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The Optimality of the Genetic Code

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Irreverend
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« Reply #30 on: September 21, 2009, 20:16:32 PM »

So one times near-optimal life code, plus one times Mecchie's brain equals designer proved, QED.

Wow, what's next for you, Mecchie?
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Teleological
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« Reply #31 on: September 21, 2009, 20:45:07 PM »

No and no.
Huh? So what is the purpose of this again?
From the OP:
The purpose of this thread is to discuss recent findings on the optimality of the genetic code.

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« Reply #32 on: September 21, 2009, 20:50:48 PM »

Why are you ignoring me, Mecchie? Is it 'cos I is not optimal?
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cyghost
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« Reply #33 on: September 21, 2009, 21:50:34 PM »

From the OP:
The purpose of this thread is to discuss recent findings on the optimality of the genetic code.
But that is what I am not getting. It is optimal yet there are other more optimal codes. (one gets degrees of optimal??) So what does this optimal code mean? I'm curious here and this is your thread. I was hoping for some enlightenment.
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Teleological
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« Reply #34 on: September 21, 2009, 22:07:48 PM »

From the OP:
The purpose of this thread is to discuss recent findings on the optimality of the genetic code.
But that is what I am not getting. It is optimal yet there are other more optimal codes. (one gets degrees of optimal??)
With regards to error minimization. Your point being? There are other parameters as well.

So what does this optimal code mean? I'm curious here and this is your thread. I was hoping for some enlightenment.
Which optimal genetic code? We are discussing the optimality of the genetic code (the SGC) (as stated in the OP). Error minimization is not the only parameter.

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cyghost
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« Reply #35 on: September 22, 2009, 08:01:05 AM »

With regards to error minimization. Your point being? There are other parameters as well.
Which you said above is not the be all and end all of optimality. I fail to understand this. Please explain.
Quote
Which optimal genetic code? We are discussing the optimality of the genetic code (the SGC) (as stated in the OP). Error minimization is not the only parameter.
So what about it? What are we discussing about it? And didn't you admit that for the rest of your parameters we'll have the same kind of thing as we see for parameter 1? Other possibilities, more optimality, different starting points, resulting in different optimal codes, etc etc. What is going on here?
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Teleological
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« Reply #36 on: September 22, 2009, 08:23:53 AM »

With regards to error minimization. Your point being? There are other parameters as well.
Which you said above is not the be all and end all of optimality. I fail to understand this. Please explain.
What is not the be all and end all of optimality?

Which optimal genetic code? We are discussing the optimality of the genetic code (the SGC) (as stated in the OP). Error minimization is not the only parameter.
So what about it? What are we discussing about it?
Other parameters to consider as well. Not only one.

And didn't you admit that for the rest of your parameters we'll have the same kind of thing as we see for parameter 1?
No. That you will have to read up on and find out for yourself. You might find that the code is very optimal for other parameters and even more optimal, or not, if all the different paramaters are taken into consideration. I am not guaranteeing that that is the case as there has been no study whereby various parameters have been taken into consideration.

Other possibilities, more optimality, different starting points, resulting in different optimal codes, etc etc. What is going on here?
More parameters? Take all the parameters into consideration? etc..
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cyghost
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« Reply #37 on: September 22, 2009, 08:38:26 AM »

What is not the be all and end all of optimality?
Your 9 parameters.
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Other parameters to consider as well. Not only one.
Yes and?
Quote
No. That you will have to read up on and find out for yourself. You might find that the code is very optimal for other parameters and even more optimal, or not, if all the different paramaters are taken into consideration. I am not guaranteeing that that is the case as there has been no study whereby various parameters have been taken into consideration.
So what is this about again?
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More parameters? Take all the parameters into consideration? etc..
Okay. Do it.
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« Reply #38 on: September 22, 2009, 09:15:33 AM »

What is not the be all and end all of optimality?
Your 9 parameters.
You sure those are 9 different parameters for optimality? I gave nine points...

No. That you will have to read up on and find out for yourself. You might find that the code is very optimal for other parameters and even more optimal, or not, if all the different paramaters are taken into consideration. I am not guaranteeing that that is the case as there has been no study whereby various parameters have been taken into consideration.
So what is this about again?
Errr,  Huh? from the OP:
The purpose of this thread is to discuss recent findings on the optimality of the genetic code.

