Annoying creationists

[delphi_ote]

That's bit broader than I meant.

I was just hoping you saw something interesting I had missed.

It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution.

If we're going for an entirely accurate model, that's going to be extremely difficult, maybe even impossible. But people are definitely working on these problems in bioinformatics and evolutionary computation. If our friend has something interesting to say, I'm certain people in those fields would listen.

I'm being a bit of a Devil's advocate here, as "satan" as the the Book of Job put it. I'm naive enough to think that we might back away from the name calling to, if not agreeing on anything, valuing the process.

I was more than willing to hear the man out until he proved he couldn't retract a very simple error.

 

[joobz]

That's bit broader than I meant. It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution. There seems to be a snag. Perhaps there isn't one after all. It's just it seems that way to me now, and I'm not a scientist, so I'm open to be corrected. I've never thought that Darwin was the last word on evolution. So it seems to me that disputes of this sort can encourage progress. If there is a real snag in the classic theory, I look forward to exciting developments. Dr. Kleinmann may be annoying in this context, but I hope he's not superficially dismissed. A pain, right? But pain often serves a purpose that that should be addressed, even if you chase it away with an advil.

I'm being a bit of a Devil's advocate here, as "satan" as the the Book of Job put it. I'm naive enough to think that we might back away from the name calling to, if not agreeing on anything, valuing the process.

If you double back over the thread, you'll notice that I've given kleinman ample time to present his case and I have acknowledged that his critique of the model is valid. He found a problem with the model. Paul acknowledged where the limitations to the model are. However, The conclusion that kleinman generalizes it to real life is the problem. No person on this thread has ever claimed that darwin was the end all of evolutionary theory. Far from it in fact. But to state that the entire concept is wrong because some computer program doesn't work is just juvinile.

I've been willing to discuss with kleinman and listen to him when many have ignored him. I invite you to go back a check the transcripts. As he says, "google is watching." Between us, he was the first to throw verbal stones. He is the one who refuses to acknowledge when he was blatantly wrong about entropy and thermodynamics. His whole concept of 'time too long' in the model is a poor arguement. There is no new knowledge he has provided.

No, kleinman is just a noisy gong. loud and clangy but devoid of substance. He is of no use to anyone.

As I said. Science moves on without him. We don't know where it's going. It's the nature of discovery, but we don't hide what we discover. We don't change observations to fit our theories. We fit our theories to observations. As we learn more, we will change and improve.

this is completely opposite of kleinman's desire. He offers nothing worthwhile. I am done with him.

 

[Beleth]

I’m the “Annoying Creationist” Paul Anagnostopoulos is pissed off at.

I'll take that as a Yes.

How did you arrive at the Creationist conclusion?

 

[Paul C. Anagnostopoulos]

I added the bold face to your quote. Your theory about Rcapacity says the exact opposite. I will summarize your hypothesis:
If Rcapacity = 2 * binding site width is less than Rfrequency then ev will not converge. The mathematics of ev is saying that it is more difficult to evolve narrow binding sites on larger genomes.

I wish you'd stop calling it a theory. If I need a 12-bit code and I've only got 8 bits, it just won't work, period.

However, in real life, there are two issues. On the one hand, a narrow binding site wouldn't have sufficient bases to contain a code unique enough* to be useful in genetic binding. On the other hand, a wider site can contain a unique code, but is it harder to evolve the ligand? Actually, I really don't know. Point taken.

~~ Paul

* Yes, yes, I know.

 

[Paul C. Anagnostopoulos]

We don’t have to ignore the effects of mutagens, how high of a mutation rate to you think can be maintained in a living organism?

I don't know, but perhaps we have sex to show for it:

http://news.nationalgeographic.com/news/2001/07/0709_sexorigin.html

~~ Paul

 

[Paul C. Anagnostopoulos]

That's bit broader than I meant. It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution. There seems to be a snag. Perhaps there isn't one after all. It's just it seems that way to me now, and I'm not a scientist, so I'm open to be corrected. I've never thought that Darwin was the last word on evolution. So it seems to me that disputes of this sort can encourage progress. If there is a real snag in the classic theory, I look forward to exciting developments. Dr. Kleinmann may be annoying in this context, but I hope he's not superficially dismissed. A pain, right? But pain often serves a purpose that that should be addressed, even if you chase it away with an advil.

