Freethought & Rationalism Archive

NeilUnreal · 05-11-2003, 10:28 AM

(Coming out of lurk mode.)

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Arikay ...unless the computer is now inteligent.

Which is exactly my job! (Although I admit to being way behind. :banghead: )

-Neil

NialScorva · 05-11-2003, 11:35 AM

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Originally posted by Albert Cipriani
[B]Now Wait A Minute (times 100 billion minutes!) Rufus,
You can�t just fillip a zero off 100 billion as if it were a gnat and call it a day. You guys are celebrating the proof of evolution here based upon virtual mutations that deviate by many many orders of magnitude from the biological facts.

No, they're not celebrating "the proof of evolution". The proof of evolution is a done deal, no further proof needed. What this article shows is that the *algorithm* is sufficient to produce complexity on the order that creationists/IDist say that can't be produced. Shaving an order of magnitude or two off really doesn't make that much difference. The trick to mutation in a GA is to get the right amount of noise in the entire system, where the noise is roughly mutation_rate * population_size. You can decrease one so long as you increase the other.

Albert Cipriani · 05-11-2003, 04:02 PM

Nic said it best:

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The only things that I see the mutation rate affecting are the cases where they had a detrimental mutation that was "rescued" by a later mutation such that the two had a net benefit.

The article made a point of stressing the fact that detrimental mutations preceded the evolution of EQU, that without the detrimental mutations, EQU may not have evolved. In the real world, those deleterious mutations would not have been rescued immediately by the artificially high mutation rate. They�d have had to wait for many generations for another mutation to snatch success from the jaws of defeat, and in that timeframe, been swallowed up by death.

Salmon says:

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Why does the mutation rate matter?

Because evolution, as a theory that explains the process by which complexity extant today may have developed from the simplicity of yesterday, is a time-contingent process. Speeding up the mutation rate is functionally equivalent to extending the amount of time organisms had to evolve. But in reality, the time evolution had to do its magic is fixed, perhaps 3 � billion years max. So increasing the mutation rate seems like cheating, seems like pretending evolution had more time than it did to produce what it did.

Nial says:

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Shaving an order of magnitude or two off really doesn't make that much difference.

Then why do it? For fools like me, recovering psudo-creationsists, it seems suspicious. Evolutionists should show some compassion on us and not make it any more difficult than it already is to believe their theory.

Nial says:

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The trick to mutation in a GA is to get the right amount of noise in the entire system, where the noise is roughly mutation_rate * population_size. You can decrease one so long as you increase the other.

This I cannot understand. Wouldn�t a population size of one have the same propensity to mutate (according to Peez, 1e-6 per gene)? Evolution is not a puppet master lowering mutation rates commensurately with rising population sizes. What am I missing?

Thank you all for lending me your intelligence on this perplexing subject. � Sincerely, Albert the Traditional Catholic

Lobstrosity · 05-11-2003, 05:23 PM

Quote:

Originally posted by Albert Cipriani
This I cannot understand. Wouldn�t a population size of one have the same propensity to mutate (according to Peez, 1e-6 per gene)? Evolution is not a puppet master lowering mutation rates commensurately with rising population sizes. What am I missing?

What I think you're missing is that there are two different ways to define "mutation rate": mutations per unit time or mutations per replication. In general the two are not the same thing, but they are mathematically related. Peez's mutation rate is clearly a measure of mutations per gene per replication, which is just proportional to mutations per individual per replication. This gives you no information as to how frequently mutations enter a given population over time, however. If we assume that mutations per replication is a fixed quantity, mutations per unit time should be proportional to reproduction rate:

mutations/time = mutations/replication * replications/time

Reproduction rate is in turn proportional to population size (well, in highly simplistic models). This leads to the conclusion that the rate at which new mutations enter a population is roughly proportional to its size (let's call population size N).

replications/time = k*N for some constant k
=> mutations/time = mutations/replication * N
=> mutations/time = k' * N for some constant k'

What this means is that if you want mutations per unit time to be the fixed quantity, then you need to scale the mutation-per-replication rate inversely with the size of your population (as Nial suggests).

mutations/replication = N / (mutations/time)

If this were done dynamically over a given trial run, it would be fair to cry foul in that such a display would not represent the real world. However if each population is existing more or less in equilibrium at a fixed size, there is no problem with forcing mutations per replication to be a specific value so as to obtain a desirable mutations-per-unit-time rate.

