I *heart* Conservapedia

So much. So much! You just can't make this stuff up. God, I love Conservapedia.

LINEs, SINEs, and the Design Inference

Transposons are wacky little genes, and really kind of cool. You can see Wikipedia's explanation of transposons here, but I'll give you the short version. What I'm describing here are what Wikipedia calls Class II transposons.

A transposon is a sequence of DNA that can move around in your genome. It comes in long and short versions, and copies of it are found interspersed throughout the genome. The long ones (Long INterspersed Elements, or LINEs) encode one protein, a transposase. What the transposase does is it cleaves the transposon from its current location and inserts it elsewhere in the genome. And that's ALL it does. SINEs (Short INterspersed Elements) do even less. What they do is be sequences that the LINEs' transposases recognize, and therefore transpose. And that's fucking IT.

Transposons are quite possibly the wackiest things I've encountered all week. They don't DO anything. By which I mean, they have no influence on an organism's life cycle. They just hang out in your genome, moving around and taking up space.

I like things like transposons because they really drive the point home that we're just something that happened. When you're studying stuff in the natural world, especially biology, it can be really easy to start anthropomorphizing and attributing purpose without even realizing you're doing it. So much of biology is so fucking complex and often really quite good at what it does, and it's in all the language that we use, talking about what a given enzyme is "for," or "why" a given trait evolved, sometimes you can slip into thinking that we actually mean those things. And then you see something like a transposon, and it's obvious that it's not "for" anything. It has no purpose, no raison d'être. It does nothing but be there. And once you realize that it becomes obvious once again that that's equally true of us.

And for all that the design inference died 150 years ago with Darwin's work, it's crap like this that really makes it implausible to me. I mean, this is exactly the kind of random, pointless genomic drivel that one might expect to show up in a system of random changes that can get passed along, but a god designer would have to be some fucked up kind of surrealist to create something like this. I mean seriously. WHY WOULD YOU DO THAT?!? Why? It's strange and off-putting.

Well, okay. There is one thing that transposons do. Transposons can cause non-silent mutations. There are two main ways that they can do this, both at the insertion stage. The first way is, when they cut the DNA to insert themselves, they cut the different strands at different points, creating an overhang and a gap on each side. Then, while they're inserting, the gaps are filled in with sequences complementary to the overhangs (and therefore identical to the opposite overhangs), so when the process is complete you have two copies of the sequence, one on either side of the transposon. If this sequence was something your cell was using, well, now it has two of them.

The other way a transposon can have an effect is by inserting itself right into a gene (or promoter region of a gene, or whatever) that you were using, thereby breaking it. This is apparently the sort of mutation that caused hemophilia in the European royal families. A transposon inserted itself into the gene for a protein involved in blood clotting and bam! No more blood clots; sucks to be them.


But for all that that's an effect of transposons, it's only a real effect in the context of evolution. What would be the point of that in something that was designed?

Transposons are cool.

You Have Got To Be Fucking Kidding Me

Seriously. I can't even bring myself to wonder what the justification is. I'm sure all manner of mirth and hilarity will ensue once it goes to trial.

UPDATE:
It's been pointed out to me that not everybody has the same wacky obsessions that I do, and some context might be useful. Here it is:

Premise Media is the production company behind the ID creationism movie Expelled. XVIVO is an animation company that created a rendition of some intracellular processes for Harvard University. ERV has the whole nasty story, but basically Expelled uses a copy (as in forgery, not as in Xerox) of the XVIVO/Harvard animation. XVIVO's lawyers sent Premise a don't-do-that letter and have filed a lawsuit. Now, according to the first link up there, Premise is suing them back, on what twisted pretext I can't even imagine. Hence the hilarity. (I'm fresh out of outrage. These guys aren't competent enough to warrant it.)

The Word Dumb Has Long Ceased to Cover It

IDiots do something massively stupid and hypocritical.

Sciencey bloggosphere acts surprised

Well, no, not really. But now that I've interspersed all those letters with links, I'm not exactly inclined to go back and change my phrasing, so you're stuck with it.

Evolution: Really Damn Cool

Go check out this post by Abbie about what plasmids can do. You know what a plasmid is? Just DNA. C'est tout. I'm serious, go read Abbie's post and marvel.

On Peer Review

Recently somebody goofed. Bad. The journal Proteomics (which I had never heard of but I understand was heretofore reputable) published (Epub, ahead of print) an article that, if Myers' excerpts are representative, has conclusions that not only don't follow from any data, but are in fact unfalsifiable. This is bad. It's not only bad for the journal and the authors, it's bad for science. It is the “one peer reviewed article” that we've been smugly demanding from IDiots all this time. Bad.

