Part 999: My Fundamental Theorem of Biology

[Kylie]

What I came up with as a "Fundamental Theorem of Biology" is P = (n^a)*f, where:

P = probability of viable organisms
n = number of nested levels
a = acceleration factor
f = lowest probability of self-assembly of a fundamental element

Initially all I focused on was the 'f' factor.

Given a set of fundamental elements, S, what are the probabilities of self-assembly? For example, suppose S = <P,Q,R,S,T>. Further, suppose we define rules of the form, If C then PQ, meaning that if condition C is met, P and Q assemble (join together). If the rules can be expressed mathematically, the probability of any statement (e.g. If C then PQ) can be calculated.

Given the probabilities of all these statements, a Markov transition matrix can be created. A Markov transition matrix is just an eigenvalue problem, which means that for simple cases, we can derive closed form equations for the probabilities of self-assembly.

If we assume a simple rule such as for any list of fundamental elements, there are equal probabilities of assembling with the element preceding and following it in the list, the equation that results is: f = 1 / (2^(n-2) + sum{i=2,n}(2^(i-2))). Several cases like this can be solved. However, they quickly become so complex as to make closed form solutions impractical and numerical solutions become necessary.

One means of numerical solution is TAM (Tile Assembly Method). If one programs rules for Markov chains as described above, it can be quickly demonstrated that TAM correctly approximates the closed form cases.

In what units do you measure the acceleration factor, and how do you determine the probability of self assembly of a fundamental element? For that matter, how do you even define if something is a fundamental element or not?

 

[Amittai]

... If I could, I'd give it up for life.

No don't give up speculating! Speculating is the life!

In nature, random doesn't exist, according to investigators. But the extent of complexity appears unpredictable. (This is a bit like equivocity of analogy and analogy of equivocity.)

Instead of worrying why we can't get to the ultimate, why not let's revel in the questions we can ask, the points others raise, and a perhaps more developed version of your equation, or several equations, as components in a starting point. Runners can't run unless they have a starting point. That's why I love these threads.

 

[Subduction Zone]

No don't give up speculating! Speculating is the life!

In nature, random doesn't exist, according to investigators. But the extent of complexity appears unpredictable. (This is a bit like equivocity of analogy and analogy of equivocity.)

Instead of worrying why we can't get to the ultimate, why not let's revel in the questions we can ask, the points others raise, and a perhaps more developed version of your equation, or several equations, as components in a starting point. Runners can't run unless they have a starting point. That's why I love these threads.

I would disagree about your statement that in nature random doesn't exist. On a quantum level there is no doubt that it does. Above that it is all statistics. Also even at the macro level there appears to be randomness. Chaos theory covers that. The universe appears to be not a wind up mechanism where perfect knowledge would allow a one hundred percent prediction of what will happen next.

 

[Ophiolite]

The universe appears to be not a wind up mechanism where perfect knowledge would allow a one hundred percent prediction of what will happen next.

Although the same cannot be said of the plots of B-movies. (Just something I noticed while self-isolating on NetFlix and PrimeVideo)

 

[46AND2]

Indeed, it seems I've done a poor job.



It would be easy to write a program where something evolves. It would be easy to write a program where nothing is created until an intelligent agent intervenes. Neither of those programs would mean anything. It begs the question to assume evolution or creation in the fundamentals. If the structure is to mean anything, it must be built from first principles that make no assumptions about the result.



Indeed. That is how I wanted to approach this - to show how it all developed. I didn't get a sense anyone had the patience to follow along, so I just plopped down a result. I'm not surprised it looks thin and meaningless.

But I'm at a loss how to proceed. I might suggest something like starting at the beginning and developing something together - something all participants can engage with - but ... meh ... I dunno. Sorry.

Its not begging the question, it is recognizing that they (evolution and abiogenesis) are distinct processes with many different mechanisms. What is required for one may not be so for the other. Trying to tie them together in the same formula is adding unnecessary and detrimental complexity.

