Personal Computer Turns 40

It was 40 years ago tomorrow that the very first personal computer was demonstrated by Douglas Engelbart of the Stanford Research Institute. SRI's PC already had a few familiar accouterments, including a keyboard and mouse. Who decided to call it that? Nobody knows. Even a very primitive form of the Internet already existed, documents could be hyperlinked, and the computer had something vaguely like windows.

People watching the demo — all 1,000 of them — were blown away by the proto-PC. It was the smallest computer they'd ever seen and it didn't use punchcards. It could even edit text.

40 years ago, this was big stuff. To celebrate, I'm going to stuff a cupcake into my CD drive today and click "burn." These things can eat now, right?

You can view silent black-and-white video taken from original film of the first PC demo here. It's too bad that there's no sound, though. If there were, you could hear the guy at the back of the auditorium shouting, "Now I can haz cheezburger!"

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Swapping Bodies: Researchers Fool Brains to Think They're In Mannequins

Swedish researchers Henrik Ehrsson and Valeria Petkova have used technology to fool the brains of subjects into thinking that they're in mannequins instead of their usual bodies. It's pretty trippy stuff.

Cognitive neuroscientists at the Swedish medical university Karolinska Institutet (KI) have succeeded in making subjects perceive the bodies of mannequins and other people as their own. The findings are published in the online, open-access journal PLoS ONE, December 3.

In the first experiment, the head of a shop dummy was fitted with two cameras connected to two small screens placed in front of the subjects' eyes, so that they saw what the dummy "saw." When the dummy's camera eyes and a subject's head were directed downwards, the subject saw the dummy's body where he/she would normally have seen his/her own.

The illusion of body-swapping was created when the scientist touched the stomach of both with two sticks. The subject could then see that the mannequin's stomach was being touched while feeling (but not seeing) a similar sensation on his/her own stomach. As a result, the subject developed a powerful sensation that the mannequin's body was his/her own...

In another experiment, the camera was mounted onto another person's head. When this person and the subject turned towards each other to shake hands, the subject perceived the camera-wearer's body as his/her own...

The strength of the illusion was confirmed by the subjects' exhibiting stress reactions when a knife was held to the camera wearer's arm but not when it was held to their own.

The illusion also worked even when the two people differed in appearance or were of different sexes. However, it was not possible to fool the self into identifying with a non-humanoid object, such as a chair or a large block...

— Source: EurekAlert! Press Release

The paper, If I Were You: Perceptual Illusion of Body Swapping, goes into great detail about how and why all this works. For me, the takeaway message is that we can be fooled about things about which we are normally quite certain if we rely on our senses alone. If we can be tricked into thinking that we're not in our own body but within an inanimate, albeit anthropoid, object, we can be tricked into just about anything if some unbiased intermediate observer or technology isn't used to make sure that seeing is truly worth believing.

I'm led to wonder, too, about the so-called "out of body experience" reported by some people who have come near death. If the changes that cause the apparent projection of consciousness into a dummy (no cracks about Dubya, now!) can be induced by the application of cameras, and that experience is fundamentally electrochemical, then surely a similar effect might occur as a result of the illness or trauma that leads to a near-death experience.

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What Spore Teaches Us About Intelligent Design: The Four Lessons of Casey Luskin

I'm proud to note that I've added numerous points to my geek cred scale recently by purchasing a copy of EA/Maxis' computer game, Spore. I haven't had much time to play it, but I have managed to take a species of mine all the way to the galactic phase. My little critters, the Shub, are gleefully jetting about the galaxy, although their home world, Mloukhiye, is currently under attack. You can see a Shub there on the right. Cute, no?

I like Spore. It's a fun little game, and that's all it is. I wouldn't dream of using it as a tool with which to instruct students about evolutionary biology for a very simple reason; it's nothing like evolutionary biology. It lacks most of the mechanisms that we see driving evolution in the real world. There's no random mutation in Spore, for instance. Nor is there sexual selection, genetic drift or gene flow. In fact, Spore is essentially The Sims with characters that aren't necessarily human or even human-like. In the real world, species don't jump from being cells to having legs because they eat enough bits of nutrient floating in liquid medium. They don't grow bigger brains because they sing duets with other organisms. The real world simply doesn't work like Spore. In other words, Spore isn't evidence for or against any empirical principle. It is, after all, just a fun little game.

That, of course, isn't going to stop the ID Creationism contingent from advancing the notion that this bit of electronic fluff from Electronic Arts somehow supports their notion of how the diversity of life arose on the planet. They are not, after all, under the constraint of testing hypotheses, nor even of rudimentary common sense, because the vacuous nonsense they assert as a theory (proving that they're not even under the constraint of English usage) is just that — vacuous. They could as easily maintain that the existence of pie is evidence that prayer has the power to turn the head purple. We are thus treated to platters of blather such as an article in The Christian Post in which Casey Luskin, better known to sentient beings everywhere as Captain Clownie, yammers on about how a computer game is evidence of, and teaches users about, his favorite content-free fairy tale:

'Spore' Game Helps Players Understand Intelligent Design
Fans of a video game about evolution include young Christian teenagers and intelligent design proponents

By Katherine T. Phan
Christian Post Reporter

While the latest video-game craze, "Spore," touts the theory of evolution, taking gamers from a single-celled organism to complex civilizations, some say it also promotes God and intelligent design...

Players start the game with the task of feeding a single-cellular amoeba that eventually lays an egg after it has consumed enough blob-like nutrients in its 2-D world. The egg allows gamers to edit their simple organism into a more complex creature - with seven legs, one eye and purple skin if they so desired.

At each egg stage, players can further "evolve" their creatures to have different body structures, physical capabilities and even bigger brains – all of which affect the creatures' abilities and personalities in the game...

Let's pause right here for a moment. In Spore, players do not "evolve" their creatures, they edit their creatures. There's a big difference here. See, you have to click this little button and a new window opens. The player then spends a few "DNA points" to buy arms and legs and eyes which they choose from a menu on the left side of the screen. That isn't evolution by any definition, of course. Is it intelligent design? Sure, assuming that the player isn't a member of the Discovery Institute, barring appropriate use of the word "intelligent" in this context. However, is it evidence for what Luskin and his Creationist clown car assert? Is this how the designer designs? Is he constrained by a budget of DNA points amassed by creatures eating blobs of algae? Well, the truth is... I don't know. Since one of the assertions these numbskulls make is that we can't know anything about their designer (whom, for the sake of simplicity, I'll refer to as Bob the Builder henceforth), he could be clicking away at a menu on some celestial computer somewhere and we could all be nothing more than critters in a pangalactic Sporepedia. However, I am unaware of the proponents of ID ever having advanced this notion beforehand... which, for their purposes, is just fine, since their vacuity isn't constrained by the requirement of predictiveness, anyhow. Unlike real scientists, IDolators are free to make it up as they go along. Everything they do is ad hoc.

And here we have the first thing that Spore really does teach players about Intelligent Design; one can say nearly anything (real biology is barred from discussion, of course), and ID pseudotheory can find a way to accommodate it. Chalk one up for Captain Clownie. We've all learned a valuable lesson. To continue with the article, then:

"Anyone can see that Spore is not really about evolution by the Darwinian mechanism; it's about evolution by intelligent design," Casey Luskin with Discovery Institute, a leading intelligent design think tank, wrote on the group's affiliated blog Evolution News & View...