It is also being held up as a failure of the peer review process, and I can see why. But there's something important that's getting lost in the (justifiedly) panicked shuffle, and I want to talk about it. My intention is that this post be a reference that people can point to in the fight I know is coming. So here it is.

There are two things that peer review can mean. I'll call them peer review(S) and peer review(G). Peer review(S) is what people normally think of when we talk about peer review. It's the process whereby a journal sends articles to just a few experts in the field, and those experts read and evaluate the article to recommend whether it should be published and, if so, what changes should be made first. When a reviewer is reviewing an article, she is looking for two things. One, she is looking for good science: Is the methodology sound? Is the measure valid? Do the conclusions actually follow from the data? and so on. And two, she is looking for integrity: Is the methodology well enough described to be reproduced? Are potential sources of error disclosed? Do citations accurately represent their sources?

This is an incredibly important process. Whatever I may say later in this post, I want it understood that one cannot overstate the importance of this process. It serves several functions. Firstly, it keeps out the rifraff. Writings from the likes of John A. Davison don't generally make it as far as a reviewer, but some less gibbering nonscience will, and the reviewers can keep it from getting published. This is good, not only because it keeps the rest of the community from having to slog through mountains of nonsense, it also means that nonexperts reading the journals (such as science reporters) are less likely to come away from them believing the nonsense, which is good for everyone.

Secondly, it helps the editor to keep her biases from dictating what gets published. As important as it is to keep gibbering idiocy out of a journal, it's equally important to let legitimate disagreement in, and that's a big part of what peer review(S) is for.

But here's the thing. Not everything that has ever passed peer review(S) is still believed today, and the reason for that is what I'm calling peer review(G). The review process doesn't stop once the article is sent to a typesetter.

Once an article gets published, it doesn't just sit there in some sciencey archive, revealed truth to be believed from here on out. It gets tested. This is where the real strength of the scientific institution lies. Many more people will read the article than reviewed it. Most will read it with a critical eye, asking themselves if the conclusions follow from the given data. Some will check the sources to see if they say what they're claimed to say. And a few will check the results. They'll re-run the numbers, redo the experiments, do different experiments to check for convergence.

Peer review(G) is what allows someone (but not everyone) who publishes books rather than articles to still be taken seriously as a scientist. It's what decides how reliable a journal is.

As important as peer review(S) is (and dammit, it is) peer review(G) is more important. Peer review(G) is how hoaxes get identified. It's how knowledge moves forward. The real test of the strength of a conclusion is whether it stands the test of time and rigorous retesting, not whether it can make it past a couple reviewers.

So while I agree that what happened with Proteomics is an obscene failure of peer review(S), at best a truly embarrassing mistake and at worst an apalling miscarriage of the process, ultimately this is a success story for the peer review process. A process which "Mitochondria, the missing link between body and soul: Proteomic prospective evidence" is failing, by the way.

Best. Sentence. Evar.

From Pandagon's Amanda Marcotte:

To sane, normal people, the willingness to engage in slavery denialism is a sign that someone is both delusional and a rabid racist, but to the Discovery Institute, it no doubt showed a stellar willingness to stand up to the tyranny of reality.

I'm Not Sure

But I think Seth may be right.

He says that the Intelligent Design assertion fails, not because that something looks designed shouldn't be taken as evidence that it is designed, but rather because

Living things don't look like they were designed. They don't look remotely designed, at any level, from super-macro to super-micro. From forests to molecules, the incredibly paucity of structures or systems that even vaguely resemble human creations is astonishing. Sure, we've copied natural features to supplement our terrible, inefficient, and ridiculous attempts at designing usefull things. But nothing that we do looks even a little like the inside of a cell, ccd chips don't look like retina, we can't build a decent sphincter and as for proteins... don't even get me started. We can't even model the mechanisms of protein folding, much less design something that works like one. Nothing designed looks or behaves anything like a protein.

I'm not sure, though. I'm not convinced that saying something is more complicated than anything we can design necessarily implies that it therefore doesn't look designed. And I think maybe Seth is misinterpreting Dawkins. I doubt very much that any biologist (well, except Behe), would say that living things look designed once they're examined properly. But I think it is the case that on first, uncritical glance, living structures can look designed. Once we understand how evolution works, of course, then that becomes a better explanation for what we see, because it accounts for inefficiencies and suboptimal configurations that intelligent design wouldn't bring about. So on more detailed examination living things don't look designed, because they instead look evolved.

Of course, this is all very fuzzy, because we talk about things that may or may not "look designed", but we never really say what 'looks designed' means. I think we need a specific definition for that term, but I'm not going to provide it because I'm tired.