 

[Amittai]

I would disagree about your statement that in nature random doesn't exist. On a quantum level there is no doubt that it does. Above that it is all statistics. Also even at the macro level there appears to be randomness. Chaos theory covers that. The universe appears to be not a wind up mechanism where perfect knowledge would allow a one hundred percent prediction of what will happen next.

Though nothing is pure random, non-linear dynamics (recursion) theory does confirm that the extent of complexity does appear unpredictable, as I stated. Nature being big, and we not knowing how big the universe is, we don't know how big a subject it is.

 

[Amittai]

Here is a very nice C S Peirce resource:

Commens | Digital Companion to C. S. Peirce

 

[Subduction Zone]

Here is a very nice C S Peirce resource:

Commens | Digital Companion to C. S. Peirce

If you are using him as a resource he is rather outdated. Once again, at the quantum level all of the evidence shows events to be statistical. Not predetermined.

Quantum indeterminacy - Wikipedia

Experimentation trumps philosophy.

 

[Amittai]

If you are using him as a resource he is rather outdated. Once again, at the quantum level all of the evidence shows events to be statistical. Not predetermined.

Quantum indeterminacy - Wikipedia

Experimentation trumps philosophy.

Surely we don't know what "predetermined" is. Surely we should treat statistics as the gift they are. Why would Peirce, as a chemist and coastal surveyor, as well as being insightful into language, not like statistics? Popper proposes propensity fields. Newman tries to get us interested in degrees of inference for our degrees of assent.

Do those who accuse others of being off-pat, try to cloak that they are off-pat in a slightly different direction?

I am told Peirce was constantly trying to revise the terminology of his earlier pronouncements. And I was flagging him up as one of many. He had to combat some shallow tendencies that, as Menand describes, unfortunately took root in some of the work of Dewey, James and Wendell Holmes. He tried to devote logic to the relative contrasts between individuating and non-individuating sciences which, I am told, Rickert and Windelband flagged up.

The article you have linked to is wonderful. I get a huge amount out of pondering Schrodinger's Cat. Heisenberg and Godel are my heroes. Duhem and Quine commented on some of the same things.

Do you think Amittai wants to be a lookalike? No (having made a late start) I want to pull together, for those around me, the best quality building blocks my forebears and contemporaries have generously left to hand. I'd have got nowhere without methodical realism, retroduction and projectivity.

Half of my argument goes into this thread and the other half goes into the "rational basis of faith" one. I've commented on words in numeorus threads. Shall have to recompile the lot soon (apologies )

 

[Amittai]

Resha, I came across this, on the secret life of plants, from a contributor to the "Peirce List" the other day:

quote

In some theories of ontology, the focus on scientific principles tends to omit or downgrade the importance of goals, intentions, and feelings. Such issues are often deprecated as "anthropomorphic". Other systems, which emphasize neuroscience, downgrade any kind of memory or reasoning that is not based on neurons. Even the field of biosemiotics puts more emphasis on animals with brains than single-celled protozoa, which have no neurons. The semiotics of plants was usually ignored.

But in recent years, biologists have discovered the complex methods of communication, memory, and learning by plants. For a review of those methods, see "The secret life of plants: How they memorize, communicate, problem solve, and socialize": The Secret Life of Plants: How They Memorize, Communicate, Problem Solve and Socialize

These developments show the importance of broadening the foundations of ontology to include phytosemiotics as well as zoosemiotics. Those issues are fundamental to every aspect of life from bacteria on up. They cannot be dismissed as "unscientific".

unquote

 

[Ophiolite]

Resha, I came across this, on the secret life of plants, from a contributor to the "Peirce List" the other day:

quote

In some theories of ontology, the focus on scientific principles tends to omit or downgrade the importance of goals, intentions, and feelings. Such issues are often deprecated as "anthropomorphic". Other systems, which emphasize neuroscience, downgrade any kind of memory or reasoning that is not based on neurons. Even the field of biosemiotics puts more emphasis on animals with brains than single-celled protozoa, which have no neurons. The semiotics of plants was usually ignored.

