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Author Topic:   Fixation of genetics - program
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 16 of 27 (62717)
10-25-2003 11:12 AM
Reply to: Message 14 by Fred Williams
10-24-2003 1:51 PM


Re: Rei sloppiness
[This is a reply to a message on this topic that Fred accidentally posted in the Fred Williams' Mutation Rate Article Obsolete thread at Message 27.]
Hi Fred,
When I didn't see a reply from Rei yesterday I started composing my own, but went to bed before I finished. This morning I see Rei has posted a reply, and it says pretty much what I would have said only better, so I'll just post this as it is. This *does* have some very useful additional information, probably worth reading, but that's my opinion. Enjoy!
--Percy

Hi Fred,
First, nice job noticing that bug where the percentages don't add up. That I didn't notice that bug myself really puzzled me, so I went back to the code and saw that I never bothered to check this because Rei had included a check right in the code:
 if (fabs(MUT_PERCENT_MINUS_90 + MUT_PERCENT_MINUS_50 + MUT_PERCENT_MINUS_20 +
MUT_PERCENT_MINUS_10 + MUT_PERCENT_MINUS_5 + MUT_PERCENT_MINUS_1 +
MUT_PERCENT_NOCHANGE + MUT_PERCENT_PLUS_1 + MUT_PERCENT_PLUS_2 +
MUT_PERCENT_PLUS_5 + MUT_PERCENT_PLUS_10 - 100.0) < 0.0001)
{
printf("Error: Mutation rates aren't sufficiently close to 100%.\n");
return 1;
}
So I figured she had it covered and never bothered to check. So why isn't this code detecting the problem? Especially since this checking code itself has a bug because MUT_PERCENT_MINUS_2 isn't included, so instead of being just 4% short of 100% it's 10% short?
The answer is that the direction of comparison is wrong - she should be using ">" instead of "<". Correcting these problems and running again the program produces the same results but with overall fitness increasing at a slower rate.
So now that we've got that little bug out of the way, let's move on to address your specific criticisms.
So let’s consider your example (aka fantasyland), that produces an increasing fitness average across the population. Well, for starters you selected a beneficial mutation rate of 1 out of every 12 (8%)!!! A whopping 1 out of 25 have a 10% advantage! No wonder your program succeeded!
How you could find that bug while ignoring the significance of Rei's way high deleterious rates, all the way up to 90% while the favorable rate is 10% max, is beyond me. Perhaps you're using a biased selection mechanism, Fred? Beyond that, the program's harmful mutation rate is a whopping 42%. The likelihood of a harmful mutation is 10.5 times more likely than a beneficial mutation. But let's try an even lower beneficial mutation rate and see what happens. Setting it to 1% (I set the beneficial rates to .4, .3, .2 and .1, and I added the remainder to the neutral mutation rate) so that the harmful mutation rate is 42 times greater we find...THE SAME THING. Fitness increases, but of course more gradually.
Certainly as we increase the ratio of harmful mutations to beneficial mutations there will come a point where fitness no longer increases. Where is that point? Let's try setting the beneficial mutation rate to .1%, making the harmful mutation rate a whopping 420 times greater. This one was a struggle in the early generations with fitness gradually decreasing during the first 10's of generations, but by generation 60 enough good genes are becoming fixated that fitness has once again begun increasing, and steadily thereafter.
We set the beneficial mutation rate even lower, making harmful mutations 4200 times more likely. Trying this we find that as before fitness decreases in the early generations, but by generation 90 fitness begins increasing again, and steadily thereafter once more, though at the slowest rate yet, as expected.
At some point harmful mutations will outnumber beneficial mutations to such an extent that the small number of beneficial genes that become fixated cannot overcome it and fitness won't increase, and in fact will likely decrease steadily and cause eventual extinction. But let's examine how well these experiments with mutation rates support your assertions. You said the following:
You can make many things happen when you tinker with the mutation ratio and selection. In your example you tinker mightily with the mutation ratio to create your fantasyland.
It doesn't appear that Rei had to do much tinkering. Whether the harmful mutation rate was 42 times greater, 420 times greater, 4200 times greater, fitness still increased, so your assertion is false.
You *do* raise a pertinent question:
What primarily matters is the ratio of beneficial mutations to deleterious mutations, and that realistic selection is occurring.
The program was to illustrate the principle that random chance can produce improved fitness. Even if this is not your current position, in the past you have denied that this is possible even in principle. The program demonstrates that this claim is false. You go on to make related comments:
No one believes the frequency of beneficial mutations is 1 in 1000, let alone your fantasyland 1 in 12! Is 1 in a million possible? Unlikely. It certainly isn’t supported by the years of research on bacteria and drosophila where we can only find a handful of questionable examples.
The evidence of beneficial mutations in bacteria is unequivocal, and Drosophila experiments are useful more for understanding heredity, not beneficial/harmful mutation ratios. I'm guessing we don't have a good idea of what the beneficial/harmful ratio is outside the bacterial realm, but in that realm beneficial mutations are so likely that they happen over and over and over again. Is it one in a thousand? A million? A billion? I don't know, Fred, (please realize that doesn't mean no one knows - I'm not a biologist) but whatever the ratio the results of bacterial experiments on this are very clear that beneficial mutations are sufficiently common that they can be depended upon to turn up in experiment after experiment after experiment.
A standard experiment in university biology programs has the experimenter begin with a single bacterium which reproduces in a controlled environment so that he can know when adaptational mutations emerge. There are biology departments at so many universities that experiments along these lines must get performed for educational purposes alone at least a hundred times a year.
--Percy

