Darwin Unhinged: The Bugs in Evolution

If bringing up pheromones is unhelpful, can someone explain why? The connection between DNA and a polypeptide seems to be the same as the connection between a pheromone and a behaviour.

Has somebody offered a definition for "code" which includes DNA, but not pheromones? The mapping of ideas was brought up, but DNA isn't an idea. It's a description of which base sequences have become associated with which amino acids.

Linda

Firstly, how do you define a code? Does it involve encoding and decoding? Are there rules? Can it be represented symbolically? Does it convey meaning or determine function? Is it structured (not haphazard)?

All excellent questions.

"Different languages, for example, give different names to the same object precisely because there is no necessary connection between names and objects."

Here is a critical point. Is there a "necessary connection" between a particular codon and the amino acid it codes?

"Signs, meanings, and conventions, however, do not come into existence of their own. There is always an ‘agent’ that produces them, and that agent can be referred to as a codemaker because it is always an act of coding that gives origin to semiosis."

Note the scare quotes around 'agent.'

~~ Paul

"Signs, meanings, and conventions, however, do not come into existence of their own. There is always an ‘agent’ that produces them, and that agent can be referred to as a codemaker because it is always an act of coding that gives origin to semiosis."

Note the scare quotes around 'agent.'

~~ Paul

If you read further in he document you will find he makes a distinction between mind and "organic" as agents. What he means by organic and how it differs from mind I have not been able to fathom.

[Note: these paragraphs are not necessarily contiguous in the original document]

The sequences of genes and proteins, in short, have precisely the characteristics that define signs and meanings. They are codemaker-dependent entities made of organic molecules and are, therefore, organic signs and organic meanings. All we need to keep in mind is that signs and meanings are mental entities when the codemaker is the mind, but they are organic entities when the codemaker is an organic system

Organic information and organic meaning, in short, are not intrinsic properties of the molecules that carry them, and this raises a new problem. What kind of entities are they?

We conclude that organic information has the same scientific status as the physical quantities because it is an objective and reproducible entity. But we also conclude that it does not have the status of a derived physical quantity because it cannot be expressed by anything simpler than itself. This means that organic information has the same scientific status as the fundamental physical quantities, i.e., that it is a fundamental (or irreducible) entity of Nature (a similar conclusion was also described in Küppers 1990 and 1992).

By the same token, the rule of the genetic code that a group of three nucleotides (a codon) corresponds to an amino acid is equivalent to saying that that amino acid is the organic meaning of that codon. Anywhere there is a code, be it in the mental or in the organic world, there is meaning. We can say, therefore, that meaning is an entity which is related to another entity by a code, and that organic meaning exists whenever an organic code exists (Barbieri 2003a).

Modern biology has readily accepted the concept of information but has carefully avoided the concept of meaning, and yet, organic information and organic meaning are both the result of natural processes. Just as it is an act of copying that creates organic information, so it is an act of coding that creates organic meaning. Copying and coding are the processes; copymakers and codemakers are their agents; organic information and organic meaning are their results.

1. The sequence used by a copymaker during a copying
process is organic information.

2. The sequence used by a codemaker during a coding
process is an organic sign.

3. The sequence produced by a codemaker during a
coding process is an organic meaning.

4. Organic information, organic signs, and organic meanings
are neither quantities nor qualities. They are a new
kind of natural entities, which are referred to as
nominable entities.

5. Organic information, organic signs, and organic meanings
have the same scientific status as physical
quantities because they are objective and reproducible
entities that can be defined by operative procedures.

6. Organic information, organic signs, and organic meanings
have the same scientific status as fundamental
physical quantities because they cannot be reduced to,
or derived from, simpler entities.

So, if I read him correctly, he seems to be saying that, as some might say that mind or consciousness is a fundamental, so too is organic information or meaning. I'd prefer to class them together as a single phenomenon.

Do we have to play this game? I'm happy to acknowledge that it's a code. But if the central argument is that a code cannot evolve, doesn't it make sense first to define exactly what a code is? Apparently handwaving is sufficient.

Well let's use a closer analogy. Suppose we have a computer instruction set in which each instruction occupies the same number of bytes (say 2), and that all of the possible codes already have a meaning. Suppose that you want to develop new hardware that can access more instructions, but can still run all the existing binary software.

I hope you can see the problem - you can't extend the instruction length because then 2-byte instructions in the old software might be interpreted as a new 3-byte instruction - and crash the program. You most certainly can't solve the problem by making random changes to the hardware, looking for something that works, because whatever change you make will crash the program!

In real life, the solution might be to have two 'addressing modes', one for legacy software and one for new stuff, but that is really a dodge equivalent to stuffing two computers in one box - but how else do you evolve the genetic code in terms of the number of bases per amino acid? Sure it could evolve a little by acquiring an extra DNA base or two, but in fact life manages with just 4 bases, but the number of bases per amino acid is much harder to change.

