A peek: Natural selection reduced diversity on human Y chromosomes

| 71 Comments

In science we often get together with other scientists and present preliminary results before the publication of the manuscript.  I think that attending meetings is an excellent opportunity to learn what other people are working on, share the research that I am currently engaged in, and both give and receive feedback about the analysis and interpretations.

In this case, I presented a poster at the scientific meeting I attended, the 2013 annual meeting of the Society for Molecular Biology and Evolution, about work that was recently accepted for publication (expected to be published in January). I’m working on an accessible research blog post about this work. In the meantime, here is the description from the poster this summer, and the pdf version of the poster (you can also download the preprint version here):

Description

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.

Wilson Sayres, Melissa; E. Lohmueller, Kirk; Nielsen, Rasmus (2013): Natural selection reduced diversity on human Y chromosomes. figshare
http://dx.doi.org/10.6084/m9.figshare.806296

71 Comments

Is the time scale which you are observing diversity long enough that what you could be seeing is purifying selection in the past? It is thought that loss of functional loci on the Y occurred, through processes like Muller’s Ratchet. When you see more sites that have purifying selection than there are Y-linked coding sites, could that be an observation of past selection? So selection at locations that no longer have any function.

This should come as no suprise to anyone because all that natural selection is known to do is reduce existing genetic variation. It is Nature’s executioner and eliminator, and not an agency responsible for the proliferation of diversity.

https://me.yahoo.com/a/UIFqpY46nexU[…]agSA6W#dd2ba said:

This should come as no suprise to anyone because all that natural selection is known to do is reduce existing genetic variation. It is Nature’s executioner and eliminator, and not an agency responsible for the proliferation of diversity.

Bizarre musing from a non-biologist: Would it be possible for natural selection to encourage or reward diversity and variation (of course it can’t directly cause it)? Imagine a species in which individuals are attracted to mates that are the most UNlike the average. There would have to be limits, of course, but I don’t see why even potentially deleterious variations couldn’t seem attractive to mates. Many species have ‘expensive’ equipment that isn’t good for much except attracting mates (e.g., peacock tails). Suppose the females of a species, instead of being attracted to just one (or a small set) of features (like big antlers), instead went for the guy that was the most unusual, whether that was the tallest, shortest, darkest, stinkiest, or whatever? And each female could vary from others in what she viewed as attractive (they don’t all go for the tall guys), and they could even go for a different trait next season.

That seems to me like a potentially powerful breeding strategy (within limits), as it would encourage diversity and reward variation. Do we see a hint of that in male humans who are attracted to ‘exotic’ females?

Joe Felsenstein said:

Is the time scale which you are observing diversity long enough that what you could be seeing is purifying selection in the past? It is thought that loss of functional loci on the Y occurred, through processes like Muller’s Ratchet. When you see more sites that have purifying selection than there are Y-linked coding sites, could that be an observation of past selection? So selection at locations that no longer have any function.

It could be evidence of past selection. Alternatively,it could perhaps positive selection acting on the highly repetitive ampliconic regions, which we did not test. These ampliconic regions are not included in the single-copy coding regions we originally modeled because they are transcribed in the testis, but the extent to which they are translated is unknown.

Just Bob said: Bizarre musing from a non-biologist: Would it be possible for natural selection to encourage or reward diversity and variation (of course it can’t directly cause it)? Imagine a species in which individuals are attracted to mates that are the most UNlike the average. There would have to be limits, of course, but I don’t see why even potentially deleterious variations couldn’t seem attractive to mates. Many species have ‘expensive’ equipment that isn’t good for much except attracting mates (e.g., peacock tails). Suppose the females of a species, instead of being attracted to just one (or a small set) of features (like big antlers), instead went for the guy that was the most unusual, whether that was the tallest, shortest, darkest, stinkiest, or whatever? And each female could vary from others in what she viewed as attractive (they don’t all go for the tall guys), and they could even go for a different trait next season.

That seems to me like a potentially powerful breeding strategy (within limits), as it would encourage diversity and reward variation. Do we see a hint of that in male humans who are attracted to ‘exotic’ females?

Features that aren’t “good for much except attracting mates” are quite good indeed! If the goal is to pass on one’s genes, then anything that can attract and secure mates, without a tremendous drawback to oneself, can spread. And even then, “tremendous drawback” is relative. Some insect and arachnid males sacrifice their lives to their mates. This may be deleterious to the individual (because they will no longer be alive), but is not deleterious on a genetic level, because it actually promotes that individual’s fitness (i.e., it’s genes will be passed on). To my population genetics mind, a mutation is deleterious when it reduces the fitness, or the likelihood of passing on an individual’s genes.