Well-played, Captain! I agree entirely; anyone who knows anything about evolutionary biology can see that Spore is not about evolution by Darwinian mechanisms, nor by any other mechanisms seen in the real world. The thing is, so what? Computer games routinely violate the laws of physics; one might just as well state that Super Mario Brothers isn't about quantum mechanics. See, entertainment devices don't always seek to replicate the real world and Spore is not a teaching tool. It isn't science. It's a computer game from which precisely zero lessons about the universe in which we (by which I do not mean to necessarily include Captain Clownie and the Funtime Gang over at the DI) actually exist. In truth, Spore is about neither evolutionary biology nor about religiously-derived "alternative theories." It's about having a bit of fun.

But here we have our second lesson about Intelligent Design inadvertently brought to the fore by Spore: ID advocates can't tell the difference between a fantasy role-playing game and reality. Note that this is a notoriously poor sort of mindset from which to begin the genesis of anything useful to science. But they do go on:

The game even refutes many Darwinist objections to I.D., argued Luskin, including one objection that says detecting design requires knowledge about the designer.

"Browsing on YouTube I can find hundreds if not thousands of Spore creatures that were designed by people whose real names, parents' names, and tribes of origin I know nothing about. We don't have to know who the designer is, or who spawned the designer, to be able to detect design," wrote Luskin...

I'm unfamiliar with the argument that Luskin says we "Darwinists" bring up in regard to IDiocy. I am, however, familiar with two arguments that he may have crammed together here. The first is that if design is present, it should be detectable and the second is that if there is a designer present the designer should also be detectable and because that designer can be observed, even indirectly, it absolutely follows that we could say something about the nature of that designer based upon how Bob the Builder designs. We could infer, for instance, what kind of design regime it follows, what sorts of tools Bob uses, etc., all of which perforce tell us something about this veiled designer.

Captain Clownie, of course, puts his foot right in it when he says that he can't tell anything about the people who designed the Spore creatures he's found on YouTube. This may be indicative of the extent of Luskin's brain damage, since anyone lacking his degree of cognitive impairment can say any number of things about the designers of Spore creatures without even looking at the creatures themselves. For example, it's a sure bet that every single person who has designed a Spore creature has used the Spore creature creator to do so, and we can thus infer that such individuals also have access to at least one computer and furthermore know how to use it, could we not? We can make some educated guesses about what colors these designers favor, particular if we can find several of their creations and note what they have in common in this regard. More importantly, we can test our hypotheses about these junior Bobs by sending them an email and asking a few questions. Some might choose not to respond, but at least a few of them would and we could expand from our initial hypothesis to build a profile of one or more designers, look for commonalities between them and ultimately come up with some idea of what unites the kind of people who make creatures for Spore. In fact, you can bet your bottom dollar that there are people working at EA who do just this kind of thing for a living. In case Captain Clownie missed it, then, here's a clue; this discipline is called marketing. Even if Luskin didn't investigate the creators of those Spore critters on YouTube, other people make a living doing precisely that. In fact, they did so before anyone ever bought the game, and the information they uncovered was used to make predictions about who would buy Spore and how many buyers there would be long before the game itself ever hit the shelves. If they were correct, they might get a nice bonus. If they were wrong, they might get fired. This works just like science; what's known prior to an experiment (in this case, the launch of a product) is used to create a hypothesis which is then tested, evidence for and against the hypothesis is gathered, and the hypothesis is either conditionally accepted or rejected.

Here, we learn our third lesson about ID Creationism — it doesn't lend itself to inquiry. As soon as a bit of useful agitprop is formulated, inquiry ceases. Luskin didn't find anything about to say about the Spore creators because he didn't even trying once he could make some statement in support of an a priori conclusion. We have learned that Intelligent Design is, in fact, exactly the opposite of the search for the truth about the world in which we live — a most valuable lesson, indeed.

Benjamin Cormack, writing on the gaming Website GotGame.com suggested Spore may even help players understand, in a small way, the heart of God.

"As you guide and care for your creations, you may actually develop an almost parental sense of pride in watching them grow, kind of like children or sea monkeys," he wrote...

Well, that's a very long way from Captain Clownie's assertion that it isn't necessary to infer anything about Bob the Builder, isn't it? Cormack is certainly saying something about God (and, after all, that's precisely who Bob the Builder really is!) Of course, it's also a tremendous leap of logic and certainly a category error. It's based on a major statement about the nature of the designer — this designer has human emotions and, not only that, applies them in an entirely human way. Bob the Builder forms attachments to the things it creates.

We get yet another lesson about Intelligent Design, then. It has no problem with contradicting itself in order to accommodate any opinion about anything at all, so long as that opinion is one in contradiction of sound science and reason. This is, of course, a major advantage of being vacuous.

It turns out, then, that Captain Clownie is absolutely correct in his assertion, shared with numerous other IDolators, that Spore teaches players about Intelligent Design. He's just wrong about what lessons those players can learn. What Spore has done is simply to bring the termites out of Bob the Builder's woodpile to make the usual round of silly statements that those of us who still have a few working brain cells firing away can then dissect using that most incisive of scalpels, reason. In summation, we who are still in possession of this valuable faculty and who hold it in esteem learn the most valuable lesson of all about Intelligent Design from the reaction of one of its leading advocates to Spore. That is, they aren't very good tool-users. They tend to apply a cudgel when what's called for a nice, sharp blade.

The ability to use tools is a major part of what makes us humans. To be a bad tool user is, in a sense, to be an inferior human being. I would submit, then, that the ultimate lesson one can take away from all of this is about Casey Luskin himself and, based upon their assent to Captain Clownie's arguments, about the leadership and members of the Discovery Institute. They don't know how to use the one tool that makes all other possible — reason. They're not so much a think tank as they are a holding pen for the chronically deficient who have benefited from the relaxed requirements of fitness that good tool-users have engendered. Natural selection having failed to remove them from the ideological gene pool so far, we shall have to wait for the effects of some other factor to lead in the end to their inevitable extinction. Surely the very fact that this rubber-nosed know-nothing can assert that one can learn about the real world by playing a video game should be enough to demonstrate how jejune is the black hole of intellect termed "intelligent design" for all of humanity. At least, I would like to think it that obviously stupid.

I also suspect, sadly, that someone will come along to dash my hopes any minute now.

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She Dinna Have Enough Power

The rocket that was supposed to carry the ashes of Scotty, James Doohan, dinna have enough powerrr to make it into orbit and was lost. Somebody must have forgotten to charge the dilithium crystals.

Launch of Private Rocket Fails; Three Satellites Were Onboard
By JOHN SCHWARTZ

A privately funded rocket was lost on its way to space Saturday night, bringing a third failure in a row to an Internet multimillionaire's effort to create a market for low-cost space-delivery.

The accident occurred a little more than two minutes after launch, and the two-stage Falcon 1 rocket appeared to be oscillating before the live signal from an on-board video camera went dead...

The rocket was also carrying the ashes of 208 people who had paid to have their remains shot into space, including the astronaut Gordon Cooper and the actor James Doohan, who played Montgomery "Scotty" Scott, the wily engineer on the original "Star Trek" television series...

Considering the line for which James Doohan is most famous, the spacecraft not making it into orbit seems an even more fitting tribute to Scotty than if it had.

Besides, Scotty should have been beamed up, not shot into space aboard some primitive wessel.

Hyphal tip to Wormtown Taxi for the heads-up on this story.

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Transcript of Pope Benedict's Homily at World Youth Day

The following transcript of Pope Benedict XVI's homily at World Youth Day was produced by turning on the television (coverage provided by EWTN), then my laptop's speech recognition software, and then walking out of the room. The raw transcript was saved as a Microsoft Word document. I then ran Word's spelling and grammar checker and accepted whatever changes it suggested. When there was more than one correction suggested, I always chose the first one. This, then, is what the computer heard Pope Benedict say. It starts off a little clumsy, but it makes as much sense as anything I've ever heard uttered by a clergyman by the end.

