Rosio Pavoris a blog

I’m not even talking about apartheid or AIDS. I’m talking about language. Quite apart from the fact that they incomprehensibly keep pretending their dialect is a language in its own right, they keep applying the wrong words to things, and then passing them on to other languages.
Three examples.

Exhibit A: Meerkat

This is probably the most famous example, and also an odd one, because mainstream Dutch is in the wrong here too. Examine the pictures above.

The one on the left is Suricata suricatta, a member of the mongoose family. In Afrikaans this has been called a meerkat, and this has been adopted into English. In regular Dutch it’s a stokstaartje (“little stick tail”).

The one on the right is a vervet monkey (Chlorocebus pygerythrus), one of thirty-five species of Old World monkey in the tribe Cercopithecini, which in Dutch are collectively called meerkatten.

This is, of course, an absurd name for either of those, as meerkat means “lake cat”. If anything should be called this, it should be Prionailurus viverrinus, which currently labors under the descriptive but utterly boring name fishing cat.

This medium-sized cat is semi-aquatic, and while it prefers streams and swamps to actual lakes, at least the name would be sort of appropriate. Being medium-sized, it’s also meer kat than the housecat.

Let’s just agree to call Suricata suricatta suricates, okay?

Exhibit B: Steenbok

The one on the left is Raphicerus campestris, a small antelope native to southern and eastern Africa. For some reason, it was named “steenbok” after the one on the right, Capra ibex, the ibex, one of a few goat species called steenbok in Dutch. I have no idea what Afrikaners call the actual steenbok (the one on the right, that is; I know Germans call it Steinbock, and the other one Steinböckchen—that is to say, the diminutive), but the Dutch have taken to calling R. campestris “steenbokantilope”, which at least is fair enough.

Steenbok, of course, translates to stone buck (as in a male goat), which makes sense for the ibex because it lives in the Alps. It very much does not make sense for an antelope that spends its days in grassland.

Since it’s closely related to the two species of grysbok (which by rights should be spelled grijsbok), call it the fancy grysbok and stop confusing people.
Even though it’s not grey.

Exhibit C: Eland

The last one is particularly ridiculous. Yes, that’s a moose. In Dutch, meese (elk, in European, though the North-American elk is something else; that’s a different discussion) are called eland. Afrikaners named two species of antelope eland because apparently they’re blind. Even the giant eland (Taurotragus derbianus, pictured) doesn’t even come close to Alces alces in size. The common eland, Taurotragus oryx, is even smaller.

The common eland (just eland in Afrikaans) is called the elandantilope in Dutch. The giant eland is reuzenelandantilope (the prefix reuzen- meaning “giant”). If you’re going to keep the dumb name, “eland antilope” and “giant eland antilope” seem like a good compromise.

I hate Afrikaans.

Having said that, there are some words that made it into English that they get right (boomslang, for example, means tree snake, and it’s exactly that), and a lot that, while dumb, aren’t confusing (aardvark (“earth pig”), aardwolf (“earth wolf”), wildebeest (“wild beast”), hartebeest (more correctly hertebeest, “deer-type animal”); all of these are at least vaguely misspelled by modern standards). Many non-animal words that made it into English are even fully accurate: spoor, veld, trek, and, of course, apartheid.
The three listed examples, though, are bunk. The animals are awesome enough to deserve decent names of their own.

And I still say Afrikaans is just a dialect of Dutch. It’s closer to standard Dutch than, say, Limburgs or West-Vlaams, and while there’s a movement to have those recognised as separate languages, that’s a tiny, tiny minority. The only real difference is that Afrikaans has a standardised spelling and good reasons to hate the Dutch.

(But then, so do we.)

One thing that continues to annoy me whenever my internets get into a discussion about race is that invariably, very nearly everyone gets it wrong. The most recent example of this is, of course, when some Stormfront morons declared war on Pharyngula.

On the one hand you have the common racists, which are wrong for obvious and uninteresting reasons, but on the other you have the “enlightened” people who claim race is entirely a social construct, or at least of no significance whatsoever. They’re wrong too.

The following is an excerpt from Richard Dawkins’ The Ancestor’s Tale, which I finished a few weeks ago. It may be the clearest explanation I’ve seen so far.

It is genuinely true that, if you measure the total variation in the human species and then partition it into a between-race component and a within-race component, the between-race component is a very small fraction of the total. Most of the variation among humans can be found within races as well as between them. Only a small admixture of extra variation distinguishes races from each other. That is all correct. What is not correct is the inference that race is therefore a meaningless concept. This point has been clearly made by the distinguished Cambridge geneticist A. W. F. Edwards in the recent paper called ‘Human genetic diversity: Lewontin’s fallacy’. R. C. Lewontin is an equally distinguished Cambridge (Mass.) geneticist, known for the strength of his political convictions and his weakness for dragging them into science at every possible opportunity. Lewontin’s view of race has become near-universal orthodoxy in scientific circles. He wrote, in a famous paper of 1972:

It is clear that our perception of relatively large differences between human races and subgroups, as compared to the variation within these groups, is indeed a biased perception and that, based on randomly chosen genetic differences, human races and populations are remarkably similar to each other, with the largest part by far of human variation being accounted for by the differences between individuals.

