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Counting Dogs

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Recently, Mark Frank and I had a brief dialogue in the OP,“Didn’t everyone already know this about dogs?”
I’ve decided to clean it up a bit and re-post it because after my last question, I received no responses. At the outset, I would like to say that I place no blame about lack of responses on Mark Frank or anyone else in the last OP (as my post was rather quickly buried.)

Having said that, in this OP I would like somebody to address the question.

After one go around where I’d suggested that “success” should be counted as an increase in genetic information, Mark Frank corrected me, writing:

In biology success is breeding in the available environment. As a result there are about 400 million dogs in the world. There are about 200,000 wolves and they are extinct or endangered in many geographies. It is irrelevant how they would thrive without us. We are the dog’s environment and they have exploited that very effectively getting us to care for them by manipulating our parental instincts (and also providing some services).

and

I had in mind the biologist’s definition of the success of a species. This is purely and simply the species ability to reproduce in the world as it is . . . The genome is only relevant to the extent that it contributes to this. Any other definition of success leads to the odd result that a species could be highly “successful” but failing to survive.

In both cases, Mark Frank references “(I)n biology” and “the biologist’s” definition, so I will stipulate for the sake of this post that the convention in biology is that a species’ success is simply increase in number.

My response to Mark Frank:
According to your definition, evolutionary success has only to do with the genome (of the organism in question) so far as it informs the ability to reproduce “in the world as it is.” Is that about right?

In the case of domesticated dogs, I am informed that there is a loss of genetic information. And, you stated that dogs enjoy (numerical) success. Dogs, whether by breed or by number, are successful because of their responses to specific environmental nuances (e.g. we like dogs that chase sheep without eating them, so we feed them kibble and help them reproduce). This is easily measured by the increase in number of dogs (as compared to wolves, for example). One might even suggest that even if the narrative concerning sheep and kibble is just that, an unscientific narrative. Numbers don’t lie. Is that about right?

Onward:
Michael Behe in his controversial book, The Edge of Evolution, writes that such is generally the case for malaria-resistance — that the battle involves organisms “enjoying” loss of genomic info, to better get over on malaria so they can live to reproduce, (oh, and in turn, strains of plasmodium falciparum are doing likewise, sacrificing function, via loss of genetic information, to reproduce) –all of this only when necessary, or as Mark Frank suggested, “in the world as it is.”

Please, correct me if I am wrong, but don’t most (all?) scientists in the field agree with Behe’s assessment? That is, the “trench warfare” described by Behe is not actually that controversial, but an accepted finding.

It seems to me that an organism’s response to the environment (“in the world as it is”) involves dumping, if necessary, genomic information to succeed. Whether the selection is artificial or natural, the far, far, easier pathway for organisms is to lose genomic information. In fact, this is the dominant, almost universal, response according to scientific studies. . .

My question:

How could these more immediate pathways of losses of information possibly square with the evolutionary claim that natural selection (along with its numerical “success”) accounts for increased information in the genome, not only in a given organism, but for all organisms over the entire history of life on earth?

I thank you in advance for your considered responses.

