"A Mathematician's View of Evolution"

[Art Vandelay]

Which? That computer programs can evolve or that creationists would ever shut up?

~~ Paul

The latter.

 

[hammegk]

Uh, no. All possible reactions to cosmic rays, chemical mutagens, excessive heat, climate change, etc., are not coded in DNA.

Yeah, that's why I previously, specifically, excluded them.

If I'm allowed to tweak a connection arbitrarily, then yes, I would say that.

Yeah, nothing like designless code with arbitrary tweaks. No, you can't.

No. A 'response' is more than what can be contained in the 'code', and looking at it that way is what leads to the bottomless recursion.

Sorry, I don't see what you're getting at. I do not say specific, high level responses can be deduced looking at seed dna. That just builds the lathes/milling machines, that is proteins/chemistry/etc to specifications.

The chemical state of the cell is as much a part of the response as is anything at the level of 'code'. A cell inherits not only its DNA from its parent cell, but its chemistry as well. It is this chemistry (as much as anything) which determines which portions of the DNA will be translated into proteins, and when, and what will happen to those proteins.

Other than what most agree is clearer prose on your part, how do you interpret what I've said as different from that statement?

 

[Paul C. Anagnostopoulos]

Yeah, that's why I previously, specifically, excluded them.

You did?

Yeah, nothing like designless code with arbitrary tweaks. No, you can't.

I can't tweak the neural network.

Then the analogies to DNA are broken, because there is nothing to prevent arbitrary tweaks to DNA.

~~ Paul

 

[MalvernHills]

A response to Mr Scott

I knew an inability to throw away old science magazines would come in handy one day. I think the article you're after is entitled "Testing Darwin" which can be found in Discover (vol26#2). The software in question is "Avida" which according to the article annoys creationists no end.

Not sure how to type this as I've too few posts to directly hyperlink but if you fill in the gaps you can find more at Caltech:

http dllab caltech edu/avida

For those interested in this area: for no apparent reason I have a copy of Steve Grand's book "Creation - Life and how to make it" lurking on my desk. It covers many of the same issues (emergent properties etc.) outlined in the article from a game-designer perspective (Steve wrote Creatures).

 

[hammegk]

You did?

I'm not referring to dna.rna changes at seed level that are caused by destructive activity; cosmic rays, inappropriate chemicals, etc.

I thought so. What do *you* think?

I can't tweak the neural network.

Well, in the sense you can provide input to an existing structure as dictated by underlying code and past events, sure you can.

Then the analogies to DNA are broken, because there is nothing to prevent arbitrary tweaks to DNA.

Here, we're talking about working dna.rna and we're not trying to mutate it. That's another discussion you're having elsewhere.

 

[CapelDodger]

Any system which is free of external influences becomes more disordered with time.

The top-of-the-range definition, as I recall, includes "non-expanding system". An expanding system cools, so order can increase. Mind you, I'm recalling that from a long time ago.

 

[Paul C. Anagnostopoulos]

I thought so. What do *you* think?

Sorry, I didn't see that post.

Here, we're talking about working dna.rna and we're not trying to mutate it. That's another discussion you're having elsewhere.

So you're claiming that DNA has a preprogrammed response to everything except mutagens? For example, are you claiming that it has a preprogrammed response to temperature levels higher than ever existed during the evolution of the DNA?

~~ Paul

 

[CapelDodger]

I knew an inability to throw away old science magazines would come in handy one day.

That's how my loft is insulated .

For those interested in this area: for no apparent reason I have a copy of Steve Grand's book "Creation - Life and how to make it" lurking on my desk. It covers many of the same issues (emergent properties etc.) outlined in the article from a game-designer perspective (Steve wrote Creatures).

For those who haven't already, Artificial Life by Steven Levy is worth reading.

 

[CapelDodger]

Uh, no. All possible reactions to cosmic rays, chemical mutagens, excessive heat, climate change, etc., are not coded in DNA.

You left out those cunning little critters, the viruses. They're in an active arms-race with our genetic defences, unlike cosmic rays.

As to chemical mutagens, we as an industrial species are actively at war against our genetic defences, inadvertantly. Climate change, meh, look at all the climates we live in. That's social self-mutilation, not genetic.

 

[hammegk]

Sorry, I didn't see that post.

Well, I'm glad we could clear that up.

So you're claiming that DNA has a preprogrammed response to everything except mutagens? For example, are you claiming that it has a preprogrammed response to temperature levels higher than ever existed during the evolution of the DNA?

No, I'm not. And any preprogramming resides in the entire system as it exists at any point in time: dna, proteins, other chemicals, and inputs.

Or as stated more correctly, sfaik; certainly more elegantly...

But the code contained also encode the walls of the machine shop, the operators, the method of wiring the machines use to function...

I think the coding example isn't wrong. We just need to remember that there are multiple subroutines running simultaneously with each having feed back loops that affect the outcomes. It's more of a process control code.

We still don't know it completely. Think of the classic example of a caterpillar and butterfly. They have the identical genetic dna what changes is the relative expresion of that code (a field called proteomics).

 

[Paul C. Anagnostopoulos]

No, I'm not. And any preprogramming resides in the entire system as it exists at any point in time: dna, proteins, other chemicals, and inputs.

Then I don't understand what you're saying. You appear to be saying that any preprogrammed response is preprogrammed and all the other responses are not. I guess I can't disagree with that.

