Biology General interest Natural selection

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.

106 Replies to “Counting Dogs

  1. 1
    jerry says:

    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?

    Natural selection is a culling process which means that over time it will reduce the information in the gene pool. Some think this may be the cause for extinction of a lot of populations. As they loose information, the population does not have the resources to adapt to a change in environment.

    So natural selection doesn’t increase the information in the gene pool. This is why natural selection is really a diversion.

    Supposedly, the real evolutionary process goes like this. Somewhere off in the genome, mutations are going on to junk DNA which are not selected for but somehow over time will lead to a new allele. Then somehow, this allele gets expressed and has an effect on the organism’s reproductive rate and survival success.

    So when the allele poofs into expression, natural selection can now have an affect on this new allele. Has this ever happened? Probably, but not too often and there is no evidence that it ever produced anything meaningful.

    There are some times when there are small mutations to a coding region in a genome which has the effect of survival of the organism. Think fur or skin color in an animal. Again trivial but it could lead to slightly increased information in the gene pool.

    I hope this answers your question. Natural Selection is an important factor in genetics but is essentially meaningless in the overall evolution debate. But that won’t stop people from referring to the concept all the time even when they never had one good example of it ever working.

  2. 2
    Enkidu says:

    Can someone please show me where any scientist offered the variety in dogs as evidence of macroevolution? Macroevolution is defined as evolution at or above species level. Domestic dogs for all their variations are still one species.

    Dawkins in Greatest Show On Earth discusses dog variety as evidence of the creative power of evolution to produce new forms. Neil de Grasse Tyson also offers the variation in dogs through artificial selection as an example of evolutionary change. However, AFAIK neither ever said anything about dogs demonstrating macroevolution. Looks like this whole thing is a big strawnman cooked up by Creationists as yet another dishonest propaganda ploy.

    I’m willing to be corrected. Anyone?

  3. 3
    ppolish says:

    Dawkins & Tyson are not Scientists. They are “Science Communicators”. They really don’t count.

    Do out have an example of real scientists who have not said dogs are macro Enkidu?

  4. 4
    Enkidu says:

    ppolish

    Dawkins & Tyson are not Scientists. They are “Science Communicators”. They really don’t count.

    Do out have an example of real scientists who have not said dogs are macro Enkidu?

    The Creationists at the DI are the ones who specifically named Dawkins and Tyson as saying dogs are evidence for macroevolution. I’d like to see that claim supported.

    Can you do it or not?

  5. 5
    Tim says:

    Enkidu @2, 4

    With all due respect, although you are free to ask that some claims be supported, because such a claim was not made here, your comment is not relevant. Please stay on topic. The topic concerns selection, whether artificial or natural, and its apparent effect on decreasing information in the genome of organisms as they negotiate changing environments and implications, if any, for the standard narrative. Again, please stay on topic, thank you.

  6. 6
    Enkidu says:

    My apologies Tim.

    Can you please give me the scientific definition of “genetic information” as you are using it? Are you speaking of the information in one individual or in the whole gene pool? Do different alleles count as different information?

    Can you please give me the method of quantifying the “genetic information” in a genome to tell if increased, decreased, or stayed the same in any given generation?

    Thanks.

  7. 7
    mahuna says:

    Jerry@1
    “So natural selection doesn’t increase the information in the gene pool. This is why natural selection is really a diversion.

    Supposedly, the real evolutionary process goes like this. Somewhere off in the genome, mutations are going on to junk DNA which are not selected for but somehow over time will lead to a new allele. Then somehow, this allele gets expressed and has an effect on the organism’s reproductive rate and survival success.”

    OK, so which is it? Is “natural selection” a diversion? Or is “survival success” the key to evolution?

    And exactly how are these 2 terms different in practice?

    As far as I know, natural selection is measured exclusively by the rate of successful survival and reproduction. Or the net results of the reproductive rate and the survival rate.

    Humans have a very low reproductive rate compared with most other mammals, however, humans are the most successful large mammal that has ever existed, based on worldwide species population and range of environments in which we can breed successfully.

  8. 8
    Tim says:

    I got this from Biology Online:
    http://www.biology-online.org/.....nformation

    Genetic information: the heritable biological information coded in the nucleotide sequences of dna or rna (certain viruses), such as in the chromosomes or in plasmids.

    . . .which seems fine to me. I suppose that would be for both individuals as well as populations. Alleles are certainly different information. I am not sure that they would be counted as additional information.

    When you ask,

    Can you please give me the method of quantifying the “genetic information” in a genome to tell if increased, decreased, or stayed the same in any given generation?

    I confess, I cannot. I merely took it on the authority of Dr. Werner Gieffers, and so I direct you to this quote from the cited article,

    On the basis of research of many experts in the relevant fields, Lönnig proves that the enormous variability of our domestic dogs essentially originated by reductions and losses of functions of genes of the wolf.

    I don’t know how those guys do it, but apparently it is rather a common occurrence. Then, there’s this:

    Matti Leisola, professor emeritus at the Helsinki University of Technology, [calls] the book a “colossal and detailed study.”

    I hope this helps.

    Thank you for your comments.

  9. 9
    phoodoo says:

    Enkidu,

    Why would you like to see the claim that Dawkins and Tyson have used the examples of dogs as examples of macro-evolution supported? If someone went through the time and effort to show you this, what would it change in your thinking or your discussions? Their names aren’t even mentioned in this article, but so what?

    Are you admitting that Dogs are a terrible example for evolution, and that anyone who would suggest this is either stupid or mis-informed? Are you acknowledging that dogs pose a problem for evolutionary theory, in that all the changes we see in dogs appear to come at the expense of some functioning?

