Saturday, December 31, 2005

AiG: Pathetic new depths

In the desperate search for straw-men, AiG has plummeted to an all-time low: citing X-Men movie as an authority on mutation. Check it out for a grand ol' laugh!
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Wednesday, December 21, 2005

Resistance is evolution; resistance is futile

It's one thing to not understand evolution, and another (though related) thing to disbelieve it. It's quite spectacular to be a public front against evolution where nearly every word you speak or write demonstrates your continued failure to understand it in the first place... like this AiG article.

In engagements with creationism, it's quite frequent to see examples of antibiotic or pesticide resistance trotted out as examples of evolution. Indeed, they are examples of the action of natural selection in changing the genetic 'make-up' of organsims. Generally, the examples are pests or microbes. So, how do creationists respond to this? The AiG article states:
But in this example, it was known that this resistance to the antibiotic was already in the bacterial population right from the beginning of the experiment. In other words, some bacteria already had the information in their genes to be resistant. The bacteria had inherited information; so the resistance has nothing to do with evolution.

After having read this paragraph, I was geared-up for how they were going to explain that this is not evolution. However, this is how I've always understood the mechanism of evolution by natural selection: variation among members of the population will cause a variation in how well individuals can reproduce. When these variations are heritable the net effect is that the advantageous variations become more widely represented in the population. Over many generations, there is a growth and eventual take-over of this heritable variation. If this process is continued and accumulated, then continued change will occur. Very simple.

The statement that this was "inherited" information and "has nothing to do with evolution" is downright laughable. I would like to know how the folks at AiG would explain evolution without inheritance.

Lest they should explain their assertions, they follow it up with this classic canard:
Now, what about those experiments where some bacteria developed a resistance to substances over time due to mutations in their genes? Such mutations, which are mistakes in the genes, result from a loss of information (such as the loss of a control gene which regulates the pumping of the substance into the cell). Again, this is the opposite of evolution, which requires an increase in information if it were to occur.

Ah yes - good ol' loss of information. It's never really explained what is meant by a loss of information. A loss of gene sequence? 'Overwriting' the old code? I'm not really clear on what is meant. I can only suspect this options. At the risk of putting words in their mouths, I'll focus on these options until such time as a creationist defines what they mean by 'information'.

The loss of gene sequence: Quite ofthen the case with resistance evolution. Pesticides and antimicrobials often work by 'plugging' into a key protein pathway such as to block biologically necessary reactions. A loss of a certain 'non-vital' part of a protein in a pathway may change that protein's conformation and therefore render the pathogenic agent useless.

The problem is that nobody would disagree that this type of event cannot explain how you get from, say, a self-replicating RNA to a single-celled organism. Well, not by itself (it would be naïve to think that such events never would have happened during that transformation). However, the point is irrelevant because it is wholly wrong that novel traits caused by mutations always evolve this way. Gene duplications are a common source of new adaptive capacities by microbial populations. Given that nearly all our developmental genes represent duplicate/divergent copies of the exact same genes in other animals, duplication events are precisely the type of thing we need to explain major transformations in evolutionary history.

The 'overprinting' of old information. Simply stated: this is not a loss but a changing of information. It's essential for evolution to proceed. Granted, evolution to new environments (say, those containing an anti-microbial substance) will carry antagonistic consequences for adaptations to the old environment. However, this has no effect on the acceptability of evolution. Evolution does not state that organisms are Swiss Army knives becoming infinitely large with gadgets for all environments (would sound more like something an omnipotent creator could do though). No, evolution is far from omnipotent. It is limited, imperfect, and often struggling. It can make the descendents of a fish capable of living on land, but it can't make it a universal fish/tetrapod. It loses some aquatic adaptations for life on the land. Even amphibians carry a cost of their terrestriality (such as dessication, the need to return to water). Aquatic reptiles, on the other hand, must surface to breathe. There's always a cost in evolution. The loss of adaptedness in the old environment in order to cope with a new one is not contra evolution.

The other problem is bias-laden terminology: referring to mutations as "mistakes in the genes". Indeed, they are errors in copying fidelity. Whether or not they are "mistakes" depends entirely on what their effects are. Our genomes are peppered with old genes that don't work anymore. That aside (because even creationists will challenge the 'pseudo' in 'pseudogenes'), a 'mistake' can only be interpreted in light of what effect that copying error actually has - not whether or not it changes the old sequence we're accustomed to.

So to creationists, I say that efforts to undermine evolution through the use of loaded semantics and jargon buzz-wording ('information') are futile. This is a question about data and evidence. As AiG themselves point out, observations can be interpreted different ways. However, some interpretations can be shown to be unacceptable or otherwise useless. Citing difference in interpretation does not permit using demonstrably misleading or deliberately vague interpretation.
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Victory for reason in Dover

It doesn't get any better than this. A ruling against the ID pundits was forseeable, but the frank and downright scathing tone of Judge Jones ruling was the icing on the cake. It quite possibly stands as the single most indicting document against ID ever.