This is, of course, exactly the point I accepted above, not surprisingly since what I wrote was largely based on Lewontin. But see how Lewontin goes on:

Human racial classification is of no social value and is positively destructive of social and human relations. Since such racial classification is now seen to be of virtually no genetic or taxonomic significance either, no justification can be offered for its continuance.

We can happily agree that human racial classification is of no social value and is positively destructive of social and human relations. That is one reason why I object to ticking boxes in forms and why I object to positive discrimination in job selection. But that doesn’t mean that race is of ‘virtually no genetic or taxonomic significance’. This is Edward’s point, and he reasons as follows. However small the racial partition of the total variation may be, if such racial characteristics as there are are highly correlated with other racial characteristics, they are by definition informative, and therefore of taxonomic significance.

It’s not surprising that Lewontin’s¹ views are most popular in the US, where casual racism is so common many smart people are so eager to dissociate themselves from it they swing too far in the other direction.

Dawkins then goes on to say that if we have a person and we are told about his sex, we immediately know more about the shape of his genitals, though not with absolute certainty. That is to say, our uncertainty about some of his attributes is reduced. Similarly, if we are told this person is black, our uncertainty about a number of his attributes, such as (but not exclusively) the color of his skin, is reduced as well, so it’s intuitively obvious that race cannot be exclusively a social construct.

The whole thing is worth reading, though the book as a whole is not his best. If you’re going to buy it, buy the hardcover version. It’s expensive, but the book relies on pictures too much for the paperback to be very useful.

Incidentally, contrary to what aforementioned Stormfront morons claim, there is no conclusive causative link between race and IQ. It’s true that blacks on average have a lower IQ than whites in the US, but that difference disappears once you adjust for class (the lower classes tend to have lower IQs than the upper classes, of course, given the strong correlation between IQ and education levels), and the fact that blacks on average tend to be lower class than whites seems to be more of a result of discrimination based on racism than it is of anything inherent in blacks.²

Either way, this whole discussion makes me tired. Talking to either side in it is like talking to a brick wall.

¹ It should also not be surprising that Lewontin is an erstwhile compatriot of Gould’s, and a longtime opponent of the straw-man “genetic determinism” of evolutionary psychology.

² And to the “other side”, before you try to dispute the validity of IQ testing, I suggest you at least read this article (Wikipedia has an article about that article).

Memes evolve, and even creationist memes are no exception. It used to be that they denied things like antibiotic resistance in bacteria and pesticide resistance in insects even existed, but now most of the ones that actually end up “debating” sane people seem to agree that “micro-evolution” happens, but “macro-evolution” doesn’t.
The distinction is meaningless, of course, and the argument amounts to nothing more than “I believe in small changes over a small period of time, but not large changes over a large one”. The implication that there is some invisible barrier to speciation, though, still tends to stump many of the people they’re debating, because it’s not necessarily easy to come up with an example that’s simple enough for the wilfully ignorant to understand, and examples of observed speciation in bacteria doesn’t tend to impress people who only barely believe bacteria even exist, much less that it’s meaningful to speak of different species of them.

Ring species, however, are such an example. They demonstrate a gradual process of speciation, and they manage to do it in a way that’s observable in real time.

Put simply, with ring species you have a series of populations along a line or open ring (often a coastline or a river bank, actually). Each of these populations can breed with itself (obviously) and with its slightly different neighboring populations. Perhaps some populations are classified as different subspecies of some overarching species; it’s difficult to point down where one subspecies ends and the next begins, though: the populations basically form a continuum.
The punchline, though: though each population can breed with its neighbors and produce fertile offspring (which, according to a popular definition, makes them the same species), the populations at the ends of the line cannot. They are, in effect, different species.

The canonical example is the herring gull complex around the north pole.¹

The ring starts on the shores of the northern North Atlantic with the herring gull Larus argentatus. It can interbreed freely with the American herring gull Larus smithsonianus,² which occurs, surprisingly, across North America.
The North American herring gull can interbreed with the Vega gull Larus vegae, which is a subspecies of the East Siberian gull (the only other subspecies is the Larus vegae mongolicus, which isn’t relevant to our story). That in turn can interbreed with Heuglin’s gull, Larus heuglini, which can interbreed with the Siberian lesser black-backed gull Larus fuscus heuglini, concluding our trip across northern Siberia.
The Siberian lesser black-backed gull can interbreed with the lesser black-backed gull Larus fuscus, which bring us back to Europe, mostly around the Baltic Sea, though they share some territory with the herring gull.³

These gulls form a species continuum, as you can see, but the herring gull cannot interbreed with the lesser black-backed gull.
It’s hard to tell where one species ends and the next begins, but it’s undeniable that the herring gull and the lesser black-backed gull are different species.

This is just one mechanism of speciation (allopatric speciation; these gulls inhabit much the same niches, so this is nearly entirely down to genetic drift, too), but it’s a plainly obvious one.⁴

Of course, most creationists would just reply “but they’re all still birds”, which is a level of ignorance against which little can be done.
Some of the more literate ones might point out that not only are they all birds, they’re all still in the genus Larus, moving their non-existent barrier to speciation to a barrier to “genusiation”, but that’s no more to the point than to point out that all new growth on an old tree seems to happen at the bud level, with only new twigs being born, and that no new massive boughs have been added to it in decades.