    Or are you, as usual, you looking for some reason, any reason at all, to say, well, it doesn’t change my belief, its not a problem for evolution, and more denials ad infinitum ?

    Many evolutionist websites for years have used the examples of dogs to suggest that we can see the great powers of evolution by just looking at dogs. If you don’t know this, once again, you are willfully uneducated on the subject. I could show you where Dawkins has said this, but what’s the point. You don’t want truth.

  10. 10
    Enkidu says:

    Thanks for the effort Tim. The reason I ask is that this latest anti-evolution salvo about dogs isn’t saying anything that biologists haven’t known for 50 years. In a homogenous stable population the overall genetic information in the gene pool will remain basically stable too. If anything it will tend to very slowly rise as events like gene duplication followed by point mutations will increase the genome size and complexity. What happens in artificial selection is just a small portion of the overall population is chosen and bred for specific traits. This in effect creates a population bottleneck in that group. The chosen traits will usually emerge (i.e. the different breeds of dogs) but the genetic variation in each breed is greatly reduced since it no longer mixes with the overall dog gene pool. The lack of genetic diversity in each specialized breed leads to the detrimental health effects seen in bottlenecks. This is what is being touted as a “loss of information”. In reality since the dog population (and the gene pool) has grown so large in the last 10,000 years the overall genetic information in the species has actually increased.

    Sadly Creationist organizations like the DI love to take real science and spin it like this until it’s unrecognizable. It’s basically propaganda aimed at laymen.

  11. 11
    Enkidu says:

    phoodoo

    “Why would you like to see the claim that Dawkins and Tyson have used the examples of dogs as examples of macro-evolution supported?

    Their names aren’t even mentioned in this article,”

    From the DI article The Dog Delusion

    “Dawkins, for example, concluded his New York Times review of Michael Behe’s book The Edge of Evolution with a shout out to canines”

    “Neil deGrasse Tyson takes up the cry for dog breeds as a proof of macroevolution.”

    You’d have marginally more credibility if you actually read the article being discussed.

    “Are you admitting that Dogs are a terrible example for evolution”

    Dogs are a great example of evolution – the change in alleles in a gene pool over time and the ability to alter morphologies. They just aren’t an example of macroevolution as the DI dishonestly attributes to science.

    Why do you suppose the DI has to lie about the actual science all the time?

  12. 12
    bornagain77 says:

    “If anything it will tend to very slowly rise as events like gene duplication followed by point mutations will increase the genome size and complexity.”

    Actually, you have no empirical evidence that gene duplication followed by point mutations will increase functional information.

    To claim that functional information can arise in such manner without an empirical demonstration is basically the propaganda you accuse creationists of. i.e. a ‘just so’ story!

    Michael Behe finds Loss of Function Mutations Challenge the Darwinian Model – Casey Luskin – August 24, 2013
    Excerpt: “Because of the many ways in which a gene can be altered to lose function, the LOF mutation would have a rate several orders of magnitude greater than that of the GOF mutation for the duplicated gene.”
    http://www.evolutionnews.org/2.....75591.html

    Evolution by Gene Duplication Falsified – December 2010
    Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.
    http://www.creationsafaris.com.....#20110103a

  13. 13
    phoodoo says:

    Enkidu,

    Are you claiming that Dawkins doesn’t make the argument that domesticated dogs are a good example of evolution?

    And you have read The Greatest Show on Earth right? And you are still want to have this argument?

    Oh wait, I see what you are saying, dogs are an example of “micro Evolution” not macro-evolution! Very interesting.

    Tell me if you don’t mind, what is the difference between micro and macro evolution? I had this crazy impression that evolutionists considered it the same thing, silly me.

  14. 14
    Tim says:

    Enkidu @10,
    Please stay on topic. I am not interested in biologists’ knowledge of the artificial nature of dog breeding, the lack of homogeneity across breeds, or that stable populations maintain stable pools. The information you cited on bottlenecks has nothing to do with the question. So, we are left with your comment concerning duplication and point mutations. If you would like to pursue and strengthen that thought, please feel free to do so, but comments such as your entire post @11 are off topic. If you would like to pursue those, please do so elsewhere.

    As for your assertion concerning gene duplication and point mutation, please comment on either the original article, or Behe’s review of studies on malaria, thank you.

    What possible difference could the bottleneck created by artificial selection make to strengthen your point that the amount of information has increased. If the bottleneck has reduced function, your only recourse seems to be the claim that information has increased because there are more dogs. Yikes. I hope that is not all you have to offer.

    What I want to know about is the immediacy of the pathways expedited in artificial selection as well as apparent “trench warfare” described by Behe in malaria studies. All I see is loss of function and genetic information. Solutions involving loss of information and/or function at the individual organism level are described to be many factors more common than similarly efficacious point mutations. If you are unwilling to speak to these topics, that is fine. I remain curious about what evolutionary explanation could possibly turn the tide in these two examples. At this time, I remain unconvinced of the evolutionary narrative.

  15. 15
    Tim says:

    Phoodoo @13,
    Thank you for your comment, however, I must insist that we stay on topic. The micro-macro debate can wait for another day. Actually, I believe some of Mark Frank’s comments concerning the “world as it is” may have addressed that topic in a left-handed way, dispensing with both prefixes at once. Anyway, I just want this to be a dialogue about pathways, genetic information, selection, information, trajectories, etc . . . thanks again.

  16. 16
    jerry says:

    Tim,

    I gave you the correct answer in my comment.

    All this discussion about dog breeding or dog breeds is nonsense. They are all one species and can inner breed. Each breed has less genetic information which is why they have distinct features. No one holds them up as an example of evolution. If they do then they are fools.

