Reflections on my personal bacterial companions

I stopped a puck the other day.

With my leg. That's what comes with playing against these dad-gum college kids. They don't know their own strength.

The hematoma became infected, and since antibiotics aren't what they used to be my personal physician/spouse recommended diligent attention. So now the infection is mostly better.

This gave me the opportunity to wonder about three things:

1. Who creates the tough sealant (scab) atop the wound? I used to think my body did that, but, really, it's a stupid response. I need the sucker to drain, not seal. Maybe the scab is built by the bacteria?
2. Why don't infected wounds hurt more? I whack my finger and it sure hurts, but my body doesn't complain much about infections. Seems illogical ... unless the bacteria are turning off pain signals.
3. We know Toxoplasma makes rats dumb and happy - the better for cats to munch 'em and spread the infection. We think it does something similar to humans. So shouldn't bacterial infections make us feel kind of laissez-faire, less prone to aggressively treat the infection?

That was yesterday. I was inspired in part by a gruesome science fiction story of some years back about emergent sentience in bacteria (can't remember author, but I don't think it was Greg Bear).

I don't think these are original ideas, but I didn't expect to see a Carl Zimmer essay on the topic today!

I For One Welcome Our Microbial Overlords | The Loom | Carl Zimmer | Discover Magazine

.... Very often, the parasites cause hosts to do things that help the parasites, instead of themselves. For example, a protozoan called Toxoplasma needs to get from rats to cats, and to help the process along, it makes rats lose their fear of cats. Parasites can also change the diet of their host as well as the way in which their hosts digest their food....

I was reminded of this sinister manipulation by a paper that was published in Science today by Rob Knight and his colleagues. They built on previous research that revealed that mice genetically engineered to be obese have different kinds of microbial diversity in their guts than normal mice...

... Knight and his colleagues discovered a different–and more disturbing–way that microbes can make mice fat....

... Mice with a genetic make-up that alters the diversity of their gut microbes get hungry, and that hunger makes them eat more. They get obese and suffer lots of other symptoms. Get rid of that particular set of microbes, and the mice lose their hunger and start to recover. And that distinctive diversity of microbes can, on its own, make genetically normal mice hungry–and thus obese, diabetic, and so on.

When I first learned of this work, I asked Knight–with a mix of dread and delight–whether the microbes were manipulating their hosts, driving them to change their diet for the benefit of the microbes. He said he thinks the answer is yes...

If gut bacteria can change diet, then skin bacteria could make people with chronic skin infections apathetic -- the better to discourage treatment of the thriving bacterial colonies ...

Update 3/24/2010 - See also a 2006 post on viruses changing dietary behaviors ... Why would a virus fatten an animal?

The disappearing signature

I've never had a very consistent signature, but today Emily noted that it's become a genuine scrawl.

Of course this could be a sign of early Parkinsons disease, but there's a more benign explanation.

I very rarely sign my name.

Forty years ago we signed our names a lot. We wrote checks, we deposited things, some of us did it as a part of our work. In the modern world we enter passwords instead. I haven't written a check in over a year.

Signatures are going the way of the wrist watch. My children may never develop a signature.

YouTube needs a pay-per-view solution

I've not had much use for YouTube, but I do have a son who does better with video than with text. I figured I'd collect selected educational videos for him to study from, using a family video learning blog.

That was when I began to learn that YouTube sucks.

Yes, there's lots of stuff there, and some of it is well done. There's Monty Python, for example. When it comes to education in general, and science in particular, however, it's really lousy. Most of the material is both very poor quality and very old.

The problem isn't a lack of good material. There's an enormous quantity of instructional science material owned by the BBC and by the television networks. That material could be sliced, diced and repackaged to create thousands of high quality educational videos from brief demonstrations to longer expositions.

The problem is money, or lack thereof. We need a way for people who own high quality material, or who are able to create it, to get paid.

I'd like to see YouTube offer up this material with a 10 cent/min 1 day rental fee. A five minute concept demonstration would cost 50 cents to rent until midnight. A 60 minute show would cost $6.

