Gambler's Ruin is Darwin's Gain

Basically then, he's pretending that mutations are rare events?

It is always amazing how creationists, and Sal in particular, can see one thing in a text book that seems to support their presupposition and completely miss the majority of the lesson which indeed shows that their conclusion is wrong. The clue should be that the book Sal quote-mined deals with an integral part of evolution theory, namely population genetics. Also if this book was printed in 1971 and wasn't an earth shattering refutation of "Darwinism" then, why should we now expect it to be?

Prof. Felsenstein (sir), I must disagree with you about the Hill-Robertson effect - I'm not sure Sal is that advanced. I suspect he's assuming a (roughly) constant total variance in fitness so that having more genes involved reduces the average effect of each one. But I haven't pushed him on it, because I forgot to check the literature when I was at work.

I don't have access to the book in question. Do they provide an equation to calculate the odds that a mutation with s=.01 will be fixed out of a population?

Is it, by chance, the remaining 98%?

It hardly seems meaningful to infer the effectiveness of natural selection by comparing the rate of fixation in advantaged vs. neutral mutations, when in fact you are comparing "tiny" to "much tinier."

Rather, the most meaningful conclusion appears to be that genetic drift reduces the the odds of fixation of an advantaged trait by 98% in an s=.01 scenario.

I noticed in that UD post that Sal said he'd seen both "21" and "Expelled" the same day. Does he have like a job or something?

Basically then, he’s pretending that mutations are rare events?

I don’t have access to the book in question. Do they provide an equation to calculate the odds that a mutation with s=.01 will be fixed out of a population?

Is it, by chance, the remaining 98%?

It hardly seems meaningful to infer the effectiveness of natural selection by comparing the rate of fixation in advantaged vs. neutral mutations, when in fact you are comparing ”tiny” to ”much tinier.” Rather, the most meaningful conclusion appears to be that genetic drift reduces the the odds of fixation of an advantaged trait by 98% in an s=.01 scenario.

ungtss said: It hardly seems meaningful to infer the effectiveness of natural selection by comparing the rate of fixation in advantaged vs. neutral mutations, when in fact you are comparing "tiny" to "much tinier." Rather, the most meaningful conclusion appears to be that genetic drift reduces the the odds of fixation of an advantaged trait by 98% in an s=.01 scenario.

Sal really stepped into my world on this one, since I counted Blackjack for several years. I take him apart here:

http://scienceavenger.blogspot.com/2008/05/evolution-21-gamblers-ruin-and-zero-sum.html

He doesn't even understand the basics of the issues, making statements like:

"If he has a 1% statistical advantage, that means he has a 50.5% chance of winning and a 49.5% chance of losing."

Which reveals either that he is completely ignorant of the rules of blackjack, or he doesn't understand the difference between probability of victory and expected winnings.

I would also note that it is highly unlikely that Thorp's system was the one used in the movie. Blackjack counting systems improved dramatically in the 70's and 80's as computing power allowed for simulations for the first time, and his would no doubt have been surpassed in efficiency by more modern systems.

bump

Sir:

Thank you for your response. By "fixed out of" I meant eliminated as a variant. I apologize for my lax use of words.

Thanks for the equation itself, also. I greatly appreciate your time.

I agree with you that this certainly does not "refute" natural selection. However, I don't think it's "Darwin's gain," either. An s=.01 mutation may have a 40,000x better chance of fixation than a neutral one, but the more relevant fact is that the s=.01 mutation has only a 2% chance, and the neutral and disadvantageous mutations have virtually no chance at all.

The problem becomes even more severe in smaller, isolated populations (where genetic drift becomes more severe), and in the context of sexual reproduction (where each child receives only 50% of the collective genetic diversity of its parents).

I don't think this is any meaningful "gain" for Darwin at all. Rather, it's a significant hurdle that mutations have to get over to get fixed. It may be surmountable, over significant periods of time, but it is a hurdle, nonetheless.

Of course such a theoretical discussion cannot ever prove that evolution by natural selection is impossible anyway. There are always a host of other factors operating in the real world that can drastically alter the probabilities. For example, what is the dominance of the newly arisen mutation? How many offspring are produced carrying the new mutation and what is the rate of inbreeding? Are there other considerations such as hitchhiking, pleiotropy, density dependent selection, sex-linkage, etc. All these factors and many more can help to determine the initial and ultimate fate of mutations no matter how selectively advantageous they are. And then of course there is population size, environmental heterogeneity etc.

Leave it to creationists to find the end of "Darwinism" in everything they read. Why is this guy reading 37 year old papers anyway? No matter what he quote mines he will always find that science has moved on in the last thirty years anyway. How come these guys never seem to notice that? It's almost as if they as just trying to find things that someone might take the wrong way instead of really trying to learn anything about science.

Joe Felsenstein said: Some comments on the comments: J. Biggs wrote:

Basically then, he’s pretending that mutations are rare events?

No, they are rare. He's noticing that even advantageous ones very often get lost, and arguing that this refutes the effectiveness of natural selection.

AAHHHHH....The Cordova....standard with fine Corinthian Bullshit.

Dr. Felsenstein,

Thank you for responding to our discussion at Uncommon Descent. I appreciate that you would take time to respond. I have provided links from Uncommon Descent to your response here. I encourage those reading Uncommon Descent to read your response.

Many thanks for taking time to read what I wrote and offering a response here at PandasThumb.

Salvador T. Cordova

The problem becomes even more severe in smaller, isolated populations (where genetic drift becomes more severe), and in the context of sexual reproduction (where each child receives only 50% of the collective genetic diversity of its parents).

At least I have to say that Sal is probably the most polite ID/Creationist that comments here.

Mr. Felsenstein:

I greatly appreciate the explanation. Thanks.

Forgive my abject ignorance, but I've been wondering whether s=.01 is typical. I gather that if this number were even slightly larger, the probability of fixation would go up dramatically. So is s=.01 conservative? unglss seems to be saying that for evolution at this level of selective advantage, the loss rate implies that evolution will be slower than actually observed in some cases. So my guess would be that some beneficial mutations offer better than a 1% improvement. And those would be a LOT more advantageous than neutral mutations.

So where did the 1% number come from? Is it realistic?

Flint:

Seems like that's going to depend on the mutation at issue. Certain mutations (like antibiotic resistance) are going to be significantly higher than .01. The S of other mutations (like gradual changes to anatomy) are going to be much lower. Seems like you'd actually have to observe the effect of the mutation to determine the S. Yes?

At least I have to say that Sal is probably the most polite ID/Creationist that comments here.

Darwin couldn’t do high school algebra even after much effort and a tutor to spoon feed it to him. He doesn’t deserve to be in the “genius corner” of Westminster Abby. Perhaps we ought to transplant his coffin to the dunce corner.

Dr. Felsenstein wrote: Sal Cordova argued that there was little difference in outcome between advantageous and neutral mutations. He was wrong about that, and I assume that he will admit that.

This means is that natural selection is only slightly better than random chance. Darwin was absolutely wrong to suggest that the emergence of a novel trait will be preserved in most cases. It will not!

Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good. Charles Darwin chapter 4 Origin of Species

The fact that the majority of mutations, including those having a slight advantage, are lost by chance is important in considering the problems of evolution by mutation, since the overwhelming majority of advantageous mutations are likely to have only a slightly advantageous effect. Note that a majority of mutations with large effect are likely to be deleterious. Fisher (1930b) emphasized that the larger the effect of the mutant, the less it its chance of being beneficial. In our opinion, this fact has not fully been acknowledged in many discussion of evolution. It is often tacitly assumed that every advantageous mutation that appears in the population is inevitably incorporated. page 11

scordova wrote: Truly novel and beneficial mutations are rare. They don’t repeat themselves very often, and when they arise, they will likely be wiped out unless there is fairly intense selection pressure (like we see in pesticide resistance or anti-biotic resistance or anti-malaria drug resistance with sickle cell anemia).

ungtss said: Flint: Seems like that's going to depend on the mutation at issue. Certain mutations (like antibiotic resistance) are going to be significantly higher than .01. The S of other mutations (like gradual changes to anatomy) are going to be much lower. Seems like you'd actually have to observe the effect of the mutation to determine the S. Yes?

Sal said: Darwin was responsible in large part for the false assumption that “every advantageous mutation that appears in the population is inevitably incorporated”.

Sal, we aren't in 1859 anymore.

ungtss, yes, the chance of a beneficial mutation spreading throughout the population (using the numbers posited here) is 2%. The chance of the mutation going extinct is 98%.

So how many times would the same mutation have to arise to ensure that it gets fixed in the population, again assuming the numbers we are using here?

1 mutation: 2% chance of fixation
2 mutations: 4% chance of fixation
3 mutations: 6% chance of fixation
4 mutations: 8% chance of fixation
5 mutations: 10% chance of fixation
6 mutations: 11% chance of fixation
.....
33 mutations: 49% chance of fixation
34 mutations: 50% chance of fixation
35 mutations: 51% chance of fixation
.....
207 mutations: 98% chance of fixation
208 mutations: 99% chance of fixation

So if just 1 animal in a population has the beneficial mutation, there is a 98% chance the mutation will not spread and a 2% chance that the mutation will spread. Many/most mutations likely start in just this manner, with a single mutation in a single individual.

Now imagine that a 2nd animal (at some other point in time) has the same mutation. In other words, I am not saying that two animals at the same time have the same mutation (which is certainly possible); I am saying that the first mutation died out and has now re-arisen in a different animal. This mutation has the same 2% chance as the original animal, but the overall chance that the mutation fixates (either from the first or the second individual) is 4%.

The numbers above speak for themselves. Each number assumes that only a single individual has the mutation at a given time. How many times would the mutation have to "independently arise" before it is likely to fixate in the population?

Once the same beneficial mutation appears 35 separate times, it is more likely than not that it will spread through the population.

Again, I think these numbers may underestimate how easy it is because more than one individual can have the same mutation.

Mutations are rare? That's not what one hears at Sandwalk.

No one with a triple digit IQ would read that passage and think that Darwin literally meant that 100% of advantageous mutations would be passed on. What utter tripe.

It is always amazing how creationists, and Sal in particular, can see one thing in a text book that seems to support their presupposition and completely miss the majority of the lesson which indeed shows that their conclusion is wrong.

Yeah, combine Pete Dunkelberg's comment with what I said to see that it's not very hard for a beneficial mutation to spread.

The mutation just has to arise several times (and get lucky one of those time). Mutations are more common than you would expect, so "arising several times" shouldn't be too difficult.