    This is interesting how people who don’t have a clue about this actually comment here.

  17. 17
    Bob O'H says:

    Certainly evolution can happen by loss of function, and I guess when evolution is quick (as in host-parasite/pathogen interactions) it can be a quicker way to evolve resistance (although loss of function can also cause a loss of fitness in the absence of the pathogen). But there are also gains of function, e.g. through duplication of a resistance gene, followed by its mutation.

    With reference to dogs, I haven’t read Lönnig’s book, so can you summarise his arguments for why loss of information is important in dog evolution?

  18. 18
    Mark Frank says:

    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?

    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.  It may just be that the main differences between a wolf and a dog involve less genes functioning. But this is a very hard call.  A gene can be functional in one environment and non-functional or detrimental in another. 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?

  19. 19
    phoodoo says:

    Tim,

    Well I think one aspect of this discussion that is highly relevant, is that while perhaps Mark Frank accepts the definition that any genome that survives and prospers is by definition successful (can we substitute the word fit?), that seems to be a huge point of contention with many of the evolutionists posters here, and likewise at TSZ.

    There are some that argue that sometimes the less fit, or less well adapted, survive despite their lack of being well adapted. So are we using a definition that says being well adapted means one survives, or are we using a different definition of being well adapted (or more fit, or more successful, or whatever term we want to use)?

    So does success equal to fitness, or are they two completely different concepts, and if so, what is the definition of fitness?

  20. 20
    Joe says:

    ID uses Crick’s definition of biological information. Natural selection has proven to be impotent.Not only that there isn’t any methodology that demonstrates all genetic changes are accidents, errors and/ or mistakes.

    And yes sickle-cell anemia is a definite loss of function which means it is a loss of specification and a loss of information.

    And that is important because macroevolution requires an increase in biological information. And that has never been observed to happen with differing accumulations genetic accidents, errors and/ or mistakes. No one can model such a thing.

  21. 21
    Joe says:

    Emkidu:

    Macroevolution is defined as evolution at or above species level.

    That is the meaningless definition. Try the following:

    “MACROEVOLUTION: ‘Major’ evolutionary change, usually thought of as large changes in body form or the evolution of one type of plant or animal from another type. The change from our primate ancestor to modern humans, or from early reptiles to birds, would be considered macroevolution.

    “MICROEVOLUTION: ‘Minor’ evolutionary change, such as the change in size or color of a species. One example is the evolution of different skin colors or hair types among human populations; another is the evolution of antibiotic resistance in bacteria.”

    – Coyne, Jerry A. Why Evolution Is True. 2009. Oxford University Press, Glossary, pp. 268-269.

  22. 22
    Me_Think says:

    Whether the selection is artificial or natural, the far, far, easier pathway for organisms is to lose genomic information.

    Wrong. Losing genomic information is going to reduce the size of the genotype network. A reduction in size will decrease the chance of finding a new phenotype within the network. Gene mutation ,whether neutral or beneficial helps in increasing the network size.
    When the network is large, in 1 dimension a new phenotype can found within 15 steps, as dimensions increases, the search space for new phenotype reduces drastically. You can calculate the search sphere volume for any dimension using the formula Pi^(d/2)/r(d/2+1) d = dimension, r=radius of search sphere

  23. 23
    Bob O'H says:

    So does success equal to fitness, or are they two completely different concepts, and if so, what is the definition of fitness?

    Fitness is (loosely) expected success, where ‘expected’ is used in a probabilistic sense.

    One way of thinking about it is that from a starting point, you run the tape of life for a generation a lot of times, and the fitness of an allele is the average in the change in its frequency.

    (I’m simplifying quite a bit, but I only want to make the distinction between observed success and fitness clear)

  24. 24
    Joe says:

    Biological fitness only pertains to natural selection. It does not pertain to artificial selection.

  25. 25
    phoodoo says:

    Bob,

    So then if a trait that is not expected to survive better survives better, what do we call that?

  26. 26
    Alan Fox says:

    Expectations aren’t the issue. Results are. Results of observation and experiment. Like dog breeding has been a long – running experiment in the power and limits of selection.

  27. 27
    Alan Fox says:

    Remember the niche, phoodoo. Remember the niche!

  28. 28
    jerry says:

    Tim,

    This is getting out of hand with irrelevant comments. I suggest you get a basic book in genetics. Genetics for Dummies is very good and will probably answer all your questions. It is one of three or four sources I have used to find quick answers to questions like yours.

  29. 29
    Alan Fox says:

    In dog breeding, the breeder is a major part of the niche. The distinction between artificial and natural selection is, well, artificial.

  30. 30
    bornagain77 says:

    me-think in regards to,,,

    “Whether the selection is artificial or natural, the far, far, easier pathway for organisms is to lose genomic information.”

    ,,, you state,,,

    “Wrong.”,,,

    ,,,But you provide no actual empirical evidence that it is wrong,, just a bunch of imaginary reasons why you think it is wrong.,,, I too can give a bunch of reasons why it is right, but, more importantly, I can references the empirical evidence to show I am right.

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

    Thus, me think, though you may not like the evidence, as far a science is concerned you are wrong. Feynman puts your current situation, in regards to the empirical evidence at hand, like this:

    The Scientific Method – Richard Feynman – video
    Quote: ‘If it disagrees with experiment, it’s wrong. In that simple statement is the key to science. It doesn’t make any difference how beautiful your guess is, it doesn’t matter how smart you are who made the guess, or what his name is… If it disagrees with experiment, it’s wrong. That’s all there is to it.”
    https://www.youtube.com/watch?v=OL6-x0modwY

  31. 31
    phoodoo says:

    Alan, How can you possibly be so thick? Did you not even read what Bob wrote? Here, read it slowly:

    “Fitness is (loosely) expected success”.