Maybe that wouldn't be enough to unlock the vaults of the BBC. It might be too easy to steal for example. It would, however, be enough to support independent production of short format well catalogued educational video material.

Stop being free YouTube, and start being valuable.

Update 3/5/2010: Per Janek Mann, in comments, YouTube debuted YouTube Rentals in beta about 7 weeks ago:

... Introducing the beta of YouTube Rentals, a pay-to-view model on YouTube. Providing content owners a new way to generate revenue on the site, YouTube Rentals allows partners greater flexibility to monetize a variety of videos, provides full control over their content, and allows content owners to tap into the world's largest online video community.

The YouTube Rentals beta is currently available only to content owners in the U.S.

Evidently they thought it was a good idea too, though, barring time travel, they've probably been planning this for years. Obviously I'm a fan!

We need translation on Google Reader for Mobile!

After a hiatus when Google Reader social was broken, I'm back to following shares and blogs that alternate English with Chinese and other languages.

This would be a killer feature for Google Reader desktop, except that GR desktop has already killed all the feed reader competition. On a bigger scale though, embedded translation is one of the reasons that Google will (sadly) crush Apple and, over the next 20 years, machine translation will transform human civilization.

Yeah, I meant that. I've even added a new GR "label" (post tag) today called "translation".

Problem is Google Reader for Mobile doesn't do translation! Argghh. My non-English feed items (blogs, shares, etc) are unreadable on my iPhone. It's been over a year since GR desktop added translation services, and Mobile is still unilingual.

Sigh. I am 95% sure Google work on this will include the iPhone, and 5% worried it won't. If they do omit the iPhone, I may have to move to the gPhone sooner than I'd expected. That's how big this feature is. The GR Mobile translation story is just one more telling illustration of why Apple will lose its war with Google.

So, Google, for your user's sake and to encourage Apple to sue for peace sooner, please do get on this.

See also:

• 2009 will be the year of machine translation
• Google reader: now with translation services (Nov 2008!)
• Reading my writing translated
• Joy of the global web -- what's 101 mean?
• Do I make more sense in Greek?
• Gordon's stuff, now in 35 languages

Why Apple will lose the Google-Apple war

The were rumbles about Latitude, but the battle of Google Voice made the Google-Apple war public. Now it's a cliche ...

How Apple and Google's Romance Turned To Hate - Apple - Gizmodo

.. They happily worked in the iPhone's 2007 launch. Google gave Apple their maps, their search, and their mail, and Apple gave Google the best spot in their new shiny device. Apple put YouTube into the iPhone and Google made YouTube to work nicely with QuickTime, moving all videos to the h.264 standard (so Apple could avoid that nasty Flash kid). Google even optimized their web apps for the iPhone, and Apple smiled....

I like the prospect of Google-Apple competition, but this is too much. It won't end well for Apple.

Apple has brought me some very good things over the past few years, but Google makes me smarter. There is a major economic and productivity advantage for working with Google. In the medium term, on a global scale, this means Google will win.

If the iPhone doesn't have full access to Google's productivity boosting powers it will lose. No, web apps are not the answer -- the Google Voice web app is pathetic (partly this is because Google is only marginally competent at building client software -- they need to buy Palm for the engineers).

Maybe Jobs will step down. Certainly Eric Schmidt needs to go. One way or another, I hope this war ends soon.

Update 3/13/10: The NYT coverage makes it seem personal - particularly between Schmidt and Jobs. Both have enormous egos, but Schmidt is completely and trivially replaceable. The world would be better off if Schmidt were to retire.
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My Google Reader Shared items (feed)

Calvin, free will and me

I've had only a nodding acquaintance with Calvinism (TULIP, via Garrison Keillor), though I picked up a bit more thanks to George W Bush and his fellow Marketarian social Darwinists.

It wasn't until I listened to In Our Time on Calvinism, though, that I realized Calvin and I had something fundamental in common. Neither Calvin nor I believe in the myth of free will, or the myth of responsibility. (Though I do treat both as a useful fiction - especially with the kids.)

If you're a Christian, and you don't believe in free will, then you have to believe that either nobody is saved, or everyone is saved, or that God is capricious.