This message is a reply to:
 Message 14 by Fred Williams, posted 10-24-2003 1:51 PM Fred Williams has replied

Replies to this message:
 Message 18 by Fred Williams, posted 10-30-2003 6:02 PM Percy has replied

  
Fred Williams
Member (Idle past 4855 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 17 of 27 (63500)
10-30-2003 5:54 PM
Reply to: Message 15 by Rei
10-24-2003 7:33 PM


Re: Rei sloppiness
quote:
The overall mutation rate is one in 50 per gene (or trait), not one in 50 per organism.
I never said otherwise. I don’t know, maybe you missed it when I said: Your gene mutation rate is set to 1 in 50. (msg 26)
quote:
Me: The lowest deleterious rate I’ve seen from the scientific community is 1.6 per
organism/generation (after selection), yet yours is roughly 0.3 per organism.
You responded: Nope. My mutation rate was 1 in 50; 100 genes; that's 2 mutations average per organism
You are flat wrong. I am talking about the deleterious mutation rate after selection! Here again is what I wrote, please read it this time:
Your gene mutation rate is set to 1 in 50. That means out of 100000 genes, roughly 2000 will contain a mutation of some sort. At least 110 of the 120 (2000*.06) lethal mutations will be removed. For simplicity we’ll favorably assume exactly half of the remaining 720 (2000*.36) deleterious mutations will be removed (the vast majority, or 98% of comparisons will be against genes with a fitness of 1). So after one generation, at most 370 deleterious mutations will remain. This means at best only 1 in three organisms will have a deleterious mutation going into the next generation (a poisson distribution will lower the ratio somewhat, as some organisms will have multiple mutations).
Do you agree, or disagree, that at most 370 deleterious mutations will remain after 1 generation? If you think more than 370 will remain, then make a case for it here. Remember, I explicitly referred to the post-selection mutation rate, as is how the rate is often cited in genetics studies (ie see Keightley paper). Your deleterious rate clearly was U ~= .3. Feel free to deny it all you want, but denials do not equal reality. You need to make a case for it (or get it through your thick skull that the rate was U=.3).
quote:
And yet, I had one in 7 bad mutations be -90%! And check out what rates I'm going to use below...
Big deal! Lethal mutations are almost impossible to detect (if you don’t know why please seek help soon ). That is why mutation rates cited in the journals typically represent post-selection mutation rates. We just can’t account for lethals.
The rate you set your lethals to is arbitrary. In fact, I can quote quite a few evolutionists who will tell you the spontaneous abortion rate is near 50%! This means you need to boost your lethals to assure half your offspring croak! Now I never saw compelling evidence to support this evo claim, but it was made by evolutionists in their failed attempts to deal with the reproductive cost problem spelled out in my mutation rate article (more on this if asked). If these same evolutionists were to avoid a double-standard, they should be telling you right now that your lethal rate is way too low!!!! I suspect at least one of them is reading this right now, since he follows me like a shadow around the internet. You know who you are, my young apprentice!
quote:
Fatal-mutation rates are irrelevant; a fatal rate to offspring born is basically the same thing as having more offspring,
That is precisely why it is relevant, because of the impact on reproductive cost/capacity.
quote:
Let's take out all of the mutations that do nothing, because you're using them to try and skew the interpretation of the results.
Huh? I’m doing no such thing! Do you deny the existence of neutral mutations? Of course they do have bearing because they slow the rate of evolution since they eat up a proportion of the spectrum of mutations. It never ceases to amaze me what hoops evolutionists try to jump through to prop up their fairytale!
quote:
As you can see, *any* bad rate can be handled and good genes will fixate, so long as there's a large enough population.
ROTFL!!! Rei, you are so brainlocked on genetic algorithms it has blinded you to plainly obvious problems. What if you set the lethal rate to 99%, and the beneficial rate to 1 in 1000? This exposes just one of the many problems with your logic. You have no parameter to completely kill off organisms that fall below a certain threshold. Over time your program will create scores of losers (Lahooo Zahers) who will compete against one another and yield a, yep, Lahooo Zaherrr! LLLLLlll...loozer! (L on forehead) It’s like the Rodney Dangerfield joke about two ugly parents who have reallll ugly kids! In other words, your program DOES NOT ALLOW EXTINCTION! A piece of jello is allowed to mate with another piece of jello. In some cases the jello gets paired against one of the few robust organisms that have garnered a beneficial gene or two, and is highly likely to lose (alas a form of truncation selection creeps in). The beneficials odds of winning go up dramatically because they get to consistently compete with jello. No lethal mutation can possibly wipe out the robust, because there are 100 other genes to compensate for that -90% bad one you are so proud of. No burden whatsoever is placed on reproduction, so low and behold Rei can produce evolution!
This leads you to make these ludicrous claims:
quote:
Want to make the already preposterously unreasonable mutation rate numbers even worse? I've jury-rigged this as far as I can in your favor, Fred, and evolution still occurs.
This is intellectual dishonesty to the highest degree. But feel free to continue to live in your fantasyland, it is a free country after all. But while your at it, please do the following:
1) Cite for our audience just one article in any of your very own evolutionist peer-reviewed journals, just one, that supports a beneficial mutation rate of 1 per 1000 organisms! You have the audacity to lump this as a preposterously unreasonable mutation rate! You are in a dream world, Rei, a dream world.
2) Explain why mush is allowed to survive.
3) Explain why there are no lethal mutations to wipe out robust organisms in your later generations? Impervious to mutation! It’s not a bird, not a plane, it’s SUPERMAN! (ie fairytale)
Finally, I would like to see your latest source code. I suspect I’ll find additional bugs/flaws. Hmm, I’m willing to bet you set your mutation rate to 1 per 1000 genes instead of per organism, which means a whopping 1 in 10 organisms will get a new beneficial mutation each generation! Zing Pao, its a miracle!