    Do I care that you don’t agree with his definition of fitness? Not at all! I am asking HIM to explain his definition. If you want to say Bob is wrong from the get go, fine, just say you think he is wrong!

  32. 32
    Joe says:

    LoL! @ Alan Fox- Natural selection could never produce the different breeds of dogs. The difference between artificial and natural selection is obvious to an educated person.

  33. 33
    kairosfocus says:

    F/N: The breeder makes intelligently directed purposeful choices [a form of intelligent design as has been commonly noted but ignored as usual], the natural environment does not look ahead to long term goals. KF

  34. 34
    Bob O'H says:

    So then if a trait that is not expected to survive better survives better, what do we call that?

    Pure dumb luck. It can happen if either it is neutral, or slightly deleterious. The latter happens in small populations, where genetic drift dominates over selection, or when a deleterious trait is linked to an advantageous trait. Deleterious traits in dogs are a result of a bit of both: a breed is bred from a small number of ancestors, and there is strong selection for a limited number of traits.

  35. 35
    Enkidu says:

    Tim

    Enkidu @10,
    Please stay on topic. I am not interested in biologists’ knowledge of the artificial nature of dog breeding, the lack of homogeneity across breeds, or that stable populations maintain stable pools. The information you cited on bottlenecks has nothing to do with the question.

    ????

    My post at 10 was om topic. It addressed the claimed loss of information in dog breeds that you asked about. The amount of information in the dog species is spread across the entire gene pool. If through AS you create artificial bottlenecks you reduce the genetic diversity or total information in that breed but you don’t reduce the diversity or information content of the entire gene pool. The whole argument from the DI is just a big red herring.

  36. 36

    Alan Fox said:

    In dog breeding, the breeder is a major part of the niche. The distinction between artificial and natural selection is, well, artificial.

    This ranks right up there with keith’s “one cannot be absolutely certain about anything” comment for sheer self-refuting absurdity.

  37. 37
    Alan Fox says:

    Would WJM like to put flesh on the bones of his bare assertion? What is different between “natural” and “artificial” selection? Thought not. 🙂

  38. 38
    Alan Fox says:

    KF claims dog breeding is “intelligent design”. So that’s how God created humans. He bred us like we bred dogs!

  39. 39
    Enkidu says:

    Alan Fox

    In dog breeding, the breeder is a major part of the niche. The distinction between artificial and natural selection is, well, artificial.

    Yes. The breeder in AS is part of the dogs’ environment and produces a major part of the selection pressure on the small group being bred. The genes in the dogs don’t know or care what is the source of the selection pressure, or if it’s “natural” or “artificial”. They are affected by it the same in either case.

  40. 40
    phoodoo says:

    Bob O H,

    But therein lies the problem (besides that Alan Fox disagrees with you). How do you differentiate between something surviving because of sheer dumb luck, and something surviving because it is more fit? If luck wins more than greater fitness, does the characteristic that was luckier change into the characteristic that was fitter?

  41. 41
    jerry says:

    Tim,

    If you truly want to learn something, I suggest you start a new thread and limit the comments to your simple question. You are witnessing how comments descends into meaningless chaos as one person tries to tell the other person they do not know what they are saying on minutiae and often irrelevant.

    One person on the thread is Bob O’H who I believe is a geneticist and then there is Joe who has been commenting here for years. These two should be able to answer all your questions as one is pro ID and the other is not. There is nothing deep or mysterious about your basic question.

  42. 42
    jerry says:

    There is nothing deep or mysterious about your basic question.

    I should add that it has nothing to do with ID and is in no way controversial.

  43. 43
    Bob O'H says:

    How do you differentiate between something surviving because of sheer dumb luck, and something surviving because it is more fit?

    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.

    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.

  44. 44
    Alan Fox says:

    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.

  45. 45
    congregate says:

    Tim-
    In an environment that is near equilibrium, where organisms have evolved to fill most of the available niches, there is no benefit to additional information. So most changes that increase fitness will reduce information.
    On the other hand, after a mass extinction event, when there are many open niches, additional information that becomes fixed in various populations of a particular species may help those populations fill different niches. In that case increases in information would be beneficial, and would be kept by natural selection.

  46. 46
    Axel says:

    ‘This ranks right up there with keith’s “one cannot be absolutely certain about anything” comment for sheer self-refuting absurdity.’

    But for me, it did, at least, have the merit of raising my spirits, by eliciting a response from you, WJM, highlighting the anomalously vapid character of such observations on what is, after all, quite an academic kind of board.

  47. 47
    Bob O'H says:

    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.

  48. 48
    Axel says:

    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.

  49. 49
    logically_speaking says:

    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.

  50. 50
    Tim says:

    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.

  51. 51
    phoodoo says:

    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?

  52. 52
    phoodoo says:

    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.

  53. 53
    phoodoo says:

    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.

  54. 54
    jerry says:

    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.

  55. 55
    Mark Frank says:

    #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”?

  56. 56
    Joe says:

    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.

  57. 57
    Alan Fox says:

    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.

  58. 58
    Joe says:

    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? 😛

  59. 59
    Joe says:

    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.

  60. 60
    jerry says:

    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.

  61. 61
    jerry says:

    There is an interesting discussion of the sickle cell mutation in David Epstein’s “The Sport Gene.”

  62. 62
    congregate says:

    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?

  63. 63
    kairosfocus says:

    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. KF

  64. 64
    kairosfocus says:

    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. KF

  65. 65
    anthropic says:

    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?