David

Well let's use a closer analogy. Suppose we have a computer instruction set in which each instruction occupies the same number of bytes (say 2), and that all of the possible codes already have a meaning. Suppose that you want to develop new hardware that can access more instructions, but can still run all the existing binary software.

Hence the reason no computer architect assigns all the codes! ;-)

In real life, the solution might be to have two 'addressing modes', one for legacy software and one for new stuff, but that is really a dodge equivalent to stuffing two computers in one box - but how else do you evolve the genetic code in terms of the number of bases per amino acid? Sure it could evolve a little by acquiring an extra DNA base or two, but in fact life manages with just 4 bases, but the number of bases per amino acid is much harder to change.

You have to read the literature on this. There is a lot of thought given to ways in which a 1-base code could evolve into a 2-base code, and so forth. In particular, if early life employed fewer amino acids, the trick is to keep binding the original amino acids while opening up the binding of new ones. Remember, we have all of chemistry at our disposal.

Check out the wobble hypothesis:

https://teaching.ncl.ac.uk/bms/wiki/inde...Hypothesis

Another line of evidence is that the tRNA's anticodon loop and its amino acid acceptor appear to have evolved separately. So the anticodon could evolve independently of the associated amino acid.

Another interesting paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810241/

~~ Paul

I read all your posts the first time and I read them again just now. You didn't answer this question regardless of what you think. "What really chaps your arse about ToE?" You see the question I'm actually asking is, What philosophy or ideology creates this normative state of mind in you that apparently ToE cannot occur by entirely natural means?

Looking over what you've written I see you've not answered this question either.

You didn't answer this question either http://psiencequest.net/forums/thread-da...7#pid11507

No steve, this is your game and your problem, not mine. You asked me what issues I had with your version of evolution and I gave a cursory review of the issues I have with it, and didn't list any ideological reasons because the issues I have don't have to do with ideology. That you think there can be no possible other answer is further indicative of your completely walled in bias with absolutely no room to move any direction. In fact, I would love to ask you the same question: what "normative state of mind" (what an absolutely absurd phrase for this situation) makes you think it absolutely must be via purely random chance? The fact that you can't fathom how someone could come to a conclusion distinct from your own without some unwavering bias or ideology that blocks all evidence inconsistent with that view is probably the reason that you don't have any substantive discussions with people on this thread or elsewhere. You're only interested in "outing" what you assume must be people's biases because it just couldn't be that they'd disagree with you for actual substantive reasons, right? Even when they understand the material and evidence as well as (or far better than) you. 

To come back and rephrase your question entirely, which doesn't naturally follow from what you posted, and then try to tell me I didn't answer your question, is insincere. Of course I can't read your mind so maybe next time consider saying what you actually mean and you'll get a different answer.

Hence the reason no computer architect assigns all the codes! ;-)

You have to read the literature on this. There is a lot of thought given to ways in which a 1-base code could evolve into a 2-base code, and so forth. In particular, if early life employed fewer amino acids, the trick is to keep binding the original amino acids while opening up the binding of new ones. Remember, we have all of chemistry at our disposal.

Check out the wobble hypothesis:

https://teaching.ncl.ac.uk/bms/wiki/inde...Hypothesis

Another line of evidence is that the tRNA's anticodon loop and its amino acid acceptor appear to have evolved separately. So the anticodon could evolve independently of the associated amino acid.

Another interesting paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810241/

~~ Paul

Paul, before we delve into all that, can you explain what you mean by evolve in a world where we don't yet have any genes? I just don't know what you mean, unless you mean that things might pop up through random chemistry.

There is a place in J Scott Turner's book (which I hope you are going to read) in which he discusses the problems faced by pre-life. He points out that sheer diffusion is against all this hypothetical pre-life chemistry. If some wonderful new chemical forms accidentally in such an environment, it will simply diffuse away because there are no cell boundaries.

Perhaps you should give us some sort of speculative ordering for all these stages:

1) Cells without active transport across their membranes.

2) Cells with active transport across their membranes.

3) A chemical that reproduces itself.

4) The formation of some sort of genetic code.

5) The capacity to evolve by natural selection.

Without a clear ordering, it is all too easy to assume a process such as evolution that can't exist at that stage in the bootstrap process.

Hence the reason no computer architect assigns all the codes! ;-

Yes I know, but I didn't want the analogy to expand to the size of a computer architecture manual The point is that those few unassigned codes then get used as prefix codes for longer instructions - so the codes end up with irregular lengths. DNA is beautifully regular - 3 bases (or six bits if you like) per codon.


