A chance for input ... Dr. John Sanford

[Ansgar Seraph]

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

I did ask the question and the answer is simply this : because of computer memory
limitations. However, this in no way affects the worthiness / validity of the results.
If you are truly interested in getting to the truth in this area, I would strongly suggest
that you delve more into the matter. Be prepared to abandon your present beliefs.

After spending 2 1/2 days of critical evaluations with John Sanford, I am fully convinced
that Mendel's Accountant is the only honest program of its kind in existence. Programs
like Avida and others (all of which were thoroughly evaluated by Sanford et al.) are just
what I've been saying here all along : worthless / deceptive examples practicing GIGO.

I promised John that I wouldn't 'spill the beans' so I can't say very much beyond
saying that hopefully you will be able to read all about it in peer-reviewed secular
scientifically-accepted journals. His science is 100.0% sound but they are
having a hard time getting published because of the association with the
Creationist position (even though his papers have absolutely no hint --- not
one iota --- of anything even remotely connected to Creationism, ID, God, etc.).
EXPELLED rears its ugly head once again.

Jorge

Since you are back on the thread again, Jorge . . .

We've proven that the "memory limitations" line Sanford gave you was a flat-out lie and the amended "We've run larger populations but it doesn't affect fitness" line is misleading. What does Sanford have to say about that? Why are beneficial mutations hamstrung in relation to their maximal effect while deleterious mutations are given "free range"?

2.5 days of critical evaluations with Dr. Sanford should have provided a few more explanations than why populations were limited by RAM . . . the more I "delve into the matter" the more certain it becomes that Mendel's Accountant is a dishonestly-framed program.

—Sam

[wattsr1]

. . . the more I "delve into the matter" the more certain it becomes that Mendel's Accountant is a dishonestly-framed program.

—Sam

I was thinking about this, this morning.

Given how YECs always argue about science that they don't like, then why should they not write computer code in a similar way, that is, in a self-serving manner, replete with holes and inconsistencies. And from there, accuse their opponents of doing just that.

I mean, this is YEC behavior as YECs, when it comes to science. Why should YEC computer code be any different?



Regards, Roland

[Jorge]

Since you are back on the thread again, Jorge . . .

We've proven that the "memory limitations" line Sanford gave you was a flat-out lie and the amended "We've run larger populations but it doesn't affect fitness" line is misleading. What does Sanford have to say about that? Why are beneficial mutations hamstrung in relation to their maximal effect while deleterious mutations are given "free range"?

2.5 days of critical evaluations with Dr. Sanford should have provided a few more explanations than why populations were limited by RAM . . . the more I "delve into the matter" the more certain it becomes that Mendel's Accountant is a dishonestly-framed program.

—Sam

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

I've been watching you guys flinging mud back and forth like a herd of piggies.
My approach is a bit more scientific, fair and honest : simply let the author of
the program respond to your accusations. Is that okay with you people?
Or are you in such a hurry to trash whatever challenges your beliefs that
you're just going to propagate your venom without listening to the other side?

Just one potential problem : I happen to know that J. Sanford et al. are
very busy on other matters and so I do not know how much time it's going
to take to respond to you guys. Judging by the reaction that I received,
unless he answers real soon you guys will have long have buried him
and danced on his grave. Know this also : I have forwarded a few of your
results to him. I'm sure that he'll get around to it when he has the time.
In the meantime, relax and try to think of what you're going to say when you
are proven wrong. One last comment : it's amazing it's absolutely mind
boggling -- how much effort you guys spend looking for "flaws" in other
programs -- those that don't support your beliefs -- yet spend a negligible
amount of time searching for flaws in programs like Avida and other
pro-evo programs that do support your beliefs. Perhaps one day little
facts such as this will cause you people to experience a moment of truth.