(like we see in pesticide resistance or anti-biotic resistance or anti-malaria drug resistance, or malaria resistance associated with sickle cell anemia).

Once the same beneficial mutation appears 35 separate times, it is more likely than not that it will spread through the population. Again, I think these numbers may underestimate how easy it is because more than one individual can have the same mutation.

If however the intial infusion is only one mutant, then one must look at the probablity of extinction, which is extremely high. But since novel mutations involving more than a few nucleotides rarely come in more than one individual at a time, then the risk of ruin is high. Unless… we are dealing with something like malaria and chloroquine resistance. We could of course factor in the multiple appearances of the same mutant over time. It appears chloroquine anti-malarial resistance had a few multiple appearances at different times and geographical locations, thus “ruin” of chloroquine resistance was prevented by multiple entry (the mutation was relatively trivial and thus appeared abundantly in numerous places…not to mention, if I recall correctly, we’re dealing with haploids not diploids, making the odds even more favorable)…. But Behe’s point in Edge of Evolution was that HIV and malaria were still slow considering the very large trials involved, and the mutations involved were relatively trivial

Mutations aren't rare. U (the genomic mutation rate) is likely greater than one for most species (where most species means organisms visible without magnification).

It should also be noted for this discussion that exactly same mutation occurs in a population of 1,000,000 every 10-100 generations. (base pair mutation rate of ~1^-11.) So, if there is only a single nucleotide mutation which can cause some beneficial mutation with s=.01; then it will likely be fixed in the population in some 100x50=5000 generations. Now, if, as seems ridiculously more likely, there are perhaps a couple dozen different ways to get the same phenotypic effect, that would be reduced substantially.

Chris Bell:

Once the same beneficial mutation appears 35 separate times, it is more likely than not that it will spread through the population.

Agreed, assuming s=.01. But that's still a particularly steep hurdle for mutations to jump before they "make it."

I would also think you would have many mutations (most?) for which the s is going to be well under that. Particularly in cases where s is 0 until a number of highly interdependent mutations come to work together (IC?).

I wonder if anybody has done research to determine the s-value of observed, real-world mutations. I wonder what the methodology would be for that.

ungtss said: The problem becomes even more severe in smaller, isolated populations (where genetic drift becomes more severe), and in the context of sexual reproduction (where each child receives only 50% of the collective genetic diversity of its parents). I don't think this is any meaningful "gain" for Darwin at all. Rather, it's a significant hurdle that mutations have to get over to get fixed. It may be surmountable, over significant periods of time, but it is a hurdle, nonetheless.

Larry boy:

It should also be noted for this discussion that exactly same mutation occurs in a population of 1,000,000 every 10-100 generations. (base pair mutation rate of ~1^-11.) So, if there is only a single nucleotide mutation which can cause some beneficial mutation with s=.01; then it will likely be fixed in the population in some 100x50=5000 generations. Now, if, as seems ridiculously more likely, there are perhaps a couple dozen different ways to get the same phenotypic effect, that would be reduced substantially.

I wonder how often a single nucleotide mutation has an s of .01. My guess is not very often. For the effect to be phenotypically significant and advantageous, you're going to need a number of SNMs to work in concert. That pushes your numbers back.

ungtss said: I wonder if anybody has done research to determine the s-value of observed, real-world mutations. I wonder what the methodology would be for that.

I was taking issue with Darwin’s statement: Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good. Charles Darwin chapter 4 Origin of Species

It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good;...

Yet many of these eggs or seeds would perhaps, if not destroyed, have yielded individuals better adapted to their conditions of life than any of these which happened to survive. So again a vast number of mature animals and plants, whether or not they be the best adapted to their conditions, must be annually destroyed by accidental causes, which would not be in the least degree mitigated by certain changes of structure or constitution which would in other ways be beneficial to the species. But let the destruction of the adults be ever so heavy, if the number which can exist in any district be not wholly kept down by such causes,—or again let the destruction of eggs or seeds be so great that only a hundredth or a thousandth part are developed,—yet of those which do survive, the best adapted individuals, supposing that there is any variability in favourable direction, will tend to propagate their kind in larger numbers than the less well adapted.

Several writers have misapprehended or objected to the term Natural Selection. Some have even imagined that natural selection induces variability, whereas it implies only the preservation of such variations as arise and are beneficial to the being under its conditions of life.

ungtss said: I wonder how often a single nucleotide mutation has an s of .01. My guess is not very often. For the effect to be phenotypically significant and advantageous, you're going to need a number of SNMs to work in concert. That pushes your numbers back.

Can't Sal just be used as something to point at and ridicule as an example of the concepts of disgusting failure and dishonesty? Why even bother turning over his rock to look at him, since NOBODY really cares?

You can’t really play both sides of the field my friend. As populations become smaller the chance of fixation becomes larger, so you are wrong. In a population of 1, a beneficial mutation, if it occurs, has a 100% probability of becoming fixed. The problem is that what really matters is RELATIVE rates of fixation. So, either your premise, that absolute probabilities of fixation ”[are] a hurdle” is correct but your statement ”The problem become even more severe” does not follow logically, or your premise is incorrect. Chose one.

Forgive me -- I'm not tracking with your thought.

Your "population of 1" example is flawed in two ways. First, it's silly to argue about the "chances" of a mutation fixing in a population of one, because the mutation is already fixed. Second, as Mr. Felsenstein explained, these calculations are for sexual reproduction -- so if you have a population of one, the chances of the mutation fixing are 0, because the individual will have no one to breed with, and the mutation will therefore die out with the individual.

As to the effect of population size on the chance of fixing, Mr. Felsenstein already explained to me that the effect is really negligible, at least when working with reasonably large numbers. Indeed, with a population of 1000, the chances of a mutation fixing still round to 2%.

But most importantly, I don't seen the contradiction in your mind between the hurdle of genetic drift and my (recently corrected) opinion that a reduced population had a significant effect on the probability of a mutation fixing.

ungtss said: I wonder if anybody has done research to determine the s-value of observed, real-world mutations. I wonder what the methodology would be for that.

ungtss said: I wonder how often a single nucleotide mutation has an s of .01. My guess is not very often.

ungtss said: But that's still a particularly steep hurdle for mutations to jump before they "make it."

I noticed in that UD post that Sal said he’d seen both ”21” and ”Expelled” the same day. Does he have like a job or something?

ungtss said: But most importantly, I don't seen the contradiction in your mind between the hurdle of genetic drift and my (recently corrected) opinion that a reduced population had a significant effect on the probability of a mutation fixing.

Your ”population of 1” example is flawed in two ways. First, it’s silly to argue about the ”chances” of a mutation fixing in a population of one, because the mutation is already fixed. Second, as Mr. Felsenstein explained, these calculations are for sexual reproduction – so if you have a population of one, the chances of the mutation fixing are 0, because the individual will have no one to breed with, and the mutation will therefore die out with the individual.

I guess I'll write and suggest that they cancel the upcoming Congress on Evolutionary Computation, since Sal says this stuff doesn't actually work.

Makes me wonder why all that stuff *does* work, though. Is some intelligent designer sneaking in and tweaking some bits during our computations (just like he does in biology)?

D'ya suppose we can catch him red handed?

Salvador T. Cordova said: Darwin was responsible in large part for the false assumption that “every advantageous mutation that appears in the population is inevitably incorporated”.

Charles Darwin said on page 145 of the first edition of Origin of Species With respect to the difference in the corolla of the central and exterior flowers of a head or umbel, I do not feel at all sure that C. C. Sprengel's idea that the ray-florets serve to attract insects, whose agency is highly advantageous in the fertilisation of plants of these two orders, is so far-fetched, as it may at first appear: and if it be advantageous, natural selection may have come into play. But in regard to the differences both in the internal and external structure of the seeds, which are not always correlated with any differences in the flowers, it seems impossible that they can be in any way advantageous to the plant: yet in the Umbelliferæ these differences are of such apparent importance-the seeds being in some cases, according to Tausch, orthospermous in the exterior flowers and cœlospermous in the central flowers,—that the elder De Candolle founded his main divisions of the order on analogous differences. Hence we see that modifications of structure, viewed by systematists as of high value, may be wholly due to unknown laws of correlated growth, and without being, as far as we can see, of the slightest service to the species.

Charles Darwin said on page 84 of the first edition of Origin of Species Can we wonder, then, that nature's productions should be far "truer" in character than man's productions; that they should be infinitely better adapted to the most complex conditions of life, and should plainly bear the stamp of far higher workmanship? It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life. We see nothing of these slow changes in progress, until the hand of time has marked the long lapse of ages, and then so imperfect is our view into long past geological ages, that we only see that the forms of life are now different from what they formerly were. Although natural selection can act only through and for the good of each being, yet characters and structures, which we are apt to consider as of very trifling importance, may thus be acted on.

scrutinising the whole constitution, structure, and habits of each creature, —- favouring the good and rejecting the bad

Some day a creationist will say, "whoops, my bad, I'm sorry."

Larry Boy:

ungtss said:

I wonder if anybody has done research to determine the s-value of observed, real-world mutations. I wonder what the methodology would be for that.

You know us scientist, we just assume we are right with out ever bothering to check with good old mother nature until someone who has done no research questions us.

Wait . …

Thats not right.

Oh, here we are:

http://scholar.google.com/scholar?q[…];btnG=Search

(Orr’s paper near the top is particularly cool, but it doesn’t answer your question.)

I'll ignore the unnecessary and arrogant snark, and thank you for the link.

I'd be curious to see if the cells that experienced beneficial mutations retained their survival benefit in a different medium, of if these "beneficial mutations" were medium-specific.

I'd also be curious to see exactly what those mutations DID to the cell that increased fitness.

Larry Boy:

I feel morally obligated not to be a total a$$ to people, and I try very hard not to be. I know some of my responses to you have been terse, but I would like you to consider the fact that you are presuming to have deep penetrating insight into a field you have not researched at all. Perhaps you can see how arrogant that is of you. Do you truly think you are that much smarter than a host of noble prize winners? I do not advocate arguments from authority to support positions, but perhaps you could be humble enough to read some of the thousands and thousands of meticulous investigations into evolution which have been written. Your flippant ”wondering” is insulting. If you really care, why don’t you find out?

My "flippant wondering" is the expressed curiosity of a non-scientist who is learning about biology and genetics in his free time the best way he can, and was genuinely articulating an honest question. I am not claiming to have "deep penetrating insight." I am "thinking critically." Not all of us have the luxury of being full-time, employed scientists. Neither should we feel obliged to accept "just-so" stories that define paradigms, a la Kuhn.