The first two options are simpler, but the first makes Christ seem rather pointless and the second can't create a successful social movement. Only the third option, that God is capricious, will produce the right mixture of fear, pride, power and scorn - particularly when coupled with the Marketarian principle that God rewards the righteous with worldly power. The principles of natural selection ensure that, absent free will, the theology of a capricious God will win.

I've never liked Calvin, but at least now I understand his logic. Of course, were I a Christian, I'd follow Occam and choose the simpler assumption that everyone is saved. Calvin didn't let his logic get in the way of a good power base, so he made a different choice.

See also:

• Bad genes, bad people and a crisis of punishment?
• Addiction and disease: My comments on the TIME Science blog
• Changing attitudes about mind and responsibility: Patricia Hearst
• Diminished responsibility: the next cultural battleground
• Free Will RIP - The Economist on preemptive punishment
• Marketarianism (Label)

Update 3/9/10: This meme is circulating. I've added a "meme watch" tag to this post.

Update 4/7/10: Sci Am article - no free will. One more sign of social acceptance.

How I discover people to follow - on Google Reader

Buzz has been a great disappointment.

It's not all bad though. Google built a lot of Buzz on the Google Reader Shared Item experiments, and as a side-effect they fixed the long broken social bits of Google Reader.

So now I'm enjoying enlisting new unpaid specialists to sort and manage the world's information flow for me. It's like having my own team of incredibly expensive super-smart uber-analysts -- except I don't pay them anything.

Mwaahh-ha-ha-ha!

Ok, so maybe the evil laughter is a bit much. After all, they're free to follow what I share, and we're all feeding the hivemind. It who laughs last is Skynet, as the saying goes.

How do I use Google reader to enlist my witting info-drones?

I look for the "like" link on posts that I like a lot, but that don't have many other "likes". I then click the "like" link and scan the names and associated metadata, looking for people who are different from me -- different nationality, age, gender, profession, etc. Then I look at their shared items. If they've shared interesting things that are new to me, I follow them. I also add them to my special "x-reader" group which allows them to comment on anything I share (should they decide to follow me, though most will not).

None of this worked reliably a month ago, but it works now.

My "People you follow" section is now becoming my strongest information source. I'm able to follow fewer feeds directly, as I now outsource the processing chore to my fellow minions.

Quite nice, really.

Update 3/2/2010: I'm also again trying Google Readers "show in my language" feature to start following non-English "likes". I believe Google's Translation feature is extremely disruptive and amusingly under appreciated. This is how the really big things often come - quietly in the night. Note that the latest betas of Chrome for Windows now incorporate translation services into the browser. I'm looking forward to an English-Chinese-English view of my posts that will allow me to optimize my English writing for English-Chinese automated translation.
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My Google Reader Shared items (feed)

Tea is the gateway drug to Militia movement

The Sepoy mutiny (IOT) is traditionally said to have begun with a rumor that new rifle cartridges, which soldiers had to bite to use, were greased with pig and cow fat.

The rumor spread quickly, and enraged many. It sounds plausible to me, but Melvyn Bragg's 3 guests all agreed that the truth was irrelevant. The rumor was a spark on dry kindling. It didn't have to be true, and refutation was irrelevant.

When a people are prepared to believe, beliefs are powerful and fungible.

I thought of that story when I read David Barstow's epic study of the all-white Tea Party movement. The Tea Party movement is rife with fear and rumor, and it is ready to believe.

The Tea Party had its roots in the GOP, but now it's largely lead by Glenn Beck. Wildly popular with a part of the GOP base the Tea Party is a threat to the corporate heart of the GOP - and Beck's Mormonism is an issue for GOP evangelicals.

So the Tea Party is mixed blessing for the GOP. That's a problem, but it's not the big problem.

The real problem is that the Tea Party is proving to be a "gateway drug" to the pro-terrorist Militia movement and a wide range of the far right fringe parties. Timothy McVeigh wannabes are warming up, just as they did for Clinton.

Challenging times.