(Incidentally, there’s an interesting parallel in linguistics, with the dialect or language continuum. Flanders is a good example of it, with most of its many, many dialects being intelligible to its immediate geographic neighbors, but people on one end of the region not being able to understand a damn thing people on the other are saying. It can probably be argued that the Limburgs dialects make Dutch form a language continuum with German.)

¹ I’m aware of the Liebers/de Knijff/Helbig paper, and I slightly disagree with its conclusion that the Larus species complex does not represent a ring species. Regardless of how it was formed, it’s a ring now. There may be contexts in which it’s not useful to speak of it as a ring species, but that isn’t relevant here.
If you want to argue about this, by all means do.

² And, indeed, is almost indistinguishable from it to the untrained eye. The American herring gull is a bit bigger, though.

³ The taxonomic story is actually a bit more complex than that, obviously. For instance, the gulls in the eastern part of the range of the Heuglin’s gull are often considered a separate subspecies (Larus heuglini taimyrensis, or the Taimyr Gull), but some people believe these to just be the result of interbreeding between Heuglin’s gulls and Vega gulls; and of course most species names are in dispute: the Vega gull is sometimes classified as Larus argentatus vegae, and people seem to be confused over what the Siberian lesser black-backed gull actually is.
This is something for taxonomists to squabble over, though, and I’m not convinced it’s a productive use of anyone’s time.

⁴ If the Liebers paper makes you nervous, there are other, less controversial examples of ring species, including Ensatina salamanders around Central Valley in California, and greenish warblers around the Himalayas.

After watching a few more videos by and about creationists on the YouTube, I realised that not only do I have more computing power at my fingertips than most scientists in history could ever have dreamed of and a greater-than-average ability to use said power, I also have a neat, educational, and easily implemented project to use it for.

Perhaps you remember the weasel program, but in case you don’t, here’s how my implementation worked:
The user enters a string consisting of characters from a certain pool (in our case, just capital letters and spaces). The program generates a random string of character from that pool, of the same length as the string the user entered. Every “generation”, the program takes one character in that string at random, and replaces it with another random character from the pool; it then compares the new (offspring) string and the old (parent) string to the target string the user entered, and discards the string that’s least like the target. The other one goes on to be the parent in the next generation.
This continues until the program’s own initially random string matches the user’s.

It’s a very simplistic example of Darwinian evolution, and while the point of it can be missed by people aiming to miss it, it demonstrates the power of evolution quite well.

Of course, casually running the program, seeing the number, and nodding absent-mindedly before forgetting all about it is no way to treat a nice algorithm, so I decided to drive the point home by modifying it a bit.

I decided to do a series of tests with successively longer strings (starting with one character, working up to fifty), and record how long it took on average to get from the random starting string to the target string (which is now just a series of As; I hope you realise why this doesn’t matter). The pool of characters was brought down from 27 possible characters to 10, to speed up execution times¹, and each test was then run five thousand times, to get rid of statistical artifacts.
The results were then plotted on a graph:

The X axis is the length of the string. The Y axis is the number of generations it took to get from a random starting string to the target. The blue line is the results my program found. The red line is how long you’d expect to take on average if you just rerolled the string entirely, which is how most creationists seem to think evolution works (the “tornado through a junkyard” fallacy).
For a string of length 50 this number is (10⁵⁰)/2, so forgive me for cutting it off the graph pretty early on.

There are some odd spikes the large sample size should have gotten rid of, which I blame on java.util.Random crapping out², but the trend is pretty clear all the same. (Edit: yeah, the problem was indeed that, and specifically how Java caches things in ways that breaks seeding random number generators. I fixed the issue as best I could and ran the program again; the results are here, and the spikes are indeed gone.)
It took about half an hour to run on my laptop, and the results are even clearer than I expected. Rather than the exponential growth in the number of generations needed so many creationists “predict”, there’s a linear one, which is much healthier.

You can debate how directly this applies to real-life evolution, since organisms tend to have genomes rather larger than fifty base pairs (though their pool of characters is only four, not ten), but they also tend to have more than one kid, and evolution is a trend over an entire population, not just one lineage, and they tend to have more than one mutation per generation (not to mention a bunch of other ways to stir things up, like chromosomal crossover), and sexual reproduction makes a whole new mess of everything.
The point, though, is to show the power of the Darwinian process; specifically, that it’s not just random chance, but something much, much more powerful.

Of course, people can show you all kinds of graphs and give you all kinds of programs to run, but it’s much more satisfying if you do it yourself and understand what you’re doing.
So I’m not going to post my code. Do it yourself. You have the algorithm (and if you think it sucked, improve on it (and post in the comments)), write your own code. It’s simple enough, it’s fun, and it’s quite gratifying.

¹ I also made a multi-threaded version of the program which works with a pool of fifty characters and goes up to string lengths of 500, and it’s been running on my reasonably pathetic cluster for the past two hours. I expect it to finish in a few weeks, unless the fans give out again and the entire cluster shuts down.

² ENTERPRISE TURKEY SOLUTIONS

This took a while to finish. In part because I’m reading too many books at once, but also because it’s so depressing I had to put it down a few times.
Silent Spring, by Rachel Carson, published in 1962, is single-handedly responsible for revitalising the environmental movement around the world. I wanted to read it just for historical context, but the message is so powerful and important that it’s still a very important book.