I don’t follow; why is that a ”particularly steep hurdle” given the fact that mutation rates are surprisingly high? Pick any specific non-lethal human mutation possessed by a single person, and I’d be willing to wager that somewhere in this world another human has the same mutation. Hell, there are thousands of people alive at this very moment who are allergic to light.

It's not a hurdle to a mutation surviving for a time (as in the case of non-lethal mutations) -- but it is a hurdle to a mutation FIXING in a population. Even beneficial mutations don't have an easy slide to taking over the population. The same beneficial .01 mutation will have to occur a good number of times, on average, before it fixes in a population. Thankfully that's the case with deleterious mutations -- otherwise we might all be allergic to light.

Someone needs to make a nice GUI. Get a couple control knobs that let you change selection pressure, mutation rate, etc. It would be highly informative.

That'd be cool.

Larry:

Look at the equations. Smaller populations have an increased chance of fixation of any mutation.

You said that the high probability of beneficial mutations being lost is a hurdle to evolution. You said this problem is worse in small populations. Beneficial mutations are more likely to be fixed in small populations. My example, while perhaps not perfect, will communicate this to you with a moments thought.

Are we clear?

"Whoops, my bad, I'm sorry."

Larry Boy said: Some day a creationist will say, "whoops, my bad, I'm sorry."

David Stanton said: No matter what he quote mines he will always find that science has moved on in the last thirty years anyway. How come these guys never seem to notice that? It's almost as if they as just trying to find things that someone might take the wrong way instead of really trying to learn anything about science.

ungtss said: It's not a hurdle to a mutation surviving for a time (as in the case of non-lethal mutations) -- but it is a hurdle to a mutation FIXING in a population. Even beneficial mutations don't have an easy slide to taking over the population. The same beneficial .01 mutation will have to occur a good number of times, on average, before it fixes in a population. Thankfully that's the case with deleterious mutations -- otherwise we might all be allergic to light.

another way of looking at this is to note that the 20% survival rate is very large compared to the chance of a 1%-advantage mutation arising. It's essentially an irrelevant filter: beneficial mutations arise with a reasonable enough frequency, as is already well established. The beneficial ones then take over the population in a way the neutral ones don't. Whether you take it as "beneficial mutations arise" or "beneficial mutations arise and fix" is irrelevent to the basic mathematical soundness of the ordinary, well-established population genetics Cordova has so much trouble understanding.

Nat Genet. 2007 Oct;39(10):1256-60. Epub 2007 Sep 9. Links Comment in: Nat Genet. 2007 Oct;39(10):1188-90. Diet and the evolution of human amylase gene copy number variation.Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287, USA. Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

Shebardigan:

Well said. I'd add that the sort of paradigm-dependent thinking you describe is not limited to religious fundamentalism. It crops up in all areas of thought, both secular and religious. The fundamental problem is working backward from dogmatic theoretical conclusion to facts selected and interpreted to justify it, instead of working forward from facts to tentative, theoretical theory to explain them.

You find backwards thinking everywhere -- religious fundamentalism and the Structure of Scientific Revolutions. You find it in economics (Keynesian vs. neoclassical) and you find it in psychology (freudian vs. behaviorism), etc.

Blaming fundamentalism is to blame the symptom, not the disease. The disease is backward thinking, whether in religion or elsewhere.

My own reading of the literature implies that mutation rates are usually not limiting for evolution. It is selective pressure. The NS of RM+NS.

We now know due to multiple sequencings of the human genome that any 2 individuals may differ by 15-20 million nucleotides. Much higher than thought.

IIRC, the number of base pair differences from one generation to the next due to mutation runs around 100 in humans. Most being neutral. Unfortunately, while I recently read this, I can't remember where right now.

Chris Bell:

I understood what you meant. My point was that a beneficial mutation, even if it has a very small chance of becoming fixed in a population individually can still easily become fixed if the mutation is common. (The word ”common” here can still point to a very low probability occurrence, say 1 in a million.) In other words, if the mutation occurs several independent times, one of those times will result in ”spread” even if chances are low for each individual occurrence.

That’s why I mentioned an allergy to light. It’s very unlikely to spread through the population because it’s clearly harmful. However, thousands of people have it. This is probably because it is an ”easy” mutation to get. A corresponding beneficial mutation would easily spread through the population–not because it’s chances of spreading are high individually, but because it gets to play the game so many times.

If I told you I would pay you $20 if you could draw the Ace of Spades from a deck in one try, you will likely not win the money if you only get one shot. If I let you play 30 times, however, I think you’ll have my money.

Agreed. But from my limited reading on the topic, it appears that beneficial mutations are the exception, rather than the rule. It seems difficult to believe, then, that beneficial mutations are the "easy" ones to get. Do you have any studies referring to "common" beneficial mutations?

ungtss said: It's not a hurdle to a mutation surviving for a time (as in the case of non-lethal mutations) -- but it is a hurdle to a mutation FIXING in a population. Even beneficial mutations don't have an easy slide to taking over the population. The same beneficial .01 mutation will have to occur a good number of times, on average, before it fixes in a population. Thankfully that's the case with deleterious mutations -- otherwise we might all be allergic to light.

Larry Boy:

Oh all right, first I suppose I should apologize again, I continued to be snarky.

Now responding: The relevance of the rate of fixation of mutations is entirely dependent on the right at which they arise. For instance, if a mutation is so miraculously improbable that it will only arise once, and we need that specific mutation to go to fixation for the evolutionary edifice to stand, then its chance of being lost is of concern. However, if all of the beneficial mutations we need to explain evolution arise at a fairly high rate, then we should not worry. Now, we have ample evidence that beneficial mutations arise at a high rate. (in fact, they are so common that it has occasionally been reported that they are MORE common than deleterious mutations.) So empirical evidence lead us to believe that the relatively low chance of fixation of any given beneficial mutation is more than compensated by a large supply of mutations.

I'm curious about these reports of beneficial mutations being more common than deleterious ones. Where would I find this research?

To confirm this for yourself you should verify a handful of facts. Fossils which lay geometrically beneath other fossils should rationally be older. Add this a priori expectation to the observation that fossils resemble modern organisms more and more as we get higher and higher (read closer to the surface and present) the geological strata. Also, well in excess of 99% of fossil organisms have no apparent modern counterparts, and almost all of the seem to show a distribution of traits which seems to be a mixture of some modern organisms. This leads to Ken Miller’s statement that he has almost seen fistfights break out over whether something is a reptile-like-mammal, or a mammal-like-reptile. Blah blah blah. The growth of coral atolls alone can push back the age of the earth to a couple million years. Blah blah blah. The heat at the center of the earth, mid oceanic ridges, the continental drift, cosmic background radiation, not to mention comparative genomics, blah blah blah.

Unfortunately, all these "evidences" turn out to be "paradigm-dependent" for their persuasive power, in my estimation. That is to say, they can be interpreted multiple ways. That is why I am more interested in the observable, falsifiable science of the matter.

By analogy: what is more convincing to prove that Abraham Lincoln was a historically real person, a picture, or a long philosophical argument about the historicity of various combinations of letter in the English language? Why not verify the truth of something in the most direct way possible?

I wouldn't find either to be particularly persuasive. Letter combinations are irrelevant to his existence, and there are as many old fictional pictures as old non-fictional pictures. In fact, more. Just look at the characters on the old Egyptian tombs. In that case, the most direct means of verification available is a variety of historical accounts, and physical evidence consistent with those accounts.

The way that genetic variation occurs is the only real way we have of trying to resolve the question (and yes, I still consider it a question) of its origin. All the other evidence I've seen is paradigm-dependent, and therefore not really evidence at all.

It's a real expert arguing the technical details of his field. RED ALERT! FACTUAL ARGUMENT ENCOUNTERED! ALL ID PROPONENTS, FULL RETREAT! ABANDON PREMISE! ACT POLITE AND PRETEND YOU WERE MISUNDERSTOOD!

Throw up some out-of-context quotes from Darwin as a smokescreen and run like hell! Mince words and pretend you were talking about something else! Whatever you do, don't acknowledge your argument was just half-cocked bullshit pulled from page one of a text you don't understand to dupe religious rubes!

Don't worry. In a few weeks, you can forget this entire discussion with Dr. Felsenstein ever happened and use these exact same debunked arguments in lectures and writings anyway. It's not like the creationist rubes will check your work. In fact, maybe you can find some way to quote mine this discussion so it looks like Felsenstein supports your claims!

Larry Boy said: By analogy: what is more convincing to prove that Abraham Lincoln was a historically real person, a picture, or a long philosophical argument about the historicity of various combinations of letter in the English language? Why not verify the truth of something in the most direct way possible?

One hole in the coin toss example is an expanding population. The math only works for a fixed population size. The probability of the selection criteria changing and selecting a previously neutral mutation or increasing the reliance on a beneficial mutation increases with the number of generations the mutation exists within the population. An expanding population allows proliferation of neutral and beneficial mutations through large subsets of the community. When things get tight, and the population becomes fixed, how many coin tosses would it take to eliminate a neutral mutation if it already existed in 100,000 of the 1,000,000 members?

MememicBottleneck:

Agreed. And also, when in nature do we observe a constant population? I think the answer is roughly "never."

ungtss: Rather, the most meaningful conclusion appears to be that genetic drift reduces the the odds of fixation of an advantaged trait by 98% in an s=.01 scenario.

ungtss: but the more relevant fact is that the s=.01 mutation has only a 2% chance, and the neutral and disadvantageous mutations have virtually no chance at all.

Flint: So where did the 1% number come from? Is it realistic?

ungtss said: MememicBottleneck: Agreed. And also, when in nature do we observe a constant population? I think the answer is roughly "never."

Josh:

Perhaps never, but then again, some populations are essentially constant (ie population size changes are so small that they can be neglected). Also, we could set things up to model things *as if* population sizes were constant. Biologists in the past century have gotten pretty good answering these types of questions.

Seems like in the real world, all the vagueries of climate, catastrophe, and predators keep most populations moving up and down. What are some organisms with essentially constant populations?

A good example of a number of neutral characteristics existing in a population just waiting for a bit of selective pressure. Most likely left over unexpressed genes from an ancestor. I'd bet my chicken's teeth on it.

"Still just a lizard"

You want to make a hardy strain of staph, you grow a lot of them, kill most of with a strong antibiotic, expand the population again and repeat. Granted, this is single cell, but the principle is the same.