  66. 66
    jerry says:

    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.

  67. 67
    jerry says:

    The previous was for KF.

  68. 68
    jerry says:


    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.

  69. 69
    Enkidu says:

    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.

  70. 70
    kairosfocus says:

    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. KF

  71. 71
    Tim says:

    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?

  72. 72
    Alan Fox says:

    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.

  73. 73
    Enkidu says:

    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.

  74. 74
    Mark Frank says:

    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.

  75. 75
    jerry says:

    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.

  76. 76
    Joe says:

    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.

  77. 77
    Alan Fox says:

    This paper indicate how genetic changes in domestic dogs are apparently linked to how they interact with humans.

    Loss of information? Hard to see it that way.

  78. 78
    Joe says:

    Alan Fox:

    It’s the ratcheting RV+NS+RV+NS+RV+NS+etc that gives the evolutionary process its power to change.

    Power to change allele frequency. Drift does that too. You need much more than changing allele frequency to explain the diversity of life.

  79. 79
    Joe says:

    Mark FRank:

    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.

    You cannot assume the very thing that you are trying to test.

    I would argue that the path from wolf to dog is not a loss of function, but it doesn’t matter.

    Wolf vs dog, wolf wins. For dogs that’s a loss 🙂

  80. 80
    jerry says:

    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.

    Within these changes to genomes environmental and reproductive pressures work to change allele frequencies. The result is called natural selection.

  81. 81
    jerry says:

    Tim,

    Delete my comment 75. My iPad is not behaving very well. It is a duplicate.

    When you delete it, delete this request.

  82. 82
    Bob O'H says:

    phoodoo @ 51 –

    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.

    This is a bit extreme! Yes, there are differences between the lab and the field, but there are also similarities. If someone looks at fitness in the lab and wants to use that to make predictions about the field then they have to make the argument. There are a few lines of argument possible, e.g. that the trait is the sort that would not be strongly affected by the environment, or the experiment could be done under different conditions, which represent variation that is likely to be important for selection. Also, predictions from lab-based experiments could be compared to field data.

    phoodoo @ 52 –

    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?

    If the phenotypes are selected by man, then they are fitter. The fact that we have ended up with dogs with different phenotypes just means that we have applied different selection pressures on different dogs. So the fitness of one particular trait will depend on the breed it finds itself in.

    phoodoo @ 53 –

    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.

    I’m sorry, I don’t understand this point. If the expected change in frequency is positive, then a phenotype is more fit by definition, regardless of whether the initial frequency is low or high. I suspect you are confusing the change in frequency with the frequency itself.

  83. 83
    william spearshake says:

    Joe@20: “And that is important because macroevolution requires an increase in biological information.”

    Says who? Getting back to dogs. If the only evidence we had of modern dog breeds were fossils, they would be classified as several different species. If you saw numerous fossils of old bull mastiffs, and numerous fossils of old chihuahuas, without knowing the history, you would assume different species, maybe different genera (OK, any sane person would).

    And these huge differences were the result of reduced information (variation) at least at the breed level. But for any individual dog, the amount of information has not changed much, if any.

  84. 84
    Bob O'H says:

    Tim @ 71 –

    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?

    First, I’d rather not get into the endless debates about what is information, so I’ll assume you are equating loss if information with loss of function. My apologies if this causes problems, but it seems to be a reasonable interpretation of what you’re arguing.

    Anyway, selection will act on the variation that’s available. But it is mutation (and recombination and other processes, but let’s stick to mutation to simplify things) that initially creates the variation. Thus selection will act on new functions if mutation create function, and conversely if mutation destroy function then selection will act on this reduced function. As it’s usually easier to destroy or create, mutation will tend to act to reduce function. And often this reduced function reduces fitness, so these tend to get weeded out.

    But sometimes removing a function can increase fitness. This would be particularly common in a new environment, for example when a human goes “oh, that looks nice”, or when a pathogen has evolved a new virulence.

    So if there is a gain of function, selection can act on it. And there are are examples of the evolution of a gain in function.

  85. 85
    rhampton7 says:

    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?

    Dog breeds aren’t the only example of micro-evolution within Canidae. That’s why I asked, in the previous thread, if the African Wild Dog (Lycaon pictus) was examined. Like dogs, wolves, coytoes, dingos, and some jackals, it too has 78 chromosomes. As you can see in the link, there are quite a number of species and sub-species.

    Do we know for certain that all of these animals exhibit only loss of information? Because if some of them show a gain in information/function, then the point about dog breeds falls apart.

  86. 86
    Enkidu says:

    rhampton7

    Do we know for certain that all of these animals exhibit only loss of information? Because if some of them show a gain in information/function, then the point about dog breeds falls apart.

    We’ll never know because there is no clear objective quantitative determination of either information of function. There’s certainly a loss of overall genetic diversity in each specialized breed but is that the same thing?

    Take the dachshund as an example. It was bred specifically to have short legs so it could go into animal burrows and flush out prey. Seems to me that’s a gain of function. But an IDer will then argue it lost the ability to jump high fences so it lost function. There’s no objective way to tell what’s a gain and what’s a loss.

    It’s pretty common practice in the ID world to never define their terms so there’s always plenty of wiggle room.

  87. 87
    jerry says:

    I believe we can safely assume that a typical dog breed results from a loss of alleles. So we can say there is loss of information since there are fewer alleles in this particular population when breeding is controlled by humans. This does not mean that there is necessarily a loss of function in the breed. In fact there may a tremendous gain in some function. After all what was the purpose of the breeding? (Since nearly all dogs can inner breed, gene flow could restore all lost alleles and the other characteristics that come with the restored array of alleles.)

