Response to the Anonymous Creationist

I've got an anonymous creationist (AC) who keeps piling one absurd statement on to another in the comments on a post below. I'm going to move the discussion up here to keep it from getting lost. This post is addressed directly to him.

The problem at this point is that you think you're not being taken seriously because you're a "skeptic" of evolution. The truth, however, is that you're not being taken seriously because your arguments are really, really bad. Let me give just a few examples of the statements you have made that are either incoherent, false or meaningless:

Examples of adaptation are now known to be even more dependent on adaptation mechanisms than was previously thought.

Totally meaningless. Adaptation is now known to be dependent on adaptation mechanisms? No shit. This is as profound as saying that bird flight is entirely dependent on a bird's ability to fly - the obvious response is simply "DUH". It's a statement totally devoid of any content. Of course adaptation is dependent on adaptation mechanisms; what else could it depend on, for crying out loud? Most amusingly, you even qualify it by saying that adaptation is "now known" to depend on adaptation mechanisms "more than previously thought". So tell me, AC, what evolutionary bioogist in the past thought that adaptation was not based on adaptation mechanisms? Give us some names.

When you say your theory is the only reasonable explanation for something, you are making a claim about all other possible theories. In other words, a claim that is not scientific.

Again, just a complete non-statement. What is science about if not determining the best explanation (read: theory) for a given set of data? What makes this statement even more ridiculous is that you don't bother to offer any other possible explanation for the data. So when I point out evolution is the only reasonable explanation for the successional order of appearance of animal forms on earth, do you say, "No, here's a better explanation"? Nope. You say, "Oh, that's not science". And you could not possibly be more wrong. Finding the best explanation for the data is precisely what science intends. Compounding the stupidity of this statement is your other attempt at explaining away successional order of appearance:

You are the one touting the successional appearance of life on earth which evolution does not predict. Complexity increase is not a prediction of evolution.

Once again totally non-responsive because the successional order of appearance that I detailed had nothing to do with complexity, it had to do with similarity to ancestral forms - the first amphibians being the most fish-like and becoming progressively less fish-like and more like modern amphibians as new species appear; likewise, the first birds being the most reptile-like and becoming less reptile-like and more like modern birds as new species appear (the earliest birds were literally feathered theropods, with teeth, no bills, unfused vertebrae, pneumatic bones, a more reptilian brain with the cerebellum situation behind the brain rather than over it, a long bony tail, an archosaurian pelvic girdle, and many other traits that, over time, were lost and modern avian traits emerged as birds evolved). This pattern of appearance is found in every single lineage, and it is the only pattern that could possibly be consistent with evolutionary theory. Indeed, that pattern MUST be there if evolution is true. If modern birds appeared suddenly in the fossil record, rather than appearing in the order of most reptile-like to slightly less reptile-like and more modern in the correct temporal and anatomical orer, there would be no way to explain the pattern with evolution. Thus, your statement that evolution does not predict this pattern of appearance is just plain stupid. 100%, incontrovertibly false. And to make it worse, you present us with this absurd caricature of evolutionary theory:

A gull population no longer interbreeds with a neighboring population of gulls, so therefore elephants could have evolved from mice.

You then claim that this is not a caricature, but is "precisely what evolutionists are saying". Utter bullshit, and anyone with the slightest understanding of evolution would know that. The fact that you don't shows how little you understand the subject you're talking about. The caricature is in the fact that you choose two vastly different types of animals, elephants and mice, and say that evolutionists claim that one evolved from the other. That's nonsense. You might as well have said that evolution claims that Tyrranosaurus rex evolved into hummingbirds, it would sound that absurd. But of course, that isn't really what evolution says because you've left out all of the detail in between to make it appear that evolutionary theory claims that this happened all in one big step, a T. rex gave birth to a hummingbird. But of course it doesn't say that. It says that a species related to T. rex split, with a slightly modified theropod with feathers splitting off from a lineage of theropods without feathers (it even appears that we have identified the point mutation that takes place that allows feathers to form rather than reptilian scutes), and then that species split off into a variety of other species that were slightly less like the theropods they evolved from, with the newer species showing adaptations in a wide range of traits that allowed for the development of powered flight, with teeth being replaced over successive speciations by bills like we see in birds today (although birds still retain the gene for making teeth, but it is suppressed - bird embryos develop the buds for teeth, but they don't actually form teeth. Evolution explains this quite easily, as the suppression of gene expression for a trait that is no longer used. Is there some other explanation for it? It would be totally pointless for an intelligent designer to have an embryo develop part of a trait and then suppress it and go in a different direction), and numerous other adaptations over millions and millions of years that eventually led to the modern bird forms we see today, including the hummingbird.

And again, it's this pattern of appearance that is absolutely necessary in order for evolution to be true. If modern birds just appeared in the fossil record without all of those forms leading in the right temporal and anatomical order from theropod dinosaurs to modern birds, with the pathways of adaptation traced through a wide range of traits from primitive (meaning virtually identical to theropods) to modern (meaning with all of the exclusively avian traits we see in birds today), there would be no way for evolution to explain the sudden appearance of birds. But the data clearly shows this pattern, and it shows the exact same pattern in every single lineage - early mammals are the most reptilian and they gradually become less reptilian and more modern as the class diversifes and new species emerge, early amphibians are the most fish-like and they gradually become less fish-like and more modern as the class diversifies and new species emerge, and so on through every major animal group.

And the sum total of your response to this has been to claim that evolution does not predict this pattern, which is obviously false since it is logically the only pattern that evolution could predict. And you confused it with complexity, which is not a part of the argument at all. The pattern is primitive ---> modern, not simple ---> complex. An amphibian is not more "complex" than a fish, a reptile is not more "complex" than an amphibian, and so forth. But the patterns of appearance within each of those groups does go from primitive (closest to the ancestral group it is believed to have evolved from) to modern (with traits exclusive to that group today). Then there's this bizarre statement:

Natural selection works when there are useful competitors to select from. We find examples of this in the immune system and in adaptation. Very complex systems that provide the pathways. For example, when bacteria are under stress, they increase their mutation rate, and the mutations occur at hotspots that help to explore meaningful adaptations. This isn't nonsense.

