A chance for input ... Dr. John Sanford

[FreezBee]

Yup. I also can't see any reason why beneficial and detrimental mutations need to be handled differently, since the only differences between them are the sign and average magnitude of their effects.

Roy

Possibly because beneficial mutations will lead to there being more mutations, which leads to more memory needed to represent those mutations, while detrimental mutations will lead to fewer mutations (supposedly the individuals with detrimental mutations have fewer offspring), which leads to less memory needed to represent those mutations.

I've had a look at the algorithms of Mendel's accountant (see e.g. this article), not a very thorough look, I admit, but this far it seems, as if the very representation of mutations favors the detrimental ones. However, I can't exclude that a close look might change that impression


- FreezBee

[wattsr1]

Possibly because beneficial mutations will lead to there being more mutations, which leads to more memory needed to represent those mutations, while detrimental mutations will lead to fewer mutations (supposedly the individuals with detrimental mutations have fewer offspring), which leads to less memory needed to represent those mutations.

I've had a look at the algorithms of Mendel's accountant (see e.g. this article), not a very thorough look, I admit, but this far it seems, as if the very representation of mutations favors the detrimental ones. However, I can't exclude that a close look might change that impression


- FreezBee

Many, many moons ago I did a year's worth of accounting as a subject in an applied science degree course. There we were taught what are called the Generally Accepted Accounting Principles:-

http://en.wikipedia.org/wiki/GAAP

We also learnt that following the GAAP an accountant could make a $100m loss become a $100m profit or a $100m profit become the equivalent but as a loss - all depending on what the company/accountant wished to achieve.


Perhaps it is with reason that this program is called "Mendel's Accountant". It uses the GAAP (but with respect to mutations) with as much fluidity as accountants can sometimes do (but with respect to money).



Regards, Roland

PS Apologies to all accountants of course.

[Dr.GH]

Yup. I also can't see any reason why beneficial and detrimental mutations need to be handled differently, since the only differences between them are the sign and average magnitude of their effects.

Roy

I can, if you want to predetermine the results with an easy excuse to dupe your creationist followers.

[Ansgar Seraph]

Here's the very latest input that I've received from John. It is SOOOO refreshing to be
dealing with a person with integrity and scholarly attitude for a change (from you people)
that I can hardly contain myself. Pay attention to the way it's supposed to be done
and you may actually learn something :

**********************************************************************************

Hi Jorge - Please tell these folks that I appreciate their
interest in Mendel, and if they see certain ways we can make
it more realistic, we will try and accommodate them.

Mendel is fundamentally a research tool, and so offers a high
degree of user-specification. There is no inherently "realistic"
population size - it just depends on what circumstance you
wish to study. The default setting for population size is set
at 1000 because it is convenient - whether you are using the
Windows version on your laptop, or any other computer, you
are less likely to run out of memory. We are proceeding to
study population size and also population sub-structure. I
believe larger populations should realistically be set up as
multiple tribes with a given migration rate between tribes.
Under these conditions we see little improvement with larger
population sizes. But they are welcome to do bigger runs if
they have the memory resources.

Truce for a moment, Jorge.

Dr. Sanford seems to welcome that we perform large runs in MENDEL but suggests that we use MENDEL's ability to sort the population into tribes. To do this, and to run the program using C instead of Fortran, we need the Linux version, which has been pulled from the download site on SourceForge. Since Dr. Sanford responds to your e-mails (I didn't get an answer today so I have no idea if he reads his Cornell mail during summer), could you ask him to provide the Linux version of MENDEL 1.4.1? He can ask Dr. Brewer to put it on SourceForge or can attach the tarball in an e-mail to you and you can e-mail it to me; I'll host the file on my Box.net account indefinitely.

I would be sincerely grateful for the Linux distribution of MENDEL and am willing to pay handsomely in TWeb pearls.

—Sam

[Roy]

Possibly because beneficial mutations will lead to there being more mutations, which leads to more memory needed to represent those mutations, while detrimental mutations will lead to fewer mutations (supposedly the individuals with detrimental mutations have fewer offspring), which leads to less memory needed to represent those mutations.

Except that in MA everyone has detrimental mutations, to the extent that those who carry the less damaging detrimental mutations will have more offspring and those detrimental mutations will spread almost as much as the beneficial ones.

Remember, you only have to run faster than the dwarf.