The book is mainly concerned with indiscriminate pesticides (biocides) such as DDT and various chlorinated hydrocarbons. The book is, of course, famous for inspiring a movement that would very quickly get most of these banned, and it’s very obvious why.
She describes the various projects in the ’50s and ’60s that used these biocides, and how they have a tendency to not just affect the insects or plants targetted, but also, through a process of bioaccumulation in which the pesticides get stored in the bodies of animals in greater and greater doses as they travel up the food chain (that is, a single insect may contain X amount of DDT; a bird that eats twenty of those insects would contain 20X, and because it passes from the system only very slowly, it will remain there while that bird keeps eating insects, or while it is eaten itself), with the result that in the end, applications of these biocides end up killing enormous numbers of larger animals; several projects she described have been successful in wiping out all birds, squirrels, and fish in the (generally very large) treated areas, while not affecting the target insects very much at all, except by removing its natural predators, which, of course, is rather counterproductive.
And of course it’s not just dangerous to birds and the like. She documents a number of cases of human casualties; hardly surprising, given the toxicity of the products involving. Even if death doesn’t occur, permanent brain damage is far more common than it should be, in people handling or just being casually exposed to these supposedly safe products.
And even forgetting the immediate toxicity, there are long-term effects to be considered. Many of the products she talks about (including DDT) are powerful carcinogens. And speaking of long-term effects, insects, with their short generation times, are, of course, going to build up a resistance (and already have), so people will only keep using more and more dangerous pesticides.

She ends the book with alternative approaches to insect control, mostly through introducing natural predators of the insects involved. This has the advantage of being much cheaper and species-specific, and there’s no danger of developing resistance. Or, of course, poisoning your cat.

It’s all very, very depressing to read. If nothing else, it destroyed the myth that “if it’s bad for you, the government wouldn’t allow it!”. Fortunately, Carson’s book made a difference and got all of the products she discusses essentially banned; DDT was banned in the US in 1972, and in most of the rest of the world over the next few decades. Dieldrin, aldrin, endrin, chlordane, heptachlor, and its ilk soon followed.
Regulations on biocides and pest control became stricter and more sane, and most of the projects Carson describes would now be immediately dismissed as retardedly reckless.

Still, it’s alarming how many assholes are out to reverse the DDT ban. The meme that a DDT ban caused thousands/millions/billions of preventable deaths due to malaria is still out there, and for some inexplicable reason gaining support, even though it’s complete nonsense.
It’s important to remember that these people, regardless of their motivation (be it Kool-Aid-flavored ignorance or outright malice (well, greed; same thing)), are very directly working to kill your children.
This is only barely hyperbolic.

(If Rachel Carson and the things she cares about interest you, Deltoid is a very interesting blog that often deals with DDT nutjobs.)

This is something that’s been annoying me recently.
If you’ve ever had a discussion with a creationist (not, like, a run-of-the-mill creationist whose only argument is “evolution is false because my pastor says it is”, but a creationists who thinks his views are defensible), chances are that at one point, they said something like “evolution is false because it can’t even explain how life began”, or something along those lines.

And if this was on a public forum, chances are also good the very next reply was from a non-creationist, saying that evolution doesn’t deal with the origin of life, only with how life behaves when it’s already there, and that what he’s thinking of is abiogenesis, and this has nothing to do with evolution one way or the other.
That possibly annoys me more than the actual creationist, because it shows that the person either doesn’t understand evolution, or that he’s copping out.

Evolution isn’t separable from abiogenesis; it doesn’t have to be. This is because evolution doesn’t just apply to living things (unless you specifically define life as “that which evolves”, which is probably too permissive a definition, in my opinion), and there is no clean break between life and non-life anyway.
The break between evolution and abiogenesis is artificial and contrived.

Evolution

How do you define (Darwinian) evolution?
There have been many definitions over time, but for the most part, they require randomly variable heritable traits on the one hand (genes, for example), and a (non-random) selection process on the other.

Does something have to be alive for evolution to apply to it?

When you’re talking about life, viruses always seem to come up.
By most accounts, they aren’t alive. They’re strands of genetic material in a simple protective coat of protein. They don’t eat, they don’t drink, they can only reproduce by literally being copied by a host cell’s copying apparatus, which is a relatively simple chemical reaction.
They’re large but simple aperiodic crystals, and they aren’t alive.

But evolution obviously applies to them. They grow resistant to medication used against them, they adapt to changing host environments, and they even speciate (though virus speciation isn’t entirely comparable to speciation of higher organisms, because they’re so damn simple).¹

Abiogenesis

Abiogenesis is simply about evolution applying to prebiotic molecules similar to viruses (but even simpler) and the chemical reactions they go through.²
It’s not something that magically happened before evolution kicked in. It’s inextricably intertwined with evolution, and evolution is a very important tool in understanding how it worked.

Now, it’s true that if we didn’t have any clue how abiogenesis could possibly have happened, evolution is still a fact, in the same way that umbrellas don’t stop working because we don’t know where rain comes from, but that’s no reason to claim rain and umbrellas are unconnected.