But this is precisely how evolution works! Of course natural selection works where there are competitors to select from (that is, when there are different phenotypes with differential survivability). The fact that you cite this as though it was evidence against evolution approaches the surreal. First you claim that the mechanisms of evolution are not sufficent for evolution to take place, then you claim that mutations occur that help bring about meaningful adaptations. How do you think speciation is supposed to take place, for crying out loud? If mutation provides a variety of genotypes and resulting phenotypes upon which natural selection can operate, and this helps to "explore meaningful adaptations", then why is that not sufficent to explain speciation? When this process of preserving meaningful adaptations (which you admit goes on in nature) takes place in one subset of a species that is reproductively isolated from another subset of that species (which obviously goes on in nature, with a wide range of causes, as species get spread out over a large area with diverse environments within the ancestral range), why would that not lead to speciation over time? Obviously it would. This is exactly what is required for evolution to be true, with new species splitting off from old ones, each new species being slightly modified from the ancestral species, then a slightly modified species splits off from that one, and so forth, and over time, through successive speciation and adaptation to new environments, you end up with a species that is considerably different than an ancestral species from a few million years before that eventually spawned it (this is an oversimplification, in fact, because it's not a linear process of A--->B--->C--->D, but is more like a bush, with multiple species splitting off from a lineage, with most of them dying out and some being preserved). But it is exactly that kind of diversification that is required for evolution, and you've just admitted to the very mechanism by which this diversification takes place and for some reason, you think this is a strike against evolution. I'm sorry, but that's just bizarre and absurd.

Then there is this ignorant statement:

Endogenous retroviruses converge to the same, homologous insertion site.

You say this as though it just explains away the use of retrovirus sequences to indicate common ancestry. When a retrovirus inserts a copy of its own genome into a host's genome at a specific spot, it can be identified as such. When this happens in a sperm or egg cell, then all of the retroviral DNA is inherited and will be present in the genomes of every descendant from that point on. I assume you agree on how this takes place, since you refer to a "homologous insertion site". But here's the key - there are at least 7 places where the same retroviral DNA is present at the exact same location in both chimps and humans. This fact ONLY makes sense if there is common ancestry because the sequence would be present in every branch of the lineage from the point of insertion. The only alternative explanation would be that, purely by chance, the same exact retrovirus inserted the same exact DNA sequence into the same exact location (out of some 30 or 40,000 genes in the human genome, keep in mind) in entirely unrelated species. And it didn't just happen with those 7, it had to happen with this same amazing luck in every eukaryotic species on the planet. And when you build a phylogenetic tree based upon shared retroviral sequences, guess what? It looks exactly like the phylogenetic tree that evolution had built before anyone even knew about these sequences and how it took place (for one of the many papers that built just such a phylogenetic tree, look here. Obviously, the notion of all 30,000 retroviral sequences that are identified in the genome having being inserted separately, by pure coincidence, into the same points in the genome of thousands of different species in just such a manner that it mimics perfectly the phylogenetic relationships shown by anatomical and fossil evidence, is patently absurd. The only logical explanation is common ancestry. You do not, of course, respond to any of this, you just brush it off as a mere appearance of homology without dealing with the substance of the argument at all. Then you breeze on to what you think are problems for evolution, resulting in even more incoherent statements.

For instance, you keep repeating that homologous traits can develop from non-homologous processes. Well, duh. Yes they can. This is called convergent evolution, where a similar trait develops in two disparate species through different pathways. You keep repeating this as though the fact that convergent evolution takes place in some circumstances means that homologies don't count as evidence for evolution. Well this might be true IF there was no way to distinguish between convergent and non-convergent evolution. But since we can now increasingly determine the various genotypic pathways for each trait at the phenotype level, it's fairly easy to distinguish between the two. But even prior to genetic sequencing, there was often fossil evidence that could distinguish convergent evolution from non-convergent evolution. For instance, the famous panda's thumb. It's not really a thumb, of course, it's an example of convergent evolution, in this case the adaptation of one of the bones in the wrist to serve a similar function to the thumb in primates. How do we know that? Well, we can see this adaptation take place by following the fossil evidence, which shows this adaptation taking place. Since natural selection would tend to favor the same traits in similar environments, the fact that similar traits can develop through distinct genetic pathways is hardly a problem for evolution. In fact, it's a pretty powerful demonstration of natural selection.

It also must be noted that the evidence from homology is not limited to phenotypic traits. In fact, most of the evidence comes from protein sequencing, not more conspicuous traits like wings or eyes. The endogenous retroviruses discussed above are a good example of how such sequences are used to construct phylogenetic trees. You can use specific protein sequences to compare between species and construct such a tree, and compare the whole set of trees to the basic evolutionary tree of nested hierarchies, and guess what? They match about 99% of the time. You can find an anomoly here and there in specific sequences, but as a rule such trees show precisely the relationships that evolution would predict. This leads to some bizarre statements about genetic homologies on your part. Like this one:

Second, genetic comparisons between the human and mouse genomes shows near identical non functional sequences. An evolutionist once told me that this type of finding would falsify evolution.

