A Jingle from the Lockheed Skunk Works

There's no confusion!
We aim to implement fusion!
It's a tougher catch than lightning in a bottle.

But we can do it!
We made the Blackbird and flew it,
And we circumnavigated at full throttle.

Yes, some are skeptical
That our receptacle,
For holy fire might be a mayonnaise jar.

So we'll assure 'em,
Our R&D is kosher for Purim,
And this'll be our best result by far!

Hedge funds: don't short us!
Federal watchdogs: don't report us!
It'll take a while, so journalists: rake some muck!

Still, we're not kidding.
We're doing DARPA's bidding,
And soon we'll ship reactors on a truck!

(WaPo on Lockheed)

Department of Health And Human Services Threatens Blogger Over Satirical Posts

The blog Addiction Myth is devoted to a very out-of-the-mainstream proposition about medicine: that the entire concept of drug and alcohol addiction is a scam perpetrated by law enforcement, rehab groups, and the entertainment industry. By contrast, the United States Department of Health and Human Services is devoted to mainstream medical and scientific propositions1 It is perhaps inevitable that these two worldviews would conflict one day.

But it was not inevitable that HHS's Office of General Counsel would bumptiously threaten Addiction Myth over obviously satirical posts. That, given minimal good sense, could have been avoided.

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The Necrogenomicon

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 23andme.com 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?

Georgia On My Mind

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: http://online.wsj.com/news/articles/SB10001424052702304384104579141600675336982

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. 2 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?

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You say you want a convolution

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.