You’re right. But it’s a good start for MA.
I would very much like to know what @Joe_Felsenstein thinks about MA.
I haven’t run Mendel’s Accountant. I was deterred by warnings about viruses in the download when I tried to download it. I can only rely on their description of what it does. This was somewhat odd in the way they applied selection, and as far as I can tell did not allow recombination within chromosomes. It seemed set up to have a very large effect of Muller’s Ratchet in each chromosome.
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Really? That that can’t be right. I am going to ask him about it.
Well, it was described as doing that when I looked. Might have changed since.
Go ahead and run MA with a starting population of 8 and any other parameters you want. Let us know how long the population survives, OK?
Sorry but MA is a scientifically worthless bad joke.
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Here is a small excerpt from an article by Sanford describing MA:
« The computer program “Mendel’s Accountant” (hereafter referred to simply as Mendel) has been developed to provide a biologically realistic forward-time numerical simulation of mutation accumulation [5]. This is a highly flexible program which for the first time effectively models natural mutation distributions, environmental variance, and improved modeling of linkage/recombination »
So it seems that MA does allow recombination, right?
Not sure that @Joe_Felsenstein nor @swamidass would consider MA as a bad joke.
Since Sanford wrote MA as a tool to specifically get the GE results he wanted what makes you think his glowing description of the program is honest or accurate?
Give us a few examples of where any genetic researchers anywhere besides Sanford or his YEC friends have used MA in their published results.
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At the time I looked at their description, some years ago, they had blocks of chromosome and no recombination within blocks. They may have improved it since.
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How big were the blocks? Small enough blocks and it should be a good approximation.
In the paper below, they run an experiment considering 1000 linkage bocks in the human genome.
http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf
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1000 linkage block are not likely enough. I’d be more convinced by 1 million blocks. Perhaps showing convergence as they increase the number of blocks would help too. But 1000 is very difficult to imagine being sufficient.
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@Joe_Felsenstein and @glipsnort how many recombination hotspots are their in the human genome?
What proportion of recombination events are inside vs outside the hotspots?
I’ve just had a look; in Genetic Entropy, Sanford says that « the human genome is a composite of roughly 100,000-200,000 linkage blocks ». So I don’t know why he has set it at 1000 in the simulation I was referring to at 30. But my guess would be that he has chosen this low value in order to be generous to the evolutionary scenario. IOW, had he chosen to set it at 200,000, the fitness decline would have been faster. What do you think?
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Setting it too low, as @Joe_Felsenstein noted, makes the simulation very different than reality, in a way that makes removing negative variants essentially impossible. This choice of parameters hurts his argument, because he is not modeling something comparable to human evolution here.
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I think I’m still waiting for you to show those examples of non-YEC genetic researchers using Mendel’s Accountant in any published papers.
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Giltil, can you please show us where Mendel’s Accountant was ever vetted and demonstrated to be an accurate representation of actual biological processes as Sanford claims? MA was published in 2007 in the obscure mathematical journal SCALABLE COMPUTING: PRACTICE AND EXPERIENCE which only looked at the math involved. To my knowledge no confirmation of Sanford’s claims for MA have ever been done by qualified geneticists or evolutionary biologists.
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As Josh already noted, this is backwards. A smaller number of linkage blocks implies that there are larger stretches of the genome within which recombination is rare, leading to high linkage disequilibrium. All else being equal, this will lead to a lessening in the efficiency of natural selection to remove deleterious variants and promote beneficial variants compared to a scenario where more of the genome is readily shuffled by recombination.
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That seems like a reasonable number. I recall (from back in the day when I was helping study them), that typical blocks in human were roughly ~20 kb long, which would mean 150,000 blocks. Of course, plenty of recombination also happens outside of hotspots, but I don’t recall quantitative estimates offhand. (No, wait, I found one early estimate in Simon Meyers 2005 Science paper: “Typically, 80% of the recombination occurs in 10 to 20% of the sequence”. But I think that 10-20% was considerably inflated by coarse resolution in defining the size of hotspots.)
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To be clear, I don’t think GA is a joke. I think Sanfords work should be engaged with seriousness and respect. He deserves a hearing.
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