Judge Jones did not shy away from pointing out liars and various dishonest and underhanded measures used by the IDists in order to advance their case. His statement bears numerous references to the over religiosity of ID.

Need I say more? I think this event speaks volumes for itself. I think I'll raise a glass tonight.

Cheers!
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Monday, December 12, 2005

Species is as species does... Part II - What teeth will tell

Another question that comes up is more specific, but is also an example drawn from dogs. It's frequently charged that if a palaeontologist had found the skeleton of a thylacine (or Tasmanian 'wolf' or Tasmanian 'tiger'), they would probably classify it (incorrectly) as a dog, rather than as a marsupial. The reason, we are told, is because the skeleton of a thylacine "looks like" a dog's, more than it does that of a marsupial such as a kangaroo or koala.

Here's a wolf skull. For our purposes, entirely like that of a typical domestic dog.



Now here's the skull of a thylacine



Upon first inspection, it's hard to see how a palaeontologist could possibly distinguish the two skulls. The reality is that it's very, very easy. Turn the skull over and look at the teeth. Here's dental arcade of a thylacine:



Note that there are four molars, the last three being nearly identical except in size. Now look at the tooth arcade of a dog:



One of the defining features of modern placental mammals is that they never have more than three molars. This already separates the thylacine skull not only from dogs, but all placentals. In this case, the dog only has two molars and a single premolar modified into what is called a 'carnassial' - a shear-like tooth for cutting meat. Note also that the thylacine skull has a pair of palatal fenestrae: window-like openings on the bottom of the skull, a character found in marsupials such as wombat skull. The dog skull clearly does not. (Don't confuse it with the passages seen behind the dog's palate - this is the choana, or internal nostril. The thylacine has this feature in addition to the palatal fenestrae, but it's not seen in the picture). These actually amount to only a few of the numerous differences in the skull that distinguish placental mammals from marsupials.

The fact that systemtatists and palaeontologists can identify marsupials from their bones is evidenced by the sabre-toothed marsupials. These forms look very similar to the familiar sabre-tooth cats. Despite only being known from fossils, they have been distinguished by palaeontologists as marsupial and placental carnivoran, respectively. This is because there are numerous aspects of the skull, such as dental characters discussed above, that can be used to unambiguously distinguish them. In addition to skull and dental characters, marsupials bear a prepubic bone (ofthen called the "marsupial bone") that projects forward from the front of the hips. It appears to be related to the pouch that marsupials use to carry their young. When entire skeletons are available, it serves as nother character to distinguish these two groups.

Here we see that not only would palaeontologists know how to separate the thylacine from dogs on the basis of bones alone, but that they routinely do distinguish marsupials from placentals in the fossil record. The evolutionary history of organisms is long and complex. Even if two organisms happen to take on very similar general appearance, the traces of their ancestry are often still documented by other parts of their anatomy. Palaeontologists and systematists search for these traces which are held in the shared unique characters held between members that share common ancestors - rather than relying on overt general similarities.

Just as in other sciences, common sense often betrays reality in systematics. This is not to say that reality never betrays systematics, either - it certianly can. Indeed convergence and incompleteness can frequently play havoc with the reconstruction of phylogeny (evolutionary relationships). However, sticking things together by overt similarity is not how things are done. Systematists look for nested sets of these shared unique similarities which, as we have seen with dogs and now marsupial vs. placental mammals, that are most useful in uncovering the true nature of evolutionary relationships.
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'Species' - Part II

Here's something annoying about using Blogger: it publishes your post in queue according to the day you started the draft not on the day you chose to publish. As a result, here's a link to Part II of 'Species is as species does..." which now appears a few posts down (as opposed to in the place of this... grrr!

Edit (15/12/05): Well, after a few days and the help of Coturnix, my eyes suddenly gained the ability to see the "Change Time & Date" feature! My oh my. I have to stop writing these late at night!
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Saturday, December 10, 2005

Infidel Guy appearance

The show went really well and lasted two hours! I was able to cover a very broad range of topics and feel quite satisfied. I've been getting a lot of good feedback, so it sounds like people were both enjoying it and learning something. If you're a member over at Infidel Guy you can download a recording of the show.
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Wednesday, December 07, 2005

Internet radio appearance: Live With the Infidel Guy

For those of you who don't know, I'll be appearing this Friday at 8PM Eastern (December 9, 2005) on the Infidel Guy internet radio show with Reggie Finley. I'll be talking about evolution and the fossil record and taking up a few of those really popular creationist canards. I believe the show takes callers if you're interested in asking questions.

Edit: I'd like to welcome all the new traffic from the Infidel Guy site! Thanks for stopping by, I hope you find something of interest here!
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Species is as species does... Part I - Variation vs. Speciation

People often ask me about species in the fossil record, and they are often posing some good questions. This will be the first of a three-part series of entries that I am going to do on this topic.