This message is a reply to:
 Message 15 by Rei, posted 10-24-2003 7:33 PM Rei has replied

Replies to this message:
 Message 20 by Rei, posted 10-31-2003 12:49 PM Fred Williams has not replied

  
Fred Williams
Member (Idle past 4855 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 18 of 27 (63501)
10-30-2003 6:02 PM
Reply to: Message 16 by Percy
10-25-2003 11:12 AM


Re: Rei sloppiness
quote:
How you could find that bug while ignoring the significance of Rei's way high deleterious rates, all the way up to 90% while the favorable rate is 10% max, is beyond me.
That bug wasn't hard to find becuasse the positives moved into play way too quickly (in just a few generations). I knew something had to be wrong.
As far as the rest, Read my reply to Rei, and just maybe, just maybe, you will see the illusion, unwitting as it probably was. Perhaps your following words might be that wop against your dome to turn the light bulb on:
quote:
At some point harmful mutations will outnumber beneficial mutations to such an extent that the small number of beneficial genes that become fixated cannot overcome it and fitness won't increase, and in fact will likely decrease steadily and cause eventual extinction.
Hmm. But Rei wrote: As you can see, *any* bad rate can be handled and good genes will fixate, so long as there's a large enough population. Perhaps you need to correct her?
Bottom line is that Rei’s fantasy program doesn’t allow extinction, and instead permits mush, the mellow yellow jello to survive and compete. There is no parameter to remove individuals below some threshold.
quote:
in that realm beneficial mutations are so likely that they happen over and over and over again.
This is a huge exaggeration. Countess experiments on Drosophila invariably produce less viable flies than the original wild type. If the beneficial rate were even 1 in a billion we would have know this by now. Now consider bacteria. The problem is the same. The mutated type is invariably less viable than the wild type in the original environment. Only stressing a bacterial population seems to cause these beneficial mutations. Why is that? Why is there so little evidence where a random copy error produced a mutated bacteria more viable than the parent in the original, stable environment?
One estimate of beneficial u is between 2*10^-9 and 5*10^-10 (The fate of competing beneficial mutations in an asexual population Genetica. 1998;102-103(1-6):127-44. Gerrish PJ, Lenski RE.)
I have to be blunt and say that no one in his or her right mind would propose a beneficial rate of 1 in 1000! This is called la la land, not science.

