Annoying creationists

[Apathia]

Myriad,

Thank you for your clear summary. I find the clarity worth the process of "Annoyance" in this thread.

 

[joobz]

Virtually everything is unknown in abiogenesis and the theory of evolution. There is no plausible explanation how RNA bases could form in the primordial soup, there is no plausible explanation how these bases could link up nonezymatically to form the first functional ribozymes, there is no plausible explanation how these ribozymes could initiate protein synthesis and form DNA, there is no plausible explanation how this collection of chemicals could remain stable long enough and in one place long enough to combine and form the first living thing, there is no explanation of what kind of selection process would allow for such chemical reactions, and now ev shows that once you have living creatures, random point mutations and natural selection is so slow that you don’t have enough time to evolve any fundamental gene or genetic control system. The abiogenesis and the theory of evolution is a long list of speculations each with its own set of highly improbable unknowns.

bolding mine.
If someone provides a plausible mechanism, are you saying you'd change your mind? No, you are using it as an escape hatch. when ever we present data to the contrary, you claim it is "not plausible".

So, can you provide data why you feel ID is plausible?

 

[hammegk]

So, can you provide data why you feel ID is plausible?

For me, the order we all notice in perceived reality at every level of observation greater than Planck length.

 

[Dr Adequate]

Your own evolutionarian mathematical model argues against your case.

You have degenerated from an amusing buffoon into a bore. Can't you think of some new lies?

I haven't had a good laugh out of this thread since last you mentioned thermodynamics.

 

[Yahzi]

I want to know what mysterious expertise anyone has to have any conclusions about what most people would say is a thing that is inherently beyond human comprehension.

I agree with the above statement; but I had to read it five times to figure what it's saying.

 

[joobz]

For me, the order we all notice in perceived reality at every level of observation greater than Planck length.

At least you acknowledge that that is a personal reflection to fulfill your own preceived reality and not something you try to apply to all observers.

So far, I got to say that I've enjoyed your postings. Thank you

 

[kjkent1]

For those who might be interested, here's a review of some details of how ev actually works:

(redacted...)


Respectfully,
Myriad

Thanks. That was helpful. I'm sure kleinman will have a number of objections to your explanation -- so, I shall withhold further comment until the argument narrows again.

 

[Soapy Sam]

Myriad- Thank you for your description. It confirms my suspicion that while Ev may be an interesting early attempt , it is in no meaningful sense an accurate model of evolution. This is no to criticise the attempt; the Wright Flyer was not an F22 for similar reasons.

It does support my simple observation that if the result of a model does not reflect reality, it is the model , not reality which we must improve.

(Why this should be hard for to see is beyond my understanding ).

 

[Paul C. Anagnostopoulos]

Myriad- Thank you for your description. It confirms my suspicion that while Ev may be an interesting early attempt , it is in no meaningful sense an accurate model of evolution.

I disagree. It models the evolution of binding sites well enough to demonstrate that Rsequence approaches Rfrequency, which was exactly the point of writing it. Furthermore, when selection is turned off, the information content of the binding sites drops back to zero. Also, the generations required to evolve the binding sites varies linearly with the mutation rate. And so on.

The characteristics of binding sites are an important issue in biology.

http://www.ccrnp.ncifcrf.gov/~toms/paper/oxyr/latex/

http://nar.oxfordjournals.org/cgi/content/abstract/25/24/4994

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=200970&tools=bot

If what you mean is that Ev does not model a significant portion of the real-world evolutionary landscape in exact detail, then I agree. Models of real-world evolution are going to be of necessity somewhat generic, unless you are willing to model chemistry in excruciating detail.

~~ Paul

 

[cyborg]

unless you are willing to model chemistry in excruciating detail.

At which point is it easier to just do the chemistry.

It's going to be pretty difficult for a computer of any design with a program of any cleverness to beat the pure simplicity of just using the real world. The basic point of computer models is that sometimes using the real world is impractical. It's a trade-off. No free lunch and all that.

 

[Myriad]

I'm glad people have found my summary useful. Fringe benefits of insomnia...

However, I did omit discussion of the actual original purpose of the model, so anyone looking up the original paper on ev might be surprised to find that it's all about showing that Rsequence approaches Rfrequency, as a facet of Dr. Schneider's work on binding sites and his efforts to promote "sequence logos" as an improvement on "consensus sequences" as the most effective way to evaluate and document known binding sites and search for unknown ones. I didn't discuss Rsequence because it's not really among the issues Kleinman raised, and in fact, the model does not use the calculated values of Rsequence internally in any way. The behavior of Rsequence, like the concept of "generations to convergence," is strictly an output of the ev model.