Yes, there can be selection away from the average. I think this is called disruptive or diversifying selection (there may be other names or types). I don’t know about cases of diversifying selection in humans, except for a recent talk I saw suggesting that variation in human faces may evolve under diversifying selection, to assist with identification of one another (to be submitted soon). That said, there is no evidence that this has anything to do with ‘exotic’ variation.

Thanks, M.

Do you think it might be possible for a species to become genetically ‘programmed’ to look for diversity in mates? And probably along with that would be a genetic tendency to actually BE more diverse – to mutate more frequently, since an obvious (but not drastically harmful) mutation would be THE way to get laid. IOW, might a species evolve a tendency to frequent mutation, along with an evolved mating preference for the unusual?

I don’t think selection for the most diverse phenotype would lead to a higher genome-wide mutation rate in vertebrates, what with long generation times, relatively small effective population sizes, and a whole host of other selective pressures. But in species with short generation times and large population sizes, like viruses, perhaps it could. Some, like HIV, mutate very quickly, and it seems that having a lot of standing variation, as well as the ability to mutate quickly, allows HIV to propagate and adapt very well.

In animals, some loci are prone to accumulating more variation, but on the autosomes (non-sex chromosomes, and non-mtDNA) I don’t think this is because of a higher mutation rate (that is, I don’t think polymerase is more error prone in some areas versus others, but it could be). For example, the MHC complex, involved in the immune response, is a very diverse locus, and there is some evidence that animals preferentially choose mates with MHC loci that are different from their own.

Some plants also have regions of their genome with increased (relative to the rest of their genome) variability that are involved in reproduction, specifically reducing/preventing self-fertilizations.

That said, even with selection for variation at one locus, a lot of factors play into mate-choice, and there will be a lot of purifying or positive selection acting in the rest of the genome.

Just Bob said:

Do you think it might be possible for a species to become genetically ‘programmed’ to look for diversity in mates? And probably along with that would be a genetic tendency to actually BE more diverse – to mutate more frequently, since an obvious (but not drastically harmful) mutation would be THE way to get laid. IOW, might a species evolve a tendency to frequent mutation, along with an evolved mating preference for the unusual?

In birds you often see selection favoring how well a male builds a nest, or how good he does the 2 step, or in some cases it is apparently on looks alone. Who knows what kind of instinctual programming is going on, but you can bet this behavior wasn’t handed down.

I can’t imagine this kind of programming, being inclined to look for something out of the ordinary in these situations. I would think the out of the ordinary might be a red flag, but who knows? There may be some preference for longer or shorter feathers, or pointier toes, or a lighter or darker coloring, or any number of cues the female is looking for, but I’ll put $1.50 on out of the ordinary being akin to the ugly drunk going home alone…in species with tendencies to have this programming. All bets are off when it comes to other species, especially ours.

This highly speculative opinion based on many hours of watching nature series, and spending more than a fair share of my youth observing drunken humans in their natural habitat.

The pop gen experts can correct me, but I think selection can increase diversity if it is balancing selection. That’s supposed to be what drives the high diversity of HLA alleles. Of course that doesn’t apply to effectively haploid regions like the Y.

M. Wilson Sayres said: Yes, there can be selection away from the average. I think this is called disruptive or diversifying selection (there may be other names or types).

Frequency-dependent selection is a good one. One would suspect that this is active in the human HLA system, which would account for their being so many alleles (like pngarrison said). And it should function in any system in which an organism is trying to avoid a predator’s search image.

This should come as no suprise to anyone because all that natural selection is known to do is reduce existing genetic variation. It is Nature’s executioner and eliminator, and not an agency responsible for the proliferation of diversity.

I suspect that this remark is from a banned individual, but will comment on it, rather than reply to it.

Despite the interesting discussion of disruptive/diversifying/frequency-dependent selection above, imperfect nucleic acid replication (often termed “mutation”), and subsequent necessary diversity of offspring, is the major source of diversity in the biosphere.

So although there can be selection for diversity, there will be diversity with or without such selection, due mutation.

And of course, mutation is necessary for frequency-dependent selection. There could be no frequency-dependent selection in a hypothetical population of totally identical clones with perfect nucleic acid reproduction.

Thus the remark is wrong on two levels. It is directly wrong in its claim that there cannot be selection that increases diversity. And it is more indirectly but more profoundly wrong in its misleading implication that the theory of evolution posits selection as the source of diversity. Imperfect nucleic acid replication is the main ultimate source of diversity.