This is patently false. In fact, genetic comparisons show exactly the opposite - that in functional sequences, using the nucleotide comparison method, the affinity is 70% for the functional sequences but only 40% for the overall genome when the non-functional sequences are factored in. Why? Because the non-functional sequences are allowed to mutate without natural selection to conserve the order. The rate of change in non-functional sequences is orders of magnitude higher than in functional sequences, for obvious reasons. You can see the actual sequence data here, and it shows that when comparing the two genomes, 91% of the coding exons are of the same length, while only 1% of the non-coding intron sequences are of the same length. That is precisely the opposite of your claim that they show near identical non-functional sequences (introns are the sequences that don't code for proteins, exons are the sequences that do).

More importantly, you continue to ignore the big picture of genetic homologies. By comparing specific gene sequences between species (including the ERVs) you can build phylogenetic trees that show the degree of affinity between the genomes. And those phylogenetic trees show the same pattern of nested hierarchies as the trees based upon fossil and anatomical evidence. Thus you have multiple lines of evidence all leading to the same conclusion. Is there a better explanation for this? If there is, you certainly haven't offered one. Then again, you seem to think, as you claimed above, that determining which theories have more explanatory power somehow isn't a part of science.

Lastly, you seem to think that convergence and contingency are somehow at odds with each other, but you don't use the word "contingency" in a coherent manner. For instance, this strange statement:

Now about the homologies. They are a very important evidence for evolution. Why are they so important? Because it is the contingent process which, we are told, explains them so well. You see, there is no reason why all these critters should all have the pentadactyl pattern (although in fact the pattern itself varies widely). Why should functions as different as climbing, walking, grasping, digging, etc., all have the same pattern? Why? The answer, we are told, is obviously because the process is contingent.

I honestly have no idea why the word "contingent" is in that sentence at all - it doesn't fit. Contingency only means that something is dependent upon prior events, and everything in the world is "contingent". The reason why all these different species have the same pentadactyl pattern is because they share a common ancestor that had such a pattern, and that pattern has been adapted to different purposes depending upon the needs of that species. Unlike an omnipotent designer, evolution can only work by successive modification of existing phenotypes and genotypes. The sharing of the pentadactyl pattern, successively modified in various species to adapt it to the local environment, is obviously the sort of data that is explained by evolution. Do you have a better explanation for it? If so, you aren't sharing it.

So far, all of your arguments are either incoherent, irrelevant or just plain false. Your primary tactic seems to be to respond to each line of evidence by saying, "Well it doesn't PROVE anything". But time and time again, I've detailed lines of evidence that are, at best, explainable only by evolution and, at worst, entirely consistent with it. The only thing you have left is to look for those areas in which the evidence is as yet incomplete (the precambrian fossils, for example) or to go down to the hyperdetails and say that evolution hasn't yet explained every minute detail of how every single species evolved since the beginning of life on earth. But this is true of all scientific theories, even gravity (as noted, we don't even know what gravity IS - but you aren't therefore a "skeptic" on that one, are you?). The fact that evolution explains all of the data so well, and for some of the data is the ONLY coherent explanation, is a very compelling reason to believe that it's true. And again, if you have a theory that explains this evidence better - or that explains phenomena like ERVs at all - then by all means, bring it up so we can examine it.

Update: Our anonymous creationist has left yet another comment with yet another very badly conceived argument. Here it is, in all its glory:

In fact, evolution does not predict homologies to be prevalent. Imagine a vertebrate without the pentadactyl pattern. That would not mean evolution is false. In that species, the pattern simply would be viewed as having not been preserved. Imagine only a single vertebrate with the pentadactyl pattern. Again, that would not mean evolution is false. The pattern would simply be viewed as having evolved in that one species, and no where else.

The pentadactyl pattern shows up repeatedly over many millions of years. This homology easily could have morphed into something else with no harm to evolution. And it is the rule rather than the exception that development is not conserved in homologies. Very similar designs come from different development paths. Evolution does not predict this.

First, it's quite easy to "imagine" a vertebrate without the pentadactyl pattern. One need only go fishing to find lots and lots of vertebrates without it. Second, the pattern does not show up "repeatedly" over millions of years, it shows up "continually" over millions of years - that is, every terrestrial vertebrate has the same pattern (even horses, which have hooves, show the same pentadactyl pattern in embryonic development, then development is suppressed and the same starting point used to come to a different ending). The wing of a bird (and a bat), the forelimbs of primates, cats, dogs, bears, alligators - every amphibian, reptile, mammal and bird - shows this same pattern.

Let's remember the phylogenetic tree that evolution uses to show the divergence of those groups: Fish ---> amphibians ---> reptiles ---> mammals and birds (from two different types of reptiles, mammals from therapsid reptiles, birds from theropod reptiles). Every terrestrial tetrapod (4 limbed land animal) is thought to have evolved from one of the early amphibian species. Is it a mere coincidence, then, that every single vertebrate species that appeared from that point on, over the course of the last 350 million years, used a variation on the same limb structure, no matter how wildly different they were in every other way? Better yet, is it a mere coincidence that the very same digital pattern is also found in the closest non-amphibians, the lobe-finned fishes like Eusthenopteron? From an evolutionary perspective, this makes perfect sense - since every species thereafter was descended from this species, and evolution can only work through successive modification of existing body plans, it is perfectly reasonable that we see this perfect nested heirarchy when it comes to limb development.

Most powerfully, we see that in those descendant species that have severely altered the pentadactyl pattern - as in horses, who have hooves, and in birds, who generally have 3 digits on their claws - we see in embryonic development the pentadactyl pattern and it is then suppressed or altered. We can even pinpoint the specific developmental gene mutation that suppresses the expression of the 4th and 5th digit in birds, for example. Again, from an evolutionary perspective, this makes perfect sense. What is the creationist explanation for it? Why would an omnipotent designer have bird embryos go through the stages of development for the pentadactyl pattern and then suppress the expression of 2 of the digits? That's very inefficent. From an engineering perspective, given the range of functions for tetrapod limbs - swimming, flying, burrowing, climbing, grasping, etc - there is no reason why the pentadactyl pattern should be used for all of those functions. An omnipotent designer could have come up with much more efficent designs for those functions without such a pattern. But evolution, which is not omnipotent and must work only through modification of existing body plans, must create in this manner.