Briefly, Rsequence is a measure of the amount of information in the binding sites, calculated from the genome sequences at the binding sites of a given individual creature in the model population (just as it can be calculated for any real genetic control system in any real genome, if the binding sites and their sequences are known). While ev might not be sophisticated in its model of genetic variation (most genetic algorithms, for instance, include, at least, recombination in addition to point mutation), it is (to my knowledge) unique and valuable in incorporating a well-defined measure of the amount of information gained by a given genome though the process of point mutation and selection.

I find the clarity worth the process of "Annoyance" in this thread.

I appreciate the compliment, but let's not take this "clarity" idea too far. Don't forget that Kleinman has gone to great lengths to be annoying, for our benefit. It would be most ungrateful of us to turn the discussion to clarification of the facts or useful discussion of the science.

Respectfully,
Myriad

 

[articulett]

I appreciate the compliment, but let's not take this "clarity" idea too far. Don't forget that Kleinman has gone to great lengths to be annoying, for our benefit. It would be most ungrateful of us to turn the discussion to clarification of the facts or useful discussion of the science.

Respectfully,
Myriad

I find his conviction interesting, and I appreciate your model. I could not figure out why he was sticking with this evolution via point mutation model when we know so many ways that genomes can be altered through time. Plus, I'm always bothered by the notion of "adding to the genome" that creationist like to talk about. Do they mean base pairs, genes, gene expression, function--? No matter how great the computer program is, it doesn't help if you can't say what you are testing for. And unless it includes all the ways we know that changes can occur to a genome, it's ridiculous to extract the exclusion that it evolution couldn't have happened unless some intelligent designer had a hand in it.

What becomes of the people who believe that evolution is a dead theory in 10 years when the data is even more stellar and obvious. Do they just get more and more cloistered in their illusion? Do you think Kleinman just can't understand why Shepard's model is inept? I just think it's so strange that he must believe all these scientists all over the world are working with a false theory while he and his theistic friends have the truth which is obvious in his math problem. Do they imagine that one day, Dawkins etc. will say, "gee, it's impossible for the genome to evolve without a designer--we need to start looking for evidence of the designer--the math shows that a designer is necessary because there's not enough time to evolve when you factor in a point mutation rate of "x"!"

Do they ever question themselves? I hope the new sim game "spore" factors in more than a point mutation algorithm for the evolution of creatures...or it will be a long slow game.

 

[kleinman]

Annoying Creationists

The point you are missing is that when you use realistic mutation rates and genome lengths, it takes huge numbers of generations to evolve only a few loci in the ev model.

I'm not missing this point -- you repeat it frequently, and I am acknowledging that it is important.

I have to continually repeat this because so many whining and whimpering evolutionarians keep saying that I am moving the goal posts.

However, the issue, "now," is whether the generational requirements would be reduced given other "realistic" parameters, such as actual organism survival rates, external environmental stresses, other types of genetic changes, such as recombination, and different types of mutation "mistakes" (i.e., I note that the EV program only codes two types of mistakes), none of which appears to have been contemplated by the EV model.

Recombination without errors can not create a new gene; recombination with natural selection can cause loss of alleles. Other forms of mutations such a gene and chromosomal duplications require point mutations to create new genes. Feel free to use frame shift mutations, inversions and other kind of mutation you can think of in ev to see if you get more rapid convergence. I think you underestimate how much Dr Schneider has contemplated his model. He has had this model for more than 20 years.

Also, on the other side of the coin, someone could impose a specific set of changes at some specific point (a "design"), and then continue to run the program, to see whether the design would start to substantially deteriorate, and how long that deterioration would require. If deterioration occurred quickly, it would suggest a rather crappy design, and it would also suggest that continuous intervention by the designer would be necessary to maintain the species continuum.

Turn off selection in the program and the binding sites quickly revert to random. This is an interesting point you raise. In order to sustain a particular sequence in the binding site region of ev, the selection process must be maintained forever. Whatever selection process that would lead to the evolution of a sequence of bases must never be removed otherwise that sequence of bases would quickly disappear.

If you could find a selection process that would speed up convergence in ev, I think evolutionarians would raise a glass to you from one end of this forum to the other. Delphi would raise a glass either way.

