The year of the personal genome

Want to buy a slightly used genome?

Back in 2000, Craig Venter and Francis Collins (and Bill Clinton) announced the completion of “the” human genome. Not to take anything away from that achievement, but genomes are just as varied as humans. Whose genome was the human genome? Or to come at it from another direction: if they popped that first draft genome into a baby printer, who would it come out looking like? The Celera version would probably look an awful lot like Craig Venter, because he just couldn’t stop himself from secretly “volunteering” his own DNA to the project.

More recently, Venter gave up any pretense of secrecy and published the most thorough human genome to date: both sets of 23 chromosomes for… Craig Venter. And not only that, it’s published on PLoS Biology, so you can go inspect every nucleotide. Or you can just print out this poster for your room. Think of it as a pin-up for the bio-geek set (I see London, I see France, I see someone’s 16 base pair non-genic heterozygous indel).

So old Craig gets to see all of his genes. Do you want to see yours? If so, you’re in luck, because, as noted in Technology Review, several new companies have set up to service your genomic needs. While you can’t get the royal (i.e. accurate and thorough) treatment that Venter and James Watson get, you can do pretty well.

23andMe, DeCodeMe, and Navigenics all will take something like $1000 from you and send you a bunch of genomic data. As many have observed, the exact value of the data is a sketchy. You may learn some things that will do little more than make you anxious.

Even so, I suspect these services will be a commercial success. There is a desire to know what cards you’ve been dealt that somehow trumps any rational medical value. When it really comes down to it, knowing about your personal DNA is almost more of an aesthetic experience than anything else. So it makes sense that there’s a company that can turn your DNA into art. That may be the most reasonable thing to do with your genes, at least for now. Hang them in your living room.

The best proof I’ve seen that biology is going mainstream is this ad for a PCR machine. Check out the insanely high production values on this video that’s peddling a piece of lab equipment for the white coat crowd. Amazing.

Everything is a myth

Good stories always trump facts. A good story is like brain glue. It stabilizes loose piles of memory inventory, thereby relieving some of your mental strain. This is why we have famous people say the things they should have said: because your brain is always trying to relax.

For example, did Galileo, while being tried in the Vatican for his heretical astronomy, say Eppur si muove (nevertheless, it moves)? Answer: no. But he should have. So he might as well have. Let’s just agree that he did and save ourselves a bunch of trouble, eh?

You’ve probably come across the “famous Goethe quote” that goes like this.

Whatever you can do or dream you can, begin it. Boldness has genius, power and magic in it.

Sadly, Goethe said no such thing. My friend Bill (a Star Chamber contributor from way back) sent me this debunking link: German Myth 12 – The Famous Goethe Quotation. It’s a fascinating story. As the piece says, “Far too many online quotation sites have been slapped together and seem to ‘borrow’ quotes from each other, without much concern as to accuracy.” I’ve run into this phenomenon before myself, so I wasn’t surprised to find the “Goethe quote” here, here, here, here, and here.

It’s too bad, because it’s still a great quote, and a great quote looks better when it hangs off a big name. How disillusioning to learn that what Goethe really said (in Faust: Der Tragödie zweiter Teil) was “I am a jam doughnut!”*

Must all our favorite stories turn out to be untrue? It reminds me of that old line from Mark Twain: “Everything is a myth.”** Or was it Winston Churchill*** who said that?

* Not true.
** Also not true.
*** There never was a “Winston Churchill”

The edges of knowledge: Wikipedia tailings and dross

One of the nice things about Wikipedia is the fact that you can go to it for information about new cultural trends. Want to know what a flash mob is? How about Leetspeak… what’s that? Wikipedia can tell you, with reasonable accuracy and long before more sober references chime in. Still, even Wikipedia has its limits. As you approach the cultural hinterland where barbarians be, the Wikipedian frontier guards regularly eject submitted material.