In fact, it is in the area of non-functional homologies that we find the most powerful evidence for evolution. For example, there is a laryngeal nerve that runs from the cranium to the larynx. It's a homologous structure found in both fish and tetrapods. But it isn't a direct connection, the nerve is routed through a tube near the heart. Now, in fish, the most primitive species in which it is found, this is a virtually direct connection. But in later species of tetrapods that evolved from fish, it is no longer direct. In giraffes, for example, this nerve has to go an extra several feet to get to the heart and then back up the neck to the larynx. Very inefficent design, but it makes perfect sense from an evolutionary perspective. And there are lots and lots of examples of non-functional homologies - teeth that begin to grow in embryonic development and then are re-abosrbed (in birds and cows and baleen whales, for example); hipbones in whales; the reversed wiring of the photoreceptors in the human eye; and so on.

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Ed, this is way to much effort for one troll creationist.

niucons-
I don't do it for the anonymous creationist, as they are likely impenetrable. Anyone who could say in public the ridiculous things he has said can easily invent more ridiculous justifications to preserve his beliefs from analysis. I do it for two reasons. First, because I am just constitutionally incapable of allowing nonsense to go unrefuted. Second, because I may well have readers who aren't familiar with the evolution/creationism debate in this kind of detail and they might benefit from seeing such bad but sophisticated sounding arguments get thoroughly debunked.

Thanks Ed,

I for one really appreciate your effort in posting such a comprehensive overview.

I have to agree with DonM. Keep up the good fight Ed!

I think Terry Gillam got it right in Time bandits:

Evil: God isn't interested in technology. He cares nothing for the microchip or the silicon revolution. Look how he spends his time, forty-three species of parrots! Nipples for men!
Robert: Slugs.
Evil: Slugs! HE created slugs! They can't hear. They can't speak. They can't operate machinery. Are we not in the hands of a lunatic?

By GeneralZod (not verified) on 03 Dec 2004 #permalink

In retrospect, I was dead wrong. Keep up the good work Ed. The update was very entertaining and educational.

I like it. Yes he is an unimportant little ignoramus but it's always fun to see ignorance get nakedly displayed for all to see. We humans still love to stop on occasion and go "Oooooo! Burn! He got burned!"

It is also good to see examples of sound refutations as someone who is still learning to argue with the same kind of people. Thanks for the entertainment Ed!

By Joshua White (not verified) on 03 Dec 2004 #permalink

Ed writes:

Your arguments are really, really bad. Let me give just a few examples of the statements you have made that are either incoherent, false or meaningless: "Examples of adaptation are now known to be even more dependent on adaptation mechanisms than was previously thought." Totally meaningless. Adaptation is now known to be dependent on adaptation mechanisms? No shit. This is as profound as saying that bird flight is entirely dependent on a bird's ability to fly - the obvious response is simply "DUH". It's a statement totally devoid of any content. Of course adaptation is dependent on adaptation mechanisms; what else could it depend on, for crying out loud? Most amusingly, you even qualify it by saying that adaptation is "now known" to depend on adaptation mechanisms "more than previously thought". So tell me, AC, what evolutionary bioogist in the past thought that adaptation was not based on adaptation mechanisms? Give us some names.

Me:

How about trying again with my full quote this time?

"Examples of adaptation are now known to be even more dependent on adaptation mechanisms than was previously thought. Natural selection works when there are useful competitors to select from. We find examples of this in the immune system and in adaptation. Very complex systems that provide the pathways. For example, when bacteria are under stress, they increase their mutation rate, and the mutations occur at hotspots that help to explore meaningful adaptations. This isn't nonsense."

I was assuming some minimum level of knowledge, and did not type out the details that would have made it more clear. I guess I was wrong to assume this as it appears you are unaware of the significance of these findings. Adaptation comes about by what are now known to be complex mechanisms. Evolution cannot explain how these mechanisms arose. For instance, in addition to bacteria (under stress) increasing their mutation rate, a fraction of the population increases their mutation rates even higher. Furthermore, the mutations themselves are not random throughout the genome but are concentrated in certain areas that can produce helpful changes. In other words, pathways of adaptation are already laid out. The point is that the small scale change that once served as evidence for evolution is now known to be due to mechanisms whose origin evolution cannot explain.

Ed quoting me and then commenting:

"When you say your theory is the only reasonable explanation for something, you are making a claim about all other possible theories. In other words, a claim that is not scientific."

Again, just a complete non-statement. What is science about if not determining the best explanation (read: theory) for a given set of data? What makes this statement even more ridiculous is that you don't bother to offer any other possible explanation for the data. So when I point out evolution is the only reasonable explanation for the successional order of appearance of animal forms on earth, do you say, "No, here's a better explanation"? Nope. You say, "Oh, that's not science". And you could not possibly be more wrong. Finding the best explanation for the data is precisely what science intends.

Me:

You said this on the other thread and I let it go. You are making forceful, black/white, statements about a deep and subtle topic. And to the point here, a scientist, as scientist, ought never says his theory is the only reasonable explanation for something. You can say a theory is the best of a given set of theories, but that is a very different statement.

