Biological warfare attracts some troubled scientists

Perhaps Bruce Ivins was responsible for the anthrax attacks.

On the one hand, the Bush FBI's credibility is negative. That is, if the FBI told me the sun was shining I'd get an umbrella. In that vein it's noteworthy that they keep tweaking their leaks...

Doubts over the anthrax case intensify -- except among much of the media - Glenn Greenwald - Salon.com

... What did the FBI do in response to that rather devastating hole in its theory being pointed out? It just leaked a completely different story to the Post about when and how Ivins mailed ...

On the other hand there are supposed technical developments ...

The Anthrax Case: From Spores to a Suspect -- Enserink 2008 (812): 1 -- ScienceNOW
By Martin Enserink

The scientific evidence against Bruce Ivins, the 62-year-old Army scientist who killed himself while about to be indicted for the anthrax murders, is finally emerging. Last week, the Federal Bureau of Investigation (FBI) laid some of its cards on the table. One key document, scientists say, now enables a reconstruction of the trail that led the FBI from the deadly letters back to Ivins's lab at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) in Fort Detrick, Maryland...

... The key to understanding the investigation is that the anthrax used in the attacks didn't have a single, uniform genetic makeup, a source close to the investigation says. Each of the envelopes likely contained many billions of spores; within such a population, there are always subpopulations of cells bearing mutations that set them apart from the majority. The same minorities would presumably have been present in the "mother stock” of anthrax from which the spores were prepared.

However, standard sequencing--which would require the DNA from thousands of spores--would have resulted in a "consensus sequence" for the spores, in which such rare mutations were simply drowned out. To find them, researchers used a different technique: They grew spores from the envelopes on petri dishes, generating hundreds or even thousands of colonies per dish, each the progeny of a single spore. They then searched for colonies that looked different from the majority; the affidavit mentions variations in "shape, color, texture."... Next, they set out to find the mutations that made those colonies different.

To do that, the FBI used a brute-force approach: It had the entire genomes of the bacteria in the minority sequenced. TIGR--which merged into the J. Craig Venter Institute in 2006--sequenced "probably somewhere between 10 and 20" such genomes in the years after the attacks, Salzberg says. TIGR could not handle live anthrax cells itself; the FBI gave the lab purified DNA ...

Comparing the sequence of the variant colonies to an original B. anthracis strain called Ames, widely used in research, identified a number of mutations, says Salzberg; they included single-nucleotide polymorphisms, a change of a single base pair, and tandem repeats, in which a short piece of DNA is repeated a variable number of times.

The FBI then had scientists at other labs develop tests that allowed them to screen any anthrax sample for four of these mutations....

... with the four tests, the FBI examined more than 1000 anthrax isolates, collected from 16 labs that had the Ames strain in the United States and several more in Canada, Sweden, and the United Kingdom. In only eight of those samples, they found all four mutations seen in the envelope samples; and each of these eight, the affidavit says, was "directly related" to a "large flask" of spores, identified as RMR-1029, which Ivins had created in 1997 and of which he was the "sole custodian."

... It's also unclear how many of the 1000 samples had fewer than four, but more than zero, of the mutations. "If a whole bunch of them had two or three," that would increase the odds that the perfect match at USAMRIID was just a false positive...

... Science aside, the affidavit relies heavily on circumstantial evidence...

One of the weak points in the affidavit is Ivins's motive, says Gregory Koblentz, a biodefense specialist at George Mason University in Fairfax, Virginia... A glaring omission, meanwhile, is any evidence placing Ivins in Princeton, New Jersey, on any of the days the envelopes could have been mailed from there...

I'll take the skeptical side of things. The FBI has shown a nasty combination of incompetence and aggressiveness over the past decade. There's no evidence that they've reformed.

On the other hand, there's some reason to suspect that biological warfare attracts troubled scientists. The innocent Steven Hatfill was a convenient FBI fall-guy because of a murky past and questionable judgment. Bruce Ivins probably suffered from lifelong mental illness, perhaps a variant of paranoid schizophrenia.

Maybe we ought to be doing a better job of evaluating people who want to work with bioweapons?

Just saying.

Reason without science - the music of the spheres

Fifteen hundred years of fascinating nonsense. That's what I think as I listen to In Our Time's "The Music of the Spheres".

It's all rather like Freudianism - but he only lasted about 70 years.

What drives these examples of unreal reason?

I think of the underlying memes as attractive antigens that bind to our cultural and biological "memetic receptors" (it's hard to escape those immunology lectures). They're hypnotically interesting, and in age of scholarship without science they flourish like metastatic weeds.

