Browsing the archives for the Science category.

Damn, It's Good To Be a Mathematical Gangster

Fun, Geekery, Science, Travel

Via one of my favorite science fiction authors, Michael Flynn:

I have just one question: after you chop a mutineer up into infinitesimal pieces, don't you just end up with two mutineers?

Hmmm. I suppose this would explain the origin of Joe-Jim Gregory.


The Necrogenomicon

Politics & Current Events, Science, Technology

Msgr. Falda: The language of the Necrogenomicon is arcane; its meaning recondite. If we give it, in its many variants, into the hands of the people, there's no telling what they may do with it!

Bro. Laxman: But, with respect: it already resides in their hands, and hearts, and indeed in all parts of them. It lives in them, and through them, and they in and through it. Most literally.

Msgr. Falda: But it requires interpretation. Trusted interpretation. Authoritative interpretation….

Bro. Laxman: To be sure, many details of life benefit from the wisdom and insight of experts. But nobody wants to do away with authorities and experts. It's merely that the people want to read the language of the text themselves, and perhaps consult with others who know more than they.

Msgr. Falda: This cannot be! If the people read for themselves a text they do not, and probably cannot, comprehend– and if they follow the guidance of whomever they will rather than that of a rightful shepherd of the flock– then they may go astray, not only in understanding but most certainly in action as well!

Bro. Laxman: But the people may already consult whomever they will, and go as they choose, and understand according to their lights, and act, possibly, in manners untoward.

Msgr. Falda: Precisely! And uncovering these truths to them all at once, in bulk, and without appropriate commentary may mislead them further! What if one of them comes to a false understanding and seeks to cut off his right hand?

Bro. Laxman: We already govern the chirurgeons, my lord.

Msgr. Falda: But… but what if one of them seeks to foment rebellion?

Bro. Laxman: We already regulate the militia, my lord.

Msgr. Falda: And what if one of them, for want of understanding, annoys a deacon with babble and the ill-gotten fruit of a meandering mind?

Bro. Laxman: Then he will tell him to stop, my lord. And perhaps help him to understand the limits of his own horizon. Knowledge is seldom fatal, and even a false understanding will seldom bring about grievous harm….

Msgr. Falda: But we are the gatekeepers, Bro. Laxman! We are the gatekeepers.

Bro. Laxman: And each of the people, my lord, is the gate. Shall we keep it closed and guarded as for war, or open as for peace, its perimeter defended?

The FDA reckons that the product provided by 23andme is medical equipment, and that some subset of the corresponding service constitutes medical advice. So the FDA wants a piece of the actionto be sure that the people are protected from the dangers of possibly false or misleading information coming through unauthorized, unregulated channels. 23andme has been draggin' its feet in response to FDA demands, perhaps because of disagreement about whether personal genomics, a new application of new technologies, actually falls squarely within the current regulatory regime.

BoingBoing provides a cartoon and a cluster of links to articles that offer a fresh and useful overview of the issues at hand.

A bunch of dead people gave me their chromosomes. Ever since, I've been trying to figure out to how organize and use them. Not too long ago, I sank a Frank' into the "Health and Ancestry" personal genomics kit from 23andme. Just in time, since the FDA has asked them to stop making sriracha until the neighbors' complaints can be mollified. Last I heard, 23andme is making nice in words about compliance and cooperation but declining actually to comply… for now. "Can't we all just get along? I'm sure there has been some sort of misunderstanding. We've made a hash of it with our tardy replies, but we do, genuinely, truly, from the bottoms of our heart, love and respect you. It's not you; it's us."

(BTW, feel free to use me as a referral once they sort things out! That'll add $5 to my book-buyin' fund. ;) )

Did the results of my test solve any deep mysteries? No, although I learned some things about my ancestry that I hadn't previously known and have since confirmed genealogically. Did health information spur me to bum rush the medical staff at my PCP's office and demand that they do X, Y, and Z forthwith? Not at all. Was it entertaining and informative? You betcha! And did it prompt me to try to learn more about genetics, genomics, and gymnastics? Indeed, it did. I was floored by the exercise, which set a high bar, and I wouldn't call my efforts so far a ringing success, but that's ok since I'm just horsin' around.

Herewith, some observations. First, 23andme takes a conservative approach to analysis; if you download your genome info, upload it to GEDMatch, and run some alternate analyses offered as freeware by genetic hobbyists or rogue professors, you may see more– or different– information about haplogroup classifications and ethnic origins. Using a different commercial service, such as FamilyTreeDNA, may likewise provide more granular results. But for 99 clams, 23andme delivers the essential and allows some speculative tweaking to see alternate results. That's good enough for the casual consumer; those on a mission may need more.