Jorge

[Tiggy]

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

I've been watching you guys flinging mud back and forth like a herd of piggies.
My approach is a bit more scientific, fair and honest : simply let the author of
the program respond to your accusations. Is that okay with you people?
Or are you in such a hurry to trash whatever challenges your beliefs that
you're just going to propagate your venom without listening to the other side?

Just one potential problem : I happen to know that J. Sanford et al. are
very busy on other matters and so I do not know how much time it's going
to take to respond to you guys. Judging by the reaction that I received,
unless he answers real soon you guys will have long have buried him
and danced on his grave. Know this also : I have forwarded a few of your
results to him. I'm sure that he'll get around to it when he has the time.
In the meantime, relax and try to think of what you're going to say when you
are proven wrong. One last comment : it's amazing it's absolutely mind
boggling -- how much effort you guys spend looking for "flaws" in other
programs -- those that don't support your beliefs -- yet spend a negligible
amount of time searching for flaws in programs like Avida and other
pro-evo programs that do support your beliefs. Perhaps one day little
facts such as this will cause you people to experience a moment of truth.

Jorge

Jorge's Answer, Cliff Notes Version:

Bluster
Evade
Bluster
Bluster
Hand Wave
Excuse
Bluster
Evade
Bluster
Bluster
Big bluster for finale


So Jorge, when will you be providing the entire contents of the email you supposedly sent to Sanford with my questions, and his entire answer?

Hate for everyone to have to think you made up the whole exchange from whole cloth.

- T

[Ansgar Seraph]

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

I've been watching you guys flinging mud back and forth like a herd of piggies.
My approach is a bit more scientific, fair and honest : simply let the author of
the program respond to your accusations. Is that okay with you people?
Or are you in such a hurry to trash whatever challenges your beliefs that
you're just going to propagate your venom without listening to the other side?

Just one potential problem : I happen to know that J. Sanford et al. are
very busy on other matters and so I do not know how much time it's going
to take to respond to you guys. Judging by the reaction that I received,
unless he answers real soon you guys will have long have buried him
and danced on his grave. Know this also : I have forwarded a few of your
results to him. I'm sure that he'll get around to it when he has the time.
In the meantime, relax and try to think of what you're going to say when you
are proven wrong.

Yes, I am sure they are busy with legitimate business. That's understandable. If I were traveling to Creation camps and touting my software to impressionable minds as being a legitimate piece of genetics modeling, I'd want to defend it sooner rather than later, however. Given Sanford's response thus far, I'm not sure he has that same zeal.

And it's not like people have been pointing and guffawing at "dis 'ere Creo code" . . . sfs1, a human genetics researcher who works in this specific field, has been offering detailed explanations for what's wrong in MENDEL. I ran a simulation where the population's fitness declined at a linear rate even though the beneficial mutation rate was 90%. That's nine of every ten mutations increasing the organism's fitness . . . and the population's fitness still plunges downward.

One last comment : it's amazing it's absolutely mind
boggling -- how much effort you guys spend looking for "flaws" in other
programs -- those that don't support your beliefs -- yet spend a negligible
amount of time searching for flaws in programs like Avida and other
pro-evo programs that do support your beliefs. Perhaps one day little
facts such as this will cause you people to experience a moment of truth.

Well, Jorge, even if you were right, that's the nature of perspective and bias. That's why Science uses peer-review; the problems invisible to one researcher are likely visible to another. It is on this requirement of peer review that YEC/ID scientists are glaringly deficient, whether it be Sanford, Baumgardner or Behe.

You yourself could do with Avida as we have done with MENDEL . . . but you don't. I don't particularly blame you for that, since I do not understand genetics either and rely on the expertise of others . . . but at least I'm making an effort to understand the competing paradigms. What did you glean from your two and a half days of critical evaluation of MENDEL and genetic entropy if you are unable to even introduce Sanford's line of reasoning?

—Sam

PS — And, of course, no one has forgotten about Baumgardner's very scientific vist to TWeb.

ETA: Here is one article describing the function of Avida, showing 17 citations. You can hardly say that Avida doesn't receive critical peer review.

