Saturday, January 31, 2009

Do It Yourself Biology in Seattle

I finally was able to attend one of the DIYBio meetings this weekend, and now my mind is reeling from all the interesting possibilities I heard.  DIYBio is an organization of people who like to study and do amateur experiments in biology.  Like me, most of the members think state-of-the-art biotech is becoming more accessible to normal people and want to take advantage of it.

The meeting was organized by a guy who has set up his own private lab at an industrial building he rents for $250/month in a rundown part of Seattle.  He’s stocking the lab with used, but usable equipment he buys from eBay:  a $40 PCR machine, for example, plus incubators, reagents, centrifuges, and much more – all at very reasonable, amateur prices.

Here are some of the ideas for DIYBio:

  • “Bio Beer”, just like the real thing only with specially engineered properties to make it glow in the dark, or with built-in resveratrol  (the anti-oxidant that makes red wine so healthy).
  • Abalone shells: a substance so strong the US Army wants to use it as armor.
  • Biodiesel, made from specially-engineered high-fat algae.
  • Bacteria that eat polyethylene, making any plastic biodegradable.
  •, an organization that is making devices to let paraplegics walk.
  • Artificial meat: go after the $1M PETA prize for growing chicken breasts without chickens.
  • Personal genomics: learn more about – and maybe manipulate -- your own genetic code.

The concept reminds me of the original Homebrew Computer Club, from California, which I attended a few times myself before its own success caused it to peter out in the mid-1980s.  Just a bunch of amateurs, all with day jobs doing something else, but convinced that the plummeting prices of technology are making for a revolution that we want to join.


[flickr photo from dullhunk]

Friday, January 23, 2009

Worst economy since the Great Depression

From the Jan 13th issue of Time Magazine:

The slump is the longest, if not the deepest, since the Great Depression. Traumatized by layoffs that have cost more than 1.2 million jobs during the slump, U.S. consumers have fallen into their deepest funk in years. "Never in my adult life have I heard more deep- seated feelings of concern," says Howard Allen, retired chairman of Southern California Edison. "Many, many business leaders share this lack of confidence and recognize that we are in real economic trouble." Says University of Michigan economist Paul McCracken: "This is more than just a recession in the conventional sense. What has happened has put the fear of God into people."

(oops, forgot to mention the year: this article is from 1992, during what in retrospect turned out not to be much of a recession at all.) [via Marginal Revolution]

If you’re one of those who thinks President Obama is inheriting “the worst economy since the Great Depression”, please check out two years: 

1982 [via David Leonhardt in NYTimes]

The first big blow to the economy was the 1979 revolution in Iran, which sent oil prices skyrocketing. The bigger blow was a series of sharp interest-rate increases by the Federal Reserve, meant to snap inflation. Home sales plummeted. At their worst, they were 30 percent lower than they are even now (again, adjusted for population size). The industrial Midwest was hardest hit, and the term “Rust Belt” became ubiquitous. Many families fled south and west, helping to create the modern Sun Belt. Nationwide, the unemployment rate rose above 10 percent in 1982, compared with 7.2 percent last month.

and, of course, 1973.

I wouldn’t trade today’s situation for either of those two years, and not just because today’s economy is by comparison so much better. It’s impossible to know the future, so who knows and maybe things will get a lot worse. But meanwhile it’s important not to over-react based on over-dramatic headlines.

Sunday, January 18, 2009

American Creation [book]

We want to believe that the present is messier and more dangerous than the past. Why can't we live in a time with a Jefferson or an Adams or a Washington? Why are we stuck with Bush and Clinton (or as we'll soon see) Obama?

The idea behind this book is that things looked pretty messy at the time back then too.

A few examples

  • Thomas Jefferson was despised as someone intensely political, but apparently unaware of his backstabbing ways. He teamed up regularly with James Madison and founded the first opposition party -- all while insisting he didn't believe in political parties.
  • Valley Forge was the low point of American history, with many soldiers dying and almost no hope of victory. Hope only arrived, in fact, during the early Spring with news that France was now supporting them.
  • If there ever was a chance to achieve a morally good ending to the colonists interactions with native Americans, the Creek Indian chief Alexander McGillivray was probably it. The guy was half-white, well-educated, commanded a large and well-organized nation, and signed an equal treaty with George Washington and the new American government in the early 1790s. But unfortunately he was also what today we would call a corrupt warlord, who double-crossed the Americans and died at age 34 of alcoholism.

Ellis' big idea is that the real innovation of the American Founders was to stumble upon a system of government that, instead of resolving differences permanently, provided a framework for on-going discussion and experimentation with government. Unlike other places, America became a place where it was okay to be in opposition.

Although I liked the main theme, I thought the book could have used more organization. It flows more like a series of unrelated essays. A better book is Ellis' earlier Pulitzer Prize winning Founding Brothers.