Comments
Enkidu:
Given all the genetic evidence that is readily available today the whole ID claim that evolution can’t produce new information or new functions is just plain silly.
That is NOT the claim. For one ID is OK with intelligent design evolution producing new functions. ID is not anti-evolution.Joe
November 3, 2014
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Readers should be aware that not only have the formation of new alleles (= new information) been empirically observed the formation of novel genes has been studied in detail. There are many instances of relatively young novel genes and their regulatory control which have been identified. The genetic mechanisms for the formation of both new alleles and novel genes are well known.
Readers should also note that none of this disagrees with anything I have said nor does it in anyway contradict ID. Here is the last paragraph of the paper which is essentially the same as what I said.
Ultimately, differences observed between species are due to differences at the genome level. Genomic studies are revealing the extent of these differences—in gene number, in encoded functions, in expression—and are also revealing the mechanisms involved in the evolution of genomes. The analysis of particular newly evolved genes provides information in finer detail, which hopefully can be generalized and help to understand the evolution of new genes and new functions. Equally as important as the formation of new coding sequences is the formation of regulatory regions responsible for new patterns of expression as well as the processes leading to spread and maintenance of the novel gene in the population. Bacterial genome studies have made very clear that, at least in bacterial species, a great part of the genes are not shared by all individuals of a species [75]. Different strains of the same species share a core genome containing genes present in all strains; however there is also a pan-genome consisting of genes present in only a subset of strains. As more complete genome sequences become available, we will be able to determine if similar patterns are observed in eukaryotes.
jerry
November 3, 2014
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Jerry
My guess is that when this becomes common in about 15-25 years from now, there will be little evidence of novel gene formation leading to major evolutionary changes.
If you accept common descent (and I imagine that includes everyone in this particular discussion) then there is absolutely no question that novel alleles have been created many, many times in the past.  That is the only way to get from a bacterium to a mammal. The question is how. So what kind of evidence are we actually looking for? Suppose we observe mutations happening to form new alleles as we know must have happened. Is this evidence for design or not? I don’t think it is going to answer anything. With respect to Tim’s question.  I would argue that the path from wolf to dog is not a loss of function, but  it doesn’t matter. If there is no gain in function in this case then that is a problem for any explanation that is trying to account for new function in life.  It doesn’t distinguish between natural variation or guided variation. Mark Frank
November 3, 2014
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Tim you've had your question answered several times. The posts made about AS and evolutionary gain/loss of genetic information were on topic. You seem very unwilling to listen to anything except what you want to hear. I thought your goal was to learn. Yes, evolution can produce new information and new functions in the long run. I guess I was under the impression that it was all about little easy steps and that the easiest step with the “most fit” outcome is “always” “selected”. Here the easiest step is either loss of function or loss of genetic information. What gives? You are not considering the whole population. You are only looking at one narrow subgroup that was subjected to artificial selection pressures then extrapolating those AS results back onto the whole population. That is wrong.Enkidu
November 3, 2014
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Tim asks:
All I am asking is this: in the light of these two narratives, one where phenotype-change is sought and one where genotype is studied, does natural selection whether process or result, for crying out loud suggest that evolution is a producer of novel information in the long term? I guess I was under the impression that it was all about little easy steps and that the easiest step with the “most fit” outcome is “always” “selected”. Here the easiest step is either loss of function or loss of genetic information. What gives?
No evolutionary biologist is suggesting the selection element in evolution produces new genes. Variation occurs in the genome of a population by various routes, mutation, duplication recombination etc.. Selection is a "winnowing" or "sieving" process whereby alleles that are less fit-for-purpose become less prevalent or lost for good whereas better-for-purpose alleles predominate and may fix. It's the ratcheting RV+NS+RV+NS+RV+NS+etc that gives the evolutionary process its power to change.Alan Fox
November 3, 2014
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Enkidu writes:
the whole ID claim that evolution can’t produce new information