[oxmixmudd]

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

I've been watching you guys flinging mud back and forth like a herd of piggies.
My approach is a bit more scientific, fair and honest : simply let the author of
the program respond to your accusations. Is that okay with you people?
Or are you in such a hurry to trash whatever challenges your beliefs that
you're just going to propagate your venom without listening to the other side?

Just one potential problem : I happen to know that J. Sanford et al. are
very busy on other matters and so I do not know how much time it's going
to take to respond to you guys. Judging by the reaction that I received,
unless he answers real soon you guys will have long have buried him
and danced on his grave. Know this also : I have forwarded a few of your
results to him. I'm sure that he'll get around to it when he has the time.
In the meantime, relax and try to think of what you're going to say when you
are proven wrong. One last comment : it's amazing it's absolutely mind
boggling -- how much effort you guys spend looking for "flaws" in other
programs -- those that don't support your beliefs -- yet spend a negligible
amount of time searching for flaws in programs like Avida and other
pro-evo programs that do support your beliefs. Perhaps one day little
facts such as this will cause you people to experience a moment of truth.

Jorge

My experience so far with YEC 'scientists' and science is that the most likely response
is Sam and Sts will get is a brow beating over why they don't interpret the Bible the same way He does, and how evil they are for not supporting a fellow Christian's attempts to 'defend the Bible'.

As for actual science, or a discussion of whatever problems there might be, if it happens, it will only go to the point a fatal flaw is discovered, and then revert to the above.

These guys have ZERO interest in how accurate their efforts are. They are only interested in protesting evolution in whatever means they can to whomever will listen.


Jim

PS I would welcome being proven wrong in this regard. But sadly, to this date, not one of the 'big guns of YEC' has behaved in such a way as to show I am incorrect.

[Faid]

On a slightly tangential note, I read Sanford's supposed response to jorge, and it doesn't make sense. He says:

jcs - The rate of mutation for mice and man should be roughly equal per cell divison,
or per day (their genomes are about same size).

Um, no. Roughly equal per cell division is not the same as equal per unit time! We are talking about cell divisions in the germline: That means that species with shorter generation times are subject to more germline cell divisions per unit time, and therefore accumulate more mutations.

That's why, IIRC, molecular clocks in mice run about five times faster than in humans.

Either Sanford was talking about something else entirely (mutation rate in somatic cells, perhaps), or someone messed up.

[Jorge]

Yes, I am sure they are busy with legitimate business. That's understandable. If I were traveling to Creation camps and touting my software to impressionable minds as being a legitimate piece of genetics modeling, I'd want to defend it sooner rather than later, however. Given Sanford's response thus far, I'm not sure he has that same zeal.

And it's not like people have been pointing and guffawing at "dis 'ere Creo code" . . . sfs1, a human genetics researcher who works in this specific field, has been offering detailed explanations for what's wrong in MENDEL. I ran a simulation where the population's fitness declined at a linear rate even though the beneficial mutation rate was 90%. That's nine of every ten mutations increasing the organism's fitness . . . and the population's fitness still plunges downward.




Well, Jorge, even if you were right, that's the nature of perspective and bias. That's why Science uses peer-review; the problems invisible to one researcher are likely visible to another. It is on this requirement of peer review that YEC/ID scientists are glaringly deficient, whether it be Sanford, Baumgardner or Behe.

You yourself could do with Avida as we have done with MENDEL . . . but you don't. I don't particularly blame you for that, since I do not understand genetics either and rely on the expertise of others . . . but at least I'm making an effort to understand the competing paradigms. What did you glean from your two and a half days of critical evaluation of MENDEL and genetic entropy if you are unable to even introduce Sanford's line of reasoning?

—Sam

PS — And, of course, no one has forgotten about Baumgardner's very scientific vist to TWeb.

ETA: Here is one article describing the function of Avida, showing 17 citations. You can hardly say that Avida doesn't receive critical peer review.