More parameters? Take all the parameters into consideration? etc..
Okay. Do it.
Err... Are all the parameters known? Which parameters have been tested so far?
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« Reply #39 on: September 22, 2009, 10:12:19 AM »

You sure those are 9 different parameters for optimality? I gave nine points...
No I am not sure how many parameters there are, which is why I have been asking you for a list.
Quote
Errr,  Huh? from the OP:
The purpose of this thread is to discuss recent findings on the optimality of the genetic code.
So what about the findings? So far I have it is optimal but it could have been more optimal and from any starting point we get optimality - some more than others (considering one parameter). What does this mean?
Quote
Err... Are all the parameters known? Which parameters have been tested so far?
You tell me, you're the one wanting to discuss this. I am just trying to catch up and lagging way way behind it seems.
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« Reply #40 on: September 22, 2009, 10:22:40 AM »

You sure those are 9 different parameters for optimality? I gave nine points...
No I am not sure how many parameters there are, which is why I have been asking you for a list.
Errr, there is no list of parameters to test the optimality of the genetic code. However, a few have been tested so far. Look among the 9 points.

Errr,  Huh? from the OP:
The purpose of this thread is to discuss recent findings on the optimality of the genetic code.
So what about the findings? So far I have it is optimal but it could have been more optimal and from any starting point we get optimality - some more than others (considering one parameter). What does this mean?
For the one parameter yes. It means by taking into consideration only one paramater, the code is very optimal and other codes could have emerged that are also very optimal and even more so with regards to that one parameter... error minimization. Use the information, don't use it.


Err... Are all the parameters known? Which parameters have been tested so far?
You tell me, you're the one wanting to discuss this. I am just trying to catch up and lagging way way behind it seems.
I did in the OP. Those are all the known parameters that I know of.
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« Reply #41 on: September 22, 2009, 10:38:48 AM »

Errr, there is no list of parameters to test the optimality of the genetic code. However, a few have been tested so far. Look among the 9 points.
We're discussing this. Part of the discussion proses should be you giving straightforward answers to questions. I get the distinct feeling I am being led around the nose here. Sort of a vague sense of wtf. Now. Looking among the 9 parameters (how can there be 9 parameters now when you objected to this a second ago? How many are there?) we know at least one which gives a result that simply makes no sense to me ie it is optimal [whatever that really means] but it could have been more optimal and starting from any point will result in optimality (various forms thereof some better than others)

I asked you whether any of the other parameters have similar results which didn't get me a clear answer.

Which result for which parameter stands out for you and why?

Quote
For the one parameter yes. It means by taking into consideration only one paramater, the code is very optimal and other codes could have emerged that are also very optimal and even more so with regards to that one parameter... error minimization. Use the information, don't use it.
How?

Quote
I did in the OP. Those are all the known parameters that I know of.
As oppose to unknown parameters that we don't know of? Okay. So we can have a list then? Of parameters, tested parameters and results?
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« Reply #42 on: September 22, 2009, 11:04:15 AM »

Errr, there is no list of parameters to test the optimality of the genetic code. However, a few have been tested so far. Look among the 9 points.

We're discussing this. Part of the discussion proses should be you giving straightforward answers to questions. I get the distinct feeling I am being led around the nose here. Sort of a vague sense of wtf. Now. Looking among the 9 parameters (how can there be 9 parameters now when you objected to this a second ago? How many are there?)

9 points, not 9 parameters... Like I said, there is no list of parameters to test the optimality of the genetic code. However, a few have been tested so far. And they are listed among the 9 points... not parameters.

we know at least one which gives a result that simply makes no sense to me ie it is optimal [whatever that really means] but it could have been more optimal and starting from any point will result in optimality (various forms thereof some better than others)

What does optimal mean? An extract from article two explains the concept:

Quote
The structure of the genetic code is manifestly nonrandom [3]. Given that there are 64 codons for only 20 amino acids, most of the amino acids are encoded by more than one codon, i.e., the standard code is highly redundant; the two exceptions are methionine and tryptophan, each of which is encoded by a single codon. The codon series that code for the same amino acid are, with the single exception of serine, arranged in blocks in the code table and the corresponding codons differ only in the third base position, with the exceptions of arginine and leucine, for which the codon series differ in the first position (Fig. ​(Fig.1).1Figure 1). The importance of the nucleotides in the three codon positions dramatically varies: 69% of the point mutations in the third codon position are synonymous, only 4% of the mutations in the first position are synonymous, and none of the point mutations in the second position are synonymous. The structure of the code also, obviously, reflects physicochemical similarities between amino acids; e.g., all codons with a U in the second position code for hydrophobic amino acids (see Fig. ​Fig.11Figure 1 where the blocks of synonymous codons are colored with respect to the polar requirement scale [6] (PRS), which is a measure of hydrophobicity). The finer structure of the code comes into view if synonymous codon series that differ by purines or pyrimidines are compared [7]. Related amino acids show a strong tendency to be assigned related codons [3,4,8]. Generally, the standard code is thought to conform with the principles of optimal coding, i.e., the structure of the code appears to be such that it is robust with respect to point mutations, translation errors, and shifts in the reading frame. The block structure of the code is considered to be a necessary condition of this robustness [9].


I asked you whether any of the other parameters have similar results which didn't get me a clear answer.

I don't have an answer, you will have to find that out for yourself.

Which result for which parameter stands out for you and why?
All of them are equally interesting at the moment.

]For the one parameter yes. It means by taking into consideration only one paramater, the code is very optimal and other codes could have emerged that are also very optimal and even more so with regards to that one parameter... error minimization. Use the information, don't use it.

How?

I don't know.

I did in the OP. Those are all the known parameters that I know of.

As oppose to unknown parameters that we don't know of? Okay. So we can have a list then? Of parameters, tested parameters and results?

Errr, the OP is there for all to read. Everyone is welcome to extract what they want from it. try and add information as well. As is, I am not sure of all the parameters, and the OP post mentioned a few. You are going to have to dig up all the different parameters that have been tested. That requires a bit of effort and time and time is not exactly on my side now. But, if it makes you feel better, these articles should help you:

Early Fixation of an Optimal Genetic Code
Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape
The genetic code is nearly optimal for allowing additional information within protein-coding sequences
A Neutral Origin for Error Minimization in the Genetic Code.
Does codon bias have an evolutionary origin?
Optimality of the genetic code with respect to protein stability and amino-acid frequencies
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cyghost
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« Reply #43 on: September 22, 2009, 12:21:44 PM »

9 points, not 9 parameters... Like I said, there is no list of parameters to test the optimality of the genetic code. However, a few have been tested so far. And they are listed among the 9 points... not parameters.
My bad. So we don’t know how many parameters or what an overall picture would give us. I see.
Quote
Generally, the standard code is thought to conform with the principles of optimal coding, i.e., the structure of the code appears to be such that it is robust with respect to point mutations, translation errors, and shifts in the reading frame. The block structure of the code is considered to be a necessary condition of this robustness [9].
That’s cool. So we know for at least one parameter this is rather pointless. How about the other parameters which were tested?
Quote
I don't have an answer, you will have to find that out for yourself.
Is that the same as “I don’t know”? That would be rather weird, giving our history.
Quote
I don't know.
And that*is* an “I don’t know” answer, no doubt about it. I am flabbergasted and shocked to the core of my being. I always knew there are so many things you don’t know and yet it has been a complete mindboggling experience in futility to get you to admit to such. Here we have two in one post! What now? Shocked
Quote
Errr, the OP is there for all to read. Everyone is welcome to extract what they want from it. try and add information as well. As is, I am not sure of all the parameters, and the OP post mentioned a few. You are going to have to dig up all the different parameters that have been tested. That requires a bit of effort and time and time is not exactly on my side now. But, if it makes you feel better, these articles should help you:
No worries, I am in no rush here and would rather have you explain things to me than try and wallow through that sludge of information. I am still trying to get to grips on the whole concept of what this all means and I am sure I’ll get you to answer eventually, even if it is a “I don’t know” answer. As you well know by now I have no problems with giving and accepting such. My problem has always and will always be with making shit up.
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Teleological
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« Reply #44 on: September 22, 2009, 12:27:09 PM »

Quote
Generally, the standard code is thought to conform with the principles of optimal coding, i.e., the structure of the code appears to be such that it is robust with respect to point mutations, translation errors, and shifts in the reading frame. The block structure of the code is considered to be a necessary condition of this robustness [9].
That’s cool. So we know for at least one parameter this is rather pointless.
Not really pointless. They discovered where on the fitness landscape the code is situated with respect to error minimization. Hardly pointless science there.

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