See also:

• Glenn Beck's white nationalist fans - Glenn Beck - Salon.com
• The fears of the GOP base - last defenders of America
• The roots of Klan 2.0 and 912 – A justified fear of change
• Palin, Noonan, and the fears of euro America
• Historian wanted: The American Liberty League and 1930s Fascism
• Frank Rich - The Axis of the Obsessed and Deranged - NYTimes.com

Snitty Apple Console message

I've been having OS X issues lately, so I've spent time in the Console (yes, the days of full function OSs are limited).

I liked this particular message:

2/28/10 10:32:19 AM [0x0-0x294294].com.microsoft.Excel[6407] Sun Feb 28 10:32:19 Stanford-MacBook-2.local Microsoft Excel[6407] : The function `CGPDFDocumentGetMediaBox' is obsolete and will be removed in an upcoming update. Unfortunately, this application, or a library it uses, is using this obsolete function, and is thereby contributing to an overall degradation of system performance. Please use `CGPDFPageGetBoxRect' instead.

Reflections on friends who vote GOP

I have not been a fan of the modern GOP. I see today's GOP as the party of torture, corruption, thoughtless bellicosity, cynical manipulation of American fears and hatreds, bad policy, anti-science, anti-reason, and so on. I also disagree with most GOP values, though my support for abortion rights is unenthusiastic.

And so, when a good person and a friend writes asking when I might join the "sane" party, I am taken aback. My Dems are often (mostly?) corrupt, pompous and venal - but I do think of them as the saner party. How can good people feel the GOP is the sane alternative? It is suspiciously convenient to say these people are delusional. Instead I'll try to examine their beliefs along four chasms - Facts, Values, Faith and Tribe. I think I can understand their beliefs best in those terms.

Facts

Not everyone obsessively follows hundreds of blogs and uses selected super-readers as fact filters. More reasonably, but unfortunately, not everyone reads factcheck.org. If you live in some parts of the country, and if you don't read online news or the New York Times, you will be told many things that are not true. More perniciously, you won't hear of anything that might change your perceptions.

If you believe the chain letters, or the WSJ OpEd page, or Murdoch's newspapers, you may well believe the Democrats are insane.

This seems like the easiest canyon to bridge. Facts, after all, can be tested. Predictions can be falsified. In reality, however, Vulcans are few. People may be attracted false facts because they support three other chasms.

Values and culture

What do the strong owe the weak? When do the ends justify the means? What are the limits to tolerance? What far can Americans move from a cultural mean?

These are fundamental differences. A good and generous person may feel they owe nothing to the weak save what they choose to give. That person is a natural supporter of the GOP. These are legitimate distinctions

Faith

We usually think of Faith in terms of Deities, but there can also be a Faith in Markets. Faith, by definition, is not amenable to discussion. If you believe the true duty of all men is to serve a particular deity, then your first political choice must be to support the Party closest to your deity. If you believe that Markets are infallible, then you must support a Party that shares your belief.

The chasm of Faith is a legitimate distinction between the GOP and the Democrats. Even religious Democrats tend to accept theological tolerance -- even when that tolerance is theologically inconsistent. The GOP has a much stronger claim to the Christian fundamentalist vote.

Tribe

Humans support their Tribe. It is especially hard for a member of a powerful Tribe to see its time is passing. The GOP is the Party of the White Tribe, and in particular of the White Male Tribe. The Democratic Party has a much blurrier Tribal identity, but if you're non-White or Gay or Lesbian it's a natural home.

The GOP and Dems are separated by chasms of Fact, Faith, Values and Tribe. The chasm of Fact seems easiest to cross, but often choices of Fact serve needs of Faith, Values and Tribe. Good persons, by reasons especially of Faith, Values and Tribe, may feel my party is less than sane.

Surviving corporate life - stand or sleep

Pity the American office drone. This week we see our premature demise from multiple angles ...

Stand Up While You Read This! - Olivia Judson - NYTimes.com

...It doesn’t matter if you go running every morning, or you’re a regular at the gym. If you spend most of the rest of the day sitting ... you are putting yourself at increased risk of obesity, diabetes, heart disease, a variety of cancers and an early death. In other words, irrespective of whether you exercise vigorously, sitting for long periods is bad for you...