Which is patently false and what's worse, it has no bearing on what we are talking about. Please, stay on topic. Mark Frank defined success by looking at numbers. We dialogued albeit briefly about the environment and the "world as it is", since then he has been respectful and pushed the conversation forward whereas the majority of the rest have insinuated that "the question is just so basic", that "selection is not what I think it is" and this last one (cited), where the whole ID claim is that evolution cannot produce information. Perhaps my question was just too subtle. Can we stipulate, please, 1) that dog breeding is a form of artificial selection that includes pressures that would in theory constitute a severe and rapid change in environment (on an evolutionary scale). 2) that dog breeds have responded to this selection pressure remarkably fast (again, compared to evolutionary time scales). 3) that what we see is a general loss of function apart from the selective pressure 4) that the pathways "used" by dogs without exception also reflect a loss of integrated information 5) in sickle trait/malaria, the story is largely the same. As each organism serves in some respect as the environment for the other the easier pathway toward success (remember, measured by number) has been a sort of trench warfare. All I am asking is this: in the light of these two narratives, one where phenotype-change is sought and one where genotype is studied, does natural selection whether process or result, for crying out loud suggest that evolution is a producer of novel information in the long term? I guess I was under the impression that it was all about little easy steps and that the easiest step with the "most fit" outcome is "always" "selected". Here the easiest step is either loss of function or loss of genetic information. What gives?Tim
November 3, 2014
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E: Novel body plans, starting with the first, and the >no new info beyond" threshold is 500 - 1,000 bits for cosmic resources. If you dismiss this, all you have to do is show on observation the creation of 500 - 1,000+ bits of FSCO/I by blind -- non intelligently directed, non foresighted -- chance and/or mechanical necessity. As we have pointed out for years. KFkairosfocus
November 3, 2014
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jerry My guess is that when this becomes common in about 15-25 years from now, there will be little evidence of novel gene formation leading to major evolutionary changes. It will be beyond both resource availability and deep time, no matter how long the time is. Even the length of a trillion universes. Readers should be aware that not only have the formation of new alleles (= new information) been empirically observed the formation of novel genes has been studied in detail. There are many instances of relatively young novel genes and their regulatory control which have been identified. The genetic mechanisms for the formation of both new alleles and novel genes are well known.
Novel Genes from Formation to Function Ponce et al International Journal of Evolutionary Biology: Vol 2012, 821645, p.9 Abstract: The study of the evolution of novel genes generally focuses on the formation of new coding sequences. However, equally important in the evolution of novel functional genes are the formation of regulatory regions that allow the expression of the genes and the effects of the new genes in the organism as well. Herein, we discuss the current knowledge on the evolution of novel functional genes, and we examine in more detail the youngest genes discovered. We examine the existing data on a very recent and rapidly evolving cluster of duplicated genes, the Sdic gene cluster. This cluster of genes is an excellent model for the evolution of novel genes, as it is very recent and may still be in the process of evolving.
The paper has a good overview of the observed recent evolution of the Sdic gene cluster in Drosophila
The Sdic gene is a recently evolved chimeric gene in D. melanogaster, discovered and described by Nurminsky and colleagues in 1998 [47, 68]. This gene possesses several unique features that provide an exceptional opportunity for the study of new gene functions, the fate of gene duplications, and the evolution of male reproductive traits.
Given all the genetic evidence that is readily available today the whole ID claim that evolution can't produce new information or new functions is just plain silly.Enkidu
November 3, 2014
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So eliminating alleles reduces information in the population gene pool, and changing proportions of the alleles has no effect on the amount of information?
Yes, because we are talking about what alleles are available in the gene pool. So if there are less total alleles, there is less information. If it is just the frequency of alleles that has changed then the information has not changed since theoretically all are available for expression in a new environment. This is a simplification I understand because there are a lot of other things besides alleles. For example, control sequences both genetic and epigenetic and other processes. Then there is the unknown source of information for body plans. Also there is the measurement of this information.jerry
November 3, 2014
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The previous was for KF.jerry
November 3, 2014
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I am waiting outside a house with wi fi. So I have time to answer on my iPad. All I am doing is stating what is considered the likely process. Mark seems to think there is enough variation creation for major evolutionary advances. So does Allan MacNeill. You doubt it will even come close. I am squarely with you on this. But in order to have credibility, it is necessary to consider how it could have taken place. All this is easily testable in the future when genome sequencing gets dirt cheap and computer algorithms will search the various species for all their meaningful differences and similarities. Any progression from one allele to another will be documented and any formation of a brand new new allele will probably be documented as to where it began and where it ended up. What sequence in the genome was the place of its beginning and how it progressed over time. My guess is that when this becomes common in about 15-25 years from now, there will be little evidence of novel gene formation leading to major evolutionary changes. It will be beyond both resource availability and deep time, no matter how long the time is. Even the length of a trillion universes. It is coming.jerry