Ed:

Once again totally non-responsive because the successional order of appearance that I detailed had nothing to do with complexity, it had to do with similarity to ancestral forms - the first amphibians being the most fish-like and becoming progressively less fish-like and more like modern amphibians as new species appear; likewise, the first birds being the most reptile-like and becoming less reptile-like and more like modern birds as new species appear (the earliest birds were literally feathered theropods, with teeth, no bills, unfused vertebrae, pneumatic bones, a more reptilian brain with the cerebellum situation behind the brain rather than over it, a long bony tail, an archosaurian pelvic girdle, and many other traits that, over time, were lost and modern avian traits emerged as birds evolved). This pattern of appearance is found in every single lineage, and it is the only pattern that could possibly be consistent with evolutionary theory. Indeed, that pattern MUST be there if evolution is true. If modern birds appeared suddenly in the fossil record, rather than appearing in the order of most reptile-like to slightly less reptile-like and more modern in the correct temporal and anatomical orer, there would be no way to explain the pattern with evolution. Thus, your statement that evolution does not predict this pattern of appearance is just plain stupid. 100%, incontrovertibly false.

Me:

Once again you are missing the point. The successional order of appearance is, of course, typical. But you are wrong that "This pattern of appearance is found in every single lineage." I pointed out the trilobites, as an example. You are also wrong that "it is the only pattern that could possibly be consistent with evolutionary theory." Evolution makes no such prediction. Life could be one long history of a planet full of bacteria according to evolution. In fact, life could have never evolved at all according to evolution. Furthermore, evolution does not require a gradual succession. Temporarily high rates of change are commonly considered in evolution. New designs abruptly appearing (eg, the trilobites) can be accommodated by evolution by appealing to a combination of fossil inadequacies and high rates of change. I think the point you want to make is that there is, generally, a successional order of appearance. That's certainly true. But this is not a prediction of evolution.

Ed:

And to make it worse, you present us with this absurd caricature of evolutionary theory: "A gull population no longer interbreeds with a neighboring population of gulls, so therefore elephants could have evolved from mice." You then claim that this is not a caricature, but is "precisely what evolutionists are saying". Utter bullshit, and anyone with the slightest understanding of evolution would know that. The fact that you don't shows how little you understand the subject you're talking about. The caricature is in the fact that you choose two vastly different types of animals, elephants and mice, and say that evolutionists claim that one evolved from the other. That's nonsense. You might as well have said that evolution claims that Tyrranosaurus rex evolved into hummingbirds, it would sound that absurd.

Me:

Tyrranosaurus rex evolving into hummingbirds remains controversial. On the other hand, it is not controversial within evolution that elephants *are* supposed to have evolved from a mouse-like creature (which is the common ancestor of the marsupials and placentals).

Ed:

But of course, that isn't really what evolution says because you've left out all of the detail in between to make it appear that evolutionary theory claims that this happened all in one big step, a T. rex gave birth to a hummingbird. But of course it doesn't say that.

Me:

I said no such thing.

Ed:

birds still retain the gene for making teeth, but it is suppressed - bird embryos develop the buds for teeth, but they don't actually form teeth. Evolution explains this quite easily, as the suppression of gene expression for a trait that is no longer used. Is there some other explanation for it?

Me:

This is a joke right? I think I've now figured this out. You are caricaturing an evolutionist. Here I've been arguing seriously with you, and you've been pulling my leg the whole time. Of course, birds don't have genes for making teeth. They make teeth when embryonic tissue, such as from a mouse, is used to induce such growth. If birds had such genes they'd have long since been riddled with crippling mutations since they are non functional. But then again, you knew all that. You're just pulling my leg.

Ed quoting me and then commenting:

"Natural selection works when there are useful competitors to select from. We find examples of this in the immune system and in adaptation. Very complex systems that provide the pathways. For example, when bacteria are under stress, they increase their mutation rate, and the mutations occur at hotspots that help to explore meaningful adaptations. This isn't nonsense."

But this is precisely how evolution works! Of course natural selection works where there are competitors to select from (that is, when there are different phenotypes with differential survivability). The fact that you cite this as though it was evidence against evolution approaches the surreal. First you claim that the mechanisms of evolution are not sufficent for evolution to take place, then you claim that mutations occur that help bring about meaningful adaptations. How do you think speciation is supposed to take place, for crying out loud? If mutation provides a variety of genotypes and resulting phenotypes upon which natural selection can operate, and this helps to "explore meaningful adaptations", then why is that not sufficent to explain speciation? When this process of preserving meaningful adaptations (which you admit goes on in nature) takes place in one subset of a species that is reproductively isolated from another subset of that species (which obviously goes on in nature, with a wide range of causes, as species get spread out over a large area with diverse environments within the ancestral range), why would that not lead to speciation over time? Obviously it would. This is exactly what is required for evolution to be true, with new species splitting off from old ones, each new species being slightly modified from the ancestral species, then a slightly modified species splits off from that one, and so forth, and over time, through successive speciation and adaptation to new environments, you end up with a species that is considerably different than an ancestral species from a few million years before that eventually spawned it (this is an oversimplification, in fact, because it's not a linear process of A--->B--->C--->D, but is more like a bush, with multiple species splitting off from a lineage, with most of them dying out and some being preserved). But it is exactly that kind of diversification that is required for evolution, and you've just admitted to the very mechanism by which this diversification takes place and for some reason, you think this is a strike against evolution. I'm sorry, but that's just bizarre and absurd.

Me:

Well said, but you confuse explanation with evidence. What you give here is a good explanation of the evolution view. And while it certainly is not impossible, from a scientific view it is pretty far out. First, the process you are talking about makes a bird's beak change shape or size a bit. It can make a subpopulation become non interbreeding. And so forth. This is trivial compared to the magnitude of change you are talking about.

And as we experiment with it and try to extrapolate the change, we invariably end up with lower fertility. Things don't work as well as you try to tease out evolutionary change. Does this mean it is impossible? Of course not. Who knows, maybe there are evolutionary pathways we don't know about. But at this point, from an experimental point of view, it is not likely.

Well, do we at least have a theoretical pathway, showing how the mutations came into play, led to improved fitness under some new condition (or neutral changes that later could be selected under a new environmental condition), and how a large number of these could serendipitously lead to the creation of some new contrivance, like histone IV or electrical organs? No, we have no such evidence even at the theoretical level. All we have is speculation.