Roy

[FreezBee]

Except that in MA everyone has detrimental mutations, to the extent that those who carry the less damaging detrimental mutations will have more offspring and those detrimental mutations will spread almost as much as the beneficial ones.

Remember, you only have to run faster than the dwarf.

Roy

Yes, that's an interesting point

From what I've understood about Genetic Entropy, Sanford claims that the human genome accumulates detrimental mutations at a rate of 1-2% per generation. Why are there then more humans now than ever before?

A detrimental mutation is one that makes its carrier less fit than other members of the population, so it really makes not too much sense.

Sure, for small populations, you may risk that overall fertility is too small to keep up the population, but for humans that's hardly the case. 'Fertility' here isn't simply the ability to produce offspring, but to keep the offspring alive long enough to reproduce, and for humans that ability is more dependent on social organization and technology than on biology.


- FreezBee

[Tiggy]

Yes, that's an interesting point

From what I've understood about Genetic Entropy, Sanford claims that the human genome accumulates detrimental mutations at a rate of 1-2% per generation. Why are there then more humans now than ever before?

A detrimental mutation is one that makes its carrier less fit than other members of the population, so it really makes not too much sense.

Sure, for small populations, you may risk that overall fertility is too small to keep up the population, but for humans that's hardly the case. 'Fertility' here isn't simply the ability to produce offspring, but to keep the offspring alive long enough to reproduce, and for humans that ability is more dependent on social organization and technology than on biology.


- FreezBee

Another big flaw in Mendel is that in real life, whether mutations are deleterious, neutral, or beneficial is dependent upon environmental context . For example, a mutation that makes your skin bright red may be detrimental to your ability to hide from predators if you live in a snow field. Later that same mutation may be very beneficial if you live in a field of bright red flowers. Mendel assumes that all mutations have a fixed relationship to fitness that cannon be changed even by changing environmental context.

Also, in real life mutations may combine with other mutations and change their mutational class. As we saw in Lenski's E coli experiments, mutations that are neutral or even slightly deleterious by themselves can combine to produce a highly beneficial overall result.

Mendel thus fails as an accurate simulation of evolution because it does not model observed reality.

- T

[wattsr1]

Another big flaw in Mendel is that in real life, whether mutations are deleterious, neutral, or beneficial is dependent upon environmental context . For example, a mutation that makes your skin bright red may be detrimental to your ability to hide from predators if you live in a snow field. Later that same mutation may be very beneficial if you live in a field of bright red flowers. Mendel assumes that all mutations have a fixed relationship to fitness that cannon be changed even by changing environmental context.

Also, in real life mutations may combine with other mutations and change their mutational class. As we saw in Lenski's E coli experiments, mutations that are neutral or even slightly deleterious by themselves can combine to produce a highly beneficial overall result.

Mendel thus fails as an accurate simulation of evolution because it does not model observed reality.

- T

Where's Jorge?

[Dr.GH]

Where's Jorge?

I could not care less.

(really)

[Tiggy]

Where's Jorge?

- T

[Jorge]

Latest input that I received from John Sanford (below) :

Once again I remind you guys to have a look at the way it's supposed to be done.
Note the scholarship, the maturity, the quest for truth above all. Sooo refreshing !
Without further ado ...

I haven't raised any claims of fraud, nor am I clamoring for an immediate response. I have the following problems with model, based on what I've seen here.

1) There does not seem to be an option for true soft selection. Even if deleterious alleles do not affect fertility, they still cause the population to become extinct. This is not an accurate model of real genetics.

2) The default value for the maximum beneficial value of mutations is much too low. Real-world estimates of positive selection coefficients for humans are in the range of 0.1, not 0.001.

3) The starting population is genetically perfect, and all deviations from that state increase the chance of extinction. This does not accurately model an evolutionary process, in which no population ever achieves perfection, merely adequacy. The fact that an ideal organism would have a major competitive advantage compared to the real one does not imply that the real one is nonfunctional or doomed to extinction. This is not a model of biological evolution.

Finally, I also have a technical problem with the program as a software tool. It does not seem to be possible to run it indefinitely, nor have I seen any cases where it has even been able to run to equilibrium (or better, steady state). Whether that is because it continues to track mutations after they fix I don't know (that's my guess), but it means it is essentially useless as a research tool. It should be possible to simulate a population of size, say, 20,000 for 200,000 generations. What would the memory requirements for that set of parameters be? Is the program really able to use the extra memory?