How’s this for an example of selection increasing diversity: Females of a species, say deer, are ‘programmed’ to favor a certain trait in males, say big antlers. There will naturally be a bell-curve of antler sizes, with a few lucky well-endowed bucks at the extreme big end, say the 9th stanine. Since those guys will likely sire more offspring than the general run of bucks in stanines 4, 5, and 6, then (assuming there is a heritable component to antler size) there will be more unusually large antlers in the next generation. Thus the deer population has become more diverse. Instead of big antlers being very rare, there are now more of them mixed into the population.

Maybe one needs to make a distinction between genetic diversity and phenotype diversity?

As I understand it, a genome (or a subset of it) will acquire diversity through mutation and drift, even without selection. With selection, it would still acquire diversity, I’m guessing somewhere around the same amount of it, but the differences would have some affect on anatomy or biochemistry.

But for phenotype diversity, that would seem to need variation and selection acting in a repeating loop of some sort, emphasizing or optimizing some trait that deals with something in the environment. If the something is another species that is also evolving, this could be a positive feedback loop. With lots of species evolving in different ways, and sometimes speciating, that would increase overall diversity.

Does that make sense?

Henry

harold said: Thus the remark is wrong on two levels. It is directly wrong in its claim that there cannot be selection that increases diversity. And it is more indirectly but more profoundly wrong in its misleading implication that the theory of evolution posits selection as the source of diversity. Imperfect nucleic acid replication is the main ultimate source of diversity.

You can’t “select” anything without discarding something else. Natural selection reduces both genetic diversity and phenotypic variation as much of it is not useful.

https://me.yahoo.com/a/UIFqpY46nexU[…]agSA6W#dd2ba said:

You can’t “select” anything without discarding something else. Natural selection reduces both genetic diversity and phenotypic variation as much of it is not useful.

You’re assuming an individual. In a POPULATION many different features can be selected for–or at least not selected against–thus adding to the DIVERSITY within the species. Some examples that I’m personally familiar with are color phases in many N. American snake species (e.g. cornsnakes Pantherophis guttatus) and eyespots (ocelli) in redfish Sciaenops ocellatus.

… models of purifying selection are consistent with observed Y diversity.

IANABiologist, but my first thought on reading this was that relatively few males have fathered the majority of sons for enough generations to create a genetic bottleneck.

Are most of us descended from harems?

Just Bob said:

https://me.yahoo.com/a/UIFqpY46nexU[…]agSA6W#dd2ba said:

You can’t “select” anything without discarding something else. Natural selection reduces both genetic diversity and phenotypic variation as much of it is not useful.

You’re assuming an individual. In a POPULATION many different features can be selected for–or at least not selected against–thus adding to the DIVERSITY within the species. Some examples that I’m personally familiar with are color phases in many N. American snake species (e.g. cornsnakes Pantherophis guttatus) and eyespots (ocelli) in redfish Sciaenops ocellatus.

If a feature is selected for, that necessarily means that some other feature is selected against. Natural selection refers to differential reproduction. And there can only be a difference in reproduction due to a difference in fitness.

If a feature is selected for, that necessarily means that some other feature is selected against. Natural selection refers to differential reproduction. And there can only be a difference in reproduction due to a difference in fitness.

I’m not sure what this statement is intended to mean. If I’m at, let’s say, a cafeteria, how does selecting an additional dish select against a dish I previous picked? I wasn’t aware that biology was a zero-sum game – it certainly doesn’t look like a zero-sum game to me.

Also, I don’t see how such a claim relates to differential reproduction (and I was under the impression that “fitness” was defined in terms of differential reproduction). I suppose one might argue that selection for greater speed is selecting against the “feature” of slightly less speed. But that’s not a very useful argument.

https://me.yahoo.com/a/UIFqpY46nexU[…]agSA6W#dd2ba said:

Just Bob said:

https://me.yahoo.com/a/UIFqpY46nexU[…]agSA6W#dd2ba said:

You can’t “select” anything without discarding something else. Natural selection reduces both genetic diversity and phenotypic variation as much of it is not useful.

You’re assuming an individual. In a POPULATION many different features can be selected for–or at least not selected against–thus adding to the DIVERSITY within the species. Some examples that I’m personally familiar with are color phases in many N. American snake species (e.g. cornsnakes Pantherophis guttatus) and eyespots (ocelli) in redfish Sciaenops ocellatus.