This message is a reply to:
 Message 16 by Percy, posted 10-25-2003 11:12 AM Percy has replied

Replies to this message:
 Message 19 by Percy, posted 10-30-2003 9:45 PM Fred Williams has not replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 19 of 27 (63530)
10-30-2003 9:45 PM
Reply to: Message 18 by Fred Williams
10-30-2003 6:02 PM


Re: Rei sloppiness
Fred Williams writes:
quote:
At some point harmful mutations will outnumber beneficial mutations to such an extent that the small number of beneficial genes that become fixated cannot overcome it and fitness won't increase, and in fact will likely decrease steadily and cause eventual extinction.
Hmm. But Rei wrote: As you can see, *any* bad rate can be handled and good genes will fixate, so long as there's a large enough population. Perhaps you need to correct her?
What I said seems consistent with what Rei said. Rei said that good genes will still fixate with increasingly harmful mutation rates as long as the population is large enough, and though this possibility occurred to me while I was responding, I decided to keep things simple and not mention it.
You didn't address the main point. You claimed that Rei's beneficial rate was too high, and I pointed out that not only were the deleterious effects of her harmful mutations far greater than the beneficial effect of her beneficial mutations, but I reran her program with her highly deleterious mutations outnumbering her modestly beneficial ones by 4200-to-1 and still produced fixation and increasing fitness.
Bottom line is that Rei’s fantasy program doesn’t allow extinction...
Read the title of the thread again, Fred. This isn't a life simulation, just a demonstration of fixation. Rei's program was intended to demonstrate how good genes can fixate even in the presence of a high harmful mutation rate, which it does. Extinction doesn't even make sense when there's only one species.
quote:
in that realm beneficial mutations are so likely that they happen over and over and over again.
This is a huge exaggeration. Countess experiments on Drosophila...
As I told you, the Drosophila experiments are studies of heredity, not of beneficial/harmful mutation rates. My comment was very specifically about bacteria, and I very clearly stated this: I'm guessing we don't have a good idea of what the beneficial/harmful ratio is outside the bacterial realm, but in that realm beneficial mutations are so likely that they happen over and over and over again. Is it one in a thousand? A million? A billion? I don't know, Fred, (please realize that doesn't mean no one knows - I'm not a biologist) but whatever the ratio the results of bacterial experiments on this are very clear that beneficial mutations are sufficiently common that they can be depended upon to turn up in experiment after experiment after experiment.
Only stressing a bacterial population seems to cause these beneficial mutations. Why is that? Why is there so little evidence where a random copy error produced a mutated bacteria more viable than the parent in the original, stable environment?
One estimate of beneficial u is between 2*10^-9 and 5*10^-10 (The fate of competing beneficial mutations in an asexual population Genetica. 1998;102-103(1-6):127-44. Gerrish PJ, Lenski RE.)
I have to be blunt and say that no one in his or her right mind would propose a beneficial rate of 1 in 1000! This is called la la land, not science.
Regardless of the specific rates, whether they're 1 in 10 or 1 in a trillion, they're sufficiently likely that they can be depended upon to occur every time you repeat the experiment I described. You're dancing all over the place, Fred, but you haven't yet addressed this fact.
--Percy

This message is a reply to:
 Message 18 by Fred Williams, posted 10-30-2003 6:02 PM Fred Williams has not replied

  
Rei
Member (Idle past 7012 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 20 of 27 (63651)
10-31-2003 12:49 PM
Reply to: Message 17 by Fred Williams
10-30-2003 5:54 PM