And there are other, entirely sufficient reasons why ID is a non-starter. It makes no predictions. It has no explanatory power. It is therefore not falsifiable.
What more do we need?

So, yeah, I take it back. I think Seth is wrong.

x=moron, {x|x ε [Tory], x ε [Tories]}

I'm sure most current and former Ontarians remember the horrors of our last Tory government. Remember that asshole whose funding cuts to health care and education ran into billions of dollars? Remember the Education Minister who never finished highschool? Remember how no one in that government gave a shit what the people they were governing wanted? Good times.

Well, in case you had forgotten, or weren't here for it, or were too young to remember, or just got dropped on your head too many times as a child, and were thinking of voting PC this October, they've just stepped up with an excellent reason why you shouldn't. Not only have they come up with the worst possible solution to the problem of Ontario's publicly funded religious schools (make more of them!), their leader, John Tory, put his foot firmly in his mouth by saying that these brand new public religious schools he wants to fund would be able to teach creationism. Of course he's backpedalling like crazy now, and to be fair, I believe he is sincere in saying that he believes in evolution and meant that creationism would only be taught in religion classes,* as is apparently already the case with Catholic Schools.** But isn't it nice when they shoot themselves so squarely in the foot like that?

And, while we're on the topic, is anyone else annoyed that the Liberals and NDP are a bunch of chickenshit pansies, and the Green Party is the only party with a sensible position on this issue?

I'm actually really annoyed with the Libs and NDP right now. I'd almost rather they agreed with the Tories than take their namby-pamby no-boat-rocking status quo position. Maybe I'm naive, but I expected better from both parties. The status quo is both idiotic and discriminatory. The Tories are at least doing something, and their position does eliminate the discrimination (on the other hand it increases the idiocy, so I'm calling it a draw). Sticking with an bad situation because you'll offend some morons by proposing change is nothing but cowardice.

I'll keep an eye on these pages of The Star to see what's what, but I may end up having to vote Green this time around.

Oh, and this isn't the last time I'll say this before October 10th, I'm sure, but whether you agree with my post or not, if you're a Canadian citizen and an Ontario resident, and you're over 18 years old, please, please, please vote next month. Democracies only work when we participate.

---

*Which is all well and good but ought to be a moot point since public funding should not be fucking going to religion classes in the first place.

**Did you know this? I didn't know this.

Oh Goody!

The Lingering Poof has a new pet. What fun!

The Voters Delivered the Jab, Now Judge Jones Gives the Reverse

The Dover ID trial is over and the good guys won. The judge thoroughly spanked the ID proponents, as can be seen from the decision. Here are some of my favourite bits:

...Professor Behe remarkably and unmistakably claims that the plausibility of the argument for ID depends upon the extent to which one believes in the existence of God. (P-718 at 705) (emphasis added). As no evidence in the record indicates that any other scientific proposition's validity rests on belief in God, nor is the Court aware of any such scientific propositions, Professor Behe's assertion constitutes substantial evidence that in his view, as is commensurate with other prominent ID leaders, ID is a religious and not a scientific proposition.

and

It is notable that not one defense expert was able to explain how the supernatural action suggested by ID could be anything other than an inherently religious proposition.

It's so nice when someone really seems to get it.

More from the decision:

The Supreme Court instructed in Edwards that it has been particularly
'vigilant in monitoring compliance with the Establishment Clause in elementary and secondary schools.' 482 U.S. at 583-84. The Supreme Court went on to state that:

Families entrust public schools with the education of their children, but condition their trust on the understanding that the classroom will not purposely be
used to advance religious views that may conflict with the private beliefs of the student and his or her family. Students in such institutions are impressionable and their attendance is involuntary.

Id. (citing Grand Rapids Sch. Dist. v. Ball, 473 U.S. 373, 383 (1985); Wallace, 472
U.S. at 60 n.51).

and

After a careful review of the record and for the reasons that follow, we find that an objective student would view the disclaimer as a strong official endorsement of religion.

The decision is a long one (139 pages), but I suggest everyone at least skim it. It's good reading.

I congratulate this judge on a job well done.

(hat-tip, Pharyngula)

Why Do We Bother?

This is a companion post to In Defense of Reasoned Inquiry below. I want to talk more about why it's so important to keep creationism out of science classrooms.

First, let's take a gander over to a fundamentalist Christian blog. Rand, of A Form of Sound Words said this

As for these millions of years of evolution scientists love to throw around so much, here's a quick thought for you: can God create a mountain that has all the physical properties of being millions of years old? If He can, then the evolutionist doesn't have the "proof" he thinks he has.