If a feature is selected for, that necessarily means that some other feature is selected against. Natural selection refers to differential reproduction. And there can only be a difference in reproduction due to a difference in fitness.

I think people are confusing diversity within an isolated population, with divergence between all isolated populations.

As much as I dislike replying to trolls and creotards, I believe he is correct. Diversity within a population is decreased by selection. However, this same selection will cause divergence between two separate isolated populations. Good times breed diversity with minimal selection. Selection usually pares down the population to the fittest for the current environment. A good example of this is a PT post from just over two years ago.

Bill #6. “How and why species multiply” by Peter and Rosemary Grant”.

They studied Galapagos finches for over two decades measuring the beak sizes (as well as other attributes). The beak sizes ran the gamut from small to large, until a drought hit. The usually plentiful food sources were gone and a very high percentage of the population starved. The large and small beaked birds were able to exploit different food sources, especially the large beaked birds. Somewhere in the presentation, Rosemary states that the selection events she observed were the hardest on the birds with average traits. She presents data showing how the medium sized beaked birds all but disappeared. During the two year drought, the average size of the large beaks increased dramatically.

IANA biologist, but it is my understanding that divergence will occur between separate isolated populations, regardless of whether or not the environments are similar. Dissimilar environments will generally cause a much quicker divergence.

https://me.yahoo.com/a/UIFqpY46nexU[…]agSA6W#dd2ba said:

You can’t “select” anything without discarding something else.

and

If a feature is selected for, that necessarily means that some other feature is selected against.

IANAB, but that’s simply not true…is it?

Look, A Masked, some female deer selectively choose males with the biggest antlers. A mutation arises that allows bucks to grow antlers 10% larger than was ever possible before. Originally, there is only one buck out of millions with that trait: a homogeneous population. All the rest have a normal distribution of antler sizes. But Big Horn gets sexually SELECTED by a harem of does, and within a few generations Big Horns make up 20% of the population: a DIVERSE population. The diversity was created by SELECTION.

Will the Big Horn trait drive out all others and lead again to a homogeneous population? Not necessarily. Mega-antlers may have a metabolic cost that in hard times works against bucks with impressive headgear: a selection pressure AGAINST big antlers. The population could even oscillate. In good years mega-antlers proliferate because does preferentially SELECT them, increasing their component of the population, and thus DIVERSITY. When the drought hits, the well-racked guys suffer and the small-horned bucks preferentially survive, driving DIVERSITY in a different direction.

DIVERSITY means there are various traits in the population. In a world with varying environmental pressures, selection often increases diversity by favoring a trait that once was uncommon. Unless that specific selection factor is overwhelmingly strong and persists for many generations, the favored trait won’t completely drive out the less-favored. As flint said, it’s not a zero-sum game.

Its not Surprising to the Y chromosome about its nature. Its the humans who study it who haven’t figured it out! If man has only been around 6000 years then there would, in many elements of genetics, be a lack of diversity. We haven’t changed since Adam that much although some. At least since the fall. This would be predicted by creationist(YEC) models.

I think people are confusing diversity within an isolated population, with divergence between all isolated populations.

I rather think the confusion is about diversity change within a single generation rather than over longer periods. Frequqncy-dependent selection, or any selection, must eliminate copies of some alleles, thus reducing diversity within that generation. But frequency-dependent selection also acts to increase diversity over time by making rare alleles more common and balancing many alleles, the more the better.

A Masked Panda said:

harold said: Thus the remark is wrong on two levels. It is directly wrong in its claim that there cannot be selection that increases diversity. And it is more indirectly but more profoundly wrong in its misleading implication that the theory of evolution posits selection as the source of diversity. Imperfect nucleic acid replication is the main ultimate source of diversity.

You can’t “select” anything without discarding something else. Natural selection reduces both genetic diversity and phenotypic variation as much of it is not useful.

IANAB, but (as others have stated) it seems to me that inaccurate gene copying is the source of much of the genetic diversity. The molecules involved in gene copying are, themselves, subject to natural selection (NS). In a stable environment, it would seem to make sense that NS would select for molecules that accurately copy genes, leading to a stable population. However, in unstable environments, it would make sense for NS to select for molecules that are worse at copying genes, thus increasing diversity, thereby increasing the chances that a randomly generated mistake might prove useful in the changing. An example of a dynamic environment might be tide pools.

By selecting for inaccurate gene copying, NS could directly lead to diversity.

IANAB, but (as others have stated) it seems to me that inaccurate gene copying is the source of much of the genetic diversity.

Yes, in fact it has to be the source of all genetic diversity.