... Several strands of evidence suggest that there’s a “physiology of inactivity”: that when you spend long periods sitting, your body actually does things that are bad for you....

... consider lipoprotein lipase. This is a molecule that plays a central role in how the body processes fats; it’s produced by many tissues, including muscles. Low levels of lipoprotein lipase are associated with a variety of health problems, including heart disease. Studies in rats show that leg muscles only produce this molecule when they are actively being flexed (for example, when the animal is standing up and ambling about). The implication is that when you sit, a crucial part of your metabolism slows down.

So you can't sit -- but you can't just stand all day either ...

How siestas help memory: Sleepy heads | The Economist

... It has already been established that those who siesta are less likely to die of heart disease. Now, Matthew Walker and his colleagues at the University of California, Berkeley, have found that they probably have better memory, too. A post-prandial snooze, Dr Walker has discovered, sets the brain up for learning....

... The ideal nap, then, follows a cycle of between 90 and 100 minutes. The first 30 minutes is a light sleep that helps improve motor performance. Then comes 30 minutes of stage 2 sleep, which refreshes the hippocampus. After this, between 60 and 90 minutes into the nap, comes rapid-eye-movement, or REM, sleep, during which dreaming happens. This, research suggests, is the time when the brain makes connections between the new memories that have just been “downloaded” from the hippocampus and those that already exist—thus making new experiences relevant in a wider context.

The benefits to memory of a nap, says Dr Walker, are so great that they can equal an entire night’s sleep. He warns, however, that napping must not be done too late in the day or it will interfere with night-time sleep. Moreover, not everyone awakens refreshed from a siesta.

The grogginess that results from an unrefreshing siesta is termed “sleep inertia”. This happens when the brain is woken from a deep sleep with its cells still firing at a slow rhythm and its temperature and blood flow decreased. Sara Mednick, from the University of California, San Diego, suggests that non-habitual nappers suffer from this more often than those who siesta regularly. It may be that those who have a tendency to wake up groggy are choosing not to siesta in the first place. Perhaps, though, as in so many things, it is practice that makes perfect.

Wireless headsets mean we can do calls easily while standing, pacing, even doing some light weight lifting -- or perhaps while going for a walk (though not with an AT&T iPhone - the connection will drop). Siestas are tougher. There's much to be said for working remotely ...
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My Google Reader Shared items (feed)

Fallows on the Nexus One - feel the fear Apple

James Fallows is a senior editor at the The Atlantic, and an adventurous man with a first rate mind. He's not a tech guy by profession, but at heart he's a geek.

I put a lot of weight on his incidental tech opinions, such as his review of the Nexus One.

Briefly - he likes it. A lot. He's abandoned his beloved BB like yesterday's fish.

Feel the fear Apple. Banning Google products from the iPhone was a cowardly and desperate move. You may yet regret infuriating your geek customers.

You know how to reach me Apple. I have suggestions.

Nikon and Canon. Apple and Google. Competition is good.

Canada v USA - bring it on

I couldn't watch the first USA v Canada game. But now ...

Team Canada brings down Russia (Montreal Gazette)

... At the Olympics, Canada hadn’t defeated the Russians in any form -- as Russia, the Soviet Union or United teams since 1960, that black-and-white TV era when Canada was represented by Harry Sinden and his fellow Kitchener-Waterloo Dutchmen. Canada’s overall Olympic record against Russia just improved to 2-9.

Yes, it’s been 50 years since Canada celebrated an Olympic win over this nation, and if that number rings a bell, it should. It was also 50 years between Olympic gold hockey medals when Canada won at Salt Lake City in 2002.

Canada next faces the winner of the Sweden-Slovakia game. The US beat Switzerland so they play the Czech-Finland winner.

At this point both the US and Canada are favored to win their next games.

If they do, we're set for one hell of a showdown.

Update 3/4/2010: It was all we could have hoped for. Fabulous game. Just fantastic.

The rise of software rental (aka software as service)

I'm evaluating the combination of Notational Velocity and Simplenote (iPhone) to manage my "notes" [1], including those related to home and work. I'll have more on that in my tech blog when I've got some personal experience, but it's interesting now to look at how software pricing is changing.