The greatest cultural invention of the 2nd millennium, science, pulled the weeds. The Music of the Spheres became astronomy, mathematics, physics, neuropsychology, literature and art.

Science deserves more gratitude.

Microsoft's auto-lobotomy

In a longish article that seems designed to put Cringely on the witness stand, he outlines Microsoft's more recent alleged crimes.

It's an impressive list. Reading it I again wonder about the deal Gates made with Rove to drop the justice department suit against Microsoft. I wonder if we'll ever hear the details.

The part that really caught my attention though, was a small bit about Microsoft's policy on archived email:

I, Cringely . The Pulpit . What Goes Around Comes Around | PBS

... Months after the Microsoft/Burst settlement I received e-mail from a former Microsoft contractor:

“Now that Burst v. MS has moved out of the courts, I thought that I might add a little to what you know about this case. Back about two years ago when the judge told MS to cough up the rest of the emails that was supposed to have floated around between MS execs that discussed the Burst relationship, the team that I was on (Corporate tape backups) was asked to gather all together all of the tapes that were used during that time. Even though there was a corporate policy in place that any *.pst was to be excluded from backup capture, the effort failed. Not only did the Backup Exec software fail to filter out those pst files, but some of the involved blue badges (Microsoft employees) intentionally disguised their mail files so that they would not be recognized and included in the nightly backups. This last effort was even prohibited by policy from the VP level. As I was the one tasked to gather the tapes together from Arcus/Iron Mountain, I know exactly how many tapes were recalled for the involved servers. They filled several 240 tape trunks and were stored in the Building 11 tape vault....

I recently did an internal lecture on using Windows Search to enhance the value of email archives, to make them a part of working memory. Microsoft, as a part of a guilt-induced policy, excludes these files from backup.

The price of crime is an auto-lobotomy.

iPhone remote multiple libraries - what it means

The iPhone Remote app supports connections to multiple libraries.

Macworld | iPhone Central | Remote lets you control iTunes from iPhone, iPod touch

...There is, however, support for multiple libraries. When you start up Remote after associating with a library, it’ll take a second to reconnect, during which time you can change which library you want to use (you can also tap the Settings button in the top left corner of any list screen). That’ll give you the option to add multiple libraries, delete existing associations, and toggle a “Stay Connected” preference (not precisely sure what that does at present)...

The implications are left as an exercise to the reader.

Ok, some hints:

1. iTunes is designed for a single user. It belongs to a user account.
2. iPod and iPhone binding is not to a user, and not to a computer, it is to a user account on a single computer. Unless everyone wants to share apps, contacts, calendar, etc a single iPhone syncs with a single iTunes library.
   
3. DRM contracts are to a single user's Apple identity (formerly .mac), they can be applied to > 1 computer (the number is shrinking over time).
4. DRM is far from dead. If the music industry succeeds in toppling Apple by allowing only Amazon to sell without DRM, then they will terminate Amazon's DRM-free privileges and assume the throne of Sauron. (You knew that, right?)

It's a complex world. Looking at the way the iPhone works, it's possible that we could move to a family account that all devices would sync to -- since iCal supports multiple calendar overlays and Address Book supports multiple subsets. Gives a whole new meaning to "all for one and one for all", a meaning of particular interest to teens.

Consequences, intended and otherwise ...

My brutal Palm to iPhone migration - lessons from refactoring a geek workflow

Sometimes it's tough being a geek.

I'm a "market of one" -- when I adopt a technology I push it to the limits -- and beyond. When it dies, I have a heck of a transition to make.

My Palm to iPhone/cloud migration has been particularly tough.

Gordon's Tech: My Palm to iPhone migration challenge -- summarized

Google Docs - Palm migration is a spreadsheet that captures in a glance how very hard the Palm to iPhone migration is. There's a feed for change notification...

... Of the 10 core functions I have identified migration strategies for exactly 3 of them.

Suggestions are most welcome, but I need suggestions that allow me to migrate my
data as needed. Data lock is not acceptable for this material.

Ok, not "brutal" as in the things life routinely does to us, but tough in terms of lack of sleep and exercise. So far I've more or less migrated my personal calendar - by starting over.

Consider the tasks problem. Of the many, many solutions I've looked at, only ToodleDo (bad name) and ToDo.app come close, but ToodleDo allows operations on only one task at a time (web 1.0). That's a long, long, way from what I've grown accustomed to.

So I have to backtrack. I feel like I've moved into an alternate reality, a "past earth" where the printing press has yet to be invented but millions live on Mars. I can't migrate on a functional basis, I have to refactor what I do into different solutions.