General legal advice: stop suggesting that Delphi has a drinking problem. If it turns out in reality that he has none, and that persons who know him for who he really is, think less of him as the result of your comments here, then you could find yourself to be the "natural selection" for the role of defendant in a libel/false light attribution suit. Getting your actual ID and contact info would be trivially easy via a subpoena served on randi.org.

Oh, so his icon which says he needs a drink is a joke? I’ve used my actual ID on this and every site I have posted, unlike most of the hooded evolutionarians on this and other sites on which I have raised this issue.

Now why don’t you do your homework for your own little marketing plan and maybe you can find a way out of your cubicle you lazy, greedy Dilbert.

I am saying that your argument against evolution appears to share the same flawed basis as Dembski's argument against evolution. The difference being that your argument focuses on the Schneider model, while Dembski's argument used statistics.

Appearances can be deceiving. Dr Schneider’s computer program appeared to show mathematically how random point mutations and natural selection leads to gain in information in a genome, however when realistic parameters are used in the model, something totally different appears.

The resulting evolved genomes exhibit a property that appears to meet IDers' definition of irreducible complexity, because the binding site sequences and the weight matrix sequence must, and do, match up to each other in order for the binding sites to function.

Thank you for your very thorough description of the ev program. I have never seen a mathematical statement for irreducible complexity so I was wondering whether the application of ev when using unrealistic parameters would meet the condition of a refutation of irreducible complexity?

Because multiple changes to the genome are typically required to eliminate any one population-wide mistake, Kleinman's argument that large increases in population should have little effect on the number of generations to reach a "perfect creature" (no mistakes), because the probability of any one specific mutation occurring in the population per generation approaches 1 with a population on the order of the genome length, is invalid. The probabilities of a given combination of 2 or more mutations obviously does not approach 1 until the population reaches the order of successive powers of the genome length -- which microbial populations in nature can easily do, up to at least the third power. This prediction is consistent with test results. Every series of test runs with increasing populations has continued to show reductions in number of generations for as long as the data series is extended. Kleinman points out that the rate of reduction decreases as the population increases, but has not given any reason why we should expect otherwise if the curve has an exponent of, say, .5 or .33. Therefore Kleinman's assertion that large populations make no difference is contradicted on both theoretical and experimental grounds.

Why don’t you post the data which refutes my assertion?

Kleinman has reported that the generations to convergence increase dramatically as longer genome lengths are tested. However, what he's seeing are largely the result of effects 1 and 2. To my recollection he's never reported the results of any tests at any binding site width other than the default, so his runs never converge past genome lengths about 50,000 bases.

Feel free modify 1. (the mutation rate) in the middle of a run and see whether ev will converge more quickly. 2. (the effect of the longer genome length requiring more information to locate a binding site) is a mathematical condition imposed by information theory. Perhaps you can see a plausible way around this condition.

I have done a series where I examined the effects of site width on the rate of convergence ev and have posted the data on the Evolutionisdead forum. I’ll repost the information here for your convenience. G=2048, Rf=7, Population=64, mutation rate=1/genome per generation, weight width=1-site width.
Site Width/Gernerations for Rs >= Rf/Generations for perfect creature
6/35486
7/36920/36819
8/29745/48335
9/35009/35651
10/42747/42672
11/37899/63415
12/29658/34675
13/34201/36666
14/29726/33928
15/31448/31201
Feel free to use what ever site width you want and see if you can get a megabase genome to converge and refute my assertions.

By all accounts and according to all tests so far, reducing the mutation rate has a linear effect on increasing the generations to convergence, for reasons that should be intuitively obvious. Except for cases such as I described above where simultaneous mutations might be advantageous but individually fatal, there's no difference to a creature whether it receives 10 mutations one every 100 generations on average, or 10 mutations in the same generation, or somewhere in between. The effect of the mutation rate only becomes complex when it becomes very high (many orders of magnitude higher than what Kleinman accepts as "realistic") resulting in a mutation load that slows down or even prevents evolutionary progress.

Not quite by all accounts, I have already posted several series which show that mutation rates exhibit a paraboloid type of behavior on the rate of convergence. Of the five series I have done examining the effects of mutation rate on the rate of convergence, each has demonstrated this type of behavior. You need to run some of these cases so that you will convince yourself of this effect.