If Sanford (or co-author) wishes to address these criticisms, I would welcome the response. As it stands, however, I do not see how one can use this model to make any statements about the likely behavior of evolving populations in the real world.

*********************************************************************************************

Dear Colleague - If we can make the program more
realistic, we will. Please explain what you would like
done ... How would you have us model soft selection?

I fail to see why mutations should not cause
extinction, especially given the additive model. As we
approach zero mean fitness, many individuals will
have a fitness of zero or less - we are forced to
truncate them (if you are dead you should not
realistically reproduce), causing population size to
start to rapidly shrink. When there are less than two
individuals, we consider the population extinct.


2) The default value for the maximum beneficial value of mutations is much too low.
Real-world estimates of positive selection coefficients for humans are in the range
of 0.1, not 0.001.

That is easily re-set, but one has to consider if
it is reasonable to realistically build up a genome
by increments of 10% (I am speaking of internal
complexity - not adaptation to an external
environmental factor). I think that is like going
up Mt. Improbable using a helicopter.

3) The starting population is genetically perfect, and all deviations from that state
increase the chance of extinction. This does not accurately model an evolutionary
process, in which no population ever achieves perfection, merely adequacy.
The fact that an ideal organism would have a major competitive advantage
compared to the real one does not imply that the real one is nonfunctional or
doomed to extinction. This is not a model of biological evolution.

We do not assume an ideal starting genotype - we
assume a uniform population after a population
bottleneck - with fitness set arbitrarily at 1.0.

Finally, I also have a technical problem with the program as a software tool.
It does not seem to be possible to run it indefinitely, nor have I seen any cases
where it has even been able to run to equilibrium (or better, steady state).
Whether that is because it continues to track mutations after they fix I don't
know (that's my guess), but it means it is essentially useless as a research tool.
It should be possible to simulate a population of size, say, 20,000 for 200,000
generations. What would the memory requirements for that set of parameters be?
Is the program really able to use the extra memory?

We can turn off individual mutation tracking and just
track the net fitness of each linkage block. We get
nearly indeterminate processing - but we lose lots of
interesting data. I would be happy to cooperate with
you - if you are interested. As far as I can determine,
Mendel is now the "state of the art" in genetic
numerical simulation, and it improves every
month. Are you aware of a better research platform?

Best wishes - John Sanford

The last thing that JS did was ask me for the email address of the people performing
these simulations & asking the questions so as to jointly work towards the goal of a
more realistic & acceptable-by-all Mendel program. Collaborative science at it best.

I know that you guys are saturated with anti-Creationist propaganda floating around
out there but the fact is that we Creationists have a passionate love for truth - period!

This is from Creationists ... what the blazes is this world coming to ...



P.S. Take note : I will not send JS the email of the escaped lunatics (e.g., Tiggy)
that reside here. I will probably have more meetings with JS in the future and
I want to make sure that he doesn't have cause to scold me for sending wackos
in his direction. Right now, I can't think of anyone other than Ansgar Seraph
and sfs1 that I'd feel were a fairly safe bet. Hopefully those two aren't closet Tiggy's.

Jorge

[rogue06]

Latest input that I received from John Sanford (below) :

Once again I remind you guys to have a look at the way it's supposed to be done.
Note the scholarship, the maturity, the quest for truth above all. Sooo refreshing !
Without further ado ...




*********************************************************************************************

Dear Colleague - If we can make the program more
realistic, we will. Please explain what you would like
done ... How would you have us model soft selection?

I fail to see why mutations should not cause
extinction, especially given the additive model. As we
approach zero mean fitness, many individuals will
have a fitness of zero or less - we are forced to
truncate them (if you are dead you should not
realistically reproduce), causing population size to
start to rapidly shrink. When there are less than two
individuals, we consider the population extinct.


2) The default value for the maximum beneficial value of mutations is much too low.
Real-world estimates of positive selection coefficients for humans are in the range
of 0.1, not 0.001.

That is easily re-set, but one has to consider if
it is reasonable to realistically build up a genome
by increments of 10% (I am speaking of internal
complexity - not adaptation to an external
environmental factor). I think that is like going
up Mt. Improbable using a helicopter.

