, with all due respect, the only problem I see here is that which one refuses to accept the research right before their very eyes. Research provided by the most respected minds in their fields and universally accepted in practically every industry that run our modern day lives including Information Theory, Communication Theory, Computer Sciences, Robotics, A.I., Cybernetics...

[jeeprs]

Originally Posted by QuinticNon

What makes you think there is no outside assistance?

Perhaps I put it wrongly. What I am trying to suggest is that organism and machines are fundumentally different in that an organism can heal, reproduce, direct itself, and so on, whereas a machine can do none of these things. This is what I often think when animals or humans (or the universe for that matter) are said to be like a machine.

To re-iterate, I don't have a creationist view that God assists with the designs of tricky bits like eyes and bacterial flaggelate mechanisms. But I rather like the idea that the 'code' which results in such developments is inherent in the nature of existence. This is like an old-fashioned notion that there exist 'laws of form'.

Thanks for the very interesting references by the way, shall add to the (ever growing) list of things to read.

[QuinticNon]

Originally Posted by jeeprs

...things to read.

I've read a number of your posts on other threads. You are hitting all around this premise of Information Theory and required authorship, but don't quite have the research or terminologies to effectively put forth your position.

You are correct to suppose that organisms and machines are fundamentally different. That fundamental difference is Information. The qualities you attach to "organisms" are exactly the same qualities that distinguish "code" from "chaos".

Code "can heal, reproduce, direct itself, and so on, whereas chaos can do none of these things."

Think of code as a material lens that allows us to look into the immaterial realm of information.

"Information is information. Not energy and not matter. Any materialism that does not allow for this cannot survive in the present".
Norbert Weiner, Cybernetics p147

Chaos = Energy + Matter

Life = Energy + Matter + Information