"How do we know that two fossils - often very similar - are different species?" The especially inquisitive person will often point out an array of different dog skulls and likens it to the similar array of hominin skulls. "How do we know that these alleged hominin species can't interbreed?" The short answer is that we don't know. The difficult part is explaining why it doesn't matter all that much.

Much of the problem seems to stem from an attachment to the Biological Species Concept (BSC) as canonical truth and that knowledge of breeding compatibility has everything to do with reconstructing phylogeny. The BSC states that a species is a population of organisms that can interbreed and produce fertile offspring. It's easy to see why it causes alarm, because it obviously can't be applied to fossils. It's also invalid when applied to asexual organisms (of which there are a great, great many).

In a somewhat concerned tone, this person might also state their belief that, were the different breeds of dogs to be extinct and their skulls discovered by palaeontologists today, we might well classify them as different species. Oh the horror! They would be so dismally wrong and never even know it! Wouldn't this cause dramatic consequences for our phylogenies of animals? The answer is that it's unlikely because of the way phylogenies are reconstructed (as opposed to the way people think they're constructed).

Palaeontologists employ a modern method of systematic biology called cladistics. Cladistics ignores characters unique to individual species because these don't tell us anything about relationships. For instance, if we're trying to figure out how a cow, a trout, and a human are related, the fact that a human has an opposable thumb tells us nothing about how it is related to the cow or the trout, as neither have it. Similarly, the fact that all three have a backbone is useless (except in setting the three apart from invertebrates, but we haven't stipulated that). Instead, cladistics focuses on character that are unique and shared between broader collections of species (i.e. four limbs with digits are uniqu and shared between humans and cows, to the exclusion of the trout).

But first, let's consider how the assumption of species might affect our methods of determining relationships in the first place. Let's imagine that dogs have been extinct for several million years and that palaeontologists have discoverd a bunch of different dog skulls. They've named each distinct type of skull a new species. Suppose that the result of their cladistic analysis looks like this:



Systematists working on extant (i.e. not extinct) animals also use the very same techniques that palaeontologists use (but will employ molecular data, not just morphological data wherever they can). Assuming that the phylogenies are the correct ones, they should get a result that looks like this:



The interrelationships should be identical. The differences are only in the very tips of the branches (breeds vs. species). The assumption of 'species' or 'breeds' is trivial, because the results are the same. The question, however, is would the same result be obtained were it not already known that dogs are interfertile?

The modern complement of dog breeds are (barring some mechanical difficulties) interfertile. They are, apparently, also interfertile with wolves. If we look at an array of dogs, we can see that a key character unites all of the domestic ones: the raised frontal (or 'forehead'):



This clearly sets them apart from foxes (top) and coyotes (bottom):





(by the way, all these great skull pictures are from this fantastic site)

What should be immediately obvious is that, despite the differences between the breeds of domestic dogs, their recent common ancestry with each other is general character that they share in common to the exclusion of other canids and carnivores. This is why modern systematics focuses mostly on shared similarities, rather than on separating them by differences. Because of this fact, domestic dogs (as we know them) would probably have been classified as a single genus, even on the basis of their morphology. Perhaps they would have been classified as distinct species, but as a total group they would have been recognized as distinct from all other canids. Historically speaking, this is identical to the true phylogeny. This is not to say that we'll always have the right answer. Rather, it is to say that by being sufficiently prudent about our classification, we should still be able to uncover the broad-scale patterns of evolution, at the very least.

For palaeontologists, it will never be possible to determine interbreeding relationships. But as long as we don't take the BSC as canon (and we shouldn't), then there is no problem. Naming a new species in palaeontology simply reflects being able to point to a distinctive morphology - preferably if we can show that populations of fossil animals can similarly be categorized. If we're concerned about whether or not two different fossil species (or perhaps even genera!) are interfertile, we are hopeless. However, we should still be able to uncover relative common ancestry. In the diagrams below, we can see that the trees (evolutionary relationships) are identical. However, the taxonomy is quite different.



So a species is as species does: for the purposes of palaeontology, it identifies a range of morphological variation. Since species/breeds are always nested the same way within genera (more inclusive groups of variation), it doesn't really matter if we call them species, breeds, or varieties in fossil animals. As long as they're within the same genus (and don't take the BSC to heart), then we're saying exactly the same thing about the course of evolution. Indeed, there is no question that all the different skulls of the different dog breeds would be classified in the same genus, along with wolves based on morphology.

I'll follow this up in Part II of this post, where I will discuss another nagging question: the classification of dogs and the Tazmanian 'wolf'. If we didn't know it from living specimens (though, thanks to man, it is now extinct), would it not have been classified as a dog?
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Saturday, December 03, 2005

More rhizodonts

My first paper was published two weeks ago in the Canadian Journal of Earth Sciences (Canadian visitors have free online access), so I figure I should put up a notice on here. The work describes a new genus of rhizodontid fish from the Early Carboniferous of Nova Scotia. It was the subject of my undergraduate thesis.
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