Re: Rei sloppiness
quote:
You are flat wrong. I am talking about the deleterious mutation rate after selection! Here again is what I wrote, please read it this time:
Your gene mutation rate is set to 1 in 50. That means out of 100000 genes, roughly 2000 will contain a mutation of some sort. At least 110 of the 120 (2000*.06) lethal mutations will be removed. For simplicity well favorably assume exactly half of the remaining 720 (2000*.36) deleterious mutations will be removed (the vast majority, or 98% of comparisons will be against genes with a fitness of 1). So after one generation, at most 370 deleterious mutations will remain. This means at best only 1 in three organisms will have a deleterious mutation going into the next generation (a poisson distribution will lower the ratio somewhat, as some organisms will have multiple mutations).
1) There aren't 100,000 genes in this latest run - there are 10,000,000. Are we going by the initial run?
2) If you had read my last post, I pointed out that lethal mutations (I.e, spontaneous abortions or otherwise death before sexual maturity) are roughly the same thing as having more children. The type of organism that I had in mind when I wrote this (daphnia) actually typically has far more than 20 offspring (I think they usually have around 100, so this would be an 80% lethal rate)
3) Where on earth do you get your "assumption" that half of the "remaining" deleterious mutatations will dissapear? The program doesn't "assume" anything of the sort. If you'll look at the output, early on deleterious genes actually can be seen spreading widely throughout the population; they're in the long run overtaken, however, by the organisms that got lucky.
quote:
Do you agree, or disagree, that at most 370 deleterious mutations will remain after 1 generation?
"At most" is utterly incorrect - this doesn't use truncation selection, so it is up to the luck of the draw relative to the fitness of the organism. As discussed, your calculation doesn't even remotely reflect the program.
quote:
Remember, I explicitly referred to the post-selection mutation rate, as is how the rate is often cited in genetics studies (ie see Keightley paper)
.
You referenced a nonsensical post-selection mutation rate. You didn't base it on evidence. Please do.
[quote]And yet, I had one in 7 bad mutations be -90%! And check out what rates I'm going to use below...
quote:
Big deal! Lethal mutations are almost impossible to detect (if you dont know why please seek help soon ).
How many times do I have to mention that lethal mutations can simply be factored into the number of offspring created, and that if we're dealing with daphnia (again, the organism I was picturing when I wrote this, although it can be adjusted to any organism), we're assuming an 80% lethal rate.
quote:
quote:
Let's take out all of the mutations that do nothing, because you're using them to try and skew the interpretation of the results.
Huh? Im doing no such thing! Do you deny the existence of neutral mutations? Of course they do have bearing because they slow the rate of evolution since they eat up a proportion of the spectrum of mutations. It never ceases to amaze me what hoops evolutionists try to jump through to prop up their fairytale!
1) Actually, slowing the mutation rate enables a worse ratio of good to bad mutations to fixate, so it's a good thing in this aspect.
2) As I mentioned, I simply moved where they were factored into - they're now factored into the mutation rate itself; a neutral mutation will have the same effect as no mutation.
[quote]
quote:
As you can see, *any* bad rate can be handled and good genes will fixate, so long as there's a large enough population.
ROTFL!!! Rei, you are so brainlocked on genetic algorithms it has blinded you to plainly obvious problems.
To quote Galileo (translated), "And yet, it moves."
quote:
What if you set the lethal rate to 99%, and the beneficial rate to 1 in 1000?
Any sort of organism that has a lethal rate of 99% is also going to be producing thousands apon thousands of offspring to begin with; it's a rather daft point to focus on, for this reason. The only thing that is relevant in this respect is the ratio of organisms that live to compete with each other for breeding rights.
quote:
You have no parameter to completely kill off organisms that fall below a certain threshold.
Yes. Because I simply had them never be born to begin with, and reduced the number of offspring born. As I've said many times.
quote:
Over time your program will create scores of losers (Lahooo Zahers) who will compete against one another and yield a, yep, Lahooo Zaherrr! LLLLLlll...loozer! (L on forehead) Its like the Rodney Dangerfield joke about two ugly parents who have reallll ugly kids! In other words, your program DOES NOT ALLOW EXTINCTION!
I should make that my signature....
Please explain how my program bans extinction.
quote:
A piece of jello is allowed to mate with another piece of jello. In some cases the jello gets paired against one of the few robust organisms that have garnered a beneficial gene or two, and is highly likely to lose (alas a form of truncation selection creeps in).
I assume that you're talking about a -90% selection organism vs. a +10% selection? In short, you're comparing the reproductive success likelyhood of a child with Downs syndrome to that of a professional athlete. Yes, the reproductive success comparison between a child with Downs syndrome and a professional athlete is effectively truncation selection. And comparison between the general population (over 99% of comparisons) is almost random natural selection. That's the way of life.