A U.S. ally in the eighth of the season lasts only in this kind. Get known to have it. On a study was the Holy Father you long for as the event is the value of a man. To be on third is the challenge, not as hard as it is easy. Some thanks to our house is the kind of a show of hands as the author has a son who is of the view that he is fine and does as pretty a Eucharist as this.

All are being with the rays of the only holy thing that that is: the one of the united tens of only a light. On one of these signs, by the way, you of the U.S. lose. You’re of the view that I have the main thing. Now he’s had a lot of that all. Use a kiss and take much as follows this.

The only other thing in the year by Jose shows off a thing. I think his time in his house or many of you author the views of the eighth OP has the ad half, as high as I know. That if the ideas of the U.S. now has gotten, how does that which has offices of the infamous as long as an eighth? The real law via acts as a semblance of that’s OK. You’re only as long as they have in the ninth of this thing. As long as they are mad at us as a pizza, it’s as thick and anonymous as this. As they are false, then rather than thanks I am a thank you. Out of UFS he and his giving thing from the SISSY stand as theater at these cars. Spans of the path use a five to its hands of the eight then I’ll think as a studio takes months. SS heads of state have the highest sounds of this.

This is nice. Now he’s SS Grand Am.

As it is a sound in a phone, that is as safe a path at $10.00 as anything. My SIN got a lot of guys’ things that I’m using. The humanism is in all other Islamic eyes of the south. As a USS is a man, so long as that’s as easy as a month’s 69.

Does a man you think is something is saying that they follow a path as a thing? You’ll then say of his case that they have anything as often as a fax. It is the main thing to go as long as an SI is the fan. He has been a few having AIDS. This thing will be the key thing. To communicate his test, call this as the house. His hands as a youth a day late, as they say, then a youth is a thing they use for a fifth as that has some of the period.

From a phase of his death and taxes and fees of the same as the date and time, this season is a long haul. It says of his cause that you visit to get a visa. A thin line of a designed investigative thing is the same as a long time, is the same hands. Unknowns visit our home as a different thing than home videos that are as many as in a net view that it ends. We’ll pay his use of the state’s main and say that he’s committed a sin. Is humanism from the thick end as I’ve seen a thing orbiting the U.S.?

Is it some of his main business days? Are these safe to sign? The thing is that a DOSS is the CIA’s thirds of saying it’s easy, I think as thickly as follows. As well as a sense of him, now have many of these days in a row. You say you view thoughts as exciting if that’s lost. The fed has a name as guy. Is the stance an eighth Baghdad? As bad as the south face of a handful of zones and the status of thickness, then their house owned safety and five of a thing happen as you stop. Of all the things that they had to say, there are thumbs as long as his. You have to thumb your head at FA’s eyes.

Is there a long thing with thin thighs that got this thing? As soon as they have a thing as long as his evidence, a thick film is as safe as real law. A thinning interview that is only his own are they. A seventh anthem is a man. Spam called and came off his thing and has become an eighth day. As thick as the phone is a headphone, but only think entirely to be as thin as the data. As of yet the thumbs they expect are these. You’ll fall as I have. Is a thing they know that I am a file? Stop and fashion the Z and the author of the events was that guy. That is all my AA captain wants. Atheist, the following is the eighth man of the inning as a result. Was CS safe as a youth? Think of that.

As the Visio ZION these days, I think it’s, yeah, I think that’s anything. Saying all that they have is the days. Home has views. The path of the house is a nine now and at the van they are both a visa and a mountain goat.

I think we can all take away a few lessons from that.

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In Praise of Vista's Speech Recognition Software

I know that a lot of people hate Microsoft and think that Vista is unstable bloatware. I come not to bury Vista but to praise part of it.

I have been having some problems with my wrist lately. Long bouts of typing are painful, so I’ve been trying to minimize when keyboarding. For that reason, I’ve been using the speech recognition software that comes bundled with Vista. It’s not perfect, but it’s pretty good and does some unexpected things.

For example, I was surprised to find that the first time I said the name of the city I live in, the software recognized it and spelled it correctly. Now, if I lived in New York or Dallas, that wouldn’t be saying much, but I live in Worcester. For those who don’t live near here, that’s pronounced “woostah.” Getting that right the first time is something that eludes most humans.

In fact, thanks to a little time put into training the software, it can now recognize obscure mycological jargon. It has no problem with words like Phellinus, Fulvifomes, cystidia and pileus. It can even handle “dikaryotic nuclei,” which isn’t bad for a laptop.

This very entry has been composed entirely using only the speech recognition software. I’ve touched neither the keyboard nor mouse once while writing this. My wrist thanks you, Microsoft!

The biggest problem it has is that it doesn't work very well with Firefox. If anyone knows of a patch for this problem, please let me know.

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Mystery Mushroom: Evolutionary Theory in Action

You might remember that a few days ago I collected some mystery mushrooms that I couldn’t identify based solely on macroscopic and microscopic characteristics. This morning, I got my rDNA sequences back and I’m happy to report that I have now been able to identify the fungus based on molecular characters. This is evolutionary theory put to practical application. Waddya know, this evolution stuff really works!

Here’s my final phylogenetic tree (although I could have collapsed the weakly-supported nodes if I'd wanted):


I produced this by matching my sequence against highly similar sequences in BLAST. I aligned these using MAFFT and then cleaned up the alignment in MacClade. The cladogram shown is a neighbor-joining tree created in MAFFT with branch lengths proportionate to phylogenetic distance. Bootstrap support is shown at all nodes and is the result of 500 replications. The taxon highlighted in red is my mystery mushroom and the clade containing its closest relatives is outlined in green.

As you can see, the unknown mushroom is clearly of the genus Gymnopus and is closest to, but not identical with, Gymnopus brunneigracilis. It may be that the mystery mushroom has not been sequenced before or I might need more characters to correctly identify it to species. Nonetheless, I do now know its genus and a photograph of one of its close relatives, G. luxurians, bears a striking resemblance. Moreover, the morphology and growth habits of G. luxurians are extremely similar to those of the mushroom I collected.

Imagine for a moment that this wasn’t a mushroom I found growing in wood chips. If this had been a mysterious fungus growing out of Aunt Tilly’s ear, I would have used the exact same techniques to diagnose our (thankfully) pretend parasite. None of this would have been possible without the principles of evolutionary theory, which informed every step of the process.

Of course, if you would like to try to identify the source of my sequence without resorting to evolutionary theory, by all means feel free. Here’s a link to the actual sequence from the fungus. I would be very interested in hearing all about how you made sense of it without involving mutations or knowing the genus and its relationship to other genera sharing a common ancestor.

Or, if you feel like trying your hand at this sort of thing, you can see pretty much the same things that I saw on the way to this result by using the links provided. If you don't feel like buying a copy of MacClade, you can substitute the freeware program BioEdit. It's all evolutionary theory in action embodied in software that makes life a lot easier than it used to be in the days of dot-plots and slide rules!

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Why Don't All Taxis Have GPS Units?

I was on my way home from the lab just now and stopped off at the Mobil station at Main and Mill to pick up a pack of smokes. As I left the store, a Yellow Cab driver approached me and asked me how to get to Webster. He'd never been there before and had to pick up a fare there. I've never been there either as far as I know, so I first told the cabbie that I didn't know. I wasn't really thinking; it has been a long day.