Leaving aside for the moment the small matter of evolution and geology being different fields of study, let's take a good look at this quote. If we accept, as Rand does, that God is omnipotent, then it does of course follow that He can create a mountain with all the properties of being millions of years old. If we furthermore accept that the bible is the word of God, and meant to be taken as literally as possible, then we are left with this one, inescapable conclusion: God is willing to deceive us. The account in the bible and the evidence we see before us simply don't match. If God was responsible for both, then God has lied to us.

Now without getting into a discussion about whether God would or should lie to us (such hypotheticals bore me to tears), I just want to discuss the implications of the fact that God (if such a being exists, and is responsible for the bible in the way Rand claims He is) *has* lied. This means that we cannot trust our senses. We cannot trust the results of our experiments. If we cannot trust the world to be as our senses perceive it and our reason deduces it to be then we can't investigate anything. Let me say that again. We can't investigate anything. If we presuppose the existence of a God that falsifies evidence, the entire field of science is moot. Moot. Hell, even if we didn't have proof that this God falsified evidence, the mere fact that He could would suffice. The musings of Descartes and Hume are fun for keeping ourselves up at night, but the scientist must proceed on the assumption that her results are reliable, or she may as well not bother.

This is precisely why creationism, Creation Science, Intelligent Design, or whatever you want to call it, does not belong in the classroom. By presupposing an intelligent guidance of natural phenomena, it flies in the face of everything science is trying to achieve. It states that things are the way they are, not because of the immutability of natural laws, but because they were arbitrarily designed that way. If that is the case then there is nothing to be learned from studying them and we may as well all go home. I'm not interested in that. There is certainly the possibility that Rand or Descartes or even David Hume were right. That the universe our senses show us bears little or no relation to the universe as it really is, but as there is no possibility of bringing evidence to bear on that conjecture, it does not belong within the realm of science. Take your ID and shove it up your philosophy teacher's ass. It has no place in a science classroom.

(Thanks to my father for providing the main idea behind this post)

In Defense of Reasoned Inquiry

Nominee, Best Post

I don't know if it's only recently come to my attention, or if there has actually been an increase in recent years, but it seems to me that science is under attack in the USA. Despite having the good fortune not to live in that country, I nonetheless feel that I have a certain responsibility, as an educated, reasonable member of this global village, to help my allies south of the border to defend this most precious technique against the attacks it has been the target of.

Why is the scientific method so precious? Because it is the *only* way we have of really knowing things. Without the scientific method all we have are superstition and common sense, neither of which have particularly good track records with getting things right. The scientific method, on the other hand, with its emphasis on testing and evidence, has an excellent track record. One might even say that "getting it right" is defined by the scientific method.

For a comprehensive definition of the scientific method, I suggest you read Wikipedia's page on the topic, but I'll give the gist of it here:

1. You start off with observation. You see what's going in the world and you notice patterns, or interesting and unexpected deviations from patterns. You collect information on these patterns until you feel you have enough information to move on to step 2, which is...


2. Formation of a hypothesis. This is where you use the information available to you to make an educated guess about why or how the things you observed happen. Now you need to...


3. Test the hypothesis. A hypothesis is only as strong as the predictions it makes, and a hypothesis that only seeks to explain given observations without making any predictions about what further observation will reveal has no value at all. (We who are interested in actual evidence call these hypotheses "just so stories," with a hat-tip to Rudyard Kipling.) What your hypothesis should do is give you some idea of what to observe next, and how to go about observing it (again, for examples see the wiki article). It is very likely that, once you've performed these new observations, you will find that your data doesn't jibe 100% with your hypothesis. That means it's time to...


4. Revise your hypothesis. See if you can come up with a (testable) idea that explains your new data while still being consistent with your old data. And once you've done that, you go back to step 3.

Now, what a lot of people don't seem to understand is that you never stop repeating steps 3 and 4. There is no point at which a hypothesis is considered proven and observation and experimentation can stop. What can happen, however, is that experimental data can bear out a hypothesis's predictions over and over, so many times, with so little need for revision, that it becomes very hard to believe that a reproducible experiment will ever be performed that disproves the hypothesis. At this point the hypothesis can graduate to the rank of theory. It becomes accepted as true by a majority of members of the field, and it can be used as a jumping-off point for new hypotheses. However, it remains falsifiable. It always remains falsifiable.

Now, I hope I don't have to explain why this technique is so damned important, and what a shame it will be if a majority of Americans reject it outright, and explicitly accept the practice of creating public policy based on conclusions not reached through this technique. I hope I don't have to explain why it's so important that children be taught this technique in school. Be taught that conclusions reached through this technique are superior to conclusions reached through other methods. I hope I don't, but if I do please say so. I'll be happy to oblige with another post.