I can see the appeal of separating them. It catches the creationists off guard, and often destroys their entire argument. They don’t have a logical basis for their beliefs, so they often can’t adjust to that new bit of information by themselves.
It also gives theistic evolutionists something to feel good about, by allowing God to move into another gap. “See, evolution is real, but God still created life!”

However, when creationists say evolution is false because it can’t account for the origin of life, the mistake they’re making isn’t that they’re conflating evolution and abiogenesis—it’s that they assume we don’t have a clue how life started.

If you don’t want to explain the whole thing to them, or you don’t know enough about the whole thing to explain it to them in the first place, saying they should be separated is a handy cop-out, but a cop-out is all it is.

¹ If you do want to define life as “that which evolution applies to”, then yes, viruses are alive. But then you have to deal with things like the Weasel program also being alive.

² Darwinian evolution isn’t the only force that applied to these things, obviously—non-Darwinian selection played its part as well. But then, it still does.

Here’s another argument I’ve seen come up a few times—I don’t intend to correct every single misconception I run into on the intertron, but this one is basic and common enough it’s worth addressing.

Have humans stopped evolving?

The argument tends to go something like “normally the weak die out and the strong survive, and that’s evolution, but humans have the technology to let the weak survive so clearly we aren’t evolving anymore!”, though usually the spelling is worse than that.
This reflects some fundamental misunderstanding of evolution, and natural selection’s place in it.

Selection and Evolution

Selection (be it natural or artificial) isn’t what makes species evolve. You could say that it guides evolution, but it doesn’t drive it.
The distinction is rather important if you don’t want to make an ass out of yourself by asking stupid questions.

The real driving force—the only driving force¹—of evolution is mutation.
This is obvious if you think about it. Selection (of any kind) doesn’t produce variety, and Lamarck, obviously, was wrong.

What selection does is prune out the harmful mutations (because yes, most mutations that have phenotypic effects are harmful), and get rid of the “less fit” organisms.
“Less fit” for what? To survive and successfully breed in their habitat.

This means that if the habitat of an organism hasn’t changed in a long time, it’s likely to be relatively close to ideally suited to thriving in it, which means that the overall effect of natural selection will be to maintain the traits of the parents in the offspring.
To most people who ask this sort of question, natural selection would seem to be the opposite² of evolution in these cases.^{3 4}

If the environment the organism has to survive in has changed recently, a species can undergo very dramatic changes in relatively short periods of time, but it’s important to realise natural selection is not the driving force here—mutation is.

Selection can only act a brake on evolution. If technology enabled mankind to be free of any of the pressures of selection, we’d be evolving faster than ever.⁵

Selective Pressures on Humanity

That was the first thing I wanted to get out of the way. Next, the claim that technology enables mankind to be free of any of the pressures of selection.

It’s bullshit.

Have we cured all diseases? Malaria alone still kills between one and three million people a year, and that one we supposedly know how to cure. Even the goddamn measels claim hundreds of thousands of people each year.
And forget diseases—what about our own bodies? Cardiovascular disease is still the most common cause of death worldwide, and cancer is responsible for 13% of all deaths.
And don’t forget that most pregnancies end in miscarriage; that’s some powerful selection right there.

And technology has brought us another very potent source of natural selection: pollution.
Air pollution means that suddenly a mild asthma that wouldn’t necessarily kill you in the past becomes life-threatening. Water pollution kills over five million people a year. Soil pollution degrades the quality of our food and threatens our health. Radioactive pollution renders us sterile. Noise and light pollution increase stress levels, which leads to increased blood pressure and heart problems.

And what about sexual selection? Or will you just have kids with anyone?

Conclusion

To sum up, yes, humans are still evolving, and yes, we’re still under selective pressures.
We’ll be subject to natural selection for a long, long time, and there’s no reason to believe we won’t be subject to artificial selection for a long time after that. And even if we weren’t, we’d still evolve. I’m sure technology affects natural selection (and by extension evolution), but it doesn’t stop it.

Obviously asking questions is always a good thing, but if you’re going to base your assumptions regarding evolution on Pokémon, it might be a good idea to just pick up a book in the future.
There are plenty of good, readable books out there that will help you think about evolution. Personally, I’d recommend Richard Dawkins’ The Selfish Gene (obviously), and Daniel Dennett’s Darwin’s Dangerous Idea.

¹ Yes, sexual recombination helps, but if you only had sexual recombination as a source of variety, your total population would shrink rather exponentially; and even sexual recombination requires variety to start with, and the only source of that is random mutations.

² “Devolution” isn’t a term that makes sense, shut the fuck up. The opposite of evolution is a lack of evolution, not devolution.

³ Obviously this is related to Eldredge and Gould’s punctuated equilibrium, which predicts rather long periods with no real change interspersed with quick periods of rapid change (arms races aside), and should be distinguished from saltationism or quantum evolution. The idea of gradualism isn’t bullshit as such, it’s just a lot rarer.

⁴ Yes, I’m essentially an adaptationist. No, that doesn’t mean I don’t think neutral phenotypic effects (like the African rhinoceros’ second horn) can’t be fixed, à la spandrels. Grow up.

⁵ I like footnotes.