In a purely imaginary mental model world in which there was “perfect” nucleic acid replication, any biosphere that existed would have to be composed of genetically identical clones. We can construct a model in which they could have different phenotypes due to different environmental experience, e.g. some could have a sun tan, and some might not, but none of that diversity would be heritable. If genomes replicated perfectly they would all always have the same genome. Even if having a sun tan attracted mates and led to greater reproductive success, there would be no selection for alleles, because tanned and untanned individuals would have identical genomes.

So yes, mutation is the ultimate source of diversity.

The potential diversity generated by the fact that every second uncountable numbers of genomes in the biosphere are imperfectly replicating is constrained by contingency on what is already in the genomes, and by the chemistry of nucleic acid replication, but within those constraints is approximately infinite.

The molecules involved in gene copying are, themselves, subject to natural selection (NS). In a stable environment, it would seem to make sense that NS would select for molecules that accurately copy genes, leading to a stable population.

We also have mechanisms to repair DNA after the fact, but the net mutation rate in EVERY population is still significant.

What we observe is that these mechanisms are, empirically, nowhere near “accurate enough” to render the mutation rate totally insignificant.

However, in unstable environments, it would make sense for NS to select for molecules that are worse at copying genes, thus increasing diversity, thereby increasing the chances that a randomly generated mistake might prove useful in the changing. An example of a dynamic environment might be tide pools.

You seem to be thinking about the observation that some lineages in very unstable environments have evolved somewhat higher net mutation rates than the “biosphere average”. That is true (but not necessary for biological diversity).

By selecting for inaccurate gene copying, NS could directly lead to diversity.

That is true. Thus the oversimplified claim that NS can never lead to diversity at all is false. Selection for weaker DNA repair mechanism enzymes, as you note, for example, would lead to a subsequent increase in genetic diversity within a population.

However, imperfect DNA replication always leads to phenotypic diversity in all populations (however similar some may appear to each other, by human standards). I realize your point was that diversity can actually sometimes be selected for, but I also want to emphasize the separate point that, even if NS is selecting against phenotypic diversity, in some defined population at a given time, mutation will still keep generating phenotypic diversity.

Someone trying to argue against the theory of evolution said -

You can’t “select” anything without discarding something else.

and

If a feature is selected for, that necessarily means that some other feature is selected against.

The top statement is basically a vague semantic game, but the second statement is perfectly true, at least if we substitute a term with a meaning, such as “allele”, in place of the nebulous term “feature”.

Of course if one allele at a locus increases in frequency within a population, at least one other allele for that locus must decrease in frequency. Duh. The frequency of all alleles at a locus, at any given instant in time, must sum to 100%. (This statement is actually somewhat approximate, as gene duplication and other mechanisms create new loci all the time, as evidenced by the fact that genome sizes differ, but it’s fair to say that it’s often true.)

So what? No-one ever said otherwise.

Remember that some of the more intelligent creationists can pepper their verbose output with occasional statements that are more or less true. It’s always the case that if a creationist includes an isolated accurate statement, that statement doesn’t support their overall gist. They may be including such statements as bait, to trick science supporters into disputing the accurate statements.

… so glad you brought up the string on the Galapagos Fiches.

The Grants concluded that it was “Retrogressive Hybridization” that maintained the diversity of genotype and resulting phenotype within the various finch populations on the archipelago. Natural selection did indeed limit the diversity by favoring certain traits within isolated populations living within certain environments. Fortunately for the finches, this retrograde hybridization, (the ability for different populations to interbreed) maintained enough diversity so that if environmental condition did change, the highly specialized population (some would call them a species) wouldn’t be wiped out.

Contrary to the commonly held belief of many in the scientific establishment, mutations were not the source of diversity displayed in these finches … instead it was inherent genetic diversity in he founding members of the Galapagos finch population.

By the way … one of my favorite observations of Rosemary Grant in this video is her revelation that all of the populations of Galapagos inches can indeed interbreed and that to become completely genetically incompatible it is supposed they would need to stay reproductively isolated or over 30,000,000 years! Quite different from what I was taught in most of my biology classes growing up.

I hope you in the field are doing a better job of teaching all of the evidence.

fittest meme said:

By the way … one of my favorite observations of Rosemary Grant in this video is her revelation that all of the populations of Galapagos inches can indeed interbreed and that to become completely genetically incompatible it is supposed they would need to stay reproductively isolated or over 30,000,000 years! Quite different from what I was taught in most of my biology classes growing up.