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

I'm just sitting here, scratching my head, trying to figure out what part
of "let the man respond to your accusations" you didn't understand.

Could you spare me from the bewilderment by shedding some light on this?

Thanks!

Jorge

[sfs1]

I'm just sitting here, scratching my head, trying to figure out what part
of "let the man respond to your accusations" you didn't understand.

Could you spare me from the bewilderment by shedding some light on this?

I don't understand the source of your bewilderment. The criticism you're talking about was posted on a public forum, one where Sanford or any of his co-authors can respond at any time. Who exactly is preventing them from responding to the accusations?

When I publish something, it is fair game for critics. They don't have to come to me for approval before attacking it. Why should these authors be any different?

[rogue06]

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

I'm just sitting here, scratching my head, trying to figure out what part
of "let the man respond to your accusations" you didn't understand.

Could you spare me from the bewilderment by shedding some light on this?

Thanks!

Jorge

When and where is Sanford going to respond? Did you extend an invitation for him to post here? And why should everyone go silent while they await his response (if it ever comes) if it is being promoted as devastating blow to evolution?

[Jorge]

I don't understand the source of your bewilderment ... ... ...
The criticism you're talking about was posted on a public forum, one where Sanford
or any of his co-authors can respond at any time.

Who exactly is preventing them from responding to the accusations?

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

Are you reading-comprehension impaired? Did I not clearly write :

Just one potential problem : I happen to know that J. Sanford et al. are
very busy on other matters and so I do not know how much time it's going
to take to respond to you guys.

THAT -- other priorities -- is what prevents them from responding (at least right away).
Surely you people aren't arrogant enough to think that we all just sit around waiting
to respond to your endless accusations (hmmm ... maybe that IS what you all think.)


Even so, J. Sanford was kind enough to send me the following brief input in response to this :

"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

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

Even I [Jorge] have remaining questions after the above input but the point is this :
only un-scholarly, obtuse fanatics in a feeding frenzy accuse and condemn the
work and integrity of others without due process. What you guys need to
do is reflect on that, take ten deep breaths, and chill. I can almost
guarantee you that J. Sanford will answer you when he's able to.

EDITED TO ADD :

Just received this additional input from J. Sanford :

The fact that our runs crash when we run out of RAM is not by design. If someone can help us solve this problem we would be very grateful. We typically need to track hundreds of millions of mutations. Beneficials create a problem for us because they amplify in number. We are doing the best we can.

I would urge your colleagues [Heaven help me - John is under the impression that you people are my colleagues ... brrrrrrrr!] to use more care. In science we should be slow to raise claims of fraud without first talking to the scientist in question to get their perspective. Otherwise one might unwittingly be engaging in character assassination.

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

The above sounds to me like a very reasonable, scholarly response on ALL fronts.
It is also exactly what I've been telling you guys. Great minds think alike.

Jorge

[Ansgar Seraph]

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

I'm just sitting here, scratching my head, trying to figure out what part
of "let the man respond to your accusations" you didn't understand.

Could you spare me from the bewilderment by shedding some light on this?

Thanks!

Jorge

I multitask. You brought this whole mess up, you spent 2.5 days in critical evaluation with Sanford . . . I figure that you ought to be able to produce something of value in the conversation. That said, I invited Dr. Sanford to the discussion last night via e-mail. Hopefully, he gives us a small amount of time.

But whether Dr. Sanford shows up or not doesn't really excuse you from introducing an argument, making claims that you cannot or will not defend:

Are you reading impaired? The answer to your question is NOT under "lock and key".
I provided it clearly and concisely : 1000 is used due to computer memory (RAM)
limitations, period. Avida is GIGO because it was designed to essentially produce
what the programmers already believed. I had suspected this from my own study
and this was confirmed by Dr. Sanford's information. In Avida, numerous factors that
contribute to the occurrence and/or accumulation and/or expression of deleterious
mutations are either not taken into account at all or are 'watered down' so as to not
interfere with the assumed-to-happen evolution. Mendel corrects every one of those deficiencies.