I don't know...is anything I've just said valid? I sort of made it up as I typed it, so I guess it's up to you and others to judge. It sounded good as I was writing it, though.

Principia · 05-11-2003, 05:45 PM

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The article made a point of stressing the fact that detrimental mutations preceded the evolution of EQU, that without the detrimental mutations, EQU may not have evolved. In the real world, those deleterious mutations would not have been rescued immediately by the artificially high mutation rate. They�d have had to wait for many generations for another mutation to snatch success from the jaws of defeat, and in that timeframe, been swallowed up by death.

Read the paper, Albert. The paragraph that you should read to correct this misconception is on top of page 142.

Principia · 05-11-2003, 05:51 PM

Here's someone else who needs to read the paper before making IDiotic comments, like:

Quote:

Nelson Alonso: The fact that every EQU function acheived replication in different ways, but 3 instructions were conserved, shows that it is those 3 instructions, not surprisingly that were intelligently designed, that had functional constraint, and thus are truly IC. On the other hand, there is plasticity among the other instructions which means they is no specification there. This is equivalent to what we see with eubacterial flagella, eubacterial flagella have 20 parts which are universal and conserved, all eubacterial flagella have the same 20 parts, the rest of the parts vary, in that there is plasticity among the the other parts that are not IC.

Ah, the mutating definitions of IC and their dwindling effectiveness to an antievolutionist. Keep an eye out for this thread. I've a feeling it's bound to get amusing real fast in IDiot land.

Albert Cipriani · 05-11-2003, 08:54 PM

Principia says:

Quote:

Read the paper, Albert.

This reveals Principia presumption that Albert must either have not read the paper or have read it poorly and the further presumption that Albert must either be (a) extremely stupid or (b)extremely smart:
(a) extremely stupid to challenge his superiors over an article he had not even bothered to read, or
(b) extremely smart to challenge his superiors over an article he had not even bothered to read.

Alas, I have read the article and so am neither extremely smart nor extremely stupid, just honest. Honesty is something I recommend to you, Principia, as an antidote for presumptiveness, which is a deadly character trait for good science as well as for civil discourse.

Quote:

The paragraph that you should read to correct this misconception is on top of page 142.

Here is the paragraph to which Principia refers:

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Before the pivotal mutations, each line of descent had already experienced 50 or more steps, including beneficial, neutral and deleterious mutations. Some deleterious mutations had small effects and hitchhiked with beneficial mutations; others reverted or were compensated by mutations elsewhere. But in the case study, we showed that one deleterious mutation had genetically predisposed (through an epistatic interaction) the subsequent origin of EQU. To investigate this possibility further, we examined all of the mutations one step before the pivotal mutations. Five of the 23 one-step-prior mutations were deleterious in the backgrounds in which they occurred (including the case study). When these five were reverted in the pivotal genotypes, the EQU function was eliminated in three cases. Thus, three genotypes that first performed this complex function depended on a one-step-prior mutation that was deleterious when it appeared.

What I get from this paragraph is that �one deleterious mutation had genetically predisposed the subsequent origin of EQU.� My argument is that deleterious mutations had more chance of surviving in the high-mutation Avida environment.

I think the paragraph in the middle of page 141 is more to my point:

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The presence of deleterious mutations along the line of descent is more surprising. Fifteen of the 18 deleterious mutations reduced fitness by <3% relative to the parent, and might have hitchhiked with beneficial mutations that arose soon after in the same genetic background. However, two mutations reduced fitness by >50%. One was a point mutation that disrupted replication efficiency. Its descent, which occurred at a distant site in the genome. The other very deleterious step was a point mutation, at depth 110, that knocked out NAND, one of the simplest logic functions. ONLY TWO INDIVIDUALS HAD THIS MALADAPTED GENOTYPE, YET THEIR DESCENDANTS EMERGED AS EVENTUAL WINNERS. IN FACT, IN THE VERY NEXT STEP, THIS GENOTYPE PRODUCED THE MUTATION THAT GAVE RISE TO EQU. Was that deleterious mutation extremely lucky to hitchhike with such a beneficial mutation? Or was the deleterious mutation a prerequisite for producing the EQU function within that genome context? To distinguish between these hypotheses, we reversed this one-step-prior mutation in the genotype that first expressed EQU. This reversal eliminated the EQU function. THEREFORE, A MUTATION THAT WAS HIGHLY DELETERIOUS WHEN IT APPEARED WAS HIGHLY BENEFICIAL IN COMBINATION WITH A SUBSEQUENT MUTATION. The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important.