But in recent years, biologists have discovered the complex methods of communication, memory, and learning by plants. For a review of those methods, see "The secret life of plants: How they memorize, communicate, problem solve, and socialize": The Secret Life of Plants: How They Memorize, Communicate, Problem Solve and Socialize

These developments show the importance of broadening the foundations of ontology to include phytosemiotics as well as zoosemiotics. Those issues are fundamental to every aspect of life from bacteria on up. They cannot be dismissed as "unscientific".

unquote

A cautionary observation: the specific information used by the author of "The Secret Life of Plants" is fascinating and likely as accurate as any set of scientific data in a "frontier zone" of investigation. I find the equivocation of terms (memorize, communicate, etc.) in the link title troubling. It suggests an attempt to convince through rhetoric rather than evidence.

 

[Amittai]

A cautionary observation: ... I find the equivocation of terms (memorize, communicate, etc.) in the link title troubling. It suggests an attempt to convince through rhetoric rather than evidence.

Yes you are right - I wish a section of the Peirce enthusiasts would add more intuition to their too flat attempts at spatial thinking (some others do already).

Gary Klein in The Power Of Intuition (2004) explains how intuition is not airy-fairy but works powerfully hand in hand with logic.

 

[Ophiolite]

Gary Klein in The Power Of Intuition (2004) explains how intuition is not airy-fairy but works powerfully hand in hand with logic.

My own view of intuition was arrived at independently of any formal research in the matter, is entirely based upon personal observation and consequently may be casually disregarded as anecdotal.

Intuition is derived from one of two sources:

• Instinct - we are predisposed to react in certain ways (and, thus, to suspect certain things) under certain circumstances. This is illustrated by the classic scene in the Western, war movie, or horror film, where with nightfall the protagonist says to the group "I don't like it. It's quite. Too quite."
• Experience - our subconscious processes data and solves problems, reporting them upstream to conscious, which perceives them as an intuition.

In regard to the latter, in business I routinely deferred decisions till the following day, when such decisions could be safely deferred. This allowed me to "sleep on it". I would make sure I had studied all the relevant facts, but would then put them "out of my mind". In the morning, typically while showering, I would recall there was a problem to solve/decision to make. Pause. Then the answer was there. The solution/decision quite clear. No conscious thought involved. I commend this approach to all.

 

[Amittai]

... I would make sure I had studied all the relevant facts ...

Yes, it's like the individual cited has studied quite a lot of the facts but then miscontrues them in accordance with his own perhaps ideology-based rhetoric (as I recall some other participants did comment on that; I brought the passage in because it otherwise illustrated my point). Some Peirceans differ from the view of Subduction Zone in post 28 and hold that Peirce can help us examine the logic of life (the thread theme) whereas others, by dumbing down (bowdlerising), indeed make him "look dated".

 

[FrumiousBandersnatch]

A cautionary observation: the specific information used by the author of "The Secret Life of Plants" is fascinating and likely as accurate as any set of scientific data in a "frontier zone" of investigation. I find the equivocation of terms (memorize, communicate, etc.) in the link title troubling. It suggests an attempt to convince through rhetoric rather than evidence.

I think this is as much a problem of definition and specific semantics as it is equivocation. We usually use terms like 'memorize' and 'communicate' to describe the activities of mammals (particularly humans), and so they come with implicit baggage of complex and sophisticated assumptions and associations, yet the words can be applied in far simpler contexts. When they're used for plants, that we are accustomed to think of passive and lacking complex & sophisticated behaviours, it doesn't feel right. Perhaps we need to qualify the words according to the context involved...

This is a perennial problem of human language and abstractions - coarse-graining and trying to divide up the world into unambiguous categories. Unfortunately, much of the world we're trying to describe is not that simple, and new discoveries continually disturb our established categories and meanings.