So the combination of Palm and Outlook let me keep a large catalog of ideas and potential actions as tasks, but that workflow won't fit into my iPhone world. All the iPhone can handle as tasks are things I might actually do in the next few weeks. So I'll have to split my data stream, moving 15% forward as tasks and finding new homes for the rest (Evernote, would you please show me you don't want to lock my data?)

There are interesting lessons here that relate to my real-world job. I develop what we like to think of as "advanced" healthcare IT knowledge rich solutions. They all change what people do. Those changes have costs, costs like my Palm to iPhone transition. Even if it's for the better, the near term pain is pretty extreme.

It's good to get a reminder of what that feels like.

Splog war friendly fire - Google whacks me for the sins of others

I think I now see why the indexing speeds of my kateva.org pages wax and wane...

Gordon's Tech: The hidden curse of spam blogs - collateral damage

I've noticed an unhappy correlation.

Periodically spam blogs (splogs) will start harvesting my posts.

When they do that, email from kateva.org begins to be filtered into Gmail's spam folders, my Google PageRank falls, and the site is indexed less often.

When the splogs move on to another victim, things reverse.

I'm just collateral damage.

Ouch.

What hurts the most, really, is the decreased indexing. I like being able to search my memory collection.

Splogs fraudulently assume a part of my "data signature", so Google assigns a part of their reputation to me. Google knows "me", after all, only by my data.

It's a new form of identity theft, one that biologists would readily understand.

In the end I'm collateral damage; splog wars between Google's and the parasites are damaging my reputation -- and my memory.

Cyberwar is heck.

So, what do I do about it?

Update 8/18/08: Here's one view of the splog effect -- it's a list of splog posts generated in the past few hours from recent Gordon's Tech articles




Google is not yet omniscient. All it knows is that these posts are found here -- and in some very bad neighborhoods. We are the reputation of our data.

David Brooks - caught again

Incredibly, David Brooks is paid to write nonsense. I do it for free

Happily I can read James Fallows, who is a superb journalist. He points us to the Language Log's annihilation of Brooks. 

In addition to the obvious blunders, pay attention to the basic structure of the experiment. It's insane that people are able to publish this junk, and hilarious that Brooks transcends the junk ...

Language Log David Brooks, Social Psychologist

Those who've followed our previous discussions of David Brooks' forays into the human sciences ("David Brooks, Cognitive Neuroscientist", 6/12/2006; "David Brooks, Neuroendocrinologist", 9/17/2006) will be able to guess what's coming.

In this case, Mr. Brooks has taken his science from the work of Richard E. Nisbett, as described in his 2003 book The Geography of Thought: How Asians and Westerners Think Differently and Why, and in many papers, some of which are cited below. I was familiar with some of this work, which has linguistic aspects, and so I traced Brooks' assertions to their sources. And even I, a hardened Brooks-checker, was surprised to find how careless his account of the research is. ...

... Is it correct that if you show an American an image of a fish tank, the American will usually describe the biggest fish in the tank and what it is doing, while if you ask a Chinese person to describe a fish tank, the Chinese will usually describe the context in which the fish swim?

Answer: In principle, yes. But first of all, it wasn't a representative sample of Americans, it was undergraduates in a psychology course at the University of Michigan; and second, it wasn't Chinese, it was undergraduates in a psychology course at Kyoto University in Japan; and third, it wasn't a fish tank, it was 10 20-second animated vignettes of underwater scenes; and fourth, the Americans didn't mention the "focal fish" more often than the Japanese, they mentioned them less often.

The research in question was reported in T. Masuda and R.E. Nisbett, "Attending holistically vs. analytically: Comparing the context sensitivity of Japanese and Americans", J. Pers. Soc. Psychol. 81:922–934, 2001.

The subjects were 36 Americans at the University of Michigan and 41 Japanese at Kyoto University, who "participated in the experiments as a course requirement"...

Who's more absurd - Maureen Down or David Brooks? It's a tough contest.

What does it say about America that both are very influential and widely read?

Ouch.

Spooky action 10,000 times FTL. Yawn.

On the one hand, completely boring. Another test of QM is in complete agreement with theory.

On the other hand, this is almost as creepy now as it was when a 2007 Wired magazine article on a 1999 entanglement experiment casually noted that observer-independent reality was up against the possibility of free will. That set me off on my extended review of quantum mechanics; along the way free will seems to have come out ahead of reality.

Not quite as creepy though, because I'm getting used to living in a universe that's infinitely weirder than it seems. Here's the latest edition ...