    So loss of information does not necessarily equate with no gain of function. There may be some function lost but there may be a tremendous increase in some other function. Now this is artificial selection but it does not mean that in the wild there may also be circumstances where some function is gained while at the same time there is a corresponding loss of alleles. That is what natural selection mostly is. And this can lead to extinction when the environment changes as other functions which are necessary for survival in the new environment have been lost and are no longer possible due to a reduced gene population.

    This is all micro evolution and while interesting is not what the real evolution debate is about. For that we need massive creation of new functional variation. The question is what can do this.

  88. 88
    jerry says:

    It’s pretty common practice in the ID world to never define their terms so there’s always plenty of wiggle room.

    This is nonsense. I have been reading about ID for over 15 years and never saw this. It is one thing to take someone who might not know too much and use their ignorance as an example then to make such an absurd statement about ID in general.

    It is much more common for anti ID people to switch meaning or divert from the real issue with irrelevant examples. I cannot tell the number of times when someone who is pro naturalistic evolution to use microbe changes as examples of evolution. Then there are the moths and finches, which also are not examples of meaningful change.

    There are no examples of a new species being created through random variation. Lots of speculation. But no good evidence.

  89. 89
    Enkidu says:

    jerry

    This is all micro evolution and while interesting is not what the real evolution debate is about. For that we need massive creation of new functional variation. The question is what can do this.

    Science has known the answer for over 60 years. It’s the genetic variations that occur in a population every generation with the resulting phenotypes filtered by environmental selection pressures and which are passed on to new generations as heritable traits. Also called evolution. It’s been empirically observed in the lab and in the field, confirmed with computer modeling and the functioning of genetic algorithms. You can learn about it any any decent college or university.

    This is nonsense. I have been reading about ID for over 15 years and never saw this.

    The waffling over “information” and “function” in this dog breeding is a perfect example. CSI is another – a vaguely defined term with no objective way to identify or quantify it.

    There are no examples of a new species being created through random variation. Lots of speculation. But no good evidence.

    Except the scientific literature has tons of such evidence. Observed incipient speciation in ring species like the Ensatina family of salamanders is a good example.

    Incipient species formation in salamanders of the Ensatina?complex

    Abstract: The Ensatina eschscholtzii complex of plethodontid salamanders, a well-known “ring species,” is thought to illustrate stages in the speciation process. Early research, based on morphology and coloration, has been extended by the incorporation of studies of protein variation and mitochondrial DNA sequences. The new data show that the complex includes a number of geographically and genetically distinct components that are at or near the species level. The complex is old and apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. While the hypothesis that speciation is retarded by gene flow around the ring is not supported by molecular data, the general biogeographical hypothesis is supported. There is evidence of a north to south range expansion along two axes, with secondary contact and completion of the ring in southern California. Current research targets regions once thought to show primary intergradation, but which molecular markers reveal to be zones of secondary contact. Here emphasis is on the subspecies E. e. xanthoptica, which is involved in four distinct secondary contacts in central California. There is evidence of renewed genetic interactions upon recontact, with greater genetic differentiation within xanthoptica than between it and some of the interacting populations. The complex presents a full array of intermediate conditions between well-marked species and geographically variable populations. Geographically differentiated segments represent a diversity of depths of time of isolation and admixture, reflecting the complicated geomorphological history of California. Ensatina illustrates the continuing difficulty in making taxonomic assignments in complexes studied during species formation

    The evidence is there for anyone to examine but first you have to want to learn.

  90. 90
    phoodoo says:

    Bob,

    I am trying to stick with your definition of fitness, but that is a little hard to do, because it seems to keep changing. You said you determine what is the fittest phenotype by seeing where that phenotype falls with the mean of distribution in a population, right? So that is how you “expect” the phenotype to be the fittest, by virtue of the fact that it is most prevalent. Is this not what you said or meant?

    So new phenotypes would never be the most prevalent initially, so initially you must describe it as being less fit, correct? Because the definition of fitness is not some vague feelings about good, or worthy, its decided by a popularity contest within the population, correct?

    Also, what do you mean about a dog breed? Are you using a new definition of the concept of a dog breed to mean a new species? How do you classify them as different populations rather than simply different phenotypes? If there are less American Huskies than dachshunds, are the dachshunds a more fit animal? Or is what you are really saying is we get to first decide our population size and criteria, and only then do we decide what is the most common phenotype within a population which we just selected for measuring?

  91. 91
    Tim says:

    Well, this has certainly been entertaining, a little instructive and somewhat disappointing.

    Entertaining
    Watching the back and forth erupt.
    Instructive
    A few good ideas from Jerry, Mark Frank, even Enkidu (once! ha!) and others.
    Disappointing
    The participants, so overly invested that they cannot but trot out the stories closest to themselves without going to the trouble to examine the OP closely.

    We were lectured on . . .
    types of selection,
    micro/macro,
    then nature of selection,
    the definition of selection,
    alleles,
    bottlenecks,
    information,
    function,
    and more.

    Read the OP folks, it is about number, simply put, more dogs than wolves. That’s it. “In the world as it is,” ideas such as environment, niche, and all of the above are distractions.

    Here is what we must look at: There are way more dogs than wolves. Because we are working under evolutionary stipulation, we must assume that modern wolves and the domesticated dog both have a common ancestor. The evolutionary narrative (correct me if I am wrong, but I am not) is that the domesticated dogs are descended from wolves.

    Among domesticated dogs, the referenced article describes a review of 800 studies. Now, I have not read the research in toto, but it is not in dispute that dogs have lost function in relation to wolves. The question that I left open was “do dogs exhibit increased (integrated) information” in comparison to wolves.