Perhaps you’re already familiar with the idea behind METHINKS IT IS LIKE A WEASEL; it’s a simple program designed by Dawkins to demonstrate the enormous power of Darwinian evolution. He originally mentioned it in his book The Blind Watchmaker, and gave a demonstration of it in the accompanying BBC programme.
He also explains it in this shorter video (using a different phrase, but the idea is obviously the same):

(Earning that Public Understanding of Science badge. Near the end he also explains the title of another one of his books, Climbing Mount Improbable.)

Because I was bored, I’ve written a similar program (bytecode here, if you’re too lazy to compile) just now. It differs from Dawkins’ original design in a few ways.

First off, there’s only one offspring per generation, and rather than picking the best of the pool of kids, it simply picks the best of the kid or the parent.
Secondly, rather than each letter having a given chance to mutate, it just changes one letter per generation. This slows down the improvements early on, but it reduces the chances of reproduction severely messing up a nearly-correct string (my first test using random mutations took over six thousand generations just to get the final letter right; real evolution doesn’t work towards a goal it needs to get just right, so it’s not under that kind of restriction).
Thirdly, it actually kind of sucks, because you can’t really see it change as it goes. It just dumps data into the output window, and it scrolls too fast to actually follow. Still, you can scroll back a bit once it’s done.

I ran it a few times, and it seems to take about two or three thousand generations (that is, a few seconds; since this is kind of like bacterial asexual reproduction, that’s actually next to no time at all) to get from the random starting string to METHINKS IT IS LIKE A WEASEL. I could calculate how long it takes on average, but I’ll leave that as an exercise to the reader.

People have been talking about this recently, mostly sparked by some creationists calling it an example of Darwinian fundamentalism, followed by some atheist evolutionary biologists going “lol i dont believe it”.

Let me start by saying that evolutionary psychology, as it stands today, is indeed almost entirely pseudoscientific bullshit. This seems to be because psychology in general is pseudoscientific bullshit, and this is because people don’t really seem to know how to approach cognitive science.
The most obvious bullshit in psychology seems to derive from Freud and Jung, which is quite embarrassing, since their flaws should be immediately apparent to anyone who’s ever had the misfortune of sitting through a lecture on their ideas.

I’m not saying (Scientology-style) that psychologists are necessarily useless because of this, and that people should instead rely on dianetics/prayer/meditation/magic potions. Psychologists have value as a person for people with genuine problems to talk to, which helps more than most people realise, and like it or not, psychology is still the best we have, even if it isn’t very good.
Evolutionary psychology, of course, is doomed to inherit these flaws.

I do believe, however, that if we are ever going to make sense of human behavior, it has to be through the lens of our evolutionary history.
Obviously, I’m not a strict genetic determinist; some animal species’ behavior is clearly directly influenced by their genes (the case-building of caddisflies is a classic example, but there are countless more, and not just in the insect world), but humans are by their very nature generalists. There is very little behavior that’s hardwired (PZ wrote about this earlier, though he seems to be attacking a straw man at one point), and most specifically human behavior seems to be taught, not inherited.
This is (part of) the nature versus nurture debate again.

But it’s insane to deny that our genes play a very large part in determining who we are and what motivates us. Things like the desire to reproduce and raise children aren’t taught, and they’re a very fundamental part of what it means to be human; and they’re inescapable.
I know there are always those who want to pretend evolution doesn’t apply to humans, and that we stand outside nature, but that’s just chauvinistic nonsense.

There’s always a danger in making sweeping generalisations and jumping to conclusions (I’ll be the first to admit that my own foray into this area a while ago was an embarrassing failure), but knee-jerk dismissals of anything that looks like evolutionary psychology seem to me to be far more harmful than a few well-intentioned but ultimately ill-advised assertions.

I don’t know. Maybe there are fewer people disagreeing with this than seems to be the case, and I’m just preaching to the choir, but I wanted to get this out in the open just in case. Comments plz.

I don’t think I’ve posted this before. Carl Sagan on evolution and selection both artificial and natural. (06:24)

I finished this one a while ago, but I guess I never got around to reviewing it. What is Life? is, of course, a famous work by Erwin Schrödinger, of cat fame.
In it, he argues that chromosomes behave according to physical laws classical physics can’t really approach, since classical physical laws are statistical, and only hold for large numbers of molecules, while a chromosome is in essence just one very large molecule. He speculates that DNA is, in fact, a large aperiodic crystal, and muses about the ways in which it could encode hereditary information.

And yes, it’s all speculation. This was written in 1944, well before the actual structure of DNA became known, and, indeed, long before much of anything was known about genetics. It still speaks about DNA as being the carrier of heredity in the hypothetical, even.
What is Life? was a visionary work, and its influence is undeniable. Even today, it can still inspire people because of the intense sense of curiosity it conveys (Schrödinger was, after all, a theoretical physicist first, but he didn’t let that stop him from delving into this alien field of biology).
As a source of accurate information, though, it’s much more likely to misguide than to educate, at this point, so it really isn’t a book uninformed laypeople should be reading. Still, if you know a bit about genetics and molecular biology, it’s a very interesting read for its historic value.