Take any animal and move it to a new environment with no real preditor. It will expand until it fills the entire region and/or food source. Any differentation will become apparent at this point. The larger will exploit the smaller, those with larger/smaller/different appendages or more acute senses will adapt to different food sources, or find refuge in some different niche. The lizard I previously linked to is a very good example.

I don't feel the math in this case is very relevant to the real world. The "s" factor seems like just a bunch of s... . The value of that number, AFAICT was pulled out of a dark place when the author stood up.

ungtss said: Josh: Perhaps never, but then again, some populations are essentially constant (ie population size changes are so small that they can be neglected). Also, we could set things up to model things *as if* population sizes were constant. Biologists in the past century have gotten pretty good answering these types of questions. Seems like in the real world, all the vagueries of climate, catastrophe, and predators keep most populations moving up and down. What are some organisms with essentially constant populations?

ungtss said: But from my limited reading on the topic, it appears that beneficial mutations are the exception, rather than the rule. It seems difficult to believe, then, that beneficial mutations are the "easy" ones to get. Do you have any studies referring to "common" beneficial mutations?

As a little footnote, and as someone whose recently been learning about such things as theoretical population genetics, here's a book with (some) of the ideas here. It does a good job describing Kimura's basic ideas of neutral mutations and natural selection (that is, if you're actually interested in this stuff). It's a pretty good introduction to some ideas of evolution from a mathematical standpoint (which I think is on pretty solid foundations, actually).

ungtss wrote:

"Not all of us have the luxury of being full-time, employed scientists."

ungtss:
Any position that provides the remuneration to enable a person to have sufficient food, own a house, etc. could be viewed by the people in the world who have a job that does not enable them to buy these things could be viewed by them as a luxury.

Not all of us have the luxury of being full-time, employed _________s (insert any position that one has worked to achieve the qualifications for said position, and which job provides enough remuneration that one is enabled to own a house, etc.

If you are able to afford sufficient food and housing with the position that you have worked and trained for, then why are you implying that the job benefits of a scientist is luxurious compared to that of yours?

If a person has qualified for a job because he worked to achieve the knowledge and skills required of it, and retains that job because he continues fulfill those requirements, is that a luxury? If so, then why highlight the doing so of a scientist specifically as luxurious without mentioning many other fields in which people make the same amount of effort?

If not, then what about a scientist's job seems to be more of a luxury to you than other jobs? If you had wanted to make the effort to learn what previous scientific research had been on an area of interest to you, then to focus on an area in which little research had been done, and then created methods to try to find out new information, you could have done that. Doing that is not a luxury: it is hard work, and sometimes tedious, but always involves considerable intellectual effort at trying to understand the mechanisms in nature which are responsible for that particular manifestation of life.

You seem to want a shortcut to this knowledge provided to you by those who have done extensive introspection and rumination on the knowledge that they have worked hard to incorporate, so that you do not have to do the same yourself.

Unfortunately, a shortcut is unavailable at this time. If any scientist could provide this shortcut, s/he certainly would, so that there would be even more people available to work on and actually working on elucidating more of the myriad natural mechanisms.

If and when a future improvement of a microchip or its evolved analog is available for implantation into the brain of one who has not taken the time and done the work, then you've got your shortcut. (Not that I think that this is even close to possible within several generations, but, hey).

(Not any opinions or "world-views" inserted into anyone else's brain, just information that now requires years of effort by an individual to incorporate)

Summary: your use of the word "luxury" seems to imply that you view continuous thinking and working at the application of that thinking, and being paid to do so, as a luxury.

You’re still not following me. I’m not saying that beneficial mutations are common (in the sense of actually happening often) or that they outnumber harmful ones.

I am just saying that they can be incredibly rare AND unlikely to fix in the population BUT they are still likely to do so. A beneficial mutation can be a ”once-in-a-generation” occurrence, but that is nothing in geological time. Each new generation will see the mutation arise; each new generation is a new chance to try again. In 35 generations (using the numbers from earlier) it will be more likely than not that the mutation will be ”lucky” and begin to spread. That’s incredibly fast.

Let's identify the point of our disagreement. You appear to think we are arguing over whether genetic drift renders evolution impossible. I am not arguing that -- I would be stupid to, because it is not true. I am only stating that genetic drift is a hurdle standing in the way of evolution. I think we agree on that -- though we may disagree on the significance of the hurdle in the scope of "geologic time." I consider it to be of some significance, in concert with the improbability of beneficial mutations, combined with the fact that most mutations are s=0 or even negative until a number of independent mutations exist in concert so as to create an advantageous trait.

My question regarding "easy" mutations was in reference to your statement that "This is probably because [light allergies are] an ”easy” mutation to get." I know there are lots of "easy" harmful mutations that crop up all over the place. But where are the "easy" beneficial ones?

cyan:

ungtss wrote:

”Not all of us have the luxury of being full-time, employed scientists.”

ungtss: Any position that provides the remuneration to enable a person to have sufficient food, own a house, etc. could be viewed by the people in the world who have a job that does not enable them to buy these things could be viewed by them as a luxury.

Not all of us have the luxury of being full-time, employed _________s (insert any position that one has worked to achieve the qualifications for said position, and which job provides enough remuneration that one is enabled to own a house, etc.

If you are able to afford sufficient food and housing with the position that you have worked and trained for, then why are you implying that the job benefits of a scientist is luxurious compared to that of yours?

If I had been speaking of luxurious job benefits (like pay and benefits), perhaps your comment would be of some relevance. But I was not. If you read my comment in context, you would see that by "luxury of being a full time, employed scientist," I was referring to the fact that scientists have the "luxury" of learning about science while being paid for it, while I have to do it on my own time, after my regular job and between family obligations, without the resources afforded an employed scientist. Hence, I am at a handicap.

In the same way, I'm sure a scientist would be at a handicap with respect to the law or foreign affairs in a discussion with me. I get paid to study and practice the law and foreign affairs -- so I'm not surprised when scientists know less about it than I do.

The odd thing about many scientists I know is that they seem to think their knowledge of science places them in some sort of elite, whereby they are not required to even consider the opinions of the uninitiated. It would be like a lawyer saying, "Hey -- you don't have any right to an opinion about that law! I'm a lawyer and you're not -- you don't know anything -- so shut up and color." Nonsense, of course. You don't have to have a law degree to understand the law and have opinions on it -- although if you're going to, it helps to have lawyers around to bounce ideas off of and learn from.

That's why I'm here. To bounce ideas off those in the profession.

But I'm tired of this nonsense about how I need to just accept the opinions of those who have "ruminated" more than I have. Please. What arrogant, elitist garbage. Scientists need to put up or shut up, same as lawyers or anybody else.

ungtss has been treated with a lot of patience on this thread and even shown places where he can do further study in an area he is ignorant. He pays this by replying "But I’m tired of this nonsense about how I need to just accept the opinions of those who have ”ruminated” more than I have. Please. What arrogant, elitist garbage. Scientists need to put up or shut up, same as lawyers or anybody else."

As far as I can see people have responded politely to the ideas being being bounced off them and have only gotten frustrated when the same misunderstanding is being repeated. I think it is more a case of explain it to me in five minutes in a way I can understand or godditit.

whereby they are not required to even consider the opinions of the uninitiated.

turn it around on yourself.

do you often consider the opinions of those who know nothing about the law to be of merit?

or is it really that you consider any QUESTIONS the have about the law to be worth answering?

your questions were answered.

your opinion does NOT have merit.

sorry, that's just the way it is, and don't try to tell us you often rely on the opinions of pop-law neophytes in presenting your own ideas.

so, that said, you are either a hypocrite, or entirely disingenuous.

which is it?

Chris Bell: I am just saying that they can be incredibly rare AND unlikely to fix in the population BUT they are still likely to do so. A beneficial mutation can be a ”once-in-a-generation” occurrence, but that is nothing in geological time. Each new generation will see the mutation arise; each new generation is a new chance to try again. In 35 generations (using the numbers from earlier) it will be more likely than not that the mutation will be ”lucky” and begin to spread. That’s incredibly fast.

we would like to mention some important early work by Haldane (1949) relating the rate of evolution and gene substitution. Based on fossil records he studied the rate of change in quantitative measurements such as body size and tooth length and concluded that evolution is generally a very slow process.... (Haldane 1957, see Chapter 5), he came to the conclusion that in horotelic (standard rate) evolution, genes are substitutded once in every 300 generations (per genome) on the average page 16

Considering the amount of selective elimination that accompanies the process of gene substitution (substitutional load, see Chapter 5), the most natural interpretation is, we believe that the majority of molecular mutations that participate in evolution are almost neutral in natural selection. p 25

It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.

Historically, the word mutationism was used to refer to William Bateson’s saltationism or similar ideas, in which natural selection plays little role. Later Morgan (109) presented a more reasonable form of mutationism taking into account the role of natural selection. His view was abstract and based on a few lines of speculative arguments. However, recent molecular studies of phenotypic evolution support the basic ideas of his view and have extended it to a more comprehensive view presented in this article. If the new form of mutation theory described here is right, even in its crudest form, more emphasis should be given on the roles of mutation in the study of evolution. Masotoshi Nei

It is hard to comprehend now but, in the early years of this century when the phenomenon of mutation was first named, it was not regarded as a necessary part of Darwinian theory but an alternative theory of evolution! There was a school of geneticists called mutationists, which included such famous names as Hugo de Vries and William Bateson….The really creative force was mutation itself. Mendelian genetics was thought of, not as the central plank of Darwinism that it is today, but as antithetical to Darwinism. … we must beware of the patronizing tone of Bateson himself: ‘We go to Darwin for his incomparable collection of facts (but…] for us he speaks no more with philosophical authority. We read his scheme of Evolution as we would those of Lucretius or Lamark…the transformation of masses of populations by imperceptible steps guided by selection is, as most of us now see, so inapplicable to the fact that we can only marvel both at the want of penetration displayed by the advocates of such a proposition...” Richard Dawkins Blindwatchmaker p 308

Shebardigan,

That was a very interesting observation you made regarding "proof texts" and creationists. It has been filed.

Thank you.

-DU-

ungtss,

That you "need to just accept the opinions of those have 'ruminated' more that I have" is not what I advocate.

No scientist is required to consider the opinions of the "uninitiated". Nor is any lawyer required to do so.

Please correct me if I am wrong: a US legal law may be ruled unconstitutional by a person who is a state or US judge, ultimately by fewer than 12 people, thereby resulting in the previously legal law being not a law.

Comparatively, if possible: understanding of what mechanisms are responsible for the manifestations of nature
are examined by thousands of professional scientists world-wide for flaws, and the mechanistic explanations with the fewest flaws are tentatively accepted as provisional models.