What snag? The one where we agree that the diversity of life cannot arise solely from point mutations on random gigabase genomes in a few million years?

What classic theory? The one where we agree that Darwin didn't have the whole story 150 years ago?

By all means, Kleinman should make his case. I've been talking to him since June and I'm still waiting for the case.

~~ Paul

 

[delphi_ote]

The one where we agree that the diversity of life cannot arise solely from point mutations on random gigabase genomes in a few million years?

That's just the thing. Recent research has shown point mutation isn't the the only way genes get shifted around in natural evolution. There are a lot of different types of mutations that change the genome of an organism; especially those that sexually reproduce. Full chromosomal duplication events seem to be very important in plant evolution.* There also seems to be a lot of gene evolution caused by tandem duplication events. Really weird things happen in genomes, too. Mitochondrial DNA or Chloroplast DNA can end up in the nuclear genome. Something like 8% of the human genome consists of retroviral DNA. Lots of junk collects in genomes over time. Most of it does nothing, but some of it seems to be important for evolution and biology. How did life begin? How are genes formed? What is the importance of various types of mutation?

These are questions at the the cutting edge of molecular biology and evolutionary biology. Scientists in these fields are trying to answer them by performing experiments and working in the lab. What is kleinman's answer? What does he think the underlying mechanisms are which produced the "endless forms most beautiful"? "Godddidit" is just an excuse for ignorance. How exactly did it happen?

* I'm R. Cunningham.

 

[Yahzi]

You completely don't understand, do you? ...The model doesn't account for everything.

Son, you're trying to tell a witchdoctor that his voodoo doll ain't got no mojo.

You might as well spit into a hurricane.

 

[Myriad]

Likewise, at this rate, roughly an entire human genome of ~4 * 10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution.

(emphasis added)

"This rate" refers to the rate of information increase per generation shown by the ev model with the low-valued parameters that Kleinman is complaining about.

I just wanted to point out that not only did Dr. Schneider not claim that the ev model simulates all important factors in evolution, he explicitly stated the contrary. Kleinman usually leaves out the boldfaced sentence when he quotes this passage.

Respectfully,
Myriad

P.S. I've been playing around with the model. The curve of generations to convergence depends on the details of the selection mechanism. Change it so that ties are won by the bug whose worst mistake (greatest absolute value of the difference between the binding strength value from the weight matrix and the threshold) is less than the other bug's worst mistake, and the convergence time becomes (at least approximately) linear with respect to the genome length.

 

[Paul C. Anagnostopoulos]

P.S. I've been playing around with the model. The curve of generations to convergence depends on the details of the selection mechanism. Change it so that ties are won by the bug whose worst mistake (greatest absolute value of the difference between the binding strength value from the weight matrix and the threshold) is less than the other bug's worst mistake, and the convergence time becomes (at least approximately) linear with respect to the genome length.

Welcome, Myriad! That's an interesting result. Do you include both mistakes at binding sites and spurious bindings in the determination of the worst mistake?

~~ Paul

 

[Myriad]

Welcome, Myriad!

Thanks, Paul! As a long-time lurker, I know this is a great forum.

That's an interesting result. Do you include both mistakes at binding sites and spurious bindings in the determination of the worst mistake?

Yes. For binding sites it's how far below the threshold, for nonbinding sites it's how far above the threshold.

For the tests I've done with that selection model so far, I also pegged the threshold at zero. I doubt that makes a difference (it makes little or no difference with ev's normal selection rules), but I'd better mention it in case I'm wrong about that.

Respectfully,
Myriad

 

[Paul C. Anagnostopoulos]

Yes. For binding sites it's how far below the threshold, for nonbinding sites it's how far above the threshold.

That makes sense.

For the tests I've done with that selection model so far, I also pegged the threshold at zero. I doubt that makes a difference (it makes little or no difference with ev's normal selection rules), but I'd better mention it in case I'm wrong about that.

We're considering a parameter that allows the user to specify a constant threshold value. If you have the time, could you run your modified Evj with a genome size of about 1K, in the normal mode and the threshold=0 mode, about ten times each with different seeds, so we can see if there is a significant difference in generations to perfect creature?