Unless this statement just happens to be talking about this specific population of finches, the figure of 30My needed for speciation seems to be excessive. Didn’t chimps and humans share a common ancestor less than 10My ago? Assuming the statement to be accurately quoted, perhaps the Galapagos finches might require more time to speciate because the population currently has so little diversity?

Or is 30My a generally accepted time frame expected for speciation? (Obviously, chance and generation-length will give a distribution for time-to-speciation, but I was asking in the aggregate.)

Contrary to the commonly held belief of many in the scientific establishment, mutations were not the source of diversity displayed in these finches … instead it was inherent genetic diversity in he founding members of the Galapagos finch population.

This is an argument against a straw man (what a surprise). In fact this is arguing against what is commonly termed Lamarckism.

Of course allele combinations that already exist in a population are often, probably usually, what is selected for when environmental stresses change.

In idea that, whenever an environmental stress occurs, a mutation to deal with it suddenly occurs as well, is Lamarckism.

Mutations don’t occur by magic and are independent of the human-perceived “needs” of organisms.

No reasonable person would expect all changes in allele frequency in a population to be related to recent mutations.

Mutation is the reason that there are multiple alleles, though. It’s just that some of the mutations occurred long before the particular allele was strongly selected for.

Quite different from what I was taught in most of my biology classes growing up.

Ability to learn something is related to these factors -

Basic learning ability, plus motivation, minus bias, minus interfering mental illness.

You have never correctly learned anything about biology in your life, not in your “biology classes growing up’, not in anything else.

Your version of religion requires denial of scientific reality. Therefore your version of religion is wrong. Either someone else’s version is correct, in which case you may be going to hell for eternity or reincarnated in some undesirable way, or you’re just going to die some day. I strongly favor the latter, but of course, I can’t disprove all religions. I can say that yours is wrong, because it causes you to contradict easily observed scientific reality.

Scott F said:

Unless this statement just happens to be talking about this specific population of finches, the figure of 30My needed for speciation seems to be excessive. Didn’t chimps and humans share a common ancestor less than 10My ago? Assuming the statement to be accurately quoted, perhaps the Galapagos finches might require more time to speciate because the population currently has so little diversity?

Or is 30My a generally accepted time frame expected for speciation? (Obviously, chance and generation-length will give a distribution for time-to-speciation, but I was asking in the aggregate.)

Scott:

At abou 1:10 of the video here Rosemary refers to s study by Prager and Wilson regarding the length of time it takes for birds in general to become genetically incompatible. She also indicates that the Galapagos Finches have been radiating on the archipelago for only 3 million years.

The assumed chimp and human divergence indeed does not seem to make sense with this assertion especially considering the longer generational times for humans vs. birds. I am sure there are theories however to make the data fit the desired conclusion.

I think it is interesting that The Grants and their work are often given a great deal of emphasis in biology text books as evidence of speciation, but that their own words contradict what the text books are trying to suggest their work shows.

BTW I was wrong about the big scientific words Rosemary uses to say that the finches still interbreed. It was “Episodic Introgression” not “Retrogressive Hybridization.”

harold said:

You have never correctly learned anything about biology in your life, not in your “biology classes growing up’, not in anything else.

Your version of religion requires denial of scientific reality. Therefore your version of religion is wrong. Either someone else’s version is correct, in which case you may be going to hell for eternity or reincarnated in some undesirable way, or you’re just going to die some day. I strongly favor the latter, but of course, I can’t disprove all religions. I can say that yours is wrong, because it causes you to contradict easily observed scientific reality.

Yikes Harold. I never brought up religion. I just pointed out what the Grants actually revealed in their years of observing scientific reality.

Do these facts strike a nerve that challenges your own favored belief system?

fittest meme said:

apokryltaros said:

If you can not define the difference between “creating new genetic information” from “just effecting the way existing instructions are expressed,” then you are quibbling while engaging in the “Moving the Goalpost” fallacy.

Let’s try this. Genes are complicated sets of instructions that for simplicities sake, represent the materials list, assembly instructions, and timing for a particular morphological trait. Genes are made of thousands of precisely ordered base pairs. The mutations that have been scientifically observed either effect single base pairs in this string or are the result of insertions, deletions, or “flips” of sections of per-existing code.

“Creating new genetic information” refers to writing the complicated instructional code required to make a particular morphological trait appear in a living organism. “Just effecting the way existing instructions are expressed” refers to to the mutations that may change the way the per-existing genes produce the trait. In virtually all cases i am aware of the mutations are desegregation to the original code even though the morphological effect may have a short-term beneficial effect in a particular environment.