November 3, 2014
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CroMagnon was larger and more muscular than we are. Further, their brains were roughly 15 percent larger, judging by their skulls. Query: As humanity got smaller, weaker, and (quite literally) less brainy, did this involve a loss of genetic information over tens of thousands of years? If so, what processes developed Cro Magnon from presumed ape like ancestors in the first place?anthropic
November 3, 2014
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Jerry, just saw your remark, thought to support for a moment. Natural selection, so called is by actual definition, a culling process, not a creative one. The issue is what creates novel genetic info, and whether it can accumulate past certain complexity limits. When huffing and puffing is over, non-foresighted non-purposive engines of chance variation are indeed overwhelmingly likely to break down than build up, and the pop- mut rate- fixation time - functionality improvement requisites simply are not there to create novel major body plans. But sometimes, it is important to state the patent. KFkairosfocus
November 3, 2014
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AF: The breeder picks who mates with whom, relative to desired traits. He picks who gets castrated or spayed, and continues until he hits a wall or finds what he wants. Intelligently directed configuration through breeding, from toy dogs to Great Danes. That this is design within limits of genome and the odd mut or two, should be patent. BTW, Barbuda, two islands over, was a slave breeding plantation eventually willed to the slaves as a commune. To this day, people hereabouts talk about the particularly robust physique of the Barbuda breed. KFkairosfocus
November 3, 2014
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Jerry at 60- So eliminating alleles reduces information in the population gene pool, and changing proportions of the alleles has no effect on the amount of information?congregate
November 3, 2014
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There is an interesting discussion of the sickle cell mutation in David Epstein's "The Sport Gene."jerry
November 3, 2014
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Mark, We might get somewhere here. This was written quickly so lack of absolute preciseness may be the result.
So why do you write: Natural selection when it occurs is most often a reduction in the information in the gene pool or just a favoring of one allele over another. Frequently less alleles are then present as though natural selection were the process that created new function.
should be
Natural selection when it occurs is most often the result of a reduction in the number of alleles in the gene pool (less information) or just a favoring of one allele over another (same information). This new array of alleles may create a new function but unlikely for it to be anything major.
I should have also included comments about fixation of alleles too. My point is that the origin of variation is the prime issue and natural selection very secondary. And whether natural processes can can create the variation or not is the real issue of evolution. Have to run as I am away for rest of the afternoon here. I am not against clarifying anything I said to make it more precise.jerry
November 3, 2014
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Alan Fox:
Others have already tried explaining that resistance to malaria by the presence of (heterozygous) sickle cell gene increases fitness in populations who live in areas where malaria is rife.
Yes and it is still a loss of information.Joe
November 3, 2014
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Tim:
How could these more immediate pathways of losses of information possibly square with the evolutionary claim that natural selection (along with its numerical “success”) accounts for increased information in the genome, not only in a given organism, but for all organisms over the entire history of life on earth?
Evo answer: Because we didn't see the information build up. How can you have billions of years of evolution from prokaryotes to us without having an increase in biological information? :razz:Joe
November 3, 2014
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Bob O'H writes
One way is by doing experiments – you take the phenotype into the lab and measure fitness and/or do selection experiments. Another way is to look at replicate populations: if an allele has been fixed in small populations but repeatedly declines in frequency in larger populations, then it is probably less fit.
I fear you may be getting too technical for phoodoo. I think he is having the same problem with lab experiments as Gil Dodgen had with computer simulations.
It may also clear that an allele that has survived is less fit because there is a detrimental effect on the individual, e.g. sickle cell anaemia. Of course, that example also demonstrates the problem with such a conclusion.
This may be lost on him, too. Others have already tried explaining that resistance to malaria by the presence of (heterozygous) sickle cell gene increases fitness in populations who live in areas where malaria is rife. I keep saying "niche" but it's not penetrating.Alan Fox
November 3, 2014
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Alan Fox:
KF claims dog breeding is “intelligent design”.
It is, even if you were doing the selecting, Alan. It isn't the ONLY intelligent design mechanism but it is definitely an intelligent design mechanism. No wonder nothing gets through to Alan. He doesn't even grasp the basics.Joe
November 3, 2014
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#54 Jerry I agree with you that the issue is variation not natural selection. If variation can produce new stuff that helps the species thrive then that stuff will get selected. So why do you write:
Natural selection when it occurs is most often a reduction in the information in the gene pool or just a favoring of one allele over another. Frequently less alleles are then present
as though natural selection were the process that created new function. Natural selection can only operate on genetic material that already exist. What matters is can natural processes of variation: point mutation, insertions, deletions, tranpositions, duplications, recombination, endosymbiosis (although this one doesn't apply to dogs), epigenetics - provide sufficient variation to get new function or does something have to deliberately fiddle with it? I don't see what information has to do with it. You move from new alleles to new information without really explaining the difference if any. Why not just stick to new "alleles"?Mark Frank
November 3, 2014
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Tim, You are asking questions that are so basic that it is hard to know what you know and do not know. First, natural selection is an outcome and not a process. That will get some here upset since there has been long discussion on this in the past. The fact that you do not understand why natural selection is a diversion says you may not know very much about evolution. Natural selection does not create new variation but what does create variation is at the heart of the evolutionary discussion. That was my point. Let's just keep the discussion simple and limit discussion to sexual reproduction of which dogs certainly qualify. What happens is the individual organisms of a population (male and female dog) mate and produce offspring that are some what different from either of the parents in terms of their alleles. You have to think in terms of alleles even though more than alleles change with the offspring. At any locus in a genome where an allele exist, in another member of the population a similar but slightly different allele exists. It is possible to have several different alleles at the same locus and of course there are thousands of different loci. And to make it more complicated there are different ways of transcribing parts of an allele so that the protein coded will be different based on what section and in what order the allele is transcribed. (Someone like Bob O'H could describe this more precisely) Alleles are what are transcribed and translated into proteins. So to keep it simple, limit the discussion to alleles that already exist. The mixture in the offspring will be some combination of what is in the parents. It is possible to have a new allele in the offspring due to a couple things. One is recombination may split the parents allele and an entirely new allele could appear in the offspring. Another is that there is a mutation in one of the alleles passed on. This means that if you examine the DNA sequence in the genome of the offspring there will be a different sequence than is in either of the parents and also may not be present in any member of the population. The number of alleles in the gene pool has now increased. So it is possible to get new alleles or new information in the gene pool of the offspring. This new gene pool is then subject to the environment and some of these offspring will be more successful at producing the next generation of offspring. This will change the frequency of the alleles in the new generation and theoretically, evolution has taken place. One of the definitions of evolution is a change in the allele frequency over time. It is quite possible that some of the alleles will disappear and when this happens there will no possibility of it reappearing unless there is a fortuitous mutation. This new population gene pool could be reduced in the number of alleles in it. When this happens one may say that natural selection has occurred but it is really a trivial outcome. Natural selection when it occurs is most often a reduction in the information in the gene pool or just a favoring of one allele over another. Frequently less alleles are then present. That is what is meant by a loss of information. So natural selection results in less information not more and this is why it is a diversion in the evolution debate. Natural selection is not an outcome that produces new information but more often than not will produce less information. For real evolution to occur that is meaningful there has to be the creation of many new alleles not just at current coding sites but the creation of new coding sites in the genome. And these new alleles have to produce new proteins not seen before that eventually give the organism new capabilities. Bringing up the sickle cell mutation is really an example of diversion from the basic issue. Oh it is definitely a new allele and it definitely affects the survival of the organism but it is not an example of new information necessary to affect the evolution of organism from single cell organisms to man. That is why I pointed to the mutation of Junk DNA as a starting point. Duplicate genes are one such point but it is unlikely one would get a dramatically different protein function from what is current. It probably happens but there is no evidence that real evolution takes place this way. The way that I have seen described as having the best possibility is for massive changes in an old gene or the creation of a completely new one from various parts of the genome that have no function. The most vocal person on this is Jurgen Brosius from Muenster in Germany. But now we are getting into very complicated ideas of new allele formation. This has nothing to do with natural selection. Eventually the new proteins will cause the organisms to thrive or not. When that happens it is said that natural selection has happened. But that is really an aside from just how was the new information created.jerry