This edition also contains Mind and Matter, an essay I didn’t bother reading since I figured it would make me angry (especially since Roger Penrose wrote the introduction), and Autobiographical Sketches, in which Schrödinger talks about his life.
This is particularly interesting, since Schrödinger was, after all, a scientist during the World Wars (which is always an interesting topic; just look at Richard Feynman). Moreover, he was Austrian, so he spent much of his time on the side we never really hear first-hand accounts from. It’s nice to hear someone talk about this without the off-hand demonisation we’ve become so used to.

The Naked Ape, by Desmond Morris, is about humans, from the perspective of a zoologist.
I mostly read it because my mom loves the guy, but I’d been meaning to read it because I’d been told he touches on the neotenous ape hypothesis too. (Turns out he doesn’t say anything new.)

While the zoologist perspective is refreshing even now, forty years after it came out, most of the actual information in it is either very obvious (to anyone with half a brain) or very outdated.
A lot of religious people were apparently outraged by it, but I’m not convinced most were just because “it places man in nature”. The sections on sex and sexuality were often just gratuitous (and if I noticed, you know it has to be bad), and a much more likely source of outrage.

It really is quite dated, though, and likely to give inexperienced or casual readers completely wrong ideas about a number of things, including some basic facts of evolution.
My copy was a new edition released in 1994, and the preface made it clear Morris thought everything he wrote still applied perfectly, and wasn’t in need of updating, even though his editor had asked him to, so I’m not inclined to cut him much slack on that account. The Naked Ape just isn’t a very good book.

The Double Helix, by James Watson, is an account of Watson and Crick’s part in the discovery of the structure of DNA, and of the people involved.

A lot of people have called this a brilliant work of non-fiction, and an important step in de-mystifying science for the general public, but to me it mostly demonstrated that James Watson is a arrogant, prejudiced asshole and a condescending sexist, who has a ridiculously poor understanding of his own field, but managed to ride the coat-tails of his betters (almost all of the work had already been done long before Watson turned his attention to it, and he still had to depend on the insights of Crick, Donohue, Franklin, and others to get there in the end) and convince himself that he’s the center of the universe in the process.

It was written fifteen years after the fact, so even it’s factual accuracy isn’t something I’d put too much faith in. If it’s supposed to give people an idea of how “creative science really happens” (as one of the cover endorsements suggests), it’s no wonder most people are distrustful of scientists.

The same book written by Francis Crick (or Maurice Wilkins, or Rosalind Franklin, or anyone besides Watson) would’ve been infinitely more interesting.

Today is the 125th anniversary of Charles Darwin’s death.
Why didn’t he just evolve immortality, eh, if he’s so great? Hur hur hur.

Anyway. Pharyngula has a bit about his final moments.

As part of her blog tour, Lynn Margulis (mostly known for being Carl Sagan’s first wife, I guess) was doing Q&A in #pharyngula today.
It just ended ten minutes ago, and I thought it was rather underwhelming. I missed parts of it, but Margulis strikes me as a stopped-clock-is-right-twice-a-day type of “revolutionary”, for various reasons.
It’s a pity nobody asked her about the HIV/AIDS thing (she seems to deny there’s any connection).

If anyone’s interested in logs, there’s one here (unedited, so somewhat noisy).

(No, this isn’t an un-hiatusing.)

Roy Zimmerman appears to be awesome.

(Via this person.)

I still haven’t managed to find a paper copy of Charles Darwin’s On The Origin of Species by Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life (seriously, that’s the title; I think I’ll end up having to order it online), but LibriVox, a website that creates and makes available public domain audiobooks for free, has recently put up a set of recordings of it.
If you’d rather read, of course, Project Gutenberg has had it for a while now.

This is why I love the public domain, and the internets.

The term “just-so story” goes back to Rudyard Kipling’s 1902 collection of short stories titled, surprisingly, Just So Stories. (Thanks to Larry Moran for that link.)
The stories were aimed at children, and “explained” certain features of the world. Most of them dealt with animals.

Perhaps the most famous one is The Elephant’s Child, in which Kipling explains how the elephant got its trunk.

‘Come hither, Little One,’ said the Crocodile, ‘and I’ll whisper.’

Then the Elephant’s Child put his head down close to the Crocodile’s musky, tusky mouth, and the Crocodile caught him by his little nose, which up to that very week, day, hour, and minute, had been no bigger than a boot, though much more useful.

‘I think,’ said the Crocodile–and he said it between his teeth, like this–’I think to-day I will begin with Elephant’s Child!’

At this, O Best Beloved, the Elephant’s Child was much annoyed, and he said, speaking through his nose, like this, ‘Led go! You are hurtig be!’

Then the Bi-Coloured-Python-Rock-Snake scuffled down from the bank and said, ‘My young friend, if you do not now, immediately and instantly, pull as hard as ever you can, it is my opinion that your acquaintance in the large-pattern leather ulster’ (and by this he meant the Crocodile) ‘will jerk you into yonder limpid stream before you can say Jack Robinson.’

This is the way Bi-Coloured-Python-Rock-Snakes always talk.

Then the Elephant’s Child sat back on his little haunches, and pulled, and pulled, and pulled, and his nose began to stretch. And the Crocodile floundered into the water, making it all creamy with great sweeps of his tail, and he pulled, and pulled, and pulled.