Bottom line is that evolution must explain the original genesis of the genetic information not just the changes to existing information.

Presupposing this genetic information is indeed an example of moving the goalposts.

Let’s try this again. The morphological divergence in finch beaks is primarily produced by mutations in regulatory regions affecting the temporal and spatial expression patterns of master control genes in development. The origin of these genes is not the issue, they were inherited from the common ancestor of all of the finches. The genes were identified by micro array analysis and their expression patterns were confirmed by in situ hybridization studies.

This is the way that evolution works. You can’t say that it isn’t evolution just because it doesn’t work the way you want it to. You can’t say it isn’t true just because it doesn’t solve every problem in evolution and development. Random mutations affecting developmental pathways have been selected to produce the range of finch morphologies observed. Deal with it already.

DS said:

This is the way that evolution works. You can’t say that it isn’t evolution just because it doesn’t work the way you want it to. You can’t say it isn’t true just because it doesn’t solve every problem in evolution and development. Random mutations affecting developmental pathways have been selected to produce the range of finch morphologies observed. Deal with it already.

Fine DS, we can agree that this is the way that populations change over time. That is one definition of evolution. However I think that most of your atheist friends here wouldn’t be satisfied with that alone. I think for them the “origin of these genes” is indeed an issue.

What I have been pointing out is that neither the Grant’s nor Lenski’s (which is what I am supposing you are referring to) work demonstrate the more controversial definitions of evolution. Specifically, the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms.

Are we in agreement?

fittest meme said:

DS said:

This is the way that evolution works. You can’t say that it isn’t evolution just because it doesn’t work the way you want it to. You can’t say it isn’t true just because it doesn’t solve every problem in evolution and development. Random mutations affecting developmental pathways have been selected to produce the range of finch morphologies observed. Deal with it already.

Fine DS, we can agree that this is the way that populations change over time. That is one definition of evolution. However I think that most of your atheist friends here wouldn’t be satisfied with that alone. I think for them the “origin of these genes” is indeed an issue.

What I have been pointing out is that neither the Grant’s nor Lenski’s (which is what I am supposing you are referring to) work demonstrate the more controversial definitions of evolution. Specifically, the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms.

Are we in agreement?

You are an intelligent design advocate, right fitso? You advocate the idea that the theory of evolution is just wrong, wrong, wrong, but you have nothing to replace it. All you have is your whining and bitching about how this just cannot be right and that cannot be true.

What’s you alternative, fitso? Can you even define “design”? Can you say how to detect it? Can you say how to distinguish it from non-design?

No, I thought not. You lack the integrity to own up to your own convictions, because they are indefensible.

fittest meme said:

DS said:

This is the way that evolution works. You can’t say that it isn’t evolution just because it doesn’t work the way you want it to. You can’t say it isn’t true just because it doesn’t solve every problem in evolution and development. Random mutations affecting developmental pathways have been selected to produce the range of finch morphologies observed. Deal with it already.

Fine DS, we can agree that this is the way that populations change over time. That is one definition of evolution. However I think that most of your atheist friends here wouldn’t be satisfied with that alone. I think for them the “origin of these genes” is indeed an issue.

What I have been pointing out is that neither the Grant’s nor Lenski’s (which is what I am supposing you are referring to) work demonstrate the more controversial definitions of evolution. Specifically, the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms.

Are we in agreement?

To prove your claim that evolution is magically insufficient for “the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms,” you will need to actually demonstrate how evolution is just not good enough, as well as demonstrate how Grant’s and Lenski’s and the nylonase experiments aren’t good enough, as well as demonstrate how all of the observed instances of observed speciation aren’t good enough.

In other words, you will need to back up your Moving the Goalpost fallacy and your Slothful Induction fallacy with actual research, and not “because (you) said so”

phhht said:

fittest meme said:

DS said:

This is the way that evolution works. You can’t say that it isn’t evolution just because it doesn’t work the way you want it to. You can’t say it isn’t true just because it doesn’t solve every problem in evolution and development. Random mutations affecting developmental pathways have been selected to produce the range of finch morphologies observed. Deal with it already.

Fine DS, we can agree that this is the way that populations change over time. That is one definition of evolution. However I think that most of your atheist friends here wouldn’t be satisfied with that alone. I think for them the “origin of these genes” is indeed an issue.

What I have been pointing out is that neither the Grant’s nor Lenski’s (which is what I am supposing you are referring to) work demonstrate the more controversial definitions of evolution. Specifically, the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms.

Are we in agreement?