How are you trying to argue that the simulation parameters should be altered here? A lower rate of -90% fitness mutations? You'll find that that will actually help evolution.
By the way, I should mention again that this program also doesn't take into account the ability of organisms to assess the fitness of their mate, something that is incredibly important for higher animals (not so much for lower animals, but still relevant). In short, I'm being incredibly nice to you with this one.
quote:
The beneficials odds of winning go up dramatically because they get to consistently compete with jello.
Hey, I'll gladly lower the rate of extremely negative mutations for you if you want. But of course, you don't actually want that, because evolution would occur *more* rapidly then.
quote:
No lethal mutation can possibly wipe out the robust, because there are 100 other genes to compensate for that -90% bad one you are so proud of.
Not true. I have the genes weighted multaplicatively - you are the "product" of your traits. Would you prefer additive? It would actually help evolution. Notice a trend here? Whenever there's been a choice to be made, I've been taking the option that would hurt evolution the most.
quote:
No burden whatsoever is placed on reproduction, so low and behold Rei can produce evolution!
Not me. Reality.
quote:
1) Cite for our audience just one article in any of your very own evolutionist peer-reviewed journals, just one, that supports a beneficial mutation rate of 1 per 1000 organisms! You have the audacity to lump this as a preposterously unreasonable mutation rate! You are in a dream world, Rei, a dream world.
The ratio of positive to negative mutations is key here. Cite for me a paper that shows that negative mutations are over 1000 times more common than positive ones.
The problem with your statement is that very seldom do scientists go and monitor a population and look at every mutation, and determine "is this positive, negative, or neutral for the organism, and how much?" We can cite beneficial mutations, and we can cite negative mutations, but the ratio is almost impossible to come by, because the concept of checking every single mutation in a species would be an incredibly daunting task.
That said, you can look at different situations in the world and figure out what is realistic. For example, if you have an organism whose environment - whether it be the types and numbers of other species, the climate, etc haven't changed much over an incredibly long period of time - there's not going to be very much more it could do. Its ratio of positive to negative mutations is going to be very, very low. On the other hand, if you have an organism whose environment has suddenly changed, the ratio of positive to negative mutations is going to be very, very high. As in the example that I gave last time that you chose not to address: If you have a polar bear, and the climate starts getting colder, its fur is just as likely to mutate to be longer as it is to mutate to be shorter - a 1 to 1 positive/negative rate. Most genes in most situations won't near that 50% ratio, but ratios can be quite high.
quote:
2) Explain why mush is allowed to survive.
I'll ask again: want me to lower the rate of really bad mutations? It'll only make things evolve faster, but I'll do it if you want. Would you like that? Of course, you should realize - narrowing the curve in on zero change won't help you one bit; in fact, it'll actually enable a much faster mutation rate while good genes still fixate.
But if this is your argument, and you want it (or if you make the claim one more time) - hey, that's your choice, and I'll gladly run the sim again!
quote:
3) Explain why there are no lethal mutations to wipe out robust organisms in your later generations? Impervious to mutation! Its not a bird, not a plane, its SUPERMAN! (ie fairytale)
1) What is impervious to mutation here? Genes are selected randomly.
2) As I've had to mention far too many times, lethal mutations are factored into the number of offspring. If it will make you happy, I'll add a new variable called "lethal mutations percent", and then simply reduce the number of offspring by that percent, and then include the full number of offspring. If you're talking about a recessive lethal mutation, that's the equivalent of a strongly negative, but not completely negative, mutation - say, a -50% or a -90%. Or are you wanting me to special-case factor in this, and then reduce (correspondingly) the rate of -50% or -90% mutations? It won't help you any, but I think you already knew that when you made the claim.
(by the way, if you want me to target this simulation for any particular species, let me know; of course, keep in mind that if you go to higher animals, you'll be missing a lot of the "assessing the fitness of your mate" selection; that's why I chose to focus on lower animals).
quote:
Finally, I would like to see your latest source code.
Click on the initial link.
quote:
I suspect Ill find additional bugs/flaws.
I seriously doubt it.
quote:
Hmm, Im willing to bet you set your mutation rate to 1 per 1000 genes instead of per organism, which means a whopping 1 in 10 organisms will get a new beneficial mutation each generation! Zing Pao, its a miracle!
Enough with the accusations. Click, read, and then remark.
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 17 by Fred Williams, posted 10-30-2003 5:54 PM Fred Williams has not replied