For example, the other day I noticed that Audible.com was breathlessly promoting an interview with Vanna Bonta in which she talks about the “emerging genre of Quantum Fiction, exemplified by her controversial book Flight: A Quantum Fiction Novel.” Vanna Bonta? Quantum fiction? It all sounded pretty bogus to me. Fortunately I knew where to turn for the latest word on hot young memes: Wikipedia. Alas, quantum fiction missed the cut, being too wacky by half. But not for lack of trying. Another search revealed a Wikipedia quantum fiction article appearing in… the Wikipedia Knowledge Dump (a.k.a. WikiDumper.org).

WikiDumper isn’t proud. It lives off the picked over remains of Wikipedia fare. The editor is the thoroughly eccentric writer and fractal artist Cliff Pickover. He subtitles WikiDumper as “The Official Appreciation Page for the Best of the Wikipedia Rejects.” To which he adds: One man’s trash is another man’s treasure.

So now you know where to learn about Quantum Fiction. And Fractomancy, a fractal-based form of divination that was invented by, ahem, Cliff Pickover. And… there’s really no other way to say this… human cheese.

Self-replicating self-replicators

Back in August, I posted something about a nifty 3-D printing product called the Desktop Factory. Commenter Doug Moore made the following wisecrack:

I have a better way to save money on a 3-D printer. Just print a 3-D printer and then return the original to the store.

Yes yes, ha-ha and all that, but yesterday I came across another 3-D printing tool that has the explicit goal of doing exactly what Doug’s talking about. The RepRap device (RepRap is short for Replicating Rapid-prototyper) is being built by the ambitious Adrian Bowyer of the University of Bath. He wants his RepRap to self-replicate (within certain limitations) so that everyone will have one, thereby eliminating the need for money for all mankind.

So he’s obviously crazy, and his Rube Goldberg replicator (RubeRep) is nowhere close to replicating anything very useful, let alone itself. But he’s very clever, and rhetorically he knows how to sell his story. Let us say that the human spirit is willing but the mechanical flesh, as yet, is weak.

tomato.jpg

I know all this because I listened to his talk at PopTech. It’s a darn good talk and I recommend it. Bowyer makes some compelling comparisons to biology, and I believe that something like this will eventually succeed. When it comes to replication, I always think of the garden. That lovely tomato in your hand was assembled on-site using solar power and locally available materials (dirt! air!). It’s an existence proof: we can do at least that well. Someday. You don’t need metals from Peru or petrochemicals from Brunei. You don’t need kilns, chillers, or pressure cookers. You do need cleverness, patience, and a healthy diet fortified with eight essential vitamins and minerals. We might manage it yet.

My box folding video

After the busy December holiday season, I wanted to get back in the blogging saddle last week. But as I was sitting down to write late last Thursday night, a pipe burst in our house (we were in the middle of a nasty New England cold snap). It could have been much worse: my wife heard it right away and we were able to shut off the water main less than a minute after it happened. No major damage, but now we’re going to have to re-route the plumbing in the upstairs bathroom. Oy! Interesting aside: it was the hot water pipe, and the plumber who came the next day said that it’s usually the hot water pipe that goes. Why do you suppose?

Anyway, to get this week started I have a video which, for once, is a creation of mine. Years ago I was pondering a tiled floor and a question popped into my head: How many ways can you fold six contiguous squares into a cube? This video, done with MATLAB, is the answer to that question.

The Italian campaign in WWII

If history is written by self-flattering victors, then ambiguous and unfortunate battles are in danger of being forgotten altogether. We Americans never tire of the story of D-Day, of the great carnage on the beaches of Normandy that eventually put Allied troops across the Rhine and into the heart of Germany. But what do we know about Italy? The Allied campaign in Italy (1943-1944) is ambiguous at best and a colossal mistake at worst.