You are an intelligent design advocate, right fitso? You advocate the idea that the theory of evolution is just wrong, wrong, wrong, but you have nothing to replace it. All you have is your whining and bitching about how this just cannot be right and that cannot be true.

What’s you alternative, fitso? Can you even define “design”? Can you say how to detect it? Can you say how to distinguish it from non-design?

No, I thought not. You lack the integrity to own up to your own convictions, because they are indefensible.

Hence fittest meme’s inane strategy of claiming that evolution (or the parts that he can’t totally deny without looking like an even bigger idiot) isn’t good enough because he’s too lazy to understand the science and too lazy to acknowledge that evidence supporting evolution exists. And while throwing in repeatedly debunked Creationist fallacies for good measure.

fittest meme said:

DS said:

This is the way that evolution works. You can’t say that it isn’t evolution just because it doesn’t work the way you want it to. You can’t say it isn’t true just because it doesn’t solve every problem in evolution and development. Random mutations affecting developmental pathways have been selected to produce the range of finch morphologies observed. Deal with it already.

Fine DS, we can agree that this is the way that populations change over time. That is one definition of evolution. However I think that most of your atheist friends here wouldn’t be satisfied with that alone. I think for them the “origin of these genes” is indeed an issue.

What I have been pointing out is that neither the Grant’s nor Lenski’s (which is what I am supposing you are referring to) work demonstrate the more controversial definitions of evolution. Specifically, the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms.

Are we in agreement?

So you really want to go there? You really want to move the goalposts out into the street? Ok fine, but you aren’t going to like it.

The two genes we are discussing are BMP and CAM. BMP originated in the early metazoans, Cnidaria at least. It has an important function in pattern formation in invertebrates and vertebrates and belongs to the dpp gene family. Obviously, this is another example of cooption in evolution. As for CAM, it is a member of a gene family that was produced by gene duplication and mutational divergence. So you see, the origin of these genes is not a mystery at all. Not that that has anything at all to do with the topic of the thread or the topic of discussion.

As for the finches, they have obviously been caught in the act of speciation. This is the same way that most species on earth originated. No one cares if you believe it or not.

I could of course provide references for all of this, but experience shows that that would be worthless in your case, since you always ignore evidence and simply claim that you ain’t gonna believe it no how.

fittest meme said:

What I have been pointing out is that neither the Grant’s nor Lenski’s (which is what I am supposing you are referring to) work demonstrate the more controversial definitions of evolution. Specifically, the creation of new genetically distinct species from an original population, nor the creation of the original genetic instructions required for life itself and the novel functions displayed by the multitude of life forms.

“What I have been pointing out,” he says.

No matter how many times – in real time, no less – that we can demonstrate that an ID/creationist can’t understand, let alone respond to, a question about high school level science concepts, this is what we always see; an ID/creationist presuming to be able to critique a scientific experiment.

Mike Elzinga said:

So now all you have to do is give an ID/creationist “explanation” of how that “information” is transmitted to atoms and molecules. How does “information” push atoms and molecules around?

Mikey, Mikey… don’t you know that by ‘information’ he means magic?

Just Bob said:

Mike Elzinga said:

So now all you have to do is give an ID/creationist “explanation” of how that “information” is transmitted to atoms and molecules. How does “information” push atoms and molecules around?

Mikey, Mikey… don’t you know that by ‘information’ he means magic?

You mean I read all those Harry Potter books, saw all the Harry Potter movies, and I still didn’t figure it out?

When I was a kid I must have received the inverse of the “Ken Ham effect” on children.

Mike Elzinga said:

Does “information” decrease with distance? If so, does it decrease linearly or by some other function?

(Warning: I am not a mathematician, so the following derivation may not be accurate.)

My understanding is that in the ID world, the “information” field can be approximated by this expression: I = A/x + B*x, where “I” is the information content of a statement, “A” is a negative constant, “B” is a positive constant one or two orders of magnitude less than “|A|”, and “x” is the virtual distance from 208 Columbia Street, Seattle, WA.

The values of “A” and “B” are determined by experiment, as there is no fundamental(ist) limit to the negative value of “A”. Unfortunately, the irony meters keep melting or exploding, so it’s difficult to know for sure how dense the vacuity at the center of the ID field actually is.

Scott F said: … it’s difficult to know for sure how dense the vacuity at the center of the ID field actually is.

Easy. It’s filled with prayer, so it’s less dense than an actual vacuum.

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This page contains a single entry by M. Wilson Sayres published on December 24, 2013 8:00 AM.

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