But then, on top of all this, the very mechanisms of adaptation are now turning out to be complicated and preprogrammed. We have no evolutionary explanation for their origin. The more we learn, the more we see how clever and complicated adaptation is. Now, we must believe that evolution has created the machine that makes for, yes you guessed it, evolution.

Ed quoting me and then commenting:

"Endogenous retroviruses converge to the same, homologous insertion site."

You say this as though it just explains away the use of retrovirus sequences to indicate common ancestry. When a retrovirus inserts a copy of its own genome into a host's genome at a specific spot, it can be identified as such. When this happens in a sperm or egg cell, then all of the retroviral DNA is inherited and will be present in the genomes of every descendant from that point on. I assume you agree on how this takes place, since you refer to a "homologous insertion site". But here's the key - there are at least 7 places where the same retroviral DNA is present at the exact same location in both chimps and humans.

Me:

Yes, and they also show up at homologous insertion sites in distant species, such that common descent cannot be the explanation (but I already said that). They also show up in chimpanzees, bonobos and gorillas, but not humans. Again, not predicted by common descent. How could a retrovirus be inserted in these close species, but not humans? The fact that it shows up in those species means it must have been in the common ancestor, but if it is in the common ancestor, then it must be in humans. But it is not. Well, there is always the possibility of gene conversion, recombination, independent integration events, and so forth. With these explanations, there is no pattern that cannot be explained. But the results were surprising.

Ed:

And it didn't just happen with those 7, it had to happen with this same amazing luck in every eukaryotic species on the planet.

Me:

What? What is this about "every eukaryotic species on the planet"? This makes no sense. Maybe I'm missing something, or are you pulling my leg again?

Ed:

For instance, you keep repeating that homologous traits can develop from non-homologous processes. Well, duh. Yes they can. This is called convergent evolution, where a similar trait develops in two disparate species through different pathways. You keep repeating this as though the fact that convergent evolution takes place in some circumstances means that homologies don't count as evidence for evolution.

Me:

Well you can't fool me any longer. You know all about what I'm talking about, you're just pretending to be ignorant. You know very well that when I say homologous structures arise from non-homologous development processes that this has nothing to do with convergence. You know that with species in the same genus, you don't have "convergent evolution," and that if evolution is true we should not have the same structures in such highly related species arising from different genes or development processes.

Ed:

It also must be noted that the evidence from homology is not limited to phenotypic traits. In fact, most of the evidence comes from protein sequencing, not more conspicuous traits like wings or eyes. The endogenous retroviruses discussed above are a good example of how such sequences are used to construct phylogenetic trees. You can use specific protein sequences to compare between species and construct such a tree, and compare the whole set of trees to the basic evolutionary tree of nested hierarchies, and guess what? They match about 99% of the time. You can find an anomoly here and there in specific sequences,

Me:

"Here and there"? Please. Entire genomes are in conflict (eg, light harvesting bacteria). Entire classes of proteins (eg, mitoochondria) are in conflict.

Ed quoting me and then commenting:

"Second, genetic comparisons between the human and mouse genomes shows near identical non functional sequences. An evolutionist once told me that this type of finding would falsify evolution."

This is patently false. In fact, genetic comparisons show exactly the opposite - that in functional sequences, using the nucleotide comparison method, the affinity is 70% for the functional sequences but only 40% for the overall genome when the non-functional sequences are factored in. Why? Because the non-functional sequences are allowed to mutate without natural selection to conserve the order. The rate of change in non-functional sequences is orders of magnitude higher than in functional sequences, for obvious reasons. You can see the actual sequence data here, and it shows that when comparing the two genomes, 91% of the coding exons are of the same length, while only 1% of the non-coding intron sequences are of the same length. That is precisely the opposite of your claim that they show near identical non-functional sequences (introns are the sequences that don't code for proteins, exons are the sequences that do).

Me:

Well good, I'm glad you understand that the rate of change in non-functional sequences is orders of magnitude higher than in functional sequences. Your aggregate statistics misses the point. I'm referring to the well-known finding that *specific* mouse-human non function sequences (as well as other species comparisons as well) are essentially identical. Another falsifier for evolution.

By Response To Ed (not verified) on 03 Dec 2004 #permalink

So let's summarize the evidence, and why it obviously shows that evolution is not a good theory:

1. Fossils

Diversity over time, on earth, looks like a series of inverted evolutionary trees. You have the sudden appearance of great diversity followed by extinctions and reductions in diversity. Higher rates of evolution are required during the origin of new groups compared with the lack of evolution thereafter. The fossil species are clustered rather then forming a continuous spectrum. Most species belong to a relatively few, distinct major groups. There is a general successional order of appearance of animal forms with increase in complexity, something that evolution does not predict.

2. Adaptation

Ever since Darwin it has been known that we do not observe, nor can we create, extended biological change using adaptation or breeding techniques. Darwin relied on an unproven hypothesis: that breeding is qualitatively different than natural selection in the wild. To this day his hypothesis, that in nature extended change (beyond such minor changes as changing colors, beak size, and so forth) is somehow easier, remains doubtful. In fact, what we *have* learned makes it appear increasingly unlikely. As Ernst Mayr recently wrote:

"When we look at what happens to the genotype during evolutionary change, particularly relating to such extreme phenomena as highly rapid evolution and complete stasis, we must admit that we do not fully understand them. The reason for this is that evolution is not a matter of changes in single genes; evolution consists of the change of entire genotypes." [Mayr, What Evolution Is, 2001]

Also, the mechanisms are more complex than we envisioned, so we now arrive at the unlikely conclusion that evolution created (by unknown means) a machine that allows for evolution. Right.