November 3, 2014
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And, if we play your numbers game a little further, EVERY new phenotype is by definition less fit, as they fall well below the mean.phoodoo
November 3, 2014
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And Bob we have a further problem, and I hope Tim will appreciate how this relates back to the topic. If the phenotypes of a dog are selected by man, is that a fit phenotype or an unfit phenotype by definition? Since there are so many phenotypes of dogs, is there only one phenotype (the one that sits at the mean of your statistical distribution) that is "fit" while the rest are luck, or whatever you want to call those that aren't within the mean? It seems to me, according to you, losses of function can be considered the most fit in a group, as long as they are the most numerous.phoodoo
November 3, 2014
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Bob, How can you take the phenotype into the lab and do experiments, when the conditions in the lab are totally different from the conditions in nature. And furthermore there is no "standard" condition . Every instance, and every location is a different challenge for survival. For instance, how do you know if the peacock feathers phenotype is derived from luck or fitness?phoodoo
November 3, 2014
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Jerry@13, I did not comment on your post because although it sort of was on topic, I lost interest when you wrote "natural selection is a diversion." Then, I went to bed. Unlike many faithful posters here, I simply do not have the time to make repeated comments over the course of a day. But, in the wildly optimistic hope that we can get back to the topic, I direct your attention to Mark Frank @ 18 who writes:
This looks like a simple question but the answer is complicated as it makes a number of assumptions which I dispute. 1) information is a word with many meanings. If you take the kind of formal definition that ID proponents like to use then it is something like –log2(the probability of a given outcome assuming a uniform probability distribution over all outcomes). It is not clear how you apply that to canine genomes – what outcomes? what probability distribution? 2) I don’t think that evolutionary scientists do claim that “natural selection … accounts for increased information in the genome”. They don’t typically think in terms of increase or decrease of information. 3) It is more likely that evolutionary scientists would talk in terms of function. . . . I know nothing about canine genetics but take the famous example of human genetics. Do the haemoglobin mutations which confers resistance to malaria if there is one copy but sickle cell disease if there are two count as loss of function?
Here, he brings up many interesting ideas. I will address them in reverse order. In terms of function, rather than look for increase or decrease in the malaria-resistance-(sickle trait)-sickle-cell example, one might even just call it a change in function so MF is correct, "doing the math" here might be tricky. But what is not as tricky is regarding the vast increase from the first hypothetical life forms, whether single cells, an unknown RNA, or weird analog to a virus, to the genomes of the flora and fauna we now are able to measure. My question, again, is how, if NS only selects for increased function "in the world as it is" AND the pathways in our (and almost all?) examples for increased function seem to be "easier" or more direct via a loss of information, how does this square with the now larger genomes? In his first point Mark Frank discusses, information and its definition. For now, can we stipulate that generally more integrated information in a given genome produces more function? Ok, folks, have at it.Tim
November 3, 2014
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I have a question, Let's just suppose that natural selection and all that jazz CAN do the same as artificial selection. My question is this, would NS produce the SAME variety of dogs we have today or would there be totally different breeds that we wouldn't recognise? My guess is it would the same, what do you guys think? Sorry if this is a bit off topic.logically_speaking
November 3, 2014
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You'd have to say, though, that keith s' outranks Alan's 'non mot'. Alan was at least a little hesitant, kind of aware that something wasn't quite kosher about his remark. I don't think Keith's Mum has been advising him very well these days. I've just been on the blower to Barry Fantoni in France, where he retired, and he agrees.Axel
November 3, 2014
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I see “expected success” has a specific meaning in ecology that I was unaware of. I was meaning that when results do not confirm a hypothesis we discard it and our expectations.
Sorry, for throwing that in! I meant in the statistical sense. Without getting into technical details, it's the mean of a distribution. So in this case there are several possible changes in allele frequency, an the average of the possible changes would be the expected frequency change.Bob O'H
November 3, 2014
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