Replies to this message:
 Message 21 by NosyNed, posted 10-31-2003 1:18 PM Rei has not replied

  
NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 21 of 27 (63661)
10-31-2003 1:18 PM
Reply to: Message 20 by Rei
10-31-2003 12:49 PM


Re: Rei sloppiness
Thank you Rei. You are about to run out of Fred. I think he will duck and run shortly.

This message is a reply to:
 Message 20 by Rei, posted 10-31-2003 12:49 PM Rei has not replied

  
Fedmahn Kassad
Inactive Member


Message 22 of 27 (64446)
11-04-2003 8:18 PM


Two things. First of all, Fred mentions the miscarriage rate. I have seen several sources that reported that the spontaneous miscarriage rate is over 50%. Most of these are not even recognized as anything other than a late period. Here is a link: Recurrent Spontaneous Abortions
From the link:
quote:
15 - 20 % of all pregnancies will endup as early prenancy losses. These losses however, are those recognised pregnancies which are confirmed usually 4 to 5 weeks after conception. There is now evidence that the pregnancy loss rate before this period i.e., during the 2 to 3 weeks following conception, may be as high as 50 %.
Now if I am reading that right, it says the total miscarriage rate is 15-20% that are recognized, and about 50% that aren't.
Second, the overall mutation rate for humans is around 100. Here are some links that discuss this:
quote:
In humans and other mammals, uncorrected errors (= mutations) occur at the rate of about 1 in every 50 million (5 x 10^7) nucleotides added to the chain. (Not bad - I wish that I could type so accurately.) But with 6 x 10^9 base pairs in a human cell, that mean that each new cell contains some 120 new mutations.
http://users.rcn.com/...tranet/BiologyPages/M/Mutations.html
quote:
Our data suggest an overall mutation rate of 2.14x10-8 per base per generation, or 128 mutations per human zygote.
Mutation rates in humans. II. Sporadic mutation-specific rates and rate of detrimental human mutations inferred from hemophilia B - PubMed
quote:
The average mutation rate was estimated to be approximately 2.5 x 10(-8) mutations per nucleotide site or 175 mutations per diploid genome per generation.
Estimate of the mutation rate per nucleotide in humans - PubMed
FK

Replies to this message:
 Message 23 by Rei, posted 11-05-2003 1:39 PM Fedmahn Kassad has replied

  
Rei
Member (Idle past 7012 days)
Posts: 1546
From: Iowa City, IA
Joined: 09-03-2003


Message 23 of 27 (64548)
11-05-2003 1:39 PM
Reply to: Message 22 by Fedmahn Kassad
11-04-2003 8:18 PM


quote:
In humans and other mammals, uncorrected errors (= mutations) occur at the rate of about 1 in every 50 million (5 x 10^7) nucleotides added to the chain. (Not bad - I wish that I could type so accurately.) But with 6 x 10^9 base pairs in a human cell, that mean that each new cell contains some 120 new mutations.
And how many of those mutations do anything at all (let alone as astounding of a change to fitness as a -90%? I'd be surprised if the average human has even a 1% selectability difference from the sum of their mutations). I'd gladly narrow the range, and at the same time increase the mutation rate - the two things are counters to each other, so it won't change the outcome.
------------------
"Illuminant light,
illuminate me."

This message is a reply to:
 Message 22 by Fedmahn Kassad, posted 11-04-2003 8:18 PM Fedmahn Kassad has replied

Replies to this message:
 Message 24 by Fedmahn Kassad, posted 11-05-2003 9:29 PM Rei has not replied

  
Fedmahn Kassad
Inactive Member


Message 24 of 27 (64640)
11-05-2003 9:29 PM
Reply to: Message 23 by Rei
11-05-2003 1:39 PM


Oh, you are exactly correct. The vast majority will do nothing at all. Most of the mutations will occur in noncoding DNA. I am just pointing out a realistic overall mutation rate for humans.
FK

This message is a reply to:
 Message 23 by Rei, posted 11-05-2003 1:39 PM Rei has not replied

Replies to this message:
 Message 25 by Brad McFall, posted 11-05-2003 9:55 PM Fedmahn Kassad has replied

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 25 of 27 (64644)
11-05-2003 9:55 PM
Reply to: Message 24 by Fedmahn Kassad
11-05-2003 9:29 PM


another dime
That reading depends at least in part on the full interpretation of such like,
&14.2-The Molecular basis of mutation (Whitehouse Towards an Understanding of the Mechanism of Heredity p228) "In order to understand the aminoacid code, it is essential to know in chemical terms the nature of the changes in DNA caused by mutation. Watson and Crick (1953b) had suggested that mutation might be due to a base in DNA occasionally occurring in one of its less likely tautomeric forms (tautomerism is the wandering of a mobile hydrogen atom from one multivalent atom to a neighbouring one within a molecule. Tautomeric forms of a molecule are usually in dynamic equilibrium with one another.), so that at replication the wrong base is inserted at this position in the complementary nucleotide chain."
except that in this thread Rei said (if mutation = error) and this OPENS up the details (in the EvC post, for instance, oscillation of Percy and Ipetrich etc., on what is the exact analogy of DNA and Computation) in quote connnect context such as
&14.2p232 "However, Brenner, Barnett, Crick and Orgel (1961) postulated that proflavin causes mutation by the insertion or deletion of one of one or more base-pairs in the DNA, and not by transversion as Fresse suggested. Part of their evidence for this was that proflavin-induced mutants appeared completely to lack the normal activity of the gene, whereas mutants produced by other mutagens were often 'leaky', that is, showed some growth on strain K of the host (see &13.4)."
as AN ERROR in the age we are discussing as well. So I would not say "exactly". I may be wrong but you may have thought of DNA caused mutation not mutation caused DNA? Even if I am wrong it would still be content-wrong to say exactly but then we would have much more than a tread in this tissue at issue.