David

Wait a minute. We are talking about the evolution of the genetic code, not the evolution of proteins. The question is whether the genetic code could evolve by naturalistic means.

And how can you say this with a straight face when the alternate proposal is that some sort of intelligence did it, with no hypotheses about how it works and with no evidence of it? It is, right now, nothing but an inference from human design.

There is no genetic code table in the cell. The table was invented by humans to help explain what is going in with the chemistry. The periodic table is also a nice table to explain what is going on with valence electrons in atoms. What exactly is the difference? I'm willing to listen to a difference, but so far everyone is just accusing me of being an uncooperative curmudgeon.

~~ Paul

The evolution of a protein is a physical transformation.  You would measure the transformation in terms of changes to the elements, changes to the folding and changes in active bonding sites.

The evolution of a code is not a physical thing.  It is an informational thingy.   You would measure the transformation in terms of changes to the symbolic structures, to the sequence of activity, to the logic of the functionality being encoded and in changes to new potential molecules that would attach or be repulsed.

In my worldview both the information structured by the periodic table and a table mapping bio-semiotic information are information objects that can be actualized by a physical pattern and sequence of development.

One has been expertly constructed to match atomic properties and particle interaction states.  The mentality that did the information processing was from the natural capability of living things.

The code was constructed on bio-feedback from trial and error and is structured by successful adaptation. A limited mentality that did the information processing was from the natural capability of living things.

The periodic table is an add-on.  DNA/RNA/Ribosome communication tables are inclusive in the organism.  Other than that the are similar.  Paul you are still looking for the magic, when mind and sense of self - (human or any other living thing) are natural things.  Living things are intelligent and have designed themselves.

No steve, this is your game and your problem, not mine. You asked me what issues I had with your version of evolution and I gave a cursory review of the issues I have with it, and didn't list any ideological reasons because the issues I have don't have to do with ideology. That you think there can be no possible other answer is further indicative of your completely walled in bias with absolutely no room to move any direction. In fact, I would love to ask you the same question: what "normative state of mind" (what an absolutely absurd phrase for this situation) makes you think it absolutely must be via purely random chance? The fact that you can't fathom how someone could come to a conclusion distinct from your own without some unwavering bias or ideology that blocks all evidence inconsistent with that view is probably the reason that you don't have any substantive discussions with people on this thread or elsewhere. You're only interested in "outing" what you assume must be people's biases because it just couldn't be that they'd disagree with you for actual substantive reasons, right? Even when they understand the material and evidence as well as (or far better than) you. 

To come back and rephrase your question entirely, which doesn't naturally follow from what you posted, and then try to tell me I didn't answer your question, is insincere. Of course I can't read your mind so maybe next time consider saying what you actually mean and you'll get a different answer.

Oh, I do fathom how someone chooses to see design irrespective of what the evidence indicates. I suspect that's why you choose to be sympathetic to that position if not outright supportive.
As I said earlier, in this country I cotton no talk of design because those that squeak most loudly asserting there is design are too willing to insert their Christian God into all areas of public life undermining the liberties our Constitution grants us citizens. To think they are simply questioning the science of evolution is absurdly naive.

The web is a marvelous thing for it allows the dissemination of worthwhile ideas to spread worldwide. It also has a dark side by allowing the people with bad ideas to find each other.

Paul, before we delve into all that, can you explain what you mean by evolve in a world where we don't yet have any genes? I just don't know what you mean, unless you mean that things might pop up through random chemistry.

RNA is a perfectly good carrier of genes, though not as good as DNA. Here's a good paper on the issues with the origin of the RNA world:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331698/

There is a place in J Scott Turner's book (which I hope you are going to read) in which he discusses the problems faced by pre-life. He points out that sheer diffusion is against all this hypothetical pre-life chemistry. If some wonderful new chemical forms accidentally in such an environment, it will simply diffuse away because there are no cell boundaries.

I'll check it out, though I am not hopeful.

https://www.openlettersmonthly.com/book-...se-desire/

https://smile.amazon.com/Purpose-Desire-...geNumber=2

Perhaps you should give us some sort of speculative ordering for all these stages:

I will leave this up to the many biologists, some of whose papers I have linked. The project is ongoing and will be for some time.

Yes I know, but I didn't want the analogy to expand to the size of a computer architecture manual The point is that those few unassigned codes then get used as prefix codes for longer instructions - so the codes end up with irregular lengths. DNA is beautifully regular - 3 bases (or six bits if you like) per codon.

I think you're comparing apples and oranges. Many architectures have fixed-size opcodes. The IBM 1130 and DEC VAX come to mind. Also, in the case of the genetic code, there are exceptions, so that the same codon results in different amino acids.

~~ Paul