You apparently learned enough with Sanford to (A) explain why Avida is GIGO and (B) how MENDEL corrects that problem. The only thing you've said concretely, though, is that a population of 1000 was used in Sanford's experiments due to RAM limitations, which is demonstrably false.

—Sam

[Ansgar Seraph]

Even so, J. Sanford was kind enough to send me the following brief input in response to this :

"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

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

Even I [Jorge] have remaining questions after the above input but the point is this :
only un-scholarly, obtuse fanatics in a feeding frenzy accuse and condemn the
work and integrity of others without due process. What you guys need to
do is reflect on that, take ten deep breaths, and chill. I can almost
guarantee you that J. Sanford will answer you when he's able to.

EDITED TO ADD :

Just received this additional input from J. Sanford :

The fact that our runs crash when we run out of RAM is not by design. If someone can help us solve this problem we would be very grateful. We typically need to track hundreds of millions of mutations. Beneficials create a problem for us because they amplify in number. We are doing the best we can.

I would urge your colleagues [Heaven help me - John is under the impression that you people are my colleagues ... brrrrrrrr!] to use more care. In science we should be slow to raise claims of fraud without first talking to the scientist in question to get their perspective. Otherwise one might unwittingly be engaging in character assassination.

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

The above sounds to me like a very reasonable, scholarly response on ALL fronts.
It is also exactly what I've been telling you guys. Great minds think alike.

Jorge

Well, it sounds reasonable enough. It would seem that Sanford is aware of severe limitations in his computer software and is probably aware that MENDEL does not provide realistic results (e.g., the 90% run), possibly attributable to those limitations (sfs1 has given good reason to think there are more severe issues with the software's parameters, however). Scholarly, though? Should a scientist publish and promote a program as a devastating polemic against evolutionary theory when it is so crippled?

I've tried using MENDEL with 4GB of RAM and have never been able to make it use more than 2.2GB. How is adding more RAM going to help if MENDEL doesn't use the free RAM I already have?

—Sam

[Jorge]

Your arrogance absolutely prohibits you from admitting that you are wrong. Par for the course.

Let me now respond to your childish nonsense below :

I multitask. You brought this whole mess up, you spent 2.5 days in critical evaluation with Sanford . . . I figure that you ought to be able to produce something of value in the conversation. That said, I invited Dr. Sanford to the discussion last night via e-mail. Hopefully, he gives us a small amount of time.

I can produce lots of value here but I prefer to let authors speak for themselves - shame on me.


But whether Dr. Sanford shows up or not doesn't really excuse you from introducing an argument, making claims that you cannot or will not defend:

Answered above.


You apparently learned enough with Sanford to (A) explain why Avida is GIGO

I suspected / knew that Avida was GIGO long before I met John Sanford.
He merely corroborated what I already suspected / knew.


and (B) how MENDEL corrects that problem. The only thing you've said concretely, though, is that a population of 1000 was used in Sanford's experiments due to RAM limitations, which is demonstrably false.

—Sam

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.

The mouse question is interesting. I think one would need
to change various parameters for mouse - each species is
different. I would like to know the maximal (not minimal)
generation time - do they know? This would define the
maximal time to extinction. I have read that the per
generation mutation rate is about an order of magnitude
lower in mouse - which makes sense if there are fewer cell
divisions in the generative cells between generations.
I would be happy to do such experiments when I get the
input data.

Best - John

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

Jorge

[Faid]

Even I [Jorge] have remaining questions after the above input but the point is this :
only un-scholarly, obtuse fanatics in a feeding frenzy accuse and condemn the
work and integrity of others without due process. What you guys need to
do is reflect on that, take ten deep breaths, and chill.

And yet another irony meter is vaporized...

Jorge, think about what you just wrote. Then think about what you have said in the past about Avida.

Then look yourself in the mirror.