This message is a reply to:
 Message 24 by Fedmahn Kassad, posted 11-05-2003 9:29 PM Fedmahn Kassad has replied

Replies to this message:
 Message 26 by Fedmahn Kassad, posted 11-05-2003 10:26 PM Brad McFall has replied

  
Fedmahn Kassad
Inactive Member


Message 26 of 27 (64650)
11-05-2003 10:26 PM
Reply to: Message 25 by Brad McFall
11-05-2003 9:55 PM


Re: another dime
Brad,
You have neglected to consider the effect flux capacitance may have on the inherent instabilities of such a system. Either way, it’s a wash.
FK

This message is a reply to:
 Message 25 by Brad McFall, posted 11-05-2003 9:55 PM Brad McFall has replied

Replies to this message:
 Message 27 by Brad McFall, posted 11-05-2003 11:46 PM Fedmahn Kassad has not replied

  
Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 27 of 27 (64661)
11-05-2003 11:46 PM
Reply to: Message 26 by Fedmahn Kassad
11-05-2003 10:26 PM


Re: another die dust?
Are you talking about an instability NOT currently recognized by "flux" (Cantor cricism of infinesmals whatever the collectivity etc...) OR what Rei meant quite clearly indeed with "uncorrected" error no matter the scale of the phenomena (of change)?? There is a choice here. No I did not "neglect". I was just trying to correect some logic which can indeed conflate the explanation by using mutations to think some computer informatin DNA model vs DNA (life) INT TIME proceeding with subsequent mutations. This is EvC and not all E for example so that a simple such assumption CAN NOT BE made. Besides you seem to either not follow or purposely rupture my simply point on the logic involved. If you stick to "uncorrected error" then the issue is clear as to BEING a base pair difference but indeed there is plenty of late 60s questioning OF THIS point on change (not MINE nor my interpretation) so in the issue of THE TIME involved there ISNOT IN FACT "a wash". It is only "exact" at you said if you bring in an assumption that enables one in some/yours/any idea of a computer-soma relation assert DNA-mutation-DNA-mutation as Loop. I was making the record clear by citing the sources and keeping track of when what ideas were and are being developed and when. The chemical terms even still DID NOT conscript the dynamics for the DIRECTION of mutation in addition to it cardinal existence can go in different CHEMCIAL directions. But you would have me have it that I could tell short of something already in this post that I would be able to find the error from the mutant phenotype in any term encoded. This is not necessarily "unstable". It could be a discontinuity or nonlinear effect. But I dont know how to do it. Please do not "dumb Brad down." Then tell me how to KNOW the uncorrected error coded FROM the mutant phenotype (whether you would already know if what is not in error AND non-coding exact locations) PER GENEOTYPE. Drug discovery companies would love to have this knowledge. Otherwise you must respect the history that FIRST it was the DNA explained from the mutation not any hope of getting the mutation explained from the DNA. All and Tide clean differently no matter the fall. You can not avoid this phrasing then if you admit to some kind of notion of "error". I had left open what the age is.
The logic know involves both an "or" and an "and". You response only made the answer more difficult. So my conclusion is if you continue to igore my words/wordings you indeed can tell me whether I am looking at the left or right of your avatar but you are sneaking in the long time frame via the DNA and NOT THE MUTANT. Go ahead prove me wrong but please recognize that I do not post on the simple level of NAIG here. IF you go a second post with someone here you pretty much better be willing to retreat to some island North of Madagacar and nobely admit defeat (of course I can do the same) or you must be prepared to back up what you/one had said. I am not however going to take over the thread with polemic. just the facts man, nothing but the facts.

This message is a reply to:
 Message 26 by Fedmahn Kassad, posted 11-05-2003 10:26 PM Fedmahn Kassad has not replied

  
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