Even if one accepts the claim that the ancient prokaryotes that are the closest scenario from nature to what ev simulates must have mutation rates similar to present-day microorganisms (and no evidence whatsoever has been offered to support that claim), such a mutation rate (versus the 1 per 512 base rate that Paul used in his genome-length series) only accounts for a further increase in number of generations of a factor of about 10^4, which combined with the linear effects of expanding to "realistic" genome lengths, still does not result in evolution that's "profoundly slow" by known evolutionary time scales. There are also sound mathematical and experimental reasons to expect that higher populations would indeed compensate for lower mutation rates. For instance, if (unlike in ev) mutations were truly randomly distributed, a large fraction of the population would receive signficantly more than the expected number of mutations in any given generation.

It is you evolutionarians who are in the professional speculation business. There are known, measured mutation rates and genome lengths. If you think that there are sound mathematical and experimental reasons to expect that high populations will somehow compensate for these known, measured values, post your data, otherwise you continue to pile speculation upon speculation.

In attempting to apply quantitative results (however questionable) of ev to questions of the evolution rate of humans and other eukaryotes, Kleinman has rejected any hypothesis that sexual reproduction can account for faster, more efficient evolution. While it is true that recombination alone does not create additional mutations, mutations alone do not control the rate of information increase. The generation of combinations of mutations and the selection of such combinations is critical, as should be patently obvious to anyone who, like Kleinman, has run the ev model and observed that, taking the population into account, it can take enough generations to converge for every possible point mutation to have occurred tens, hundreds, or thousands of times over along the way. Clearly it matters what combinations of mutations appear in which individuals, and sexual reproduction generates new combinations much more efficiently while allowing the population to assimilate a considerably higher mutation load.

I have not rejected any hypothesis that sexual reproduction can account for faster, more efficient evolution. I have even suggested to Dr Schneider a means of introducing this concept into his model. Myriad, perhaps you will introduce recombination into ev and prove my assertions wrong.

It's also well-known to Kleinman, or at least it should be. One mathematical model comparing asexual to sexual reproduction is given by MacKay available at w w w.inference.phy.cam.ac.uk/mackay/itprnn/ps/265.280.pdf. (Figure 19.1 sums up the difference recombination makes very succinctly.) I'm indebted to Kleinman for pointing me to the MacKay monograph in the first place, and I've pointed out significance of the MacKay model to Kleinman on several occasions to no apparent avail.

I also have said to you, once we have finished dissecting ev, we could examine the MacKay model in more detail and see whether this model rescues you theory. I have also pointed out to you that the MacKay model contradicts your assertion that huge populations will speed evolution, apparently to no avail.

Virtually everything is unknown in abiogenesis and the theory of evolution. There is no plausible explanation how RNA bases could form in the primordial soup, there is no plausible explanation how these bases could link up nonezymatically to form the first functional ribozymes, there is no plausible explanation how these ribozymes could initiate protein synthesis and form DNA, there is no plausible explanation how this collection of chemicals could remain stable long enough and in one place long enough to combine and form the first living thing, there is no explanation of what kind of selection process would allow for such chemical reactions, and now ev shows that once you have living creatures, random point mutations and natural selection is so slow that you don’t have enough time to evolve any fundamental gene or genetic control system. The abiogenesis and the theory of evolution is a long list of speculations each with its own set of highly improbable unknowns.

If someone provides a plausible mechanism, are you saying you'd change your mind? No, you are using it as an escape hatch. when ever we present data to the contrary, you claim it is "not plausible".

I’ve been thinking about how we could get you back into this discussion besides your posting of URL’s and an occasional smiley face.

Since you are a professor of chemical engineering, why don’t you start by giving us a plausible mechanism for forming the initial RNA bases necessary to start the RNA world? Let’s make it simpler than that, why don’t you describe an experiment that would simulate the primordial world where you could generate ribose?

 

[Paul C. Anagnostopoulos]

Feel free to use what ever site width you want and see if you can get a megabase genome to converge and refute my assertions.

Here's some data I collected:

population 36
site width 8
1 mutation per 512 bases

genome size, generations
512, 3763
722, 4950
1024, 9866
1448, 11446
2048, 11189
2887, 13037
4096, 38731
5775, 34424
8192, 61365
11550, 68696
16384, 73915
23101, 136762
32768, 177424
46202, 344124
65536, 526545
92406, 707871

This fits [latex]$7.8G^{.98}$[/latex] with r=0.99. It also fits a linear equation with r=0.99, even if I discard the first half of the points.

So tell me, what do you think is going to happen between a genome size of about 100K and 1000K that's going to screw up the curve fit? I just want to know what the magic is.

~~ Paul

 

[kleinman]

Annoying Creationists

Feel free to use what ever site width you want and see if you can get a megabase genome to converge and refute my assertions.