It's with this in mind that I've weighed into the evolution/creation debate. My goal is not, and has never been, to convince creationists that they are wrong. My goal is to reach those who are undecided. Those who are at risk of being convinced by the arguments of creationists (arguments that, with their logical fallacies and factual errors, can seem quite sensible on the surface). I hope to do my part to create a more scientifically literate populace, which is, in the end, the only thing that will keep creation "science" and other such nonsense out of government, and out of the schools. Call me crazy, but I'm convinced of the capacity of science to build a better world.

Evolution at Home

Much to my chagrin, my snail tank appears to have become a prolific fruit fly breeding ground. Now, there's no way for me to permanently solve this problem, that I can think of. I can clean the tank, but as soon as I do, some of the many flies that have escaped will get back in and start breeding again. And I can't effectively get rid of the population outside the tank with newly hatched flies coming out of the tank at a steady pace. My only hope is to do my best to encourage any fruit flies in the tank to leave, and then try to reduce the population outside the tank to manageable levels. I would try putting the tank outside for a couple days but it's supposed to be in the teens and low twenties and I'm afraid that would kill the snails (10tacle, care to weigh in on this?).

So. To get rid of insects inside the apartment the safest, cleanest, cheapest, and most effective way to do this is with diatomaceous earth. It's best suited for walking insects, but it also works with flying ones, just more slowly. The primary disadvantage to this method is that it makes your apartment look like a five-year-old has been scribbling on bits of it with chalk. Much as this may fit in with my decor theme (mess, mess, and more mess), I'd rather avoid it, so I decided to start with some very clever fruit fly traps a friend told me about.

You take some small, shallow bowls, fill them most of the way with a liquid the fruit flies will like (I used hot chocolate - dairy free so it wouldn't stink), and cover them with saran wrap. Then cut a slit in the saran wrap, so the flies can get in but, because they're flies and therefore stupid, can't get out again.

Well I tried it, and the damn things work like a charm. The two in the living room and one in the bathroom are filling up with flies (don't ask me what the flies are doing in the bathroom, where there's never any food. Flies are stupid). The one in the kitchen is still pretty empty but the kitchen is actually where the problem is least serious, so that's okay.

In observing my little fly traps, though, I noticed something. I appear to have two kinds of fruit fly. Anyone with high-school level biology (and probably most people without) will be able to guess what the two kinds are. Yup, red-eyed fruit flies and black-eyed fruit flies. BUT, I noticed something else. Now, I don't know if these traits are generally linked, or if it's just a coincidence of my populations, but the red-eyed fruit flies are tending to be less than half the size of the black-eyed ones. What this means is that the little buggers can make their way out of the traps. So while the traps are filling up quite nicely with large (relatively speaking), black-eyed fruit flies, they're just providing most of the little rede-eyed ones with a nice snack. Sure, a few of the stupider, less lucky red-eyed ones die, and a few of the smaller, luckier, black-eyed ones escape, the overwhelming majority of dead flies are the black-eyed ones. I predict that, although I started off with a large majority of black-eyed flies, in a couple days I will end up with a population that is overwhelmingly red-eyed and small flies. So what, you may ask, it shouldn't make a difference what color/size the flies are. But you'd be wrong! What, I ask you, is the defining characteristic of these red-eyed flies? It's not their eye colour, or even really their size (although that's relevant). It's their ability to survive my traps. In laying out these traps I am, pretty much by definition, creating an environment that selects for flies that can survive those traps, thereby making the resulting population harder to kill. To put it in more familiar (though less accurate) terms, I've created trap-resistant flies. Well damn.


And this evolution, yes evolution, of the fruit flies in my apartment is a fact. Not a theory, but a directly observable FACT. And anyone who can observe this phenomenon and not realise that the same forces driving it exist in nature, not realise that when you come down to it, the world we have (maybe not the exact world we have, but a world that shares the key property of being teeming with hugely varied life) is the highly likely, possibly INEVITABLE, result of the advent of a molecule that just happens to replicate itself (which in and of itself isn't a particularly surprising occurrence when you think of the sheer size of the universe) is a COMPLETE and UTTER MORON!!


(Sorry, I try not to get that heated on my blog generally. I guess I've been reading way too much Creationist nonsense lately.


Frakking dumsnuts.)

UPDATE:
In response to Q. Pheevr's response in the comments: It's true that this specific example is one of not-so-natural selection, rather than speciation, but speciation is the obvious and inevitable result of this process being repeated over and over, with multiple simultaneous selection forces, over a long period of time. There's no logical way around that, and it's the people who can't see that who are morons.