For years we've "leased" software, but we've had effectively unlimited licenses. After a vendor reaches their core market (revenue), they have little incentive to continue supporting the product (costs). Few vendors have Microsoft's power to force upgrades [2]. Some very fine software has died of this "natural cause".

On the other hand "cloud" services like SmugMug have a sweet recurring revenue model. They sell their service at a yearly price, and they can be the envy of desktop vendors (SmugMug benefits from a wicked lock-in, but that's another post.)

Over the past few years, however, I've seem more vendors experiment with 1 year licenses. This is an easier sale if there's a server-side dependency. For example, after a 1 year hiatus I again pay about $20 a year for Spanning Sync, primarily so I can sync my OS X Address Book with Google Contacts.

Simplenote is floundering about with pricing, but I gather they've suffered the usual iPhone app fate - initial growth then no revenues. Judging from their recent customer reviews they've been flamed for obscuring their current sales model [3]. As of today the base application is "free", but if you look very closely at their web site you might see mention of the "premium" service. The premium service is $9/year and includes:

• no ads
• automatic backup of older notes
• create notes by email
• RSS feed
• Unlimited API Usage (free limit is 2,000 API requests/day)

This seems like a very nice set of services and well worth the price -- especially since Notational Velocity (open source, free) means there's no data lock.

The last is an essential requirement for the new model of subscription software. There can't be any data lock. You have to able to move to alternatives easily, or just walk away and be none the worse off. Both Spanning Sync and Simplenote (with Notational Velocity) meet this test.

I like this new model, as long as it's tied to data freedom. It gives me hope that the sofware I love will stick around for a while.

[1] See below. My current solution (Tooldedo Notes + Appigo Notebook) isn't bad, but I'd like to free my notes from the limitations of proprietary formats and I'd like to find a solution that will enable easier integration with Outlook/Exchange note-type functions.

• Moving Palm notes to Toodledo via CSV file - what worked. (Hard!)
• Appigo Notebook is coming to the iPhone
• Kiss your Google Notebook good-bye
• Palm to iPhone migration - address book and notes (Aug 2008 - dated)
• Toodledo gets it
• Appigo and Toodledo – nasty emergent design flaw makes a mess of my iPhone Notes and Tasks
• Evernote's import/export test (updated)

[2] Corporate customers pay for the latest version of Office even if they choose to deploy older versions.

[3] Their pricing model seems entirely reasonable. So why the heck can't they make it more obvious? I wonder if there's a language problem here ...

Update 2/25/2010: I'm still evaluating Simplenote + Notational Velocity + Simplenote Chrome extension (aka simplenote ecosystem), but that tech blog post isn't ready to publish. It is interesting, however, to note the international background:

• Simplenote - Google Chrome extension gallery (Johnston - Canada)
• Notational Velocity (OS X) - sync locally expose, spotlight, search (Zachary Schneirov - Russia)
• Simplenote Chrome plug-in: search, edit. (Jan Andersson - Sweden)

It's a creative world. The dominance of the US in software development was always unnatural; that time has passed. US Patent laws will accelerate the migration of software creativity to more rational nations.

The unreasonable effectiveness of mathematics - explained

Eons ago my peers used to puzzle over the unreasonable effectiveness of mathematics. Back in the 1960s an essay on the topic by Merci Cooper ended with this conclusion …

… The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve….

Why is it that the “the great book of the universe is written in the language of mathematics” (Galileo Galilei)?

In a recent In Our Time programme on Mathematics' Unintended Consequences I heard, from one guest, a personally persuasive explanation. It’s a fundamentally anthropic explanation that goes something like this:

1. Entities that can do mathematics arise as a consequence of natural selection.
2. Natural selection can only occur in regions of a universe that have interacting and persistent patterns (perhaps including recursion).
3. So a universe containing mathematicians will also be a pattern-based universe.
4. Mathematics is a process for describing and manipulating patterns.
5. Therefore mathematics is a language that can describe pattern-based universes, including our own.

I’m good with that.