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Author | Topic: Ratio of Deleterious Mutations to Beneficial Ones | |||||||||||||||||||||||||||||||||||||||||||||||
PlanManStan Member (Idle past 3716 days) Posts: 73 Joined: |
I was reading a paper (not necesarily the most formal thing you've ever seen, but a paper nontheless) which talked about a computer simulation called Mendel which, when the correct rates of muation, fraction of deleterious muatations, muation rate, selection efficiency, etc., it showed a trend of degeneration, leading to extinction. Do you think this poses a serious problem to evolutionary theory? I'm not well-versed in this kind of stuff (I'm an American high-school student, after all. I'm not well-versed in anything ).
Quote of the Paper I was talking about:
The user manual for
Mendel’s Accountant (http://www.mendelsaccountant.info) describes in detail how to input all the relevant data for different biological situations in the most honest way possible. Mendel’s specific results depend on the specific input data used. However the general patterns which Mendel reveals are surprisingly consistentas long as the input data which is used is even remotely realistic biologically. These general output patterns are revealed in the example given below. In this particular example Mendel’s human default parameters (see the user manual at http://www.mendelsaccountant.info) are used, except for the following exceptions: (a) the frequency of beneficial mutations is increased 10,000-fold so that the ratio of deleterious to beneficial is 9:1; (b) for simplicity, all mutations are made co-dominant. Although we use here the default mutation rate for Mendel (which is presently set at ten new mutations per individual per generation), there is growing evidence that this should be set about one order of magnitude higher. We presently use a mutation rate of only ten just to be generous to evolutionary theory, allowing for the notion that 90% of the genome might be irrelevant junk DNA. If this example employed the accepted human mutation rate (>100), the degeneration described below would be much more severe and extinction would be rapid. The default selection pressure used in this example (six children per female, four of which are selected away every generation), represents extremely intense selection.
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AdminModulous Administrator Posts: 897 Joined: |
Thread copied here from the Ratio of Deleterious Mutations to Beneficial Ones thread in the Proposed New Topics forum.
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Percy Member Posts: 22504 From: New Hampshire Joined: Member Rating: 4.9 |
Hi PlanManStan,
There must be a mistake in his program because he says this:
The default selection pressure used in this example (six children per female, four of which are selected away every generation),... Two surviving children per couple is all it takes for a population to replace itself and would never end in extinction. --Percy
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PlanManStan Member (Idle past 3716 days) Posts: 73 Joined: |
You know, I never thought of that. But wouldn't that be somewhat optimistic, considering that some of the babies will inevitably die of disease, predation, or the like? I was reading about sub-replacement fertility, which is when a population isn't having enough children, and that value can reach 3.4 children per couple in developing nations due to all the dangers.
Source: Wikipedia (yeah, I'm quite the intellectual )
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nwr Member Posts: 6412 From: Geneva, Illinois Joined: Member Rating: 4.5
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I don't know the particular software. But I doubt that it is a problem.
The thing to remember, is that there is actual evidence of evolution occurring. So software models that are inconsistent with the actual evidence are not very persuasive. Here's the thing to remember with mutations: If a population is well adapted to its environment, then most changes will be changes for the worse. That is, most mutations will be deleterious. This is just the basic principle that, if you are at the top of the mountain, the only way to go is down. For a population that is not as well adapted, there is a greater possibility of beneficial mutations. Or, in mountain climbing terms, if you are only part way up, then a random move is as likely to lead you up as to lead you down.Fundamentalism - the anti-American, anti-Christian branch of American Christianity
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PaulK Member Posts: 17828 Joined: Member Rating: 2.3 |
Aside from the general problem of trusting theoretical models strongly contradicted by the evidence, you should realise that "Mendel's Accountany" was created by the creationist J C Sanford to support his own arguments.
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Percy Member Posts: 22504 From: New Hampshire Joined: Member Rating: 4.9 |
So the next thing you have to know is how he's connecting his mutation rates to the "2 of 6 total offspring survive". That he even mentions such a number makes me think he's structured the problem solution incorrectly. The proportion of offspring that survive should be a function of the mutation rates, not something that is specified.
Also, specifying the number of total offspring (6) is arbitrary. If only 1/3 of offspring survive then an average of 5 total offspring per couple means eventual extinction, 6 total offspring means stasis, and more than 6 means eventual overpopulation. Look at it another way. Researchers have measured the point mutation rates of many organisms, including humans. It probably ranges from around 1 to a few hundred point mutations per reproductive event, depending upon the mutation rate for the organism and the size of its genome. Mendel's Accountant says that using the mutation rates researchers have measured results in extinction, so what is Mendel's Accountant trying to say? I can only guess that Mendel's Accountant is saying that since we're not extinct that researchers must have mismeasured the mutation rates. My own guess is that the Mendel's Accountant program has flaws. Are you a programmer? The program itself can be found at Mendel's Accountant. Someone must have mentioned this program here before because I apparently downloaded it a couple years ago. It's written in Perl and is tiny, far smaller than the software for this discussion board. I doubt it has any of the sophistication they claim, particularly since it arrives at conclusions that are at odds with reality. But if you're a programmer we can look through it together and figure out if what it's doing makes any sense. --Percy
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PaulK Member Posts: 17828 Joined: Member Rating: 2.3 |
quote: It's meant to say that species can only last a few thousand years before going extinct, therefore YEC.