Principia says:

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Here's SOMEONE ELSE who needs to read the paper before making IDiotic comments.

Meaning, Albert�s comments were �idiotic.� Let�s see:
1) I paraphrased Nic.
2) I asked Nial why they would shave off an order of magnitude.
3) I asked Nial to explain what I was missing.
4) I admitted my perplexity.
5) I commended y�all for your intelligence and your assistance.

How is it that my questions and compliments can be construed by you as �idiotic comments�? Until you fully assimilate several vials of the honesty antidote, I�m afraid you won�t be able to answer that. � Albert the Traditional Catholic

Principia · 05-11-2003, 09:10 PM

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Albert: What I get from this paragraph is that �one deleterious mutation had genetically predisposed the subsequent origin of EQU.� My argument is that deleterious mutations had more chance of surviving in the high-mutation Avida environment.

Compare this to your original assertion:

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The article made a point of stressing the fact that detrimental mutations preceded the evolution of EQU, that without the detrimental mutations, EQU may not have evolved.

There is simply no way to have read the paragraph you cited and drawn the conclusion that the paper was stressing any particular mechanism towards evolving EQU, much less stating that "that without the detrimental mutations, EQU may not have evolved." This last part is simply false.

All I can say is: Read the paper again, Albert. Note that in 23 cases, only 5 involved mutations that decreased fitness, and of those, only 3 were considered "highly deleterious." But do you know what the authors mean by highly deleterious?

Quote:

Meaning, Albert�s comments were �idiotic.� Let�s see:
1) I paraphrased Nic.
2) I asked Nial why they would shave off an order of magnitude.
3) I asked Nial to explain what I was missing.
4) I admitted my perplexity.
5) I commended y�all for your intelligence and your assistance.

How is it that my questions and compliments can be construed by you as �idiotic comments�?

Then, Albert, avoid making blanket assertions like the one you made above.

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My argument is that deleterious mutations had more chance of surviving in the high-mutation Avida environment.

I fail to see the point of your making an argument, here, Albert. If you are indeed honest, the first thing to admit is that you have no argument until you have mastered the basic facts. Come now, Albert. Are you telling us that you are arguing a strong point with the knowledge of evolution you display?

Albert Cipriani · 05-11-2003, 11:25 PM

Principia says:

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There is simply no way to have read the paragraph you cited and drawn the conclusion that the paper was stressing any particular mechanism towards evolving EQU

Ah, Principia, that paragraph was the one you cited, not me. Why am I not surprised that it does not articulate my point?

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All I can say is: Read the paper again, Albert.

No, that�s not all you can say. But then such disingenuousness is all I expect from you until you take a swig of your honesty antidote.

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Note that in 23 cases, only 5 involved mutations that decreased fitness.

Note, those 5 were �one-step-prior� mutations. Way prior to them, two mutations, whose reproductive fitness was reduced by a whopping >50%, were the lucky two whose �descendants emerged as eventual winners,� according to my citation.

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But do you know what the authors mean by highly deleterious?

No. But I bet you do. And I bet you won�t tell me, either. You know why? Because in addition to being presumptuous, a lack of honesty tends to induce displays of condescension.

First you call what I wrote �idiotic comments.� So I categorize what I wrote as one paraphrase, two questions, one self-effacing statement and one compliment and ask you for an explanation. To whit, you emit the following non sequitur:

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Albert, avoid making blanket assertions.

Yes sir! I won�t make such blanket assertions as you�ve made. For example, I won�t call your comments �idiotic comments� or say �you have no argument� And on top of that, I won�t even be a hypocrite, either.

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Come now, Albert. Are you telling us that you are arguing a strong point with the knowledge of evolution you display?

I�ve happily asserted at every turn that my knowledge of evolution is sparse. That�s why I�m here, to learn. What's your excuse? To display how engaging and winsome you can be in an honest give and take dialogue with your inferiors? � Albert the Traditional Catholic

RufusAtticus · 05-11-2003, 11:45 PM

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05-11-2003, 11:45 PM	#30
RufusAtticus Veteran Member Join Date: Nov 2001 Location: NCSU Posts: 5,853	Moderator's Note Hey guys, let's keep this friendly. Thanx. RufusAtticus E/C Moderator

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