In actuality, there is not a lot that is similar between the fields of law and science, other than as human endeavors. A country's legal laws are relative to a particular countries mores, and thusly are subject to the mores of a particular society at a particular time. The laws of one country may or may not influence those of another country.

In contrast, individual scientists may be influenced by their own country's laws and their own religion, but if their methods and therefore conclusions from those methods of the mechanisms of a certain natural manifestation are influenced by those things, other scientists worldwide consider those results even in the light of their own country and religious baggage, and the eventual result is a consensus as to what mechanisms are at work with less eye-blinds than that of a particular country or religion.

As to people not trained in either science (world-wide) or law (US) having opinions on any topics within these fields: opinions on every topic exist in everyone. Does that fact mean that most people in the US are equally served by being their own counsel in court, lacking a person who earned a law degree to represent them?

As far as I can see people have responded politely to the ideas being bounced off them [by ugtss] and have only gotten frustrated when the same misunderstanding is being repeated. I think it is more a case of explain it to me in five minutes in a way I can understand or godditit.

I’m afraid selectionism is going out of favor.

‘‘Natural selection can account for both slight and great differences among species, and adaptations are traits that have been shaped by natural selection.’’ Although this type of statement is quite common in the evolutionary literature,it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution.

May I suggest you spend more effort understanding and less effort quote mining these papers…

that's like asking Casey Luskin to honestly represent what happened in Kitzmiller.

to put it bluntly, it's not what they get "paid" for.

The locus classicus for contemporary critiques of adaptationism is an influential essay published three decades ago by Stephen Jay Gould and Richard Lewontin (1979). The ‘‘adaptationist programme’’ that was the target of their attack had, they claimed, committed a number of scientific sins during the forty years that it had dominated Anglo-American evolutionary biology. Central among these was its almost single-minded emphasis on selection-driven adaptation as the most (or only) important cause of phenotypic evolution.1 As they put it, ‘This program regards natural selection as so powerful and the constraints upon it so few that direct production of adaptation through its operation becomes the primary cause of nearly all organic form, function, and behavior’

"I'm afraid selectionism is going out of favor."

You've already been caught distorting Darwin out of context(and you haven't owned up to that). Now you're jumping the gun from Nei's review. Yet Nei himself writes in that 2007 paper, that "most evolutionists still believe in neo-Darwinism with respect to phenotypic evolution and are not interested in neutral evolution (19–22)."

The argument about mechanisms has been going on for decades. And possibly Nei's view will eventually prevail -- if so, it will be due to force of evidence (which he himself characterizes as being heretofore 'rather weak'). But it won't mean that species didn't evolve, it won't mean that they were Intelligently Designed, and it certainly won't give you even the slightest shred of credibility, you odious, dishonest *hack*.

It’s the age old discussion as to what drives evolution, mutation or selection.

Mike Elzinga said: There has been a similar exchange with PBH. After a few of us relented and offered some explanations, he came back with essentially the same kind of crap. It’s clear they work from some kind of script. I even detailed the technique just a few days ago and now we are seeing it in action.

Some day a creationist will say, ”whoops, my bad, I’m sorry.”

The argument about mechanisms has been going on for decades. And possibly Nei’s view will eventually prevail – if so, it will be due to force of evidence (which he himself characterizes as being heretofore ’rather weak’).

Basic difference between scientists and creationists: lesser vs greater egocentric anthropomorphism (yes, redundancy in that phrase).

First group: here is what is, in a particular instance. Given that, I'm going to try to mentally backtrack what processes resulted in this instance, and so try to predict accurately what those same processes may result in, in the future. Perhaps my efforts and joy in those efforts will result in a benefit to others if the predictions can be used to manipulate the environment in a way more friendly to humans. And then again, perhaps not.

Second group: here is what is. If I were to start with nothing 6000 years ago or more and then decide that my goal is what is currently seen by humans, what would I engineer to occur? (And what red herrings would I design into my plan, in addition to the goal, to create doubt as to my plan and consternation as to some of my inefficient, inelegant flaws within it?) Perhaps my efforts will not be admired by all, but those who find flaws with my thinking and efforts and so think that they could achieve the goal more efficiently: well, because they do not admire my engineering plans, they should endure physical pain not only while they are alive but after they are dead.

Chris Lawson said: As always, it is worth checking the original quotations. Cordova said:

I was taking issue with Darwin’s statement: Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good. Charles Darwin chapter 4 Origin of Species

What Charles Darwin really said in Chapter 4 was this:

It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good;...

Note the "metaphorically." Why did you leave that out of your quote, Mr Cordova?

It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good;...

It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good;...

Salvador T. Cordova said: I'm afraid selectionism is going out of favor.

If we do in fact find that single nucleotides are significant to function, then a 1/300 nucleotide substitution rate is incredibly slow if we are talking about the evolution of 70,000,000-90,000,000 nucleotides (like one might have to deal with in the supposed Chimp/Human divergence).

You should know that a lot (and I do mean a LOT) of scientists have been arguing for a long time against a purely adaptationist view of evolution.

Thomas S. Howard wrote: Oh, Sal's a peach, alright:

starved and stunted on the intellectual side, it is not surprising that Charles Darwin’s energies were directed towards athletic amusements and sport, to such an extent, that even his kind and sagacious father could be exasperated into telling him that “he cared for nothing but shooting, dogs, and rat-catching.”

Lies-and the thrills derived from lies-were for him [Darwin] indistinguishable from the delights of natural history or the joy of finding a long-sought specimen.

[Darwin] was able to put across his ideas not so much because of his scientific integrity, but because of his opportunism, his equivocation and his lack of historical sense. Though his admirers will not like to believe it, he accomplished his revolution by personal weakness and strategic talent more than by scientific virtue.

Sal, I imagine it has been suggested before that if you start with the evidence and derive conclusions, rather than exactly the reverse, you would avoid the more egregious errors you make with such thumping consistency.

You might also gain some insight into why those of your persuasion are not only in the minority, but share a common religious faith that *should* be completely irrelevant to the material you misrepresent. You might use some of your skill at statistical analysis to determine the likelihood that this religious correlation (essentially, 1.0) is statistically significant. And if it is, whether it suggests any possible bias. Someone as creative as you might even be able to construct a hypothesis explaining your findings, which can be tested. Ya think?

Sal really stepped into my world on this one, since I counted Blackjack for several years. I take him apart here: http://scienceavenger.blogspot.com/[…]ero-sum.html He doesn’t even understand the basics of the issues, making statements like: ”If he has a 1% statistical advantage, that means he has a 50.5% chance of winning and a 49.5% chance of losing.” Which reveals either that he is completely ignorant of the rules of blackjack, or he doesn’t understand the difference between probability of victory and expected winnings. I would also note that it is highly unlikely that Thorp’s system was the one used in the movie.

Allow me to recap both ungtss and Sal's (I use to have a pet salamander by that name. My wife says having a pet salamander is much like having a pet box of dirt.) argument. Because beneficial mutations are lost from the population at a high rate, natural selection is too slow.

The interesting part of this argument is that they provide no estimations of the time scales involved. Too slow? Why? How fast does it go? If your going to make an argument that it is too slow, don't you have to figure out how slow it is, and how fast it needs to be? Isn't this in fact the only part of the argument that matters? Yet it is a part of the argument supported only by statements like "My guess is." So w the efficacy of natural selection is indited by, as Dawkins' would say, an argument from personal incredulity. They simply find it difficult to believe that Natural selection could work if it loses 98% of beneficial mutations of small effect. Now, it turns out that we have been doing a lot of work on this, and gee, beneficial mutations are quite common if you set out to measure them:

Joseph and Hall (2004) "Spontaneous Mutations in Diploid Saccharomyces cerevisiae More Beneficial Than Expected" Genetics. 5.75% of fitness effecting mutations were beneficial. Is this rate too low?

Shaw et al. (2002) A COMPREHENSIVE MODEL OF MUTATIONS AFFECTING FITNESS AND INFERENCES FOR ARABIDOPSIS THALIANA. Evolution 56:453-463. Indicate that 50% of all mutations are beneficial. Is this rate too low for natural selection to operate effectively?

The distribution of fitness effects of mutations is an interesting question, and has yet to be resolved. No studies, however, indicate that beneficial mutations are vanishingly rare. Every look at nature seems to indicate that she will supply natural selection with ample positive variation to act upon, even if natural selection is wasteful with beneficial mutations. If anyone has empirical evidence that beneficial mutations are vanishingly rare I would like to see it.

So, as far as I can tell Sal started an argument which he couldn't take to its conclusion because he left off about half way through. He failed to recognize 2 things. 1) change over geological time REQUIRES fixation. The fact that neutral and deleterious mutations are unbelievably unlikely to fix shows that evolution proceeds at a snails pace in any direction other than adaptive ones. 2) The key issue is the rate of supply of mutations, which so far as I can tell, Sal hasn't given the slightest consideration.

Finally, we see ungtss dismiss the findings of more or less all modern science as "paradigm dependent." I am more than happy to debate facts, but if all the facts in the world can be dismissed with a wave of the hand and some magic words, I hardly see the point of discussion. So, to ungtss and now sal I will say: Who cares? It really doesn't change anything if natural selection cannot work, the world will still be 4.5 billion years old, cosmic background radiation will still only be explicable with the big bang theory. The endeavor or toss out modern science seems extremely futile to me.

I glanced at TFA, and it appears that Sal considers the rate of beneficial mutations, but fails to give any research to it at all. In fact, he assumes they are vanishingly rare w/o giving any evidence to this end. He then goes on to miss apply arguments about clonal interference to a sexual populations, butcher logic, and miss represent the scientific consensus. Altogether a good days work.

Finally, we see ungtss dismiss the findings of more or less all modern science as ”paradigm dependent.” I am more than happy to debate facts, but if all the facts in the world can be dismissed with a wave of the hand and some magic words, I hardly see the point of discussion. So, to ungtss and now sal I will say: Who cares? It really doesn’t change anything if natural selection cannot work, the world will still be 4.5 billion years old, cosmic background radiation will still only be explicable with the big bang theory. The endeavor or toss out modern science seems extremely futile to me.

You're guilty of the same backwards thinking as the fundamentalists are.

Your conclusion is "Creationists = antiscience."

In order to maintain that delusion, you have to ignore the salient facts right in front of your eyes:

1) I, a creationist, am trying to understand one particular aspect of science -- fitness distributions and genetic drift.