Quantum weirdness wins again: Entanglement clocks in at 10,000 times faster than light: Scientific American Blog

No matter how many times researchers try, there's just no getting around the weirdness of quantum mechanics.

In the latest attempt, researchers at the University of Geneva in Switzerland tried to determine whether entanglement—the fact that measuring a property of one particle instantly determines the property of another—is actually transmitted by some wave-like signal that's fast but not infinitely fast.

Their test involved a series of measurements on pairs of entangled photons (particles of light) that were generated in Geneva (aerial view at left) and then split apart by optical fiber to two villages 18 kilometers (11 miles) apart where the team had set up photon detectors. (In 2007, researchers transmitted entangled light 144 kilometers between two of the Canary Islands.)

The idea in the new experiment is that the photons in each pair of entangled pair are hitting the distant detectors simultaneously, so there's no time for them to exchange a signal. By comparing results from the two detectors, the researchers determined whether the photons were entangled or not, using a test known as Bell's inequalities.

The photons were indeed entangled, the group reports in Nature. But in reality, no experiment is perfect, so what they end up with is a lower limit on how fast the entanglement could be traveling: 10,000 times the speed of light....

.. It's always conceivable that quantum mechanics might break down (read: show some signs of everyday normalcy) if experimenters could test it the right way. In a 2007 study, researchers in Vienna tested the idea that maybe the instantaneous-ness of entanglement (called nonlocality) was consistent with hidden "variables" that can explain the randomness of quantum measurements. But no dice for that idea...

... Rudolph says we're probably stuck with instantaneous entanglement, which seems impossible to us because we're stuck in everyday space and time. "We need to understand how quantum mechanics sees space and time," he says. "I think there's probably much deeper issues.

Yep, we're stuck.

I recommend Gribbin for a layperson explanation of how bad things are, though his preferred model for understanding entanglement is currently out of fashion (and incompatible with free will).

Slate reviews swim goggles

This is a surprisingly useful review. I'm tempted by fixed optical correction goggles, but otherwise ...

The best swim goggles. - By Juliet Lapidos - Slate Magazine

Speedo Speed Socket, $24.99

This pair is roughly like the Swedish goggles in that the eyecups are exceptionally well-designed to match the bone structure of the socket and it's possible to custom-fit the nosepiece. But they're better for nonprofessional swimmers, because the soft eyepieces rest more comfortably against the skin than the hard-plastic Swedes, and because they're much easier to customize. Speedo sends along three ready-made nosepieces, each slightly different in size, and it couldn't be easier to clip them on and off.

My friends and I agreed that the Speed Sockets look sleek and professional. And for just $5 more you can get a pair with mirrored lenses, which keep out sunlight and give your face a certain T-1000, liquid metal je ne sais quoi. Because the suction isn't too aggressive, I didn't experience any pain, and the raccoon effect was minimal. These goggles deserve high marks in every category...

Ease of Use: 5
Comfort: 9
Visibility: 10
Aesthetics: 5
Value: 5
Total: 34

Obama as the Antichrist - now from McCain

We weren't suprised by the Obama is the Antichrist meme. Heck, Clinton was accused of the same role.

Now we aren't suprised that the GOP is embracing Obama as Antichrist:

An Antichrist Obama in McCain Ad? - TIME

... includes images of Charlton Heston as Moses and culled clips that make Obama sound truly egomaniacal — taps into a conversation that has been gaining urgency on Christian radio and political...

McCain/Rove and the GOP will make this the ugliest campaign in modern history. They will do anything and say anything. They'll incite paranoid schizophrenics to violent action -- whatever it takes to win.

Don't assume it won't work. America is perfectly capable of falling for this.

Need some reading? Hugo nominees online

2008 Hugo Nomination List includes links to novellas and shorter works that are now available online.

I think that's really neat.

My Peak Oil Call

On 3/10/08 I wrote:

Gordon's Notes: Oil price speculation: is it rational investment or a bubble?

...So here's my proposal for deciding if Peak Oil is on the way.

If the price of oil craters ($65) in the next 6 months then we're living in an energy bubble today and Peak Oil is more than 10-15 years away.

If the price of oil is above $105 a barrel in August of 2008 then Peak Oil is on the sooner rather than later, and the world I grew up in is shuffling away -- sooner than I'd expected....

Today a barrel of oil costs $115 or so.

I believe that's above $105/bbl. True, the price is falling, but that doesn't matter. I'll stick to my criteria.

I say Peak oil is here.

I say that despite, in my 1979 chemical engineering class, being told that peak oil was coming in the late 1980s (I think we reviewed the 1957 Rickover speech back then). I say this despite remembering Jimmy Carter's peak oil prediction in the 1970s.