    But for malaria-sickle-trait-sickle-cell the story is clearer. Again, numbers don’t lie. People who carry sickle-trait, “enjoy” loss of function, but this loss of function makes it difficult for good ol’ plasmodium falciparum to hook onto cells. That, in turn, seems to increase “function” i.e. people with sickle trait get less malaria — and that is rather functional, indeed.

    The bottom line is this: by ignoring all other narratives and looking only at numbers, we should find that in malaria the constant battle should produce novel information/function (whichever suits you) more immediately than loss of function. Or, perhaps in dogs we should see more novel information/function (whichever suits you) in comparison to wolves. We don’t. The easier pathway in both cases is the same: loss. That is what is at issue.

    I am the first to admit it. These are only two (very different) examples, and I appreciate Mark Frank’s discussion of information/function and even Enkidu and the ring-species of salamanders. Not too surprisingly, I find these only as convincing as an evidence of species formation to the extent that I have assumed evolution’s ability to create information — extrèmement limité.

  92. 92
    phoodoo says:

    Well Tim, in my opinion the topic is necessary large because its a big question. We don’t really know what is meant by information of function. Is a particular feature or trait good or bad for an organism. In evolutionary theory, there is really no way of deciding what is good or bad, other than deciding what is frequent, and what is less frequent. The more frequent (by their definition) the more good (or fit) that trait is. I don’t know if there is a definition of function, other than to say that something is either useful or not useful. I don’t think you can call a sickle cell a function, rather it is the functioning (the operation of a known system) that has gone haywire (that is clearly a loss of function in my eyes) . It just so happens that they system that has stopped working as it (was designed to-haha) usually does, means that it is harder to get one type of disease which affects that system.

    Its probably harder to get lice if you have no hair, and harder to get gall stones if you were born without a gall bladder. Are those losses or gains in functionality.

    From my point of view (an ID perspective), its pretty clear that systems are made to work a certain way. Our nervous system, or respiratory system, or circulatory system, they have many parts, all which seem to have a very specific and useful purpose. And so if one part is broken, that to me is a loss of function. But from the Evolutionists standpoint, I don’t think they can make that same claim. There is no such thing as a system. What looks like systems is really just an illusion, all are just separate parts that luckily happen to survive, if it turns out that it is lucky enough that one part can be useful with another part for further reproduction, that it sticks around. There is no such thing as a “broken” system, if nothing is really a system. When evolutionist talk of a system, really that is just convenient language, actually they are all just meaningless parts which just so happen to not destroy each other. So how can an evolutionist talk about gain of function or loss of function in any meaningful way, other than to say if something stays alive, it has function.

    That has been the whole point of my posts. If you take the evolutionists believe, there is no such thing as good or bad, fit or not fit (as ordinary people use the word fit) there is only more of one kind or less of one kind. That has been my point to Bob. If evolutionists start calling one trait good or bad, because it seems useful to a normal person, that is cheating-because to them, the best traits are simply the most frequent ones.

    I think they try to equivocate on this point, but it is still inescapable. They hedge this a bit by saying the ones they “expect” to be most numerous (how do they expect it, by counting the frequency of course). There is no system, there is no good or bad trait, there is no function, and non-function, there are only frequent ones, and less frequent ones. The frequent ones are best.

    How can you call something a system or a function, when it was never designed to be a system, it is just a random collection of parts, that happen to work sometimes.

  93. 93
    Enkidu says:

    Tim

    Well, this has certainly been entertaining, a little instructive and somewhat disappointing.

    Glad you were entertained but it’s a pity you’re so averse to being educated. You were so busy looking for anything to support your preconceived ideas on “information loss” you missed a lot of interesting science. Oh well. Like I noted above, the evidence is there for anyone to examine but first you have to want to learn.

  94. 94
    Bob O'H says:

    You said you determine what is the fittest phenotype by seeing where that phenotype falls with the mean of distribution in a population, right?

    Err, no. Nothing of the sort, I’m afraid. Fitness is the (expected) change in frequency.

    Also, what do you mean about a dog breed

    I believe it’s a standard term. But I think you need to understand the concept of fitness first, before discussing how it varies between breeds.

  95. 95
    Bob O'H says:

    The bottom line is this: by ignoring all other narratives and looking only at numbers, we should find that in malaria the constant battle should produce novel information/function (whichever suits you) more immediately than loss of function.

    Why?

  96. 96
    Me_Think says:

    Tim,

    The easier pathway in both cases is the same: loss. That is what is at issue.

    As I said earlier, the answer is no.
    Losing genomic information is going to reduce the size of the genotype network. A reduction in size will decrease the chance of finding a new phenotype within the network. Gene mutation ,whether neutral or beneficial helps in increasing the network size.
    When the network is large, in 1 dimension a new phenotype can found within 15 steps, as dimensions increases, the search space for new phenotype reduces drastically. You can calculate the search sphere volume for any dimension using the formula Pi^(d/2)/r(d/2+1) d = dimension, r=radius of search sphere

  97. 97
    phoodoo says:

    Bob,

    You answer is very puzzling. Don’t blame me if you answer as to what the meaning of fitness is is not clear. HOW do you determine the EXPECTED change in the frequency of phenotypes? I quote from YOU:

    “One way is by doing experiments – you take the phenotype into the lab and measure fitness and/or do selection experiments.

    If fitness means the EXPECTED change in frequency, and not the ACTUAL change in frequency, then that is not what you are measuring in the lab, you are measuring the actual change in frequency. You are being very imprecise with your language.