2) I, a creationist, haven't claimed anybody or anything was "magically" created, nor do I believe anything was.

3) I, a creationist, haven't suggested that any holy book is inerrant, nor do I believe one is.

4) I, a creationist, haven't suggested that the universe is only 6,000 years old, nor do I have any reason to believe it is.

But we wouldn't want to let the inconvenient facts get in the way of your conclusions, now would we? Naw. That would hurt. So let's ignore the evidence and revert back to empty rhetoric about the age of the earth and my being "anti-science," shall we? Yeah. That'll protect your fragile little delusion.

As to the "paradigm-dependent" evidence, I've learned by working with fundamentalists of all types that they are characteristically unwilling to acknowledge the paradigm-dependence of their "evidence." Arguments from "Bible verses," for instance, are paradigm dependent -- if you reject the authority of the Bible, they don't mean anything. So it is with "evidence" for universal common descent. Unless you assume universal common descent, the alleged "evidence" is not really evidence at all.

I'm not going to waste my time arguing that with you; I've learned a lot about population genetics, and that's about all I can hope for.

Thanks for the link regarding fitness distribution.

I think Darwin’s friend Huxley writing an obituary where he called Darwin’s intellect ”starved and stunted” really takes the cake…

Industry, intellectual interests, the capacity for taking pleasure in deductive reasoning, in observation, in experiment, no less than in the highest works of imagination; where these qualities are present any rational system of education should surely be able to make something of them. Unfortunately for Darwin, the Shrewsbury Grammar School, though good of its kind, was an institution of a type universally prevalent in this country half a century ago, and by no means extinct at the present day. The education given was "strictly classical," "especial attention" being "paid to verse-making," while all other subjects, except a little ancient geography and history, were ignored. Whether, as in some famous English schools at that date and much later, elementary arithmetic was also left out of sight does not appear; but the instruction in Euclid which gave Charles Darwin so much satisfaction was certainly supplied by a [258] private tutor. That a boy, even in his leisure hours, should permit himself to be interested in any but book-learning seems to have been regarded as little better than an outrage by the head master, who thought it his duty to administer a public rebuke to young Darwin for wasting his time on such a contemptible subject as chemistry. English composition and literature, modern languages, modern history, modern geography, appear to have been considered to be as despicable as chemistry. For seven long years Darwin got through his appointed tasks; construed without cribs, learned by rote whatever was demanded, and concocted his verses in approved schoolboy fashion. And the result, as it appeared to his mature judgment, was simply negative. "The school as a means of education to me was simply a blank." (I. p. 32.) On the other hand, the extraneous chemical exercises, which the head master treated so contumeliously, are gratefully spoken of as the "best part" of his education while at school. Such is the judgment of the scholar on the school; as might be expected, it has its counterpart in the judgment of the school on the scholar. The collective intelligence of the staff of Shrewsbury School could find nothing but dull mediocrity in Charles Darwin. The mind that found satisfaction in knowledge, but very little in mere learning; that could appreciate literature, but had no par[259]ticular aptitude for grammatical exercises; appeared to the "strictly classical" pedagogue to be no mind at all. As a matter of fact, Darwin's school education left him ignorant of almost all the things which it would have been well for him to know, and untrained in all the things it would have been useful for him to be able to do, in after life. Drawing, practice in English composition, and instruction in the elements of the physical sciences, would not only have been infinitely valuable to him in reference to his future career, but would have furnished the discipline suited to his faculties, whatever that career might be. And a knowledge of French and German especially the latter, would have removed from his path obstacles which he never fully overcame. Thus, starved and stunted on the intellectual side, it is not surprising that Charles Darwin's energies were directed towards athletic amusements and sport, to such an extent, that even his kind and sagacious father could be exasperated into telling him that "he cared for nothing but shooting, dogs, and rat-catching." (I. p. 32.) It would be unfair to expect even the wisest of fathers to have foreseen that the shooting and the rat-catching, as training in the ways of quick observation and in physical endurance, would prove more valuable than the construing and verse-making to his son, whose attempt, at a later period of his life, to persuade himself "that shooting was almost an [260] intellectual employment: it required so much skill to judge where to find most game, and to hunt the dogs well" (I. p. 43), was by no means so sophistical as he seems to have been ready to admit.

ungtss said: As to the "paradigm-dependent" evidence, I've learned by working with fundamentalists of all types that they are characteristically unwilling to acknowledge the paradigm-dependence of their "evidence." Arguments from "Bible verses," for instance, are paradigm dependent -- if you reject the authority of the Bible, they don't mean anything. So it is with "evidence" for universal common descent. Unless you assume universal common descent, the alleged "evidence" is not really evidence at all. I'm not going to waste my time arguing that with you; I've learned a lot about population genetics, and that's about all I can hope for. Thanks for the link regarding fitness distribution.

So, as far as I can tell Sal started an argument which he couldn’t take to its conclusion because he left off about half way through. He failed to recognize 2 things. 1) change over geological time REQUIRES fixation. The fact that neutral and deleterious mutations are unbelievably unlikely to fix shows that evolution proceeds at a snails pace in any direction other than adaptive ones. 2) The key issue is the rate of supply of mutations, which so far as I can tell, Sal hasn’t given the slightest consideration.

In actuality, there is not a lot that is similar between the fields of law and science, other than as human endeavors. A country’s legal laws are relative to a particular countries mores, and thusly are subject to the mores of a particular society at a particular time. The laws of one country may or may not influence those of another country.

In contrast, individual scientists may be influenced by their own country’s laws and their own religion, but if their methods and therefore conclusions from those methods of the mechanisms of a certain natural manifestation are influenced by those things, other scientists worldwide consider those results even in the light of their own country and religious baggage, and the eventual result is a consensus as to what mechanisms are at work with less eye-blinds than that of a particular country or religion.

That is an idealized view of science. I found Kuhn's account to fit the facts much better: scientists are influenced by social, political, and ideological, and self-interest factors same as anybody else. Many of these factors keep them within a "paradigm" of scientist, until someone, usually an outsider, brings about a paradigm shift. I'm not claiming to be that outsider. I'm just arguing that the decisions and opnions of scientists are influenced by non-scientific factors just the same as anyone else. And they also, like everybody else, often refuse to admit it -- they want to see themselves as somehow epistemologically privileged.

As to people not trained in either science (world-wide) or law (US) having opinions on any topics within these fields: opinions on every topic exist in everyone. Does that fact mean that most people in the US are equally served by being their own counsel in court, lacking a person who earned a law degree to represent them?

No -- but neither does it mean that when my little sister states an opinion about the law, I say, "Shut up! You're not trained as a scientist!" Instead, I try to separate what is falsifiable in her statement from what is her opinion; I acknowledge what is falsifiable and true; I correct what is falsifiable and false, based on my training; and I meet her opinions with, "Yes -- I can see your point of view. Other people see it this way."

I show a wonderful example of beneficial mutations spreading through a population on the HHMI Holiday Lecture Series with Sean Carrol. He uses the pocket mice of Southwestern Utah. Basically, he shows that despite the long odds of a beneficial mutation even appearing in the first place, when the mutation rate is factored in with the rate of reproduciton, the population size and a realistic amount of time, the odds of a beneficial mutation, in this case, color, are extremely likely. To strengthen the case, once predation begins to act on the natural variation within the environment, the odds go up even higher.

I quoted Darwin from the ICON-RIDS quotation and crossed checked the online version http://www.literature.org/authors/d[…]pter-04.html It appears whatever version was used, I, Salvador T. Cordova, was wrong…

Thomas S. Howard wrote: Oh, Sal’s a peach, alright:

*snip Sal's other examples of peachery: Thomas Huxley, Sir Gavin de Beer, CD Darlington*

So it is with ”evidence” for universal common descent. Unless you assume universal common descent, the alleged ”evidence” is not really evidence at all.

ungtss said: No -- but neither does it mean that when my little sister states an opinion about the law, I say, "Shut up! You're not trained as a scientist!" Instead, I try to separate what is falsifiable in her statement from what is her opinion; I acknowledge what is falsifiable and true; I correct what is falsifiable and false, based on my training; and I meet her opinions with, "Yes -- I can see your point of view. Other people see it this way."

Larry Boy:

*chuckle* I do think you have lost your temper. Well, I can’t blame you, I lost mine at points. But yes, your personally are being anti-science. I am complaining that you dismiss evidence as being paradigm dependent, when, in fact, it is not. But I could be wrong. How are comparative genomics and the fossil record paradigm dependent?

Comparative genomics:

Analysis of the similarities between genomes is only meaningful as evidence of common descent insofar as common descent is already assumed. Consider an alternative paradigm: design. If I were going to design apes and humans, I would doubtless use much of the same code to do it. After all, most of the essential functioning would be almost identical -- I'd be a fool to reinvent the wheel. Instead, I would start with an ape template, and modify the areas of it that were necessary to modify, in order to achieve my goal.

Compare it to computer programming. Computer programmers don't start from scratch with new programs. They borrow code from old programs that does the same thing. If you did a "comparative code" analysis on Word 95 and Word 97, you'd find most of it to be identical. You might analyze how different it is, apply a known rate of corruption of data on hard drives, and infer how long it would take for the code to spontaneously change from one state to the other. Or you might do a different analysis to determine how long it would take from both Word 95 and Word 97 to diverge from a common ancestor.

But none of that "evidence" is meaningful, because Word 95 and 97 were DESIGNED, and did NOT evolve.

That's what I mean by paradigm dependence.

As to the fossil record, that's much easier. Similarity only implies common descent if you assume common descent. Again, Word 95 and 97 share many similarities in form and function; but they were both DESIGNED.

I think the comparison between lawyers and scientist is somewhat misleading. Science, as a practice, is actually an epistemologically privileged way of knowing. Many people do not understand just how compelling scientific knowledge is. They assume that a little logic can prove scientific findings wrong. Scientist know that if they disagree with the facts, the facts usually win. Facts are very obstinate. That means, if evolution happened, then no matter how smart you are, you will never prove that it didn’t. I am convinced that evolution by natural selection actually happened, and therefor an honest investigation can only reveal the truth, that it happened. Lot’s of intelligent people are likewise convinced. Why don’t you look at the arguments that convinced them, like the fossil record? I would never have considered evidence of the distribution of fitness effects very compelling proof of evolution, it is merely icing on the cake.

Science is an epistemologically privileged way of knowing, but only within a very limited scope -- the scope of falsifiable, repeatable experiment -- like fitness effects distributions.