Second, the community forum at is fairly primitive. For example, email notification for followed discussion threads is an all-or-nothing affair. Searching is non-existent. Redundant threads occur because there's no fast, non-awkward way to find out whether an appropriate thread already exists.

Third (and this is probably true of all personal genomics communities at present because this industry is larval), the points of light are far outnumbered by the blobs of smog. To phrase it with greater diplomacy, the discussion forum is overrun by understandbly curious and uninformed users whose questions, and whose answers to others' questions, are flat out wrong. In the midst of all that noise, a few valiant and well-informed hobbyists (plus the occasional professional) who have dedicated themselves to the task try to set things right. Sadly, the forum software sees those contributions fade rapidly into undiscoverability.

I trust the quality of discussion will improve there, and elsewhere, as education improves and interested parties take advantage. Indeed, 23andme provides a number of informative introductory videos and simple essays that lay out the basics while identifying some of the limitations and nuances. But reading and watching videos are homework, and nothing guarantees (nor should guarantee in that sort of forum) that everyone who speaks has done that homework.

Do you have some experience with personal genomics services? What was your experience? Did you learn anything surprising or interesting that you'd like to share? What do you think of the policy issues underlying the FDA's attempt to regulate 23andme?



Effluvia, Poetry, Science

It was a formidable task, but agitators or Alinskyites have finally managed to pit the workers against the founders:

By such is my muse newly stirred:

Empirical lurkers,
We're studying workers,
And hoping to model their nest.

We've come from the foundry
To size up the boundary
And feel that old Al does it best.

We've taken great pains
To see no ant remains;
We've worked hard to effect their premoval.

You'll be happy to learn, the
New method would earn the
Fourteenth Dalai Lama's approval.


An Ode from Ur-Dad

Humor, Poetry, Science

While off to meander
The vale of Neander
I once took a gander at some lovely gal.

She was low in the hip
And smart as a whip,
But that brow ridge! It made me her pal.

I said, "Though I'm cro-magnon,
I'll be yer companion,
If you'll join me now down in the valley."

With a come-hither look,
My comparatively frail hand she took,
And we down toward the river did sally.

With no hint of neurosis,
We danced the meiosis,
And maybe a tango or two.

And that's why knuckle-dragger
Snips, like a stone dagger
Enhancing your swagger,
Now make you a bragger
'bout the chromosomes that she left to you.



Georgia On My Mind

Effluvia, Science

Bad news for the objectively anti-Neanderthal and anti-Denisovan bigots and others concerned about genetic variation among populations in the deep south of Georgia: some early hominid "species" may not be different species after all:

Early, diverse fossils — those currently recognized as coming from distinct species like Homo habilis, Homo erectus and others — may actually represent variation among members of a single, evolving lineage. In other words: just as people look different from one another today, so did early hominids look different from one another, and the dissimilarity of the bones they left behind may have fooled scientists into thinking they came from different species. (source: NYTimes)

The idea is that Homo habilisHomo rudolfensis and Homo erectus are not branches but variation within the single trunk. Further, the degree of variation among the skulls from Georgia– all evidently from a single population– is similar to, or greater than, the degree of variation among skulls from Africa. This suggests that speciation has been overprojected for Africa, too. Finally, the differences between the Georgian and African fossils are similar to the differences among the Georgian fossils. So speciation relative to migration may have been overprojected:

Naturally, some scholars affirm and some dissent. A lot of bones to pick!

[Fred Spoor from University College London] added that the very specific characteristics that had been used to define H.erectus, H.habilis and H.rudolfensis "were not captured by the landmarks that they used".

"They did not consider that the thick and protruding brow ridges, the angular back of the braincase and some details of the base of the cranium are derived features for H.erectus, and not present in H.habilisand H.rudolfensis."

Chris Stringer at the Natural History Museum in London said that the team had made an excellent case "that this remarkable new skull, with its huge jawbone", was part of the natural variation of the Dmanisi population.

But he said he was doubtful that all of the early Homo fossils can be "lumped into an evolving H.erectus lineage".

So the dispute is over which features different among the samples are sufficient to assert speciation, and which count as natural variation within a single species. Seems like we'll need more fossils before that issue can be resolved definitively. The site in Dmanisi may well provide them!

Update: interesting, slightly different coverage from WSJ:


Biology-Online And Marketeer Entitlement, Revisited


This weekend I talked about how Dr. Danielle N. Lee was called a whore by a marketeer from Biology-Online, and how Scientific American temporarily deleted her blog post about it. 1 I used it as an opportunity to discuss bad crisis management (on the part of Scientific American) and the entitled marketeer mindset (on the part of Biology-Online).