3. Comparative anatomy

Biology contains massive convergence. So striking is this finding that an evolutionist must conclude that there are strong attractors in design space. That is, for some unknown reason, certain design points are highly likely to evolve. In a world where a tremendous variety of designs are imaginable, why do so few arise? Why, over millions of years, on different places on the earth, do we find the same designs arising?

A contradiction arises because evolutionists claim homologies are convincing evidence for evolution (indeed, Darwin said comparative anatomy alone, in its various forms, should be sufficient to advance his theory). Now when this claim is made a contradiction arises. This is because, due to all the convergences, the evolutionist must also agree that there are all kinds of similarities that are *not* due to inheriting the design coming from a common ancestor. The marsupial and placental wolves could not have inherited their similar designs because their common ancestor is something like a mouse. Do you really believe that over millions of years, in different lands, the wolf is going to independently evolve twice? Well that's what evolution says happened.

From that ancestral mouse, you have flying squirrels, wolves, rats, and a bunch of other designs occurring twice, over millions of years on different continents. Yet we are supposed to be shocked that there is this pentadactyl pattern repeated in the vertebrates, and that this must be such strong evidence for a common ancestor. If we are shocked by the by the repeated pentadactyl pattern, we must be catatonic from the placental-marsupial convergence. But, and here's the rub, we *cannot* resolve the placental-marsupial convergence with common descent, like we did the pentadactyl pattern and other homologies. The placental-marsupial similarities must have arisen independently. But if these similarities could have arisen independently, then certainly the homologies could have arisen independently as well. We no longer have the mandate for common descent.

Evolutionists say homologies arise because in evolution, contingency dominates necessity. You see, there is no reason why all these critters should all have the pentadactyl pattern (although in fact the pattern itself varies widely). Why should functions as different as climbing, walking, grasping, digging, etc., all have the same pattern? Why? The answer, we are told, is obviously because the process is contingent.

This is why evolutionists say "play the tape of natural history over again, and you'll get a different result." Contingency rules necessity. But this argument falls apart because convergence is rampant in biology. Evolution tells two contradicting stories. On the one hand, homologies prove evolution because we'd never expect the same design to be repeated; but on the other hand selective pressures are acting over geologic time periods, on different continents, to bring about the same designs. This severely mitigates the homology evidence.

And what is Ed's response? All he can say is that he has "no idea why the word contingent is in that sentence at all," but that he is sure an omnipotent designer would never have used the pentadactyl pattern in all those critters. Sorry, but Ed's religion doesn't count in science. Go back to church Ed and leave science to the scientists. The irony is that Ed is blaming skeptics for being blinded by religion.

Beyond all of this, there is the simple, well known fact that homologies, very often, arise from non homologous development processes (genes or the embryonic pathway). This makes no sense, and was a real surprise for evolutionists. They still don't have anything but speculation to explain this.

4. Origin of life

Closing in on a century of research, there still is no scientific explanation for how the first cell evolved. In fact, we now know that the three branches of life do not trace back to a simple cell, instead, what we would need is a super cell. So evolutionists are calling for a non common descent early world to try to explain this. And still, we do not have explanations for how the fundamental machinery of the cell arose. The genetic code appears rather difficult to evolve. How did it evolve then? We have nothing but speculation to such questions. What science is telling us is that this is unlikely.

5. Molecular evidence

Aside from evolution not explaining how the things like the DNA code arose, it also doesn't explain how proteins arose. How did proteins such as histone IV evolve? This is a good example because histone IV is nearly identical in the different species. Did it suddenly appear? This is a general problem, but even more interesting is that we find strong conservation without functional reason (no functional constraint). Again, histone IV is a good example. Change the sequence and the critter does just fine. But we find it highly conserved. Years ago, evolutionists tried to explain the histone IV high conservation, saying that histone IV is highly functionally constrained. But we don't find this to be true experimentally. The explosion of genome data is revealing more such examples of high conservation of functionless sequences. A respected evolutionist once told me this sort of finding would falsify evolution.

What about retroviruses? Again, the pattern presents problems for evolution, with retroviruses showing up at the same location in the genome of different species, but not in intermediate species. This means the retroviruses must have inserted itself independently at the exact same location. This is a gzillion-to-1 shot if things are random. Or the evolutionist can opt for some other such unlikely explanation. Also, retroviruses show up at the same location in chimps, gorillas and bonobos, but not humans. Again, we'll need some mental gymnastics to explain this. The bottom line on retroviruses is that we still do not fully understand them. More research will help, but for now we do know they present strong problems for evolution.

By Response To Ed (not verified) on 04 Dec 2004 #permalink

And what is Ed's response? All he can say is that he has "no idea why the word contingent is in that sentence at all," but that he is sure an omnipotent designer would never have used the pentadactyl pattern in all those critters. Sorry, but Ed's religion doesn't count in science. Go back to church Ed and leave science to the scientists. The irony is that Ed is blaming skeptics for being blinded by religion.
You know what? I have tired of your stupid games, from mimicking email addresses to making the same claims that have been debunked numerous times to dodging the logic of arguments with meaningless statements that sound sophisticated but are really just a bunch of nonsense to the outright false assertions that you make without ever bothering to offer a shred of evidence for them. Like the idiotic assertion about mouse genomes that meant something entirely different than you said, and what was allegedly meant was entirely irrelevant, or this new and false claim that ERVs don't show up in some intermediate species - all completely false. But when called on it, you just move on to the next thing. You've perfected the Gish Gallop. You've taken up too much of my time as it is and it has become obvious that you are what folks in Usenet call a "tar baby" - you'll sit here and spew bullshit for weeks, perhaps months, always dodging the issue and always declaring victory. So I'm gonna cut that short. You go on home and tell everyone how you vanquished the big bad evolutionist (a stupid phrase from the get go; no one ever referes to a "gravityist"). I'm sure they'll believe you, but then they'll obviously believe anything. The rest of us adults who actually understand what we're talking about are going to sit here and laugh at you some more, but from a distance. If that doesn't appeal to you....well, tough shit. It's my weblog.