So the cabbie went back to his cab and started fumbling with a map. I got back to my car and remembered that I have a GPS unit. I took the "lady in the box" out of the glove compartment, switched her on and approached the cab.

I knocked on the window and asked the cabbie to give me the address he was trying to get to, then punched it into the unit and there they were, turn by turn directions right to the door where his far was waiting in Webster. The driver, an African fellow, thanked me profusely and waited for me to pull out of the lot ahead of him.

Now, this is reason to ponder. Why aren't taxis equipped with GPS units? There are always places that some driver is bound not to know how to get to, and a GPS unit is a lot better for such things than a paper map. As someone who absolutely lacks a sense of direction and relies on both a car GPS and a hand held unit to get me where I'm going on-road and off, I can attest to how indispensable these things really are. Moreover, I can't figure out how cabbies can earn a living these days with the price of gas through the roof. I'd imagine the last thing a driver wants to do is waste gas; every excess gallon burned is money out of his pocket and I'd be willing to bet there's not a lot in there to begin with these days.

Why, then, don't the owners of taxi fleets provide drivers with GPS units that they could sign out if they wanted them? It would probably cut a few minutes out of the time it took a driver to pick up a fare and get them where they were going, it would likely save gas, and it would help new drivers learn their way around. There are some pretty good deals on the things these days and I'm sure someone buying multiple units could work out a deal on price with a supplier.

Paper maps waste time and money. Get with the digital age, fleet owners!

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How to Levitate a Biologist or Zen and the Art of Alignment

Every day is a learning experience. Today, I learned that I can fly. I don't need an airplane and I don't need a helicopter. All I need is Macclade.

I'll assume that most of the people who read this note will never have done an alignment. It's a very meditative thing, really. One can download a bunch of sequences from GenBank for starters. Make a list of the sequences you want to download, save them as text files, clean them up, load them into Clustal (personally, I like W2 best) to generate an initial alignment, then load that initial alignment onto Macclade to fix it up. That's where the really meditative part begins. One slides colorful little blocks around to line up bases, deciding where gaps should go and what characters constitute insertions and deletions. It's very Zen, this business of alignment. The more dissimilar the sequences are the longer it takes and the more I concentrate on the task at hand to the exclusion of everything else in my environment.

And this is why all I need to fly is Macclade and a little help, which comes in the form of one of my lablings walking up quietly behind me, peering over my shoulder at the screen and asking loudly, "You believe in this stuff? All those little A's and T's?"

ZOOM!

I'm suddenly six inches above the seat of my chair. My hand has convulsed and selected four taxa which slide themselves to the top of the screen. My cytochrome oxidase subunit 1 alignment, so neatly lined up over the course of an hour, suddenly looks like red, green, blue and yellow swiss cheese. Thank Maddison that Macclade has an "undo" button.

Years ago, Maharishi Mahesh Yogi conned his followers into thinking that they could learn how to levitate based on spiritual principles. As usual, it takes science to actually get a man off the ground.

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Holy Gigabyte!

In case you were wondering what to listen to while slurping down a bottle of Jesus water, IceTech USA is here to save you! For the low, low price of $44.99, you can purchase a crucifix MP3 player. It comes with 1 Gb memory, voice recording capability (so when Jesus speaks to you, you'll have proof), FM radio, headphones and a necklace.

What better thing on which to play your Laibach collection? I suggest starting with "God is God":

Surely this is what the Angelic Choir sounds like.

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Yesterday's Festivities: Phylogeny Symposium and Such

Yesterday was consumed, happily enough, by attending the Plant Biology Initiative symposium at Harvard. As it was entitled Phylogeny Informs Biology, it probably comes as no surprise that the theme of the day was the many ways in which phylogenetic techniques are being applied to modern biology and the findings that are being produced because of this.

Traffic was awful and caused us to arrive a bit late which made us miss the opening remarks and the very beginning of Debashish Bhattacharya's seminar on endosymbiosis and the origins of plastids in eukaryotic cells. Nonetheless, I found it the most interesting session of the day (not to take anything away from the other presentations, I just find the topic particularly interesting). Erika Edwards presented her research on the application of phylogenetic techniques in sorting out the question of the importance of C3 vs. C4 photosynthesis schemes in grasses are involved in atmospheric carbon cycling through the investigation of biases in stable isotope utilization. After the first break, Lee Taylor presented on orchids of genus Corallorhiza, a devious bunch of plants that have gone from being a mutualist with mycorrhizal fungi to being a predator. In this genus, the plants have given up producing leaves and roots and the like and instead have taken to eating the hyphae that provide mineral nutrients in exchange for photosynthate in other orchids-fungus relationships. They're nasty things if you're a hapless fungal symbiont! In this instance, the driving evolutionary force is a jump between Thelephoraceae and Russulaceae, one which forms very neat clades under phylogenetic analysis. Again, Taylor's talk was particularly interesting to me because Thelephoraceae is a sister group to the polypores. Next up, David Hibbett spoke about automated taxonomy and particularly a program called MOR, which is currently under development.

The Harvard folks were very generous with lunch. Yes, they gave us sandwiches, but these were some particularly good sandwiches. My lab and members of the Pringle lab split off for a mycological luncheon in the herbarium. I learned that one of the graduate students in that lab is also doing work involving polypores, though she's looking at community structure. We'll probably be collaborating on some things, swapping specimens and collecting and the like. Funny how our paths keep crossing; I first met her in Oakland in 2000 or 2001, and now here we are on the other side of the country overlapping our work on clades that not many others are engaged with lately. Near the herbarium I noted the first mushroom fruiting bodies of the season, a number of very robust Pholiota, and now am particularly inspired to go collecting this weekend. It's a sign, I tell you!

After lunch, Susanne Renner spoke on the application of phylogeny to the question of the biogeographical diversification of plants, a session which ended with her declaration of the death of vicariance hypotheses in favor of tremendous pools of seeds limited not by dispersal but establishment. Then it was back to the grasses with Caroline Stromberg who spoke on her work using phytoliths to date the origin and diversification of grasses; it looks like they were already around by the end of the Cretaceous, pushing back their age by several million years beyond current estimates. Finally, the day's presentations ended with Michael Donoghue's talk on the application of phylogenetic analysis in resolving the evolutionary history of angiosperms, particularly Dipsacales. He also gave the concluding remarks before the symposium ended and the reception began. Donoghue is a very engaging and entertaining speaker and certainly was a good remedy to the sleepiness induced by the sporadic air conditioning in the room in which the symposium took place.

When all is said and done, it's interesting to see how large a role the reconstruction of evolutionary history plays in diverse aspects of biology and how it unites mycology, plant biology, paleontology and other such disciplines. As John Timmerman pointed out based on his attendance at an entirely different symposium, there really are controversies in evolutionary biology, but they're about the specifics, not about evolutionary theory itself. The theory, in fact, is what allows us to discover the evidence that resolves the controversies in evolutionary history, the specifics of what happens. The controversies we heard about yesterday — from whether or not the biogeographical history of grasses was driven by the rise of ungulates to whether the Cucurbitae originated in Africa or Asia — are questions for which evidence can be discovered, and not just when someone happens to find a fossil. Evolutionary biology in general is the basis upon which these histories can be reconstructed and resolved using molecular characters and biogeographical evidence. What's happening in phylogeny these days is really pretty amazing stuff for those who can make some attempt to keep up with it.

In fact, all anyone can do is make an attempt. There's so much new discovery and so much happening in general that it's probably not possible for anyone to stay on top of all of it. Still, one must make some attempt. Even a small fraction is a lot of knowledge. Anyone who says that there's "no evidence" for evolution can be accurately assessed as someone who refuses to look for any by even doing so much as reading a paper every so often.