~~ Paul

 

[hammegk]

Then I don't understand what you're saying.

Apparently not. I guess the quote from joobz didn't help.

You appear to be saying that any preprogrammed response is preprogrammed and all the other responses are not.

I think not. Is that what joobz's words said to you?

I guess I can't disagree with that.

Aww. Don't you want to argue with yourself?

 

[Paul C. Anagnostopoulos]

Apparently not. I guess the quote from joobz didn't help.

No, it didn't. What does the machine shop analogy have to say about what is preprogrammed and what is not? Is the machine shop's reaction to 200 degree temperatures preprogrammed?

~~ Paul

 

[hammegk]

It would depend on the specifics of a given situation, wouldn't it?

Black smoker temps are at 700F I believe.

 

[joobz]

No, it didn't. What does the machine shop analogy have to say about what is preprogrammed and what is not? Is the machine shop's reaction to 200 degree temperatures preprogrammed?

~~ Paul

There is definitely a cellular response that will try to take over and handle the situation. It's called the stress response. The heat shock proteins will try to prevent the thermal denaturing of other proteins...
But at that temp the materials of construction fail completely, so the code has not time to really do anything.

I think the key issue that exists here is that as you state, there are "errors' that can occur that can result in a new programming code.
a protein that had one function can with a simpple mutation possess a completely new function. You wouldn't know this until the situation arose where this function resulted in a greater survival phenotype.

That's why i stressed the issue of "mult-functioning machines."

Also, translation of DNA code isn't as simple as the one-to-one method that is taught in bio class. If you consider how antibodies are made against a new pathogen, this concept becomes readily apparhent.
When the pathogen is present, the B-cells will start to shuffle the variable region of the antibody. WHen an antibody binds well to the antigen, it is kept. This reitterates several times, until an effective antibody is made (This is a very brief description, I apologize). Anyway, once the antibody is produced, those b-cells now have effectively changed their programming to encode the new antibody for ever or at least as long as those b-cells are present.

 

[Paul C. Anagnostopoulos]

It would depend on the specifics of a given situation, wouldn't it?

Of course it would, but the point is that not everything is preprogrammed, even if you ignore mutagens.

~~ Paul

 

[Paul C. Anagnostopoulos]

There is definitely a cellular response that will try to take over and handle the situation. It's called the stress response. The heat shock proteins will try to prevent the thermal denaturing of other proteins...

Yes, there is some heat shock response. Is it entirely preprogrammed? Can it deal with all temperatures under all conditions? If the condition is new, I don't see how you could support the notion that the response is preprogrammed.

I think the key issue that exists here is that as you state, there are "errors' that can occur that can result in a new programming code.
a protein that had one function can with a simpple mutation possess a completely new function. You wouldn't know this until the situation arose where this function resulted in a greater survival phenotype.

That's one issue, yes. But surely you're not claiming that, barring mutagenic activity, all other situations have preprogrammed responses?

Anyway, once the antibody is produced, those b-cells now have effectively changed their programming to encode the new antibody for ever or at least as long as those b-cells are present.

Indeed, this is a case where reprogramming has superb survival value. But not every biological mechanism has this capability; the ones that don't cannot be said to be preprogrammed to handle all possible situations. They simply fail under certain conditions.

~~ Paul

 

[Taffer]

Something occurs to me. One part of the immune response in plants is a phenomenon called RNA interference, or RNAi. Basically, often plants contain a gene which is shared with a particular virus, and the RNA produced by this gene disactivates the virus through RNAi (oversimplification, I know, shush). Plants can also gain resistance to a virus which it was not before, by the incorperation of a viral gene. This gene was not included in the seed, but increases the complexity of the organism, and is totally independant of it.

 

[joobz]

Yes, there is some heat shock response. Is it entirely preprogrammed? Can it deal with all temperatures under all conditions? If the condition is new, I don't see how you could support the notion that the response is preprogrammed.

I don't mean that the cell knows what to do when you raise the temp X degrees. I'm saying it has preset cooping mechanisms that are coded. When these coping mechanisms don't work, the cell dies or will kill itself.

You can take cells and introduce them to a setting of hyperoxia (something that is not seen naturally). There will be a stress response that looks nearly like the heat stress response. Cells that can tune this to fit better to hyperoxia survive, those that can't don't. The difference in these cells will be mutation and possible exchange of genetic information.

That's one issue, yes. But surely you're not claiming that, barring mutagenic activity, all other situations have preprogrammed responses?


Indeed, this is a case where reprogramming has superb survival value. But not every biological mechanism has this capability; the ones that don't cannot be said to be preprogrammed to handle all possible situations. They simply fail under certain conditions.
~~ Paul

I guess I don't see what the main issue is. I have no problem thinking of the organism as preprogrammed and that once it's underway, it can either cope or not. Hopefully the genes it got will allow it to. The organisms with the golden ticket with the lucky survival code wins.

 

[Paul C. Anagnostopoulos]

I guess I don't see what the main issue is. I have no problem thinking of the organism as preprogrammed and that once it's underway, it can either cope or not. Hopefully the genes it got will allow it to. The organisms with the golden ticket with the lucky survival code wins.

I'm not sure I remember the original issue, either. It seems we're saying that it is preprogrammed to deal with the situations it's preprogrammed for, and it's a crap shoot otherwise. That's true of everything, isn't it?

~~ Paul