Saturday, January 10, 2009

Steven Pinker on Personal Genomics

The Jan 11th edition of the New York Times Magazine has a cover story by my favorite thinker describing his experiences with genome testing, and he finds the same lack of satisfaction that I have.  He coins the term “Geno’s Paradox”, to describe how with genomics it seems that the more you know the less you know.  My experience with the 23andme test is that yes, I’m glad I tested myself, but what did I really learn?  Like Pinker, I find myself using my knowledge of myself to make sense of the test results, rather than the other way around.

Some interesting takeaways from the essay:

  • He didn’t have the guts to test himself for Alzheimer’s.  [unlike me]
  • Although he has the bitterness receptor (unlike me], he still enjoys brocolli and beer.  So what good does the gene do?
  • He’s a libertarian! [like me]
  • The company Counsyl specializes in pre-natal genetic testing, a good idea before you have kids.

He doesn’t use the Taleb term “narrative fallacy”, but that’s what he means when describing the need that people have to explain why they turned out the way they did—even if it’s untrue.

some good quotes:

The most prominent finding of behavioral genetics has been summarized by the psychologist Eric Turkheimer: “The nature-nurture debate is over. . . . All human behavioral traits are heritable.” By this he meant that a substantial fraction of the variation among individuals within a culture can be linked to variation in their genes. Whether you measure intelligence or personality, religiosity or political orientation, television watching or cigarette smoking, the outcome is the same. Identical twins (who share all their genes) are more similar than fraternal twins (who share half their genes that vary among people). Biological siblings (who share half those genes too) are more similar than adopted siblings (who share no more genes than do strangers). And identical twins separated at birth and raised in different adoptive homes (who share their genes but not their environments) are uncannily similar.

[this is obvious to anyone who has children]

Although Pinker is clearly doubtful about the short-term promise of genetics testing, I actually think the situation is even more complicated.  What if much of our “environment” is determined by all those genes from the bacteria inside our bodies, some of which are inherited, some of which just arrives through whatever accidents life presents us.  In that case we’d have something with a genetic component (bacterial genes) combined with an environmental one (how we picked up the bug).  How in the world would you ever be able to analyze that amount of complexity?   But like he says:

Personal genomics is here to stay... People who have grown up with the democratization of information will not tolerate paternalistic regulations that keep them from their own genomes…There are risks of misunderstandings, but there are also risks in much of the flimflam we tolerate in alternative medicine, and in the hunches and folklore that many doctors prefer to evidence-based medicine. And besides, personal genomics is just too much fun.

Tuesday, January 06, 2009

It’s Twitter’s Turn

Every great new social phenomenon has a "fad" phase, where zillions of people join in because, well, because zillions of others are joining. A few years ago I suddenly reunited with my old friends at Apple Japan because suddenly it seemed like they all were on Orkut. That died down after a few months, and then (with Japan) it was Mixi, and a little later it resurfaced at Facebook. Now the same thing is happening on Twitter. It's fun! Every day somebody new is "following" me, and I hear snippets of updates in the lives of people who I enjoyed working closely with but for various reasons have moved on to other things and I don't keep up with as much as I wish I could.

Part of the fun is the newness of it all.  You reconnect with old friends who, unfortunately, life hasn’t permitted an easy way to stay in touch with.  And along the way you run into brand new people who are interesting and suddenly become

But we are all limited by a fundamental problem that humans can only develop so many relationships at a time.  People living in the wild usually travel in bands of 50 or so, with 150 being roughly the maximum size of the extended “band”.  Your “nation” may consist of a few hundred more than that, but it’s just not possible to be close to too many people, not at one time. Whatever you do on Twitter comes at the expense of what you do on Facebook and ultimately what you do in real life.  I’m a technology fan, so I don’t mind these other media having as much play as the real world, but still, I can only be in a few places at one time.

I’m not sure how long the Twitter phenomenon will last.  To me, it’s a basically a huge, open version of IRC or Instant Messenger—things that have been around forever and were looking for something like Twitter to take it to the next level.  I’m wondering when the commercials will hit it—you see hints of it already—and you start getting distracted from your friends by all the compelling and professionally-created content (like real-time news updates).

But meanwhile, go ahead and follow me:  I’m there now, running Thwirl and Tweetdeck, having the time of my life sending and receiving 140-character updates to great friends I haven’t seen in ages.

Saturday, January 03, 2009

My blog graphically



Graphical view of my blog

What do the colors mean?

  • blue: for links (the A tag)
  • red: for tables (TABLE, TR and TD tags)
  • green: for the DIV tag
  • violet: for images (the IMG tag)
  • yellow: for forms (FORM, INPUT, TEXTAREA, SELECT and OPTION tags)
  • orange: for linebreaks and blockquotes (BR, P, and BLOCKQUOTE tags)
  • black: the HTML tag, the root node
  • gray: all other tags