I just finished a book on the subject, The Day of Battle: The War in Sicily and Italy by Rick Atkinson. It’s a great read and does a lot to put the campaign in perspective. Atkinson gives you the viewpoint of commanders and soldiers, although I wish there were more material from the German side of the line. Atkinson refers to Italy as, at times, employing the tactics of World War I with the weapons of World War II. The reason is obvious in hindsight: there was no clear strategic directive. In France there was a simple objective. Drive your tanks into downtown Berlin. In Italy the objective was… what? A diversion from Normandy? A thrust deep into the “soft underbelly” of the Axis? A battle of attrition designed primarily to grind down German divisions? All these things? Even to the commanders, it was never clear.

Although Atkinson shows what the generals are thinking, he gives the last word to war correspondent Ernie Pyle. Here’s how Pyle sums it up.

I looked at it this way—if by having only a small army in Italy we had been able to build up more powerful forces in England, and if by sacrificing a few thousand lives that winter we would save a half million lives in Europe—if those things were true, then it was best as it was.

I wasn’t sure they were true. I only knew that I had to look at it that way or else I couldn’t bear to think of it at all.

By the way, one of the nice resources available to the modern reader of military history is Google Earth. If you want to know why Monte Cassino was so important, you can just fly there and inspect the landscape. You can also find map overlays like this one of the Salerno landings.

My uncle fought in the Italian campaign for several months before being wounded north of Rome and sent home. I’m sending him a copy of Day of Battle to get his opinion, but in the past he has highly recommended Farley Mowat’s And No Birds Sang as an unblinking memoir of what Italy looked like to an infantryman. Maybe I can get Uncle Bill to set down some of his thoughts for reading on this site…

The coming depopulation

My brother and his wife were recently in town for a surprise visit (my birthday). At one point, over lunch, the conversation turned to population growth and the woes of the world. I pointed out that all was not lost, since the Earth’s population was going to peak in this century and shrink for a long time to come thereafter.

I was challenged on this point and asked to provide a little support for my assertion.

The most forceful description of this situation that I’ve come across is Phillip Longman‘s talk at the Long Now Foundation entitled The Depopulation Problem. He’s written the entire speech out as a PDF file. It’s worth reading. It’s got some startling facts in it. It’s reasonably well known, for example, that industrialized countries like Japan and Italy are producing children at below the replacement rate, which is to say, they’re shrinking. Russia is shrinking at the incredible rate of three quarters of a million people every year. That’s nontrivial shrinkage.

People who are aware of this phenomenon in rich countries still generally believe that it’s more than made up for by high fertility in poor countries. But this isn’t true. Here’s what Longman says.

In no industrialized nation today is fertility high enough to prevent declining population. In countries as diverse as Italy, Japan, Spain and Korea, fertility rates are so low that population loss on the order of 30 to 50 percent per generation are in the works… Yet what is even more surprising is the rapid decline in fertility now seen in the developing world. The phenomenon of sub-replacement fertility has by now spread to ever corner and continent of the globe.

In short, Longman actually paints a gloomy picture of what a depopulating world may look like. That part is controversial, but the basic demographic premise is not: we’re done doubling the world’s population.

As further evidence of this point, look at the organization called Zero Population Growth, an organization that was founded by Mr. Population Bomb himself, Paul Ehrlich. That organization is not even called Zero Population Growth anymore. It’s called Population Connection. They still have plenty of good work to do with overcrowding and environmental issues, but even they agree that the population curve is flattening this century.

For all the wretched things going on in the world, that’s a pleasant thought.

Flying in the bird suit

Despite the long line of disappointed, broken, and more or less dead people who have tried to fly like a bird, it seems reasonably likely that eventually someone will succeed. They will do this not so much by flying like a bird as by safely landing like a bird. What defines flying like a bird is a matter of a pinion (sorry), but Rick sent me this NY Times video about a guy who’s making a pretty good case. He’s got a black bird suit that lets him drop from an airplane rather less like a rock and rather more like a flying squirrel. It’s a start. He still lands with the help of a parachute, but at some point he plans to dispense with that. I wish him luck. And I wonder how much his health insurance costs.

It turns out he’s not the only one perfecting a bird suit. Via tingilinde I came across this great video of someone who specializes in zipping down mountainsides, BASE jump style, in his bird suit.