Ed,

As one of the 95% who have only a basic understanding of evolution, I appreciate the many explanatory details you have provided.

At first, when I read AC's statements, I had a vague feeling that something was wrong, they didn't make sense, but I couldn't put my finger on it. Now I see some of his remarks as such an illogical interpretation of misstated data that even I can see right through them. Thanks for the time you have invested in your commentary.

His idea that bacteria under stress are more likely to mutate in areas which would lead to more adaptable outcomes shows that something more "intelligent" than evolution is involved in selecting these points was a real hoot, I nearly fell off my chair laughing!

Obviously, any bacteria which showed a preference for mutating in areas that did not lead to more adaptive outcomes died off eons ago. Only those that mutate at these more adaptive places are around today. This is a perfect example of natural selection which is a corner stone of evolution. His example supports evolution, not the contrary.

What I really don't understand is why some people have this near pathological need to maintain a supernatural explanation for phenomena that the evidence clearly shows arise from rather mundane naturally occurring processes. I know the Greeks and Romans had gods in control of the weather, the hearth, fertility and just about everything else, but geez, hasn't our ever increasing knowledge of nature served to dispel these myths? Why someone today feels it necessary to conjure up a mini-god of the genome to "explain" why bacteria under stress mutate in places which are more likely to produce adaptive outcomes when the simple process of natural selection addresses this so eloquently is well beyond my ken.

Thanks again for your cometary. Hi to Lynn. B

Ed: Bravo to you for having the patience to hang in as long as you did. I understand that you did so not for our Anonymous Creationist, as he is clearly beyond reach -- but in the hopes that if more rational minds who might be open to reason happen upon the discussion, they might benefit from the scientific evidence. I commend you for that; I ran out of patience for this hopeless character much earlier in the week.

Notwithstanding the attraction (inevitable, I suppose) of one creationist troll, the subject of your original post -- Why Americans Doubt Evolution -- is a worthwhile one and I think it deserves much more discussion. In an odd way, Anonymous Creationist added to the discussion by demonstrating, very clearly, the force that science is up against. Anonymous Creationist is the poster child for a sizeable group of Americans who simply refuse to allow the facts to cloud their worldview. They operate under the guise of science and reason, and that guise undoubtedly works very well in the creationist circles in which they travel. Those who cling to a religious worldview but who want to appear as part of the post-Enlightenment community can find some refuge in the pseudoscience that people like Anonymous Creationist put forward. In their minds, it gives them both the moral and the scientific high ground. Sadly, this group of Americans is probably beyond reach. They will hang on to their religion desperately and at all costs. Facts, reason, and honesty all take a back seat. For these people, their religion is not a healthy thing; it has crossed the line into the sort of fundamentalist dogma that has, at various times in recorded history, brought out the worst in humankind.

The good news, of course, is that not all (not even a majority) of those for whom religion is an important part of life have crossed this line. Religion helps them to live better lives, to be better people, or to cope with life's disappointments and difficulties, but it does not accomplish this at the cost of rationality. This group of Americans, to the extent that they might be uncertain of evolution, can still be persuaded. They key, I suppose, is education that starts at a young age. Once they are made to see that religion and science aren't mutually exclusive or even fundamentally inconsistent, they can accept the scientific evidence and understand that Enlightenment does not entail the death of their god.

Anonymous Creationist represents a vocal, well-organized, zealous group of people for whom faith triumphs, and always will triumph, over reason. There is a campaign underway to impose that faith upon the greater society at large. Why Americans Doubt Evolution, and the work that you and others do, Ed, is critical to the important work of reason. Not reason over faith, but reason as an element of human character. If we lose that, we are fast sliding down the slippery slope to pre-Enlightenment and all that that entails.

I'm not sure what the placental/marsupial wolf example is supposed to show as a criticism of evolution. Is it really unreasonable that the niche of "terrestrial cursorial quadruped predator" would be filled in two different lineages?

It's certain that the similarities are less "uncanny" than current antievolutionists would make them. You don't have to be an anatomist to recognize that the skulls of the two have very different shapes of bones and (of course, when talking about mammals) dentition. Yet, as recently as a conference in 2002 (IIRC), we had the spectacle of an antievolutionist opining that the two were indistingishable -- and presenting two illustrations of these animals to buttress the point. The funny thing was that it was apparent right off the bat to me that the pair were actually the very SAME illustration, with one of them flipped left to right and colorized.

A nice page with comparison of the thylacine and wolf skulls and dentition is at http://www.naturalworlds.org/thylacine/index.htm

Note the differences in neural foramina between the two.

I'm not sure what the placental/marsupial wolf example is supposed to show as a criticism of evolution. Is it really unreasonable that the niche of "terrestrial cursorial quadruped predator" would be filled in two different lineages?

Nice point Wes, and good URL.

I think the "logic" of the argument is as follows.

a) Marsupials and placental mammals separated 100,000,000+ years ago.

b) Both lineages lead to the same (or essentially the same) organism, the marsupial wolf and the placental wolf.

c) "Evolutionists" argue that if you rewind the tape of evolution, you won't get the same results.

And since you do get the same results, voila, evolution has a problem.

Of course the fact the two kinds of 'wolves' are structurally very distinct, and in fact the similarities are rather superficial doesn't phase our anonymous friend a bit. Nor does the fact similar selective pressures should lead to similar solutions (e.g. think dolphin, shark, ichthyosaur streamlining). Especially here where the animals are in the same Class already.

I think it's interesting that the Tasmanian Wolf is also sometimes called the Tasmanian Tiger, again for reasons of superficial similarity .