3) The starting population is genetically perfect, and all deviations from that state
increase the chance of extinction. This does not accurately model an evolutionary
process, in which no population ever achieves perfection, merely adequacy.
The fact that an ideal organism would have a major competitive advantage
compared to the real one does not imply that the real one is nonfunctional or
doomed to extinction. This is not a model of biological evolution.

We do not assume an ideal starting genotype - we
assume a uniform population after a population
bottleneck - with fitness set arbitrarily at 1.0.

Finally, I also have a technical problem with the program as a software tool.
It does not seem to be possible to run it indefinitely, nor have I seen any cases
where it has even been able to run to equilibrium (or better, steady state).
Whether that is because it continues to track mutations after they fix I don't
know (that's my guess), but it means it is essentially useless as a research tool.
It should be possible to simulate a population of size, say, 20,000 for 200,000
generations. What would the memory requirements for that set of parameters be?
Is the program really able to use the extra memory?

We can turn off individual mutation tracking and just
track the net fitness of each linkage block. We get
nearly indeterminate processing - but we lose lots of
interesting data. I would be happy to cooperate with
you - if you are interested. As far as I can determine,
Mendel is now the "state of the art" in genetic
numerical simulation, and it improves every
month. Are you aware of a better research platform?

Best wishes - John Sanford

The last thing that JS did was ask me for the email address of the people performing
these simulations & asking the questions so as to jointly work towards the goal of a
more realistic & acceptable-by-all Mendel program. Collaborative science at it best.

I know that you guys are saturated with anti-Creationist propaganda floating around
out there but the fact is that we Creationists have a passionate love for truth - period!

This is from Creationists ... what the blazes is this world coming to ...



P.S. Take note : I will not send JS the email of the escaped lunatics (e.g., Tiggy)
that reside here. I will probably have more meetings with JS in the future and
I want to make sure that he doesn't have cause to scold me for sending wackos
in his direction. Right now, I can't think of anyone other than Ansgar Seraph
and sfs1 that I'd feel were a fairly safe bet. Hopefully those two aren't closet Tiggy's.

Jorge

Of course there is the obvious solution of asking him to post here and hence choose for himself who's input he would like to include.

[Viktor Scott]

**********************************************************************************

"Wes Elseberry made a comment that I think could be a good title, 'Mendel's Accountant
cooks the books."


Hi Jorge - I have been traveling ... The comment ... about
"cooking the books" is, of course, a false accusation. The
issue has to do with memory limits. Before a Mendel run
starts it allocates the memory needed for different tasks.
With deleterious mutations this is straight-forward - the
upper range of mutation count is known. With beneficials it
is harder to guess final mutation count - some beneficials
can be vastly amplified. Where there is a high rate of
beneficials they can quickly exhaust RAM and the run
crashes. Wesley Brewer [one of the creators of Mendel] has
tried to avoid this by placing certain limits - but fixing this is
a secondary priority and will not happen right away. With
more RAM we can do bigger experiments. It is just a RAM
issue.

Best - John

And yet a paper that announced this program contained the following:

Mendel represents an advance in forward-time simulations by incorporating several improvements over previous simulation tools...
Mendel is tuned for speed, efficiency and memory usage to handle large populations and high mutation rates....
We recognized that to track millions of individual mutations in a sizable population over many generations, effcient use of memory would be a critical issue – even with the large amount of memory commonly available on current generation computers. We therefore selected an approach that uses a single 32-bit (four-byte) integer to encode a mutation’s fitness effect, its location in the genome, and whether it is dominant or recessive. Using this approach, given 1.6 gigabytes of memory on a single microprocessor, we can accommodate at any one time some 400 million mutations...This implies that, at least in terms of memory, we can treat reasonably large cases using a single processor of the type found in many desktop computers today.

Hat tip to antievolution.org

[Viktor Scott]

Next week I will be meeting with Dr. John Sanford to discuss several issues related
to his work and book Genetic Entropy.

Perhaps he can help you define "information" in a biologically relevant way, as you and Gitt have been toiling for - what has it been, 5 years now?

Poor fellows...

[Viktor Scott]

*************************************************************************************************




You have my deepest thanks, Faid -- I hadn't laughed this hard in over a month.




BTW, that was outstanding 'scholarly, scientific and mature' input. You're a Harvard man, right?

Jorge

I wonder if Fraudnandez even realizes how much of a hypocrite he is?