    Bob, it was you, and no one else, that said, “If someone looks at fitness in the lab and wants to use that to make predictions…”

    Now let’s be very clear here Bob, so you don’t accuse me of not understanding. When you say that fitness is the expected change in frequency and not the actual change, and then you say that someone can look at the expected (not the actual right??) HOW do you look at the expected change in a lab? You don’t. How do I know? Because you yourself said so:

    “One way of thinking about it is that from a starting point, you run the tape of life for a generation a lot of times, and the fitness of an allele is the average in the change in its frequency.”

    You also said: “Without getting into technical details, it’s the mean of a distribution.”

    So you are measuring which alleles were successful most in the past, and the ones which were successful in the past, fall into the mean of the distribution.

    Correct me if YOU were wrong Bob.

  98. 98
    phoodoo says:

    Bob, you also ignored the entire concept of function. Is there a meaning for gain of function or loss of function in the theory of evolution? How can there be? If something survives, that is all the function it needs. There is no such thing as gaining or losing function, if a system has no meaning, other than whatever survives works.

    If an albino is said to “lose” function by the normal person’s language, that is not really true in the evolutionists view. Because, maybe albinos would be the best surviving allele in some conditions. In reality its just an extreme form of blue eyes. Are blue eyes also losses of function? How about white skin? Furless skin? Without a standard of “fit” everything is just increases or decreases in their frequency in a population. If most people are albinos, then that would be their function. If most people have blue eyes, that is their function.

    If most dogs that are bred have Hip Dysplasia, then that is its function. That is Fitness according to you!

  99. 99
    Joe says:

    “And that is important because macroevolution requires an increase in biological information.”

    ws:

    Says who?

    Anyone with knowledge of biology. That leaves you out.

  100. 100
    Bob O'H says:

    phoodoo @ 97 –
    First, I should be clear that I was trying to explain things simply, so you would understand the main points. It’s not always easy to judge the optimal level of complexity in an explanation, and evidently I mis-judged it.

    Now let’s be very clear here Bob, so you don’t accuse me of not understanding. When you say that fitness is the expected change in frequency and not the actual change, and then you say that someone can look at the expected (not the actual right??) HOW do you look at the expected change in a lab? You don’t. How do I know? Because you yourself said so:

    You measure the actual change, yes. But you repeat the experiment. And the average change in frequency is the estimate of fitness. Because you have replicates, you have samples from the distribution, so you can use that to estimate the uncertainty in the estimate. Formally it gets a bit more complicated, but I hope you appreciate the idea, at least.

  101. 101
    Bob O'H says:

    phoodoo @ 99 –

    Bob, you also ignored the entire concept of function. Is there a meaning for gain of function or loss of function in the theory of evolution? How can there be? If something survives, that is all the function it needs.

    Well, I guess you missed my post at 17. After that, my involvement in the discussions turned to specifics where function took a back seat. I’m happy to return to it later, but I’d rather wait until we’ve sorted out what fitness means.

  102. 102
    PaV says:

    Bob O’H:

    Certainly evolution can happen by loss of function, and I guess when evolution is quick (as in host-parasite/pathogen interactions) it can be a quicker way to evolve resistance (although loss of function can also cause a loss of fitness in the absence of the pathogen). But there are also gains of function, e.g. through duplication of a resistance gene, followed by its mutation.

    Bob, always good to see you here.

    But let me point this out: via duplication, there is no net increase in information. Then, when there is a mutation, the vast majority of mutations are deleterious. How do you then say there is a gain of function? Don’t the probabilities associated with mutations tell us that there is some loss of function in the mutated, duplicated “resistance” gene?

  103. 103
    phoodoo says:

    Bob,

    Ok, let’s do flush this out. First, I assume that all you can really test in a lab is bacteria, so you really aren’t testing anything much in the way of competition and sexual selection, and luck of circumstances etc…

    But ok, you have one type of bacteria that has a certain mutation, and another bacteria with another mutation, and then you put them in a petri dish, and then what? You expose it to what you think might kill it? Some bacteria frequencies change (because they died) and some don’t change much, because they didn’t die. Is that it? The ones that died less are fit, right?

  104. 104
    phoodoo says:

    Or are you talking about something like fruit flies, with all kinds of cross linked genes, where its almost impossible to draw conclusions about fitness in the wild?

  105. 105
    Bob O'H says:

    phoodoo @103:

    First, I assume that all you can really test in a lab is bacteria, so you really aren’t testing anything much in the way of competition and sexual selection, and luck of circumstances etc…

    Nope, it’s been done with a lot of organisms, including eukaryotes. I’ve done selection experiments with cereal mildews, and at work have been discussing experiments on chironimids. And selection experiments have been done on many more species:

    For example, in the present symposium, we have papers about mice artificially selected for high voluntary wheel-running behavior (Rhodes et al., 2005; Swallow et al., 2005) and for basal metabolic rate (Konarzewski et al., 2005), rats selected for high and low treadmill running performance (Koch and Britton, 2005), crickets selected for high or low wing morph frequency (Zera, 2005), and stalk-eyed flies selected for male eye span (Wilkinson et al., 2005).

    There obviously are limits to what can be done in the lab – the generation time can’t be too long, and you need to be able to keep the species in the lab (so blue whale selection experiments are a few years off), but that still leaves a lot of species that can be worked with.

    BTW, if pone wanted to look at fitness of fruit flies in the wild, one could simply collect them from the wild, and not use lab stocks.

  106. 106
    Mung says:

    Mark Frank:

    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?

    It’s not our fault that evolutionists fail at information science. They should drop all pretense of there being any such thing as “information” in the genome.

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