…So tell me, what do you think is going to happen between a genome size of about 100K and 1000K that's going to screw up the curve fit? I just want to know what the magic is.

I don’t know, why don’t you run a few more points in this series and see if you can refute my assertions.

 

[joobz]

I’ve been thinking about how we could get you back into this discussion besides your posting of URL’s and an occasional smiley face.

you've been having a discussion over the past 5+ pages? I didn't notice. I've only seen you post the same already refuted nonsense over and over again. That's hardly a "discussion". So I just posted the relavent posts that refute your claims.

Since you are a professor of chemical engineering, why don’t you start by giving us a plausible mechanism for forming the initial RNA bases necessary to start the RNA world? Let’s make it simpler than that, why don’t you describe an experiment that would simulate the primordial world where you could generate ribose?

You avoid my questions, and most of everyone elses, and then you expect your's to be answered? That seems a little one sided, do you think?

Anyway, I've already traveled this road with you. I could happily speculate, but my speculations would be less informed than those in the field. regardless, you would be "unsatisfied" with any answer.

BTW, how does my position tie into the question you pose? If you were to ask me a question on thermo, mass transfer, fluid mechanics, polymer chemistry, drug delivery, reaction kinetics... the connection is clear. But alas, you do not wish to discuss science. You simply wish to continue throwing rocks.

 

[Myriad]

I find his conviction interesting, and I appreciate your model. I could not figure out why he was sticking with this evolution via point mutation model when we know so many ways that genomes can be altered through time... No matter how great the computer program is, it doesn't help if you can't say what you are testing for. And unless it includes all the ways we know that changes can occur to a genome, it's ridiculous to extract the exclusion that it evolution couldn't have happened unless some intelligent designer had a hand in it.

... Do you think Kleinman just can't understand why Shepard's model is inept? I just think it's so strange that he must believe all these scientists all over the world are working with a false theory while he and his theistic friends have the truth which is obvious in his math problem. Do they imagine that one day, Dawkins etc. will say, "gee, it's impossible for the genome to evolve without a designer--we need to start looking for evidence of the designer--the math shows that a designer is necessary because there's not enough time to evolve when you factor in a point mutation rate of "x"!"

Do they ever question themselves?

My theory is that Kleinman has an orgasm every time he reads a post proving him wrong. This makes him the happiest man on earth.

Respectfully,
Myriad

 

[kleinman]

Annoying Creationists

Since you are a professor of chemical engineering, why don’t you start by giving us a plausible mechanism for forming the initial RNA bases necessary to start the RNA world? Let’s make it simpler than that, why don’t you describe an experiment that would simulate the primordial world where you could generate ribose?

You avoid my questions, and most of everyone elses, and then you expect your's to be answered? That seems a little one sided, do you think?

Is a mean old creationist ganging up on all you poor evolutionarians? How unfair of me. At least your grammar is showing some improvement.

My theory is that Kleinman has an orgasm every time he reads a post proving him wrong. This makes him the happiest man on earth.

I guarantee that this discussion has not given me any sexual gratification; however your latest theory is an improvement over the theory of evolution.

 

[John Hewitt]

Since you are a professor of chemical engineering, why don’t you start by giving us a plausible mechanism for forming the initial RNA bases necessary to start the RNA world? Let’s make it simpler than that, why don’t you describe an experiment that would simulate the primordial world where you could generate ribose?

I could happily speculate, but my speculations would be less informed than those in the field. regardless, you would be "unsatisfied" with any answer.

BTW, how does my position tie into the question you pose? If you were to ask me a question on thermo, mass transfer, fluid mechanics, polymer chemistry, drug delivery, reaction kinetics... the connection is clear. But alas, you do not wish to discuss science. You simply wish to continue throwing rocks.

If you have time to present them, I too would be very interested in those speculations.

 

[joobz]

Originally Posted by Kleinman

Since you are a professor of chemical engineering, why don’t you start by giving us a plausible mechanism for forming the initial RNA bases necessary to start the RNA world? Let’s make it simpler than that, why don’t you describe an experiment that would simulate the primordial world where you could generate ribose?

Originally Posted by joobz

You avoid my questions, and most of everyone elses, and then you expect your's to be answered? That seems a little one sided, do you think?

Is a mean old creationist ganging up on all you poor evolutionarians? How unfair of me. At least your grammar is showing some improvement.

Dodging the questions again I see. Is it because whenever you provide an actual answer, you prove your silliness?

I'm still waiting to see why you say ev shows evolution takes too long. All of your arguments provided so far have been...well...wrong.