In his concluding remarks yesterday, Michael Donoghue said that these were exciting times. He's right, but maybe a bit conservative in his verbiage. I'd call them frenetically hyperactive times, exciting in proportion to their subject matter to the same extent that jumping out of an airplane is proportionate to pedaling a tricycle.

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Disenlightenment: Some Things Never Change

The so-called religious organizations which now lead the war against the teaching of evolution are nothing more, at bottom, than conspiracies of the inferior man against his betters. They mirror very accurately his congenital hatred of knowledge, his bitter enmity to the man who knows more than he does, and so gets more out of life. Certainly it cannot have gone unnoticed that their membership is recruited, in the overwhelming main, from the lower orders - that no man of any education or other human dignity belongs to them. What they propose to do, at bottom and in brief, is to make the superior man infamous - by mere abuse if it is sufficient, and if it is not, then by law.

Such organizations, of course, must have leaders; there must be men in them whose ignorance and imbecility are measurably less abject than the ignorance and imbecility of the average. These super-Chandala often attain to a considerable power, especially in democratic states. Their followers trust them and look up to them; sometimes, when the pack is on the loose, it is necessary to conciliate them. But their puissance cannot conceal their incurable inferiority. They belong to the mob as surely as their dupes, and the thing that animates them is precisely the mob's hatred of superiority. Whatever lies above the level of their comprehension is of the devil...

The inferior man's reasons for hating knowledge are not hard to discern. He hates it because it is complex - because it puts an unbearable burden upon his meager capacity for taking in ideas. Thus his search is always for short cuts. All superstitions are such short cuts. Their aim is to make the unintelligible simple, and even obvious. So on what seem to be higher levels. No man who has not had a long and arduous education can understand even the most elementary concepts of modern pathology. But even a hind at the plow can grasp the theory of chiropractic in two lessons. Hence the vast popularity of chiropractic among the submerged - and of osteopathy, Christian Science and other such quackeries with it. They are idiotic, but they are simple - and every man prefers what he can understand to what puzzles and dismays him.

The popularity of Fundamentalism among the inferior orders of men is explicable in exactly the same way. The cosmogonies that educated men toy with are all inordinately complex. To comprehend their veriest outlines requires an immense stock of knowledge, and a habit of thought. It would be as vain to try to teach to peasants or to the city proletariat as it would be to try to teach them to streptococci. But the cosmogony of Genesis is so simple that even a yokel can grasp it...

— "Homo Neanderthalensis," H.L. Mencken
The Baltimore Evening Sun
June 29, 1925

I ran across mention of this column in Francis Wheen's book, How Mumbo Jumbo Conquered the World, which was published in 2004. Mencken's column was written on the eve of the Scopes Trial, but things haven't changed much in the intervening 83 years since the column appeared. Perhaps that shouldn't be surprising; human nature hasn't changed much in those 83 years, either, and the Neocreationist movement is the product of the same baser motives that have always been with us — the fear of change, the desire to feel more significant than we really deserve (where would blogs be without it?), laziness... none of them show any sign of disappearing from humanity anytime soon.

This doesn't make such behavior anymore excusable, of course, particularly at a point in the evolution of information access itself that includes a potentially marvelous tool like the Internet. The noble geeks who created this medium conceived it as a means by which scientific information could be exchanged easily, and as the technology itself has grown this possibility extended beyond the walls of select institutions to anyone who cares to have access. The amount of legitimate knowledge at our fingertips now was inconceivable even within my own lifetime. When I graduated high school a quarter of a century ago, there wasn't even an inkling in the general populace of what was to come.

Sturgeon's Law applies to this medium as much as any other, though. Once access to the Internet became general, the same sort of "yokels" of whom Mencken wrote long ago began turning 90% of it into crap. It has come to serve the purpose, to a vast extent, more like the village idiot than the town hall or public university. The Internet has become the only cheap and readily available mechanism for one-to-many broadcasting for every conspiracy nut, every extremist, every know-nothing with an axe to grind on the planet. Before the Internet, it was hard for the rabble to find each other and most of those with deficient rational capacity were isolated and so obscure. Now, they can network. They can build virtual organizations. Their blatherings gain status because of mutual support and leak out into the populace at large; the "yokels" of whom Mencken wrote can now be found in Los Angeles as readily as in Toad Suck.

As for Wheen's book, I'd recommend it to those who haven't already read it who are interested in the recent history of delusional and magical thinking. My favorite quote so far from the book is a partial one from Theodore Roosevelt, a man about whom I admittedly have mixed feelings as I look back from a subsequent century upon him. Still, he was considered a great enough president to have his face on Mount Rushmore alongside Washington, Jefferson and Lincoln, so the significance of this shouldn't be lost. I reproduce the quote in context below:

In the broader field, thank Heaven, I sat at the feet of Darwin and Huxley, and studied the large volumes in which Marsh's and Leidy's palaeontological studies were embalmed, with a devotion that was usually attended by a dreary lack of reward — what would I not have given fifty years ago for a writer like Henry Fairfield Osborn, for some scientist who realized that intelligent laymen need a guide capable of building before their eyes the life that was, instead of merely cataloguing the fragments of the death that is.

— "My Life as a Naturalist," Theodore Roosevelt
American Museum Journal, Volume 18, p. 321
May 1918

Henry Fairfield Osborne was certainly a mixed bag of a scientist; he got some things right and quite a few things wrong. By today's standards, some of his work would certainly be considered racist (Osborn believed not only in a hierarchy of races but of ethnicities; people of Western European Ancestry were more advanced than those of Eastern; Osborn would have no doubt looked down upon a mongrel like me!) Still, Roosevelt was a man who went out of his way to educate himself with the best sources he could lay his hands upon at the time. I wonder how he would have viewed the nonsense that gets passed off as knowledge so often these days.

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Worcester Wireless Weather Wonder

It's an amazingly beautiful day here in Worcester. Dare I say perfect? As close as one is likely to get, certainly. It is nearly 70 degree, sunny and with a good breeze, and far too nice to be stuck in my office. I am thus not to be found there at the moment, but am instead ensconced in a quiet spot outside the university library as I type this. I've spent the morning here hard at work on a research proposal that I've just sent off for review. Thank you, Jesus, for inventing wireless networking when the earth was created 4,307 years ago this week.

Alas, my time and battery life are both growing short. I am to have lunch with a candidate for a microbiology position, then I have a symbiosis seminar to attend, and then a couple of precious hours before teaching intro bio lab in which students will be dissecting a grasshopper and a rat today to learn more about open and closed circulatory systems. I most likely won't get done until after 8:30 or later. I'd rather be doing field work on a glorious day like today but I am, indeed, biology's bitch. There are worse things to be, though, and at least I've gotten to enjoy this fine Massachusetts morning wherein springtime has made its first boisterous appearance.

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First Recorded Sounds

The first sounds ever recorded by humanity can now be heard on the web, and amazing thing. They have a ghostly quality to them, particularly the very first recording recognizable as that of a human voice. This was made on a sheet of paper coated with soot from an oil lamp by Édouard-Léon Scott de Martinville on April 9, 1860. It reproduces the voice of what sounds like a woman singing a French folk song, Au clair de la lune, Pierrot répondit.

Thomas Edison wouldn't invent the phonograph for 17 years after this was recorded.

boomp3.com
I don't know about you, but I got goosebumps listening to that eerie, scratchy, ethereal sound.

Also available are excerpts of the first human voice ever recorded (1857), though in this case the voice isn't quite as recognizable:
boomp3.com
I think this is the very first recording ever made, or at least that has survived in a condition good enough to be restored. However, it doesn't sound much like a voice at all. The person who made the recording appears to have been toying with making recordings at various speeds. This begs the question of whether some even earlier recording exists, since one might expect that someone playing with different speeds would have first recorded at a normal speed.

The recordings have been rescued and digitized by a project called First Sounds, a group created with the purpose to make the oldest recorded sounds available to the public. They give explicit permission for anyone to reproduce the sounds, but if you want to reproduce them on line it is asked that you do not hotlink them from First Sound's website. You may, however, download and host them elsewhere, which is what I've done here. A site called BooMP3 provides free, unlimited hosting of audio files and is quite handy for that purpose.

A couple of other very early recordings are also available at First Sound's websites, but these two were my favorites. I'm glad that someone has gone to the trouble of preserving them.

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The Field Work Season and Weekend Are Coming

I was hoping to go on my first officially-sanctioned collecting trip to Wachusett today. The weather is not cooperating, however. Rain and sleet and ice pellets falling from the sky do not make for good conditions to clamber about in forests on the sides of mountains. It will have to wait.

On the other hand, I'm preparing for a productive season in the field. With the remainder of my research fund for the year, I've purchased two new geek-toys. First, there's a new dehydrator capable of accommodating large polypores. It's a beauty; by removing trays, I'll be able to dry even a large Fomitopsis in one piece. The dehydrator I've been using up until now is good for small fungi, but I'd need a band saw to slice up some of the woody polypores for them to fit. This way, I can preserve not only the fungi but the beetle galleries within them intact. Such things make me happy.

Second, I'm finally getting a new handheld GPS unit. I will always love my little Magellan, but I need something more accurate and reliable under heavy tree cover plus it needs to have basemaps of South America as well as North. I should be getting a shiny new Garmin GPSMap 76Cx delivered on Monday. It'll be useful to me not only for field collections in the US but also in Trinidad should I happen to find myself there this summer.

In the meanwhile, this weekend is looking to be a good one (aside from having to grade student assignments, which I'm going to try to get through today). Tomorrow, LL and I are heading to Boston where we'll meet up with my adviser and his wife for dinner at Lala Rokh after which we'll be going to see Laurie Anderson at the Boston Opera House on her Homeland tour.

Rather than attempting to drive, LL and I are going to take the train and check in at a hotel before dinner. We're going to spend the night in Boston and then come home on Sunday morning. That way, we won't have to worry about how long the show is going to run and whether we can make the last train back to Worcester at 11:00 PM. Besides, I hate driving in Boston.

It's going to be a great weekend, and I'll have new technological toys to play with when we get back. Who could ask for more?

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Who Is the Patron Saint of Scanning Electron Microscopes?

Just kidding.

Our department is being considered for a grant that would give us a whole bunch of shiny new toys including — brace yourselves — a desktop scanning electron microscope. Our own little SEM! I would be as happy as a little girl if we had one of those right in the building. We have access to one by arrangement with another, larger, school in the area. It's a schlep across town, though, and I understand that getting time on the thing can be a serious pain in the coccyx. I haven't had the need for it yet myself, but the time will come. When it does, it would be nice to simply walk into a room and do what needs to be done without having to sign up well in advance and hope that the timing works out.

Being a smaller school, I don't know what our chances are of getting the grant. I don't even know which grant it is. All I know is that we've been good little researchers and we deserve a present! We don't have room for a departmental pony, so the SEM would really be the next best thing...

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Cow Cow Cow Cow: FDA Approves Cloning Livestock and the Fear Begins

The FDA yesterday issued its conclusion as to whether to permit the cloning of livestock whose offspring will enter the US food supply. It has found that products obtained from cows, pigs and goats whose parents were produced in this manner are identical to those from animals reproduced by means already in use. The release announcing the decision is available on the Food and Drug Administration's website.

The decision comes in the wake of a long and heated debate that has taken place over the last couple of years. There seem to be three major arguments being raised by those who oppose cloning. All three of these are based on insufficient premises. For ease of analysis, I'll note these objections as religion, pseudoscience and ecology, respectively. This is admittedly a somewhat artificial division used for convenience; many of those who object in fact blend them into a single objection or else use all three.

The Religious Objection
This objection is typified by a comment on story in Business Week on the matter:

Cloning is upsetting the balance of nature.....although cloned meat may be scientifically proven to be safe to be consumed, it is still against the law of nature.

— lionelx

Even more explicit is this comment on the same story:

Here we go against the taboos of Islam just when Mr. Bush has just collected a big cheque from the Muslim countries today, 15th January, 2008...

— Firozali A Mulla

Mulla's comment references a particular religion and lionelx's is a more general "law of nature" argument, but they're essentially the same. Both of these objections are based on the belief that there exists some supernatural set of rules that governs what we can and can't eat. This fails immediately on the fact that if such a set of laws existed, it shouldn't be possible to clone the animals in the first place. The first comment is particularly clear on the religious point of view; given that the products are perfectly safe, the very act of cloning livestock "is upsetting the balance of nature." Apparently, the domestication of animals by untold generation of selective husbandry doesn't do this. What the distinction is in reference to the "balance of nature" isn't made clear, but the fact is that raising an artificially maintained large population of one kind of animal in an area that couldn't support that population without significant human intervention is already an exceptionally unnatural situation. Why the method by which those animals reproduce should have more of an impact than the situation already has upon the natural world eludes me. Perhaps someone could explain why cloning has such a profound impact upon the "balance of nature." Breeding stock is already selected on the basis of desirable traits. Cloning speeds up the process that has been in place for thousands of years.

As far as I can tell, this objection is one made from personal belief alone. It's an insufficient reason not to allow the cloning of livestock.

The Pseudoscience Objection
A comment to the above story typifies this argument well:

Given what we know and don't know about biological proteins and how "prions" can adversely influence the reproduction of cells, who is to say our future generations won't be altered for the worse, and that the changes are so subtle and gradual that they won't manifest themselves until 2 or 3 generations later!? I am really scared. Then it may be too late and we may have altered the human race forever. Think of the Chernobyl area.

— Joey

I saw another comment on a separate story say essentially the same thing about fatty acids that Joey says about prions here but can't track it down right now.

Let's assume for the moment, based on Joey's argument, that the reason that we find prion diseases in cattle (e.g., mad cow disease) has a genetic basis. That's somewhat up in the air at the moment, by the way. There appear to be several families of prion diseases in the world and nobody knows how they're transmitted aside from the consumption of contaminated tissues. The most recent outbreak of mad cow disease in the UK, for example, appears to have been initiated when a new processing technique was used to render nervous tissues from sheep into protein meal that used a lower temperature than the previous technique and the prion proteins weren't denatured; what was mad cow disease in British cattle probably started as scrapie in sheep. This interesting bit of trivia aside, there's absolutely no reason to think that cloned animals are more likely to harbor prions than are those raised by current methods. Prions are themselves nothing more than proteins with an abnormal conformation. The twisting of the polypeptide can be the result of a genetic abnormality, but in most cases it takes place when a normal protein comes into contact with a prion. The mechanism by which this happens is not yet understood, but to make the leap to the idea that it becomes more likely because an animal has been cloned is one that isn't supported by anything we know. I find it very unlikely, in any case, that an animal from a lineage that includes a disproportionate number of individuals that have been affected by a prion disease would be chosen for cloning in the first place. The point of this technology, after all, is to speed up the propagation of desirable traits. Vulnerability to any disease will be selected against — exactly as it is in traditional husbandry.

In fact, there's no reason to think that cloned cattle, pigs or goats are substantially different from those who arrive on the farm by way of normal breeding. These animals are not being genetically modified, they're being duplicated. As the FDA release itself states:

Cloning is not the same as genetic engineering, which involves altering, adding or deleting DNA; cloning does not change the gene sequence.

Cloning and genetic modification are two entirely different issues, although those who aren't familiar with the basis of either one are likely to conflate them.

But there's one more fact that this argument ignores, and it's one that's stated in the release:

Because clones would be used for breeding, they would not be expected to enter the food supply in any significant number. Instead, their sexually reproduced offspring would be used for producing meat and milk for the marketplace.

It's not the clones themselves whose products would go on the market, but the offspring of those clones. If there are abnormalities in these offspring, it won't take long to see them and the offspring themselves are unlikely to have the one difference that we do see in clones — telomere shortening. Shortened telomere's, however, are themselves linked perhaps to early cell senescence and so, potentially, to a shorter lifespan for cloned animals. There is no reason to think that even consuming meat from an animal with shorter-than-normal telomeres poses any health risk to the consumer, and in any case that's only a problem for the cloned animal. Its offspring will have telomeres of normal length.

The objection from pseudoscience, then, is based on a combination of emotional appeal and a misunderstanding of the real situation. Animals other than livestock have been cloned for other purposes for quite some time now, and they're used for scientific investigation precisely because they're identical to their immediate ancestor and so a good way of maintaining pure strains. Thus, this argument is also insufficient.

The Ecological Objection
Of the arguments examined here, this is probably the most sensible, although that doesn't make it correct. The objection is typified by this comment:

I can only see one possible disadvantage, if a certain (profitable) breed of cow becomes the cattle of choice, widespread cloning will eliminate all diversity in the species, making the species as a whole venerable [=vulnerable] for epidemics. Which is already the case, in lesser extent, due to the extensive use of selective breeding.

— Anonymous

The author of this comment raises a good point and the comment itself almost makes the case for its insufficiency. That is, many of our crops are already effectively monocultures that lack genetic diversity. That provides the potential for a very bad situation, indeed, in cases where the environment changes due to climate flux or disease. Still, that amounts to an indictment of agricultural practice as it stands, not a reason to disallow livestock cloning. In fact, if the new technology ultimately makes it cheaper to produce animals with a very limited and regularly reproducible set of traits that are of immediate economic benefit, it will remove some of the pressure that currently works against greater heritable diversity. If ConAgra can someday halve the cost of immediately useful traits, a wise management program can use some of the surplus funds to set aside strains that have greater variety than what exists now. Whether or not big agricultural entities will do that, rather than simply taking more profits, remains to be seen. The point here is that cloning itself could increase the likelihood of it happening and doesn't necessarily make it less likely.

The objection from ecology is a sensible one as applied to agricultural practices overall, but is insufficient when applied to cloning livestock. It may be a good argument, however, for future regulation of genetic diversity. Perhaps we may someday see a government that gets this point and passes some sort of legislation that either requires or provides an additional benefit to those producers who take steps to maintain greater diversity in our food supply based upon the benefit derived from livestock cloning.

All in all, I don't see any compelling reason for consumers to be alarmed by the FDA's decision. The potential benefits far outweigh the risks, and there is always risk involved with new technology. That's good reason to analyze it carefully, but it's not justification for panic.

Just for the heck of it, I want to include one "blended" objection that shows how emotionally based these fears are when taken together — a worst-case scenario, if you will:

We need to stop playing God. People do not have the right to create. The FDA says this is a safe practice but the FDA also allows percentages of human tissue into meat products and rat pellets into popcorn. WAKE UP they are not looking out for your best interest. THis is just another way to skim off the top. And move further away from natural products which our bodies crave. The cows we are eating today are so pumped full of steroids, chemicals and genetic enhancments that their clones won't be natural animals. Down with Corporate farming, bring back the family farmer, the backbone of This country!!!

— Dale

That's what you get when you run all three objections into a single set of statements. It's all right there, complete with conspiratorial overtones and outright paranoia. Pure emotion and little knowledge; it's a volatile mix when applied to any question.

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We Didn't Have Toys Like This When I Was a Kid

Coolest toy of the holiday season for your little science geekling? Hands down, it's Eyeclops. We didn't have toys like this when I was a kid. OK, the chemistry set was pretty cool (you could make things that burst into flame back then) and the all-metal erector set held my attention for a few months. Eyeclops is better.

The concept is simple enough; it's an electronic microscope that magnifies up to 200x and plugs into a television for viewing. Cool!

Forget about buying one for the kids. I want one. I have access to much higher-powered microscopes, but I'm not allowed to take them home. This gadget even has a viewing tube for looking at insects and other small organisms, and a viewing dish for containing liquid.

I don't mean to turn this into an ad, but assuming that it isn't loaded with lead and won't burst into flames, this is an instance of "why didn't anyone think of this before?" I might even buy one just to keep on the desk at my office for the sake of geek chic. The possibilities for customization are endless, too.

Can a Talking Jesus doll magnify small object 200x and put them on TV? Didn't think so. Then again, Eyeclops can't quote John 3:16 (that's what the doll actually sounds like, by the way). Hmmm, which is more fun... looking at giant bugs on TV or listening to Bible quotes? Lemme think about that one and get back to you.

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The Best Evidence that Science Education Needs Improvement Often Comes from the Opposition

Today's Bradenton Herald includes a brief list of public comments made on the Florida Department of Education's website for comments on the new educational standards proposed for the state. A couple of these comments stood out to me as providing excellent evidence as to why there is a necessity to specifically teach evolutionary theory and to improve science education generally. They fall so wide of the mark in terms of an understanding of these things generally that they speak volumes as to where there is room for improvement.

"How can anyone accept the theory of evolution? The last time I went to the zoo the monkeys weren't evolving into a man."

This comment reveals a tremendous misunderstanding of every aspect of what evolutionary theory says. It shows that the commenter doesn't know that speciation is a process that normally (though not always) occurs over a geological scale of time, so you can't stand around at the zoo and watch captive animals turn into different species. It also fails to take into account that speciation occurs in populations, and that not every population of a given species will evolve into a new species even when other populations have done so. Indeed, there are organisms on earth which have remained unchanged for many millions of years (e.g., Limulus) and zoo animals are generally removed from the sorts of selective pressures that foster speciation in the first place. It also misses the point that nowhere in evolutionary theory is it posited that human beings are descended from monkeys, though we certainly shared a common ancestor with monkeys (and apes, and squirrels...) if you go back far enough. That ancestor itself, however, was not a monkey. This level of ignorance provides a good demonstration of why there is a need to teach evolutionary theory in schools.

If you want to challenge evolutionary theory, you may certainly do so. In fact, I'll be the first to get in line and encourage anyone to have a crack at it. However, you can't challenge something if you don't know what it is you're challenging first. I'm a professed science geek. The hairs on the back of my neck stand up when I manage to tweak the nucleotides of a chitinase gene from an insect a little bit and come up with an active site for a mammalian lysozyme. I truly am that geeky, and discovery truly is that exciting for me. If anyone can come up with real evidence that there is a fundamental flaw in the conceptual framework that we call evolutionary theory, you will have my eternal admiration as being one of the greatest scientists of all time. Until you actually know what evolutionary theory is, though, you are in no position to make such a discovery. Get educated and have at it! But if you want to call a halt to the teaching of one of the best-evidenced theories in all of scientific inquiry based upon falsehoods like those embodied in the above comment, I and others like me who have bothered to learn what the theory actually says are just going to see you as an ignoramus telling tales. You have no basis upon which to justify your opinions being considered seriously and you absolutely have failed in your attempt to challenge evolutionary biology.

"Please do not let these liberal wackos in the Washington foundations warp our young minds into thinking that their existence is an accident."

And again, this is a profound misunderstanding of what evolutionary theory says. There is nothing political in evolutionary theory. Indeed, the mechanisms by which evolution occurs are generally rather conservative in nature. For instance, when constructing a molecular clock, we often talk about the rate of mutations accumulating at something like 10^-8 per year in a given species at a given locus on a given chromosome. This is very conservative stuff and something based on observation, not on some political agenda. This is no more "liberal" than is equating pi with 3.14... Nor does evolutionary theory state that any individual's existence is accidental. In fact, part of it is the notion of sexual selection which is anything but an accident. Moreover, we acknowledge that sexual selection occurs because both observation and experimentation allow us to see it at work over and over again. Humans, we know, also make conscious choices about mating, so it can hardly be said that anyone's existence is "accidental." There's nothing in evolutionary theory that tries to dismiss the importance of families, of love between individuals, or the idea that each of us is free to find purpose in our existence. It doesn't back up the notion that such meaning is preordained by a supernatural force, though, and that's really to what this comment is objecting. Such an assertion is clearly a statement of belief, and if you want to believe that's true, fine. If you want to propose that it's a statement of the objective nature of the universe and so turn it into a scientific principle, though, you're going to have to find the same sort of evidence that I have to provide when I want to make a much less important assertion about some far more trivial item. Again, have at it! Bring on the evidence and if it's sound, evolutionary theory will be revised to incorporate this new data or tossed entirely if the model doesn't fit at all. Science deals in provisional truths, not absolutes. Old theories get revised all the time... but first you have to know what theory you're challenging.

"This is unacceptable, unless Biblical Creationism is taught alongside evolution."

Why Biblical Creationism? Why not one of the six Creation stories from the Linga Purana or the Navajo creation myth? This is typical for someone who believes that public schools should act as religious indoctrination centers. Unless one can support the idea that one creation story is better than another one by providing empirical data showing that it is correct and the others are wrong, there is no reason that one should be favored over another other than pure personal bias. The reason, then, that Biblical Creationism isn't taught along evolutionary theory is that the former is an opinion based solely on something that approaches a cultural norm while the latter is based on evidence of how the world actually works that has been subjected to rigorous testing that comes from the overall scientific method. Most of those who make this argument don't have the first idea about how hard we look at this thing we call evolution, how we test all of these mechanisms and pathways and genes and all of it, and how it does get challenged and revised within the context of valid inquiry. They don't know about it because they don't care to know about it. Does this mean we should leave students unable to mount those challenges themselves and so eventually improve upon our understanding so as to prop up some dusty religious theory, whether it is Biblical Creationism or the Hindu idea of Yugas?

"I will not allow you to teach my child this no matter what you put in your curriculum. I stand for Christ and his creation."

Funny thing about arguments like this; I've read Genesis and I can't recall Christ showing up in there at all. Beyond that, I suppose that every parent has the right to keep their child ignorant of whatever they want to so long as that child is under the age of majority. That's a sad thing, but it's perfectly legal as far as I know. However, that parent is certainly limiting that child's options later in life, after he/she becomes an adult. What are you going to do if that kid, upon reaching the age of majority and escaping this sheltering shadow of imposed ignorance, finds out about this thing called "science" and decides to pursue a career therein? Shoot him? Disown him? Lock her in the basement for the rest of her life? Evolution isn't just something taught in schools, after all. This comment is made out of fear, and fear is quite often the result of ignorance. It is also made out of a desire to impose a religious nature upon publically-funded education which, thankfully, is out of the question. Eventually, your child enters the great, big world, a world in which evolutionary theory has been tested again and again and is the glue that not only holds together biology but is drawn from and informs chemistry, statistics, and numerous other fields. Unlike the world of people who believe that the world is a neatly compartmentalized place in which you can shut out an idea by shutting out some small bit of life, it's far messier than that. Ideas and theories slop over into many disciplines, many areas, and it's not always that easy to see. If you want your child to have the wherewithal to challenge evolutionary biology, he/she must first know what evolutionary biology is.

"How is anyone's life improved by believing in evolution?"

Short answer: it isn't. Evolution is not a matter of belief but an explanation that incorporates absolutely every bit of data that we have about life in the entire universe (which, at the moment, is restricted to earth — but should we find extraterrestrial life someday, evolutionary theory will have to accommodate that new set of data or else face the scrapheap of history like any other unsupported scientific theory). However, the principles comprised by evolutionary theory have improved our lives whether any one of us agrees with it or not, and that is a hallmark of a sound theory. We posit and design new medicines based upon information that has come about as the result of evolutionary biology. We understand heredity and can predict and treat heredity diseases because of it. There is software that runs the internet and other communication networks that incorporates evolutionary principles. We select and breed plants and animals based on this knowledge. All of us, whether or not we "believe" in evolution, benefit from the products of this theory every day, although we are generally unaware of our doing so because it has become some commonplace and so integrated into our existence that we don't question and investigate these things unless it's our job to do so.

Do you have a lawn? Do you put fungicide on that lawn to keep it nice and green? Do you feel that you benefit from having a green, fungus-free lawn? Then you benefit from evolutionary biology, the principles of which led us to an understanding of the mechanisms of chitin synthesis and so to something called Polyoxin-D, a chemical which is structurally analogous to the monomers that fungi use to build the chitin which is essential to their survival. Thanks to an understanding of evolution, this compound is now commonly used in fungicides that don't harm mammals or birds (since they don't synthesize chitin) nor insects (since they use a different genetic, evolution-derived pathway for chitin synthesis that doesn't incorporate this particular competitive inhibitor). The benefit that you derive from having your nice lawn, that mundane little bit of a better life, comes to you precisely from the wonderful world of evolutionary biology. All you see is your nice, green lawn and, perhaps, a little increase in your property value. Does it matter whether you "believe" in evolution or not? That Polyoxin-D works in just the same way and just as well... but if not for evolutionary theory, you wouldn't have it. What far more important benefits would we not have if the discipline didn't exist in the first place? Again, the comment shows nothing more than the ignorance that utterly necessitates that we do a better job of educating our children about science, including (but certainly not limited to) evolutionary biology.

The very presence of comments like these don't lend any weight to the assertion that evolutionary biology shouldn't be taught as evolution in public schools and they certainly don't lend weight to some necessity that there is a competing theory that must be taught alongside evolution. All they do is demonstrate very clearly that those who oppose the teaching of evolution generally don't know to what they are opposed in the first place.

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Greetings to the AFA Readers

If you look down at the bottom of any page on this blog, you'll notice a little icon for a service called SiteMeter. SiteMeter is a useful tool that lets me see where people are coming from when they get here, how they found the blog, how many hits and page views I get per day, etc. It doesn't tell me anything more specific than that; it just gives the subscriber a general overview.

As of this morning, it seems I've picked up a couple of readers coming from the American Family Association's domain, afa.net, located down in Tupelo, MS. Greetings and welcome to Hyphoid Logic. I'm glad that you found yesterday's entry about the silliness of your proposed boycott of PetSmart for not using the word "Christmas" enough on their website and invite you to explain how evil and un-American PetSmart is in light of what reader Anti-ethnocentric mentioned yesterday in a comment about how that company does annual charity work by having customers' pets photographed with Santa Claus.

Keep on readin', AFA members! I'm delighted to see that you've found my little blog and look forward to the interactions between yourselves and the usual readers here.

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