Since then, Scientific American has practiced damage control, belatedly restoring Dr. Lee's post and offering an apology and explanation that is competently executed, if too late and ultimately rather unconvincing. Biology-Online has offered an apology to Dr. Lee, acknowledging that the conduct of "Ofek" was unacceptable and announcing his termination. Biology-Online did not identify "Ofek."

I offer one illuminating coda. In its apology Biology-Online says that "Ofek was hired to grow biology-online's relationships relationships with bloggers and scientists." In other words, as I said, a marketeer. How should we react to rude marketeers? Well, rather than Biology-Online's apology to Dr. Lee, consider what Biology-Online forum moderator "JackBean" said in a forum thread there about the situation

Please, stop acting like crazy, people. Yeah, he did what he definitely shouldn't. However, we couldn't act earlier since we didn't know about it and DNLee decided to rather write a blog about that instead of handling it with someone above Ofek. I understand that since she didn't have any other contact than him, but it's her decicion.

In other words, upon being called a whore by a marketeer, rather than writing about the experience of a marketeer calling her a whore because she refused to provide free content to improve Biology-Online's traffic and advertising revenue, Dr. Lee should have sought to speak to the marketeer's supervisor. Surely the supervisor of someone who spams scientists asking them to provide free content to Biology-Online to make money for Biology-Online will be reasonable! Why must you make such a big deal out of this?

Pressed on this, Biology-Online moderator JackBean elaborates:

I never blamed her for being called a whore, I blamed her for the delay in our team's response. That's a difference. And I blamed the anonymous users here, who registered just two days ago from being out of their mind. If they could, they would lynch Ofek. How are they different from him?
BTW Ms. Lee called our team in one of her tweets "asses", very professional from her.

Yeah! Will nobody think of the feelings of the marketeers?

Remember: marketeers are entitled assholes. If you encourage to marketeers, if you give them content, if you give them links or accept their links, if you write guest posts for them or accept their guest posts, you help them make the world a worse place.

Why would any scientist write content for Biology-Online, or even use its forum? If you know such a scientist, maybe you should ask them.


Popehat Signal: Vengeful AIDS Denialist Sues Critic In Texas


It's time for the Popehat Signal.

New Popehat Signal courtesy of Nigel Lew.  Thanks, Nigel!

New Popehat Signal courtesy of Nigel Lew. Thanks, Nigel!

Today I light the signal to ask for help for a blogger who is being sued in federal court in Fort Worth for writing about and criticizing a thoroughly creepy AIDS denialist. By AIDS denialist, I mean someone who promotes the belief that HIV does not cause or lead to AIDS. The lawsuit is contemptible. The defendant needs help. Can you step up?

Continue Reading »


You say you want a convolution

Science, Technology

Why bother with artificial intelligence when we're still pretty incompetent with natural intelligence? And yet the fact that a venture is ill advised has never stopped us before.

We aspire to control others without being able to control ourselves.

We judge others more harshly than we judge ourselves.

We take more readily than we give.

Let's talk for a moment about our brain. No, not "our brain" as in us, the crosier of Popehat. (Some blogs have a staff; we have a crosier.) I mean "our brain" as in us, the species homo sapiens somewhat laughably sapiens.

What I want to say is this: we're certainly not going to let the fact that we're baffled by our real brains impede us from trying to build fake ones, right? Perhaps aiming for artifice in matters brainial will help us grasp things actually intracranial.

Of course, if we really knew how to exercise the natural contents of our collective brainboxen, then faced with the prospect of artificial intelligence, we'd all be running around screaming, "No! Stop! Skynet! Nexus!" (Of course, some of us would be doing it with the intonations of Gene Wilder's Willy Wonka, but hey.) We'd all recognize that if we can so easily rationalize our own hypocrisy, then even if we had an anthrobotic system that was tweaked to honor the n laws of robotics, someone somewhere would hack hypocrisy and rationalization right into it. Next stop, SHODAN.

Anyhow, we are blissfully oblivious to risks. And thanks to functional MRI and kindred advances in technology, such as electron microscopy and laser-scanning light microscopy, we (as a species) now stand at the threshold of understanding the brain's architecture and adaptability. We have begun to recognize that "neural circuits tell activity how to propagate, and neural activity tells circuits how to change". It's a great time to be alive, if only for the advent of much better sci-fi.

So what would a computer program based on the way our brains actually work be like? Not one inspired by cheesy 1980s intuitions about fuzzy logic, but a rigorous adaptation of principles actually embedded in our wetware?