Nowadays, “just-so story” is mostly used in academic contexts, particularly in anthropology, sociology, and evolutionary biology, for a narrative explanation of a certain cultural practice or behavior or biological feature that is (perhaps just perceived to be) unfalsifiable.

Consider, for example, this story on how birds may have gotten their wings, from Richard Dawkins’ Climbing Mount Improbable:

Here’s one guess as to how flying got started in birds. The hypothetical ancestor, which we can imagine as a small, agile, dinosaur, runs fast after insects, leaping in the air with its powerful hind legs and snapping at the prey. Insects had evolved into the air long before. A flying insect is perfectly capable of taking evasive action, and the leaping predator would benefit from skill in mid-course correction. To some extent you can see cats doing this today. It seems difficult because, since you are in the air, there is nothing solid to push against. The trick is to shift your centre of gravity. You can do this by moving bits of yourself relative to other bits. You could move your head or tail, but the obvious bits to move are the arms. Now, once the arms are being moved for this purpose, they become more effective at it if they develop surfaces to catch the air. It has also been suggested that the feathers on the arms originally developed as a kind of net for catching insects. This is not so far-fetched as it sounds, for some bats use their wings in this way. But, according to this theory, the most important use of the arms was for steerage and control. Some calculations suggest that the most approppriate arm movements for controlling pitching and rolling in a leap would actually resemble rudimentary flapping movements.

Just-so story? Perhaps.
But it helps teach the reader how to think about evolution as a gradual process, and it also throws in the concept of exaptation. It’s a valid and valuable teaching tool.

That isn’t the only use for just-so stories, however. They can also help researchers by giving them a new angle from which to approach a certain subject.
For example, Cairns-Smith’s clay hypothesis is now generally accepted not to have been the exact mechanism behind abiogenesis, but it’s still quoted a lot as an example of the kind of mechanism that could have caused it.

Yes, it’s possible to get too caught up in just-so stories and give them more credit than they deserve (evolutionary psychology in particular seems to suffer from this), and there’s a good reason “just-so story” is often used as harsh criticism, but they’re more valuable than many people are willing to admit.

(Of course, another important problem with the concept is that it’s pretty easy for creationists (and such) to take just-so stories out of context and claim they’re evidence of poor science, or that well-tested and uncontroversial hypotheses (such as the development of the eye, still) are nothing more than just-so stories themselves.)

I don’t remember how I came across this, but it’s made of epic win.
If you have several days to spend on improving yourself, watch all of those videos. All of them. Reading his books would be better, of course, but still.
I think the biology videos are more interesting than the religion ones, but it’s all good. (Well, except for the BBC profile, which starts out promisingly enough, but then just runs itself face-first into the ground by completely misunderstanding both the entire premise of the selfish gene and the function of religion.)

Richard Dawkins makes me happy in the pants.

I was reading Daniel Dennett’s Consciousness Explained (so far it hasn’t been very impressive, though I’m only on the fourth chapter), and I saw this passage.

There is a species of primate in South America, more gregarious than most other mammals, with a curious behavior. The members of this species often gather in groups, large and small, and in the course of their mutual chattering, under a wide variety of circumstances, they are induced to engage in bouts of involuntary, convulsive respiration, a sort of loud, helpless, mutually reinforcing group panting that sometimes is so severe as to incapacitate them. Far from being aversive, however, these attacks seem to be sought out by most members of the species, some of whom even appear to be addicted to them.
We might be tempted to think that if only we knew what it was like to be them, from the inside, we’d understand this curious addiction of theirs. If we could see it “from their point of view,” we would know what it was for. But in this case we can quite sure that such insight as we might gain would still leave matters mysterious. For we already have the access we seek; the species is Homo sapiens (which does indeed inhabit South America, among other places), and the behavior is laughter.
No other animal does anything like it.

Quite apart from the point he goes on to make, this just isn’t true. Aristotle may have observed that “only the human animal laughs”, but Aristotle was wrong about a lot of things.

All four extant genera of great apes (which is to say, humans, chimpanzees, gorillas, and orangutans) laugh, though the laughter of non-humans may not always be immediately recognisable to humans. Their laughter sounds more like regular panting than actual laughter, possibly because of differences in their vocal cords.
There is evidence to suggest many non-ape primates laugh as well.

Further up the genetic stream, but probably more familiar to most people, are dogs. Their laugh sounds a lot like excited panting as well, but spectrographic analysis reveals that it’s actually quite distinct. Anyone who’s owned a dog for a while will generally be able to recognise it as well.
Experiments have been performed where dogs were exposed to a recording of a laughing dog, and its effects on their behavior was monitored. The dogs exposed to the recording were found to be more playful, and their stress levels seemed to be reduced. This suggests laughter has much the same role in dogs as it does in humans.

And finally, rats seem to laugh as well. Their laughter is ultrasonic, so humans can’t hear it, and they mostly seem to laugh while playing or being tickled.
Apparently some scientists manage to get research grants for tickling rats.

Either way, humans are far from the only animals that laugh. Some people would argue that self-awareness or the ability to identify with somebody else’s predicament are prerequisites for laughter, so animals are not really laughing in the same way that we do, but that’s just species chauvinism.

Edit: Coincidentally, John Wilkins quotes Daniel Gilbert on a topic quite relevant to this.