~~ Paul

 

[Myriad]

No problem, except that it will have to wait until next week. I'm leaving on a Thanksgiving holiday trip in the morning. While away I'll have access to the Internet but not to the system I'm running the model on.

Respectfully,
Myriad

 

[Paul C. Anagnostopoulos]

Thanks, Myriad. No hurry on running those experiments.

I mentioned your tie-breaking method to Schneider and he said to congratulate you on introducing this new method. He asked what you do when two tied bugs have the same worst mistake difference; how do you break ties when breaking ties?

~~ Paul

 

[Dr Adequate]

We don't know this, because we haven't modeled more than a measly million creatures. You won't let me extrapolate using that fitted curve, but if I did extrapolate to a lousy billion creatures, it would require 103 generations; to a trillion creatures, 21 generations. Of course, there is some asymptote it's approaching, although I haven't the slightest idea what that is.

No?

1 generation, obviously.

It is sometimes said that an infinite number of monkeys with typewriters would eventually produce Hamlet. This is an understatement. Actually, if you had an infinite number of monkeys, one of them would type Hamlet straight off.

---

The mistake Kleinman has made, or one of them, is to take a realistic value for p (the probability of a point mutation for a given base) but not for n (the population). This gives a totally unrealistic value for the probability that a given substition will occur in the gene pool per generation, which is given by:

q = 1 - (1 - p/3)ⁿ
If, for example, we take a realistic value for p of 10^-8, then for a measly million organisms, q is 0.3%. For a lousy billion, it's 96.4%.

If we use a more realistic order of magnitude for the bacteria, say something like the 10¹⁴ present in a single human gut, then my calculator isn't accurate enough to tell us the difference between q and 1.

Schneider is forced by practical constraints to take n to be small, and has compensated for this by using an unrealistic value for p to give himself a realistic value for q. This is eminently sensible, since it is the amount of variation within the gene pool, rather than the variation between individuals per generation, that determines the rate of evolution.

Kleinman, on the other hand, has chosen his numbers so that the value for q is wildly unrealistic; this is why his estimate of the time the process would take is also wildly unrealistic.

 

[Kopji]

By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the Scriptural record.

http://www.answersingenesis.org/home/area/about/faith.asp

I think you guys are great but at the end of the day you are talking to yourselves. Creationists are not arguing from a position of intellectual integrity where they might ever be wrong if you provided evidence.

 

[Paul C. Anagnostopoulos]

No?

1 generation, obviously.

Yes, that's the obvious asymptote. Somehow it doesn't seem fair to use that as the practical asymptote, however. Wait a moment, what is a "practical asymptote"? I have no idea.

~~ Paul

 

[joobz]

Yes, that's the obvious asymptote. Somehow it doesn't seem fair to use that as the practical asymptote, however. Wait a moment, what is a "practical asymptote"? I have no idea.

~~ Paul

How does this agree with Hardy-Weinberg Equilibirum? Or is that only for sexually reproducing species?

 

[Dr Adequate]

How does this agree with Hardy-Weinberg Equilibirum? Or is that only for sexually reproducing species?

I don't see how H-W E comes into it. The point is simply that if you have an infinite number of organisms, then one of them (or, to be precise, an infinite number of them) will, on reproducing, hit on exactly the right set of mutations to produce whatever it is you want. Long odds mean nothing to an infinite population.

Hence, as the population size tends to infinity, the number of generations to get any particular result tends to 1.

 

[joobz]

I don't see how H-W E comes into it. The point is simply that if you have an infinite number of organisms, then one of them (or, to be precise, an infinite number of them) will, on reproducing, hit on exactly the right set of mutations to produce whatever it is you want. Long odds mean nothing to an infinite population.

Hence, as the population size tends to infinity, the number of generations to get any particular result tends to 1.

That i get, but H-E states that with large population (along with 4 other criteria) you can suppress evolutionary changes from natural selection.

I see what you state and completely agree, but for that organism which hits the right combination, it would have to be the only surviving organism. For sexually reproducing systems, the formation of that binding site has to be dramatically beneficial for it's effect to be felt in the entire species. Otherwise, it gets diluted throughout the population.