Happily, thanks to Jeff Hawkins (the dude who founded Palm and Handspring) we can now begin to understand the answer to that question.


Michael Mann Sues NRO, Mark Steyn, the Competitive Enterprise Institute, and Rand Simberg

Law, Science

Back in July I noted that climate scientist Michael Mann had threatened to sue National Review, Mark Steyn, and others for vivid online criticism. Mann is the originator of the famed "hockey stick graph" of global warming data; he was accused of academic misconduct based on notorious hacked emails, but cleared by a Penn State investigation. Steyn quoted and linked to a post by Rand Simberg at the Competitive Enterprise Institute, the rhetorical thrust of which was that Penn State clearing Mr. Mann was no more credible than its clearing of Jerry Sandusky.

Yesterday the other shoe dropped and Mann sued NRO, CEI, Steyn, and Simberg in D.C. Superior Court for libel and intentional infliction of emotional distress (or, as I prefer to call it, Butthurt in the First Degree). The Legal Times has posted the complaint. I've reviewed it, and have some initial thoughts.

Continue Reading »


Confronting Junk Science: Keep Calm And Carry On


Various skeptic blogs, particularly those in the United Kingdom, are aflame over a magazine called "What Doctors Don't Tell You," which appears to be an uninhibited woo-fest of conspiratorial-minded pseudo-medical junk science. What's notable about the magazine is not that it exists — there's a zine for every viewpoint, even in the age of the blog. No, what concerns the skeptics is that the magazine is being carried by mainstream stores like WHSmith and Sainsbury. It's like walking into Starbucks and seeing that their newspaper rack has pamphlets about the moon landing being faked.

Some skeptics have begun to write to the corporations stocking the magazine urging them not to, which has led to accusations of censorship. I think those criticisms are off-based, but I have a few respectful words of advice to the skeptics as a free speech advocate.

First: please be aware of the opponents you face, and the rhetorical and legal arena in which you fight. In the junk scientists — let's call them "advocates of non-traditional medicine" for the sake of this point — you are dealing with a community increasingly characterized by an appetite for aggressive censorship. In the United Kingdom, you have an arena with a level of protection for free speech that — and I say this out of love, with a debt of gratitude for my common law heritage and the language I love — sucks donkey balls. It sucks so badly that we've had to pass laws specifically providing that your ludicrous defamation judgments usually aren't enforceable here. My point is this: to the extent you employ censorious measures, you can expect them to be turned against you later by your foes, with the cooperation of your largely censorship-indifferent government. Do not take up any weapon you don't want used against you.

Second: mind the rhetoric, please. Freedom of expression is threatened not only by specifically censorious methods, but by flexible and insipid memes and mottoes. When I see Keir Liddle employing the "fire in a crowded theater" image — the unprincipled nature and repulsive origins of which I discussed recently — I roll my eyes. Andy Lewis' headline "This is not an Issue of Free Speech, but of Responsible Speech" is a cringe-inducing appeal to the categorical dodge. I guarantee you that Mr. Lewis will see some future attack against his writing spun as "this isn't an issue of free speech, but of harassment/bullying/defamation/abuse." Ladies and gentlemen, using sloppy rhetoric in discussions of freedom of expression hands weapons to censors. Broader censorship will not ultimately benefit skeptics.

Third: notwithstanding the above, boycotts and complaints are an acceptable more-speech remedy, whatever the junk scientists might complain. These stores are private actors; informing them of the nature of a magazine they stock, advocating that they make a different private decision, or even threatening to boycott is part of the marketplace of ideas. Of course, if woo merchants organize some boycott that the skeptics don't like, and the skeptics argue that it is censorious, they should be called out for hypocrisy.

Fourth, I urge extreme caution in involving the government and quasi-government entities. Some skeptics advocate reporting the magazine to the government, or to non-governmental self-regulatory advertising bodies. Such reports may be based on genuinely misleading advertisements — the magazine sounds chock-full of advertisements that sound like the pseudo-medical version of x-ray specs in the back of comic books. But European advertisement regulation is already shot through with meddling silliness and the United Kingdom — and again, I say this with love — already has grave nanny-state issues. I admire the skeptical movement to the extent it pursues the goals of truth, open inquiry, and human dignity and autonomy. Ask yourselves — do governmental and quasi-governmental entities advance those goals? Does involving them in a dispute advance those goals?

Ultimately the marketplace of ideas is the best place to rebut what this magazine is peddling. I look forward to reading more critiques of the magazine and its contents in that marketplace.


What's the Frequency, Flik?