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PlanManStan Member (Idle past 3716 days) Posts: 73 Joined: |
I see. That's a really good analogy!
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PlanManStan Member (Idle past 3716 days) Posts: 73 Joined: |
Unfortunately, I'm not a programmer, I'm actually just a sophmore in high school. However, I am very interested in learning about what you were talking about, with the mutation rates leading to extinction (or rather, what Mendel's Accountant said).
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herebedragons Member (Idle past 886 days) Posts: 1517 From: Michigan Joined: |
The proportion of offspring that survive should be a function of the mutation rates, not something that is specified. Shouldn't it be a function of fitness? I see no mention of fitness. Selection pressure should be based on a "fitness threshold" so that organisms below that threshold tend to be eliminated and those above that threshold tend to survive. Selection pressure should not be a fixed number of offspring that die, that doesn't even make sense. Also selection pressure needs to vary over time, such as with predator / prey oscillations ...
and environmental fluctuations. There is also no element of randomness to the equation. We all know that not every member of a population will have 6 offspring and that even the most fit individual can be eliminated by a chance event or the even the least fit member survive. I too downloaded it sometime ago, but it doesn't seem to work now. I don't think it had anywhere near the parameters or the appropriate algorithms it needed to have to make it anywhere near realistic. Maybe you can make your own version of it that works HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem. Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.
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JonF Member (Idle past 197 days) Posts: 6174 Joined:
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This has been discussed extensively in various places, and a little here.
Mendel's Accountant (MA) is rigged to produce the result that its author desired. It's based on Sanford's oft-debunked "genetic entropy". ------------------------------------------ The simplest way to demonstrate that it's bogus is to consider the fact that there are lots of organisms with generation times that are much smaller than humans. If the MA prediction were correct, mice (with a genome about the same size as humans and 170x the generation time of humans) and Lord know what else would have gone extinct long ago. Sanford replied to this criticism as reported by Jorge Fernandez at the lost TWeb thread:
quote: Occam's Aftershave destroyed this lunacy:
quote: ------------------------------------------ The reported runs are with very small population sizes. 1,000 individuals is a population on the crux of going extinct. Again as reported by Fernandez, Sanford claims the effect is seen in larger populations:
quote: But others report differently, unfortunately mostly in the now-lost TWeb discussion. There's some graphs here (note the link at the end to the raw outputs) for a population of 3,000 and more realistic beneficial mutation rate and maximum beneficial effect 0.01, ten times larger than Sanford's. I'll post one:
Note the increasing fitness, the opposite of what Sanford reported. ------------------------------------------ The program assumes that effect of Very Slightly Deleterious Mutations (VSDMs) (which are not harmful enough to be selected against) is additive; i.e. 100 VSDMs are 100 times as harmful as one VSDM. There's no reason to believe that's true and lots of reasons to believe it's false. The effect of beneficial mutations is capped at a very low number, 0.1%. This is unrealistic; although beneficial mutations are rare the effect of one can be large. And there's no accounting for Very Slightly Beneficial Mutations (VSBMs). If VSDMs add so should VSBMs. From the manual:
quote: "Total biological functionality", whatever that is, is not what determines reproductive success and selection. One single beneficial mutation can, for example, allow one to drink milk in adulthood which can have a strong impact on reproductive success. Again as reported by Fernandez:
quote: If anyone can figure out WTF Sanford means there please let me know. Looks to me as if he didn't understand the issue. As Zachriel commented:
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JonF Member (Idle past 197 days) Posts: 6174 Joined: |
I too downloaded it sometime ago, but it doesn't seem to work now There were major and undocumented bug fixes between 1.2.1 and 1.4.1. Wesley Elsberry reported:
quote:
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
In addition to the great Tweb thread, I have found this paper worth mentioning in these discussions.
quote: In this paper, they looked at asexual endosymbionts which will suffer from genetic "meltdown" at even a greater clip due to Muller's Ratchet. What they found is slightly deleterious mutations built up there was increased negative selection for each additional slightly deleterious mutation. In other words, there is a threshold for the number of slightly deleterious mutations that a genome can incorporate. However, this doesn't result in extinction. Rather, each additional deleterious mutations is much more strongly selected against relative to the same mutations in previous generations. Sanford's model fails to incorporate increased selection as these mutations build up. Edited by Taq, : No reason given. Edited by Taq, : No reason given.
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NoNukes Inactive Member |
Here's the thing to remember with mutations: If a population is well adapted to its environment, then most changes will be changes for the worse. That is, most mutations will be deleterious. I doubt that this is correct. Perhaps it could be true about organisms who are overly well adapted to some niche environment, but I would not expect that this is true for humans for example. The fact is that most human mutations are somewhere close to neutral with respect to fitness. We know this because every human has mutations. It may be that most mutations that have some significant fitness impact are deleterious rather than beneficial, but given that such mutations are selected against, I would expect that even lop sided ratios of deleterious vs beneficial mutations would not stop the process of evolution. Edited by NoNukes, : No reason given.Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) I believe that a scientist looking at nonscientific problems is just as dumb as the next guy.Richard P. Feynman If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass
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