Once you're outside of the realm of falsifiable, repeatable experiment, and into the realm of interpretation of evidence, it is no longer epistemologically privileged. A forensics expert can determine that the marks on the bullet match the bore of my gun, but he cannot determine whether I shot the victim with it.

Interpretation of the fossil record is not falsifiable. It is the same as studying a crime scene -- you look at the leftover evidence, and develop a "theory" of what happened. But the evidence is necessarily subject to multiple interpretations. That's the nature of the beast.

You’ve already been caught distorting Darwin out of context(and you haven’t owned up to that). Now you’re jumping the gun from Nei’s review. Yet Nei himself writes in that 2007 paper, that ”most evolutionists still believe in Neo-Darwinism with respect to phenotypic evolution and are not interested in neutral evolution (19–22).”

the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer Michael Lynch The Origins of Genome Architecture, p 368

The disadvantageous mutation has probability of fixation 3.35818 x 10^-17374

Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good.

It is well known that when s, the selection coefficient against a deleterious mutation, is below ≈ 1/4Ne, where Ne is the effective population size, the expected frequency of this mutation is ≈ 0.5, if forward and backward mutation rates are similar. Thus, if the genome size, G, in nucleotides substantially exceeds the Ne of the whole species, there is a dangerous range of selection coefficients .... Mutations with s within this range are neutral enough to accumulate almost freely, but are still deleterious enough to make an impact at the level of the whole genome. In many vertebrates Ne ≈ 104, whileG ≈ 109, so that the dangerous range includes more than four orders of magnitude. If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10−6, an average individual carries ≈ 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies to high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations.

ungtss said: If I were going to design apes and humans, I would doubtless use much of the same code to do it. After all, most of the essential functioning would be almost identical -- I'd be a fool to reinvent the wheel. Instead, I would start with an ape template, and modify the areas of it that were necessary to modify, in order to achieve my goal.

But none of that "evidence" is meaningful, because Word 95 and 97 were DESIGNED, and did NOT evolve.

ungtss said: Compare it to computer programming. Computer programmers don't start from scratch with new programs. They borrow code from old programs that does the same thing. If you did a "comparative code" analysis on Word 95 and Word 97, you'd find most of it to be identical. You might analyze how different it is, apply a known rate of corruption of data on hard drives, and infer how long it would take for the code to spontaneously change from one state to the other. Or you might do a different analysis to determine how long it would take from both Word 95 and Word 97 to diverge from a common ancestor. But none of that "evidence" is meaningful, because Word 95 and 97 were DESIGNED, and did NOT evolve.

Larry Boy:

Good, now what about bad design? Phylogenise depend on neutral mutations, meaning changes that do not effect function. Why should an ape and a human have the same synonomous mutations? Synonomous mutations are in-theory totally invisable to natural selection, because they represent two alternative ways to make the exact same protein. Why should synonomous mutations reflect apparent phylogenies?

Well, your first paradigm-dependent assumption is that these "silent" mutations are in fact "silent." Recent research seems to indicate that much of the "junk" DNA is not "junk" at all. For example, this. It is entirely possible that much of that "synonymous" mutation is actually very important, just the way it is. And if it is important, it would be part of the shared design.

But none of that ”evidence” is meaningful, because Word 95 and 97 were DESIGNED, and did NOT evolve.

But it can be used as evidence that the same code was physically modified, and that word 95 and 97 were not created independently, but rather modified over time from one another, in other words they evolved by an intelligent agent. So, word 95 and 97 actually DO have common descent, whether you like it or not. chose another example please.

"Evolving by an intelligent agent" is exactly what I'm talking about -- intelligent intervention. They do not have common descent, because there was no breeding or random mutation involved. They share a common design. That's the ID hypothesis.

No, Sal is literally correct. Darwin did indeed say in that particular quote that selection is preserving ALL that are good. Not some, not most, ALL. But of course, it would be a perverse misreading to think Darwin was making such a case literally when it seems pretty obvious he was describing the general sweep of selection.

This has been a hilarious and entertaining discussion to read.

Sal has been repeatedly demolished by his intellectual betters, yet he continues to misrepresent evidence and to quote mine in order to save face. Of course to finally prove that he has been beaten once and for all, he starts quoting people who apparently criticized Darwin's character. Hilariously, even these quotes are proven to be quote-mined. Sal is the king of quote mining. It's deeply amusing to me to see him in action and to wonder how, with his dishonesty, he can sleep at night, much less call himself a Christian.

ungtss said: Analysis of the similarities between genomes is only meaningful as evidence of common descent insofar as common descent is already assumed. Consider an alternative paradigm: design. If I were going to design apes and humans, I would doubtless use much of the same code to do it. After all, most of the essential functioning would be almost identical -- I'd be a fool to reinvent the wheel. Instead, I would start with an ape template, and modify the areas of it that were necessary to modify, in order to achieve my goal.

ungtss said: Larry Boy: Well, your first paradigm-dependent assumption is that these "silent" mutations are in fact "silent." Recent research seems to indicate that much of the "junk" DNA is not "junk" at all. For example, this. It is entirely possible that much of that "synonymous" mutation is actually very important, just the way it is. And if it is important, it would be part of the shared design.

ungtss said: Larry Boy: Well, your first paradigm-dependent assumption is that these "silent" mutations are in fact "silent." Recent research seems to indicate that much of the "junk" DNA is not "junk" at all. For example, this. It is entirely possible that much of that "synonymous" mutation is actually very important, just the way it is. And if it is important, it would be part of the shared design.

Ric argued: Sal has been repeatedly demolished by his intellectual betters, yet he continues to misrepresent evidence and to quote mine in order to save face. Of course to finally prove that he has been beaten once and for all, he starts quoting people who apparently criticized Darwin’s character.

Sal: As long as you're graciously correcting your mistakes, and trying your best to act grown-up, now might be a good time for you to apologize for equating my arguments with the (alleged) surgical mutilation of innocent children.

If you’re following ID, then you can’t actually make this assumption, since ID ’theory’ is quite explicit about not being able to infer what the designer likes/dislikes to do, or its abilities. Otherwise we can infer from bad or stupid designs that the designer is only semi-competent and so on. For some reason the ID crowd generally don’t like this idea, most likely because if you are trying to peddle something to God-believing evolution deniers, telling them their God may not be up to much in the competence dept. is not a smart move.

I always found the idea that "suboptimal design" is evidence of the designer's imcompetence to be hilarious. As though the alleged designer, who did things we can't do, is incompetent because we can imagine how he/she/they could have done it better. This, even though we can't even assemble a single, functional cell from scratch.

Similarly, if you’re following ID or biblical creationism (any brand) then ask yourself this - if the complete opposite had been seen (ie a different heritable material, or completely different arrangement of the genome) to ’build’ eg chimps and humans, would this make the creator any less likely ie would you say ’there is no way this could have been the work of an intelligent designer’? I can’t see it would take any more effort for people on that side of the fence to explain it away with the designer than what is actually observed. People who accept common descent would struggle to explain such observations.

Similar design is what is observed. Similar design is consistent with both ID and common descent. It makes no sense to hypothesize some counterfactual finding inconsistent with common descent and say "Now THIS would disprove common descent." That's starting with theory, rather than fact. The facts we have are consistent with both. That's the rub.

Out of interest, how familiar are you with the evidence for common descent?

Yes. In my opinion, it is not really evidence for common descent, because it is consistent with both. That's what I'm discussing with Larry Boy.

ungtss said: "Evolving by an intelligent agent" is exactly what I'm talking about -- intelligent intervention. They do not have common descent, because there was no breeding or random mutation involved. They share a common design. That's the ID hypothesis.

Sal, how about you plug in p=0.495 (slight disadvantage) into your Excel code, watch how many players survive in the long term, compare that case with p=0.505 (slight advantage) and report the results to us? My bold prediction is virtually none will survive in the former case vs. 1.9% in the latter, which will go on to dominate the system. That's the essence of natural selection.

Cordova getting it wrong: If we do in fact find that single nucleotides are significant to function, then a 1/300 nucleotide substitution rate is incredibly slow if we are talking about the evolution of 70,000,000-90,000,000 nucleotides (like one might have to deal with in the supposed Chimp/Human divergence).

Science 21 December 2007: Vol. 318. no. 5858, pp. 1842 - 1843 DOI: 10.1126/science.318.5858.1842 BREAKTHROUGH OF THE YEAR: Human Genetic Variation Elizabeth Pennisi Equipped with faster, cheaper technologies for sequencing DNA and assessing variation in genomes on scales ranging from one to millions of bases, researchers are finding out how truly different we are from one another Deleted for length These and other studies, including a pilot study called ENCODE, completed this year, drove home how complex the genome is. There are an estimated 15 million places along our genomes where one base can differ from one person or population to the next. By mid-2007, more than 3 million such locations, known as single-nucleotide polymorphisms (SNPs), had been charted. Called the HapMap, this catalog has made the use of SNPs to track down genes involved in complex diseases--so-called genome-wide association studies--a reality. More than a dozen such studies were published this year.

Bobby wrote: I guess I’ll write and suggest that they cancel the upcoming Congress on Evolutionary Computation, since Sal says this stuff doesn’t actually work. Makes me wonder why all that stuff *does* work, though. Is some intelligent designer sneaking in and tweaking some bits during our computations (just like he does in biology)? D’ya suppose we can catch him red handed?

ungtss said: I always found the idea that "suboptimal design" is evidence of the designer's imcompetence to be hilarious. As though the alleged designer, who did things we can't do, is incompetent because we can imagine how he/she/they could have done it better. This, even though we can't even assemble a single, functional cell from scratch. It's not that funny, since we aren't the ones claiming the ability for ourselves to have designed all facets of life - the designer may be able to do more spectacular things than us, this still doesn't make it much cop though, since you'd expect something capable of designing the entirety of the world's biodiversity to be good enough to get the simple things right. Some of the designers designs are sub-standard by its own hypothetical level of ability, not ours. Similar design is what is observed. Similar design is consistent with both ID and common descent. It makes no sense to hypothesize some counterfactual finding inconsistent with common descent and say "Now THIS would disprove common descent." That's starting with theory, rather than fact. The facts we have are consistent with both. That's the rub. But this is the problem - anything is compatible with ID. This is why when making hypotheses, you need to propose potential falsifiers - which have been done for predictions based on common descent before the discoveries were made that we now take for granted (eg the discovery of DNA/the genetic code etc were based on predictions from common descent prior to its actual discovery - it could easily have turned out to not be the case). It's easy to look at the situation post hoc and say 'ah, but they are the same'. However, at one point a testable, falsifiable prediction had to be made. ID doesn't allow us to make any further predictions from what already know, since there's nothing in particular that we should expect or not expect to see. The best description I have seen of this is that it's like the rifleman that shoots a few holes in a door then draws bullseyes around where the bullets hit then declares himself able to hit the bullseye every time. Yes. In my opinion, it is not really evidence for common descent, because it is consistent with both. That's what I'm discussing with Larry Boy. I'm not sure I get your response here - I was wondering if you knew why common descent is accepted, and what the reasons for that are (eg ERVs, transposable elements etc)?