Science, Technology

The internet is pretty slick. Every attached computer has a unique address sort of like a phone number. (Sometimes, entire sub-networks lurk behind a single address through the miracles of IP and routing and such, just as entire switchboards of phones may lie behind the phone number of a main switchboard, but that's another story.)

Thanks to Transmission Control Protocol (TCP), files can be sent from one address to another with amazing efficiency. The brilliance of TCP's design lies in this: the rate at which stuff is sent automatically throttles up or down in response to network latency as measured by response time!

The Office – S5/E9: The Surplus from Vimeo.

Let's break it down. TCP is cool because "transmission control" sounds like "mission control" and that sounds like something NASA would have. But TCP is also cool because of how it works. Grossly simplified, it works like this:

  • You want to send that document requesting a pony to someone who has sent you a blind solicitation.
  • The networky stuff in your computer breaks the document into a bunch of "packets". Just like real parcels sent through UPS or Fedex or that other service, each packet is wrapped with a label explaining where it came from, where it's going, and so forth.
  • The packets follow various routes to their destination. As they arrive, the recipient (i.e., networky stuff on the other guy's computer) sends a receipt (called an "ack") to the sender. Meanwhile, the recipient uses the wrapper info to figure out whether all the packets have arrived, to put them in their correct order, and finally to reassemble the document. Transmission Accomplished!
  • The best part is the flow control. The sender starts by spraying out some packets and timing how long it takes to get a receipt for them. If the receipts come quickly, the sender sends more packets at a time. If the receipts come slowly, the sender sends fewer packets at a time (even stopping cold, if necessary). And since there's an ongoing flow of shipments and receipts and timing, the sender can avoid flooding the network but can also avoid letting bandwidth go to waste! Faster and faster! Slower and slower! No, faster! Slower! Strike that! Reverse it!

Flik, from Pixar's A Bug's Life

Now, here's the trippy science factoid du jour: researchers at Leland Stanford Junior University have discovered that Harvester Ants (including, apparently, the most venemous insect in the world) have been using TCP all along… behind Vint Cerf's and Bob Kahn's backs! Says the press release:

the rate at which harvester ants – which forage for seeds as individuals – leave the nest to search for food corresponds to food availability.

A forager won't return to the nest until it finds food. If seeds are plentiful, foragers return faster, and more ants leave the nest to forage. If, however, ants begin returning empty handed, the search is slowed, and perhaps called off.

They also found that the ants followed two other phases of TCP. One phase is known as slow start, which describes how a source sends out a large wave of packets at the beginning of a transmission to gauge bandwidth; similarly, when the harvester ants begin foraging, they send out foragers to scope out food availability before scaling up or down the rate of outgoing foragers.

Another protocol, called time-out, occurs when a data transfer link breaks or is disrupted, and the source stops sending packets. Similarly, when foragers are prevented from returning to the nest for more than 20 minutes, no more foragers leave the nest.

Further research into what these critters might teach us will be undertaken at the newly funded FourmiLab. Meanwhile, I leave you with a meditation on Proverbs 6:6 by e. e. cummings: go(perpe)go from his 1935 manuscript No Thanks (in George James Firmage, ed., E. E. Cummings: Complete Poems, 1904-1962, Revised, NY: Norton, 1994, p. 403 or thereabouts).


Your Friday Afternoon Brings A Smile To Robert Heinlein's Ghost

Geekery, Science, Technology

One hesitates to suggest that there could be a good higher than threatening to bomb one's political opponents, but human survival off this planet, indeed, human expansion into and conquest of the galaxy, may be one of those things.

As I type this, the SpaceX Dragon capsule has just docked with the International Space Station.  And you can watch it on the internet.

This is one small step for free enterprise, one giant leap for mankind.  The government won't ensure that humans escape this planet before the comet hits, giant tsunamis strike, the core reverses polarity, or the Daleks arrive.  The government couldn't find a clue if Colonel Mustard was appointed head of Homeland Security.

Private enterprise will save us, even if it has to destroy the earth to do so.


Law, Science, Technology

SHOULD APPELLATE JUDGES BE REQUIRED TO TAKE COURSES IN BASIC SCIENCE? More importantly, should they be required to pass a course on the scientific method and its application to everyday problems?

Daubert and Kumho Tire have been criticized on the ground that they require too much scientific training on the part of judges. But if the recent "pit bull" decision from the Maryland Court of Appeals is any indicator, the problem is that we don't require enough scientific training of our judges. Or any at all.

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The Triceratops will always be a real dinosaur to me, but what do I know? Caveman that I am, I still consider Pluto to be a planet.

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