Of course I'm really talking about Peak sweet light oil, and I don't mean "Peak" in absolute, or even demand > supply, I mean Peak in terms of rational market expectation of a > 70% probability that demand > supply within 5-8 years.

Basically I'm claiming that the price increases of this past year were due to praiseworthy speculation on the fundamentals rather than salacious speculation on psychology.

This means I'm expecting oil to go to Dyer's $200/bbl limit at least once in the next five years, though may transiently fall back to $80 along the way. After 5-8 years it will be very apparent that oil will be a shrinking percentage of our energy supply, and that in the absence of a severe carbon tax (or the equivalent) we'll be baking the plane with burning coal and burning tar sands.

It also means that it's now rational to invest in conservation, and to expect real estate prices to reflect increased commuting costs.

More on Peak Oil later, but I was overdue to make my promised call. (It's been a busy month!)

People didn't used to laugh when we said these things

This would be funnier if Russia weren't invading Georgia:

BBC NEWS | Europe | South Ossetia clashes intensify

...US Secretary of State Condoleezza Rice called on Russia to pull its troops out of Georgia and respect its territorial integrity...

She probably says it without irony.

The value of GrandCentral

GrandCentral is a VOIP service that gives users a phone routing service. Google bought 'em, and I signed up.

Problem is, I couldn't figure out what they were good for. Until today ...

Gordon's Tech: GrandDialer: will this help my phone bill?

But what if I could use my GrandCentral account to call Canada, then GrandCentral connects me in?

GrandDialer would make that easier:

GrandDialer, an iPhone app for GrandCentral - The Unofficial Apple Weblog (TUAW)

...GrandDialer (iTunes link) allows you to use your iPhone to call people using your GrandCentral telephone number....

This is using the GrandCentral "Click2Call" feature.

Briefly, it works. For most people this is a curiosity, but free AT&T cell calls to Montreal will pay for my iPhone.

Which explains this mysterious meeting transcript I found in my junk mail today:

... AT&T guy: "Thanks for joining us today. We really admire the work you've done at Google. We know you appreciate the fiber services we provide, and you understand why it's only fair that Google pay a bit more for the quality of service only we can provide."

Google guy's phone starts playing The Rolling Stone's "Under my Thumb".

Google guy: "Sorry about that. It's the ring tone I use for my GrandCentral calls. You understand ..."

AT&T guy: Would a 5% volume discount be ok?

AT&T is living off the big bucks they charge me for long distance calls. If they lost their long distance service they'd fall over dead.

GrandCentral could take a lot of that away -- if Google ever opened it up and created a GrandCentral widget like GrandDialer for every cell phone on the market.

In the meantime, GrandCentral is paying its way without earning a penny. They can afford to pay for my calls to Canada ...

Net security, the end of the password, and human evolution

The signs of the end are at hand.

First, this completely asinine alleged (a misquote I hope) comment from someone who must, really, know better:

BBC NEWS | Technology | Net address bug worse than feared

... Mr Silva at VeriSign said even though patches have been put in place, this doesn't mean users can sit back and relax.

'The biggest gap in security rests between the keyboard and the back of the chair,' he said.

'The look and feel of a website is not what a consumer should trust. They should trust the security behind that website and do simple things like use more secure passwords and change their password regularly...

Of course they should. They should also lose 50 lbs, run ten miles a morning, study a new language every month, and master levitation.

I really hope that was a misquote.

Next, I lose my last remaining gasket when the complexity of modern life leads to a security breach, and the need to change my 2 year old high quality primary Google account password:

Gordon's Tech: How to steal my Google account

... Yes, to steal my Google account, my primary digital identity, all you need to know is my first phone number...

1. Passwords are a complete fail. Schneier has been saying this for years. We are now into the realm of madness. We need multi-factor authentication devices that handle our secondary authentication for us. Yeah, it's not perfect, but, really, this is s#$!@# insane.
   
   
2. We live in the age of the tyranny of the mean. Even the vast majority of geeks aren't going to figure out how to sync 1Password with an iPhone. Regular folks are going to use one password everywhere and then forget it. Google, like everyone else with these asinine security question is bowing to the reality that humans didn't evolve to live in a digital world. We're maxing out right now.

This madness has to stop. The stupidity is hurting my brain.

Really, none of us evolved for this. We either need to reengineer the human mind or we need to implement better security measures.

This is going to need real help from an Obama administration, we've seen decades of banks failing to deal basic with security issues. This won't get fixed by libertarian emergence; the current system is simply providing endless prey for hungry predators.

Oh, and remember, sooner or later, we're all prey.