I would also add ungtss, since common designs are apparently evidence of a common designer, does this mean different designs are evidence of multiple designers (eg whales and fish tails and their up/down vs side/side motion)?

Dr. slpage: The 70-90,000,000 ’nucleotide differences’ between chimps and humans is the total nucleotide divergence including insertion and deletion events and large-scale chromosomal segmental duplications and the like, some of which encompass adding or subtracting hundreds of thousands or millions of nucleotides at a single pop. Each and every one of those nucleotides in fact does NOT have to be accounted for as Cordova implies.

Oh really Ric. I just provided a response to Dr. Felsenstein’s analysis of the fixation of deleterious mutations. I haven’t seen anyone try to refute my response. How about you try to refute my analysis of deleterious mutations? I invite the ”intellectual betters” to provide a solid refutation. Besides, even if I’m dumb, at least I can do high school algebra, which was more than what Darwin could do even after much effort and a tutor to spoon feed it to him.…so what does that say of Darwin?

no no no, synonous. We are not talking about junk DNA. Recent research has not show that synonymous mutations can have fitness effects, because they make exactly the same protein. Again we are not talking about junk DNA, do not confuse the issue. We are talking about changes that, in theory, can have no effect on an organisms fitness.

Now try responding to the objection.

My bad.

Well let me try to understand your argument fully. You seem to be saying that because different species share similar synonymous (and therefore selectively neutral) mutations, we should conclude they are of common descent.

Well, again, I'm not an expert in the field, but my initial impression from the little I just read is that:

1) You're assuming that the synonymous similarities are in fact mutations, rather than simply a similar identical initial code. There are many different ways to code a subroutine. The fact that the same person uses the same idiosyncratic method on two different programs is not surprising.

2) Some synonymous mutations can lead to suboptimal function (here). There is therefore the potential for selection pressure.

If I've misunderstood you, perhaps you can take a lesson from law school: if you want to be understood, you cannot assume knowledge on the part of your audience. You have to lay out your facts and arguments a step at a time, for clarity.

Salvador T. Cordova said: #2 and #3 are not natural selection mechanisms, and so if you answer #2 and #3 it underscores the point natural selection had little to do with their fixation. You can of course provide the percentages of each mechanism if you feel that will give a more accurate picture....

But they do have common descent. The differences do not represent different goals of a designing agent, but changing needs over time. In other words they were not independently designed for simultaneous release in the market, but 2000 was produced by changing the already existing 97. Clearly they are not the produces of natural selection, which requires blah blah blah, but they are 2000 is still a descendant of 97 because much of 2000 is a physical copy of 97. There was a hard drive some where where the command COPY was issued, and thus 2000 was born.

You are using the term "evolve" ambiguously. Evolution in the context of biology is different than evolution in the context of engineering and programming. The former involves no intelligent designer. The latter does. Ideas do not "evolve through random variation" in the context of engineering. They evolve through changing designs in the minds of the intelligent designers.

If you believe that an intelligent designer took the ape blueprint and modified it into a human blueprint, then you are an ID advocate, because you believe that men were intelligently designed.

ungtss, ... at first you said you were not a scientist if I recall correctly, just wondering about things. I was displeased with "Larry Boy" for his 'snarky' response to that. But later you have played the expert, indeed the uber expert, entitled to make the rules and make dogmatic declarations about what could be evidence for what, for instance. I am glad you are interested in these things. But in making these incorrect declarations as if you are in charge of science, you don't show as good a grasp of scientific practice as you think, but instead come off as a poseur. I am sorry if Larry Boy irritated you, but if you could stay in learning mode rather that teaching mode you could get more out of the discussion.

So your supposed ”take apart” is rooted in your propensity to uncharitably misread what I wrote.

Let's remind Sal that ID has NO explanations at all for the fact of evolution. And that evolution includes more than just selection, even Darwin accepted this.

Sal seems at best be barking up the wrong tree by confusing, in typical ID fashion, evolution with Darwinism.
Of course, their real objection to Darwin is that he destroyed the design inference in biology.

Similar design is consistent with both ID and common descent. ... That’s the rub.

It’s not that funny, since we aren’t the ones claiming the ability for ourselves to have designed all facets of life - the designer may be able to do more spectacular things than us, this still doesn’t make it much cop though, since you’d expect something capable of designing the entirety of the world’s biodiversity to be good enough to get the simple things right. Some of the designers designs are sub-standard by its own hypothetical level of ability, not ours.

You are assuming the designer is somehow omniscient/omnipotent, and concluding that if he were, he would have to design us in a particular way.

But what if the designer was just a person like you or me, with a much better grasp on biological engineering than we have?

If a scientist came along today that genetically engineered a reptile into an ape, but left a few rough edges (like suboptimal design -- for instance, incomplete sealing of the pereneum after the testes descend) would you say, "YOU MORON!?"

Only if you were starting with the assumption that that designer embodied the Platonic idea of God -- that is -- infinite and perfect in every way.

But this is the problem - anything is compatible with ID. This is why when making hypotheses, you need to propose potential falsifiers - which have been done for predictions based on common descent before the discoveries were made that we now take for granted (eg the discovery of DNA/the genetic code etc were based on predictions from common descent prior to its actual discovery - it could easily have turned out to not be the case). It’s easy to look at the situation post hoc and say ’ah, but they are the same’. However, at one point a testable, falsifiable prediction had to be made.

The point is that all the evidence is consistent we currently have is consistent with both. Evolution is just as malleable as ID is. That's why we have gradualism, punctuated equilibrium, and macromutation -- efforts to bend the theory to fit the facts.

ID doesn’t allow us to make any further predictions from what already know, since there’s nothing in particular that we should expect or not expect to see. The best description I have seen of this is that it’s like the rifleman that shoots a few holes in a door then draws bullseyes around where the bullets hit then declares himself able to hit the bullseye every time.

I agree. Evolutionists are guilty of the same sin.

I’m not sure I get your response here - I was wondering if you knew why common descent is accepted, and what the reasons for that are (eg ERVs, transposable elements etc)?

I'm saying the following:
1) My primary goal is to learn about those things, and allow my opinions to proceed from the evidence.
2) I find that all those "evidences" are paradigm dependent -- meaning that their persuasive power depends on assuming common descent in the first place. Much like 'scripture proofs.' They don't mean anything unless you assume the Bible is true. ERVs are subject to the same objection, in my opinion.

ungtss, … at first you said you were not a scientist if I recall correctly, just wondering about things. I was displeased with ”Larry Boy” for his ’snarky’ response to that. But later you have played the expert, indeed the uber expert, entitled to make the rules and make dogmatic declarations about what could be evidence for what, for instance. I am glad you are interested in these things. But in making these incorrect declarations as if you are in charge of science, you don’t show as good a grasp of scientific practice as you think, but instead come off as a poseur. I am sorry if Larry Boy irritated you, but if you could stay in learning mode rather that teaching mode you could get more out of the discussion

I apologize if I came off as an uber-expert.

However, I do have a fair amount of knowledge in the epistemology of evidence -- I work with evidence, proof, and alternative explanations for facts every day. I understand how the prosecution and defense have "theories" of the case -- different ways they spin the same facts to different conclusions. I understand how many people can only see the facts one way -- and are unable to grasp alternative theories of the case. We call those people "rigid."

I am more than willing to yield to scientists in their realm of expertise -- that is, the hard, experimental evidence. But I am just as qualified, if not more qualified, to speak on issues of epistemology, evidence, and paradigms. They are my bread and butter.

But I am just as qualified, if not more qualified, to speak on issues of epistemology, evidence, and paradigms.

Olegt, Sal, how about you plug in p=0.495 (slight disadvantage) into your Excel code, watch how many players survive in the long term, compare that case with p=0.505 (slight advantage) and report the results to us? My bold prediction is virtually none will survive in the former case vs. 1.9% in the latter, which will go on to dominate the system. That’s the essence of natural selection.

consider 10 individuals, each with 4,000,000,000 nucleotides in their genome. Each was gets 1 good mutation and 20,000 bad to neutral mutations in their germline. 5 successfully pass on their good genes, the other 5 are unsuccesful. It is clear which ever 5 you pick, that we’ll be killing half of what little good mutations occurred and ensuring lots and lots of what is bad are fixed into the population. The trend is clear -- an increasing proportion of what is bad. We call this Genetic Entropy.

Thank you for your suggestion. I accept your figures because I know you are adept at math, but my simulation was not comprehensive, only a pedagogical tool to illustrate some primitive concepts

ungtss said: You are assuming the designer is somehow omniscient/omnipotent, and concluding that if he were, he would have to design us in a particular way. But what if the designer was just a person like you or me, with a much better grasp on biological engineering than we have? If a scientist came along today that genetically engineered a reptile into an ape, but left a few rough edges (like suboptimal design -- for instance, incomplete sealing of the pereneum after the testes descend) would you say, "YOU MORON!?" I'm assuming that a designer capable of engineering very single living organism would have to have the capability to not make glaringly inefficient designs. On your 2nd point, firstly, if it was a person, I think we'd know about it by now as well as the fact most lifeforms existed before humans did, secondly you just push the problem back one more step to what designed that designer - eventually it always arrives back at some supernatural entity operating outside of our space and time. Conveniently, this also fits perfectly with the notion of the God the ID proponents follow. Who'd have thought? This is all beside the point, since if you are accurately following ID 'theory' as told to us by the likes of William Dembski you cannot make speculations on the designer, which is what you want to do with design being evidence for a common designer. The point is that all the evidence is consistent we currently have is consistent with both. Evolution is just as malleable as ID is. That's why we have gradualism, punctuated equilibrium, and macromutation -- efforts to bend the theory to fit the facts. I agree. Evolutionists are guilty of the same sin. Except 'evolutionists' are the ones making the predictions, doing the research and proposing the falsifiers prior to experiment. ID is just piggybacking on this, then drawing the bullseyes once the discoveries are made. It still doesn't escape the fact that there are plenty of observations now that can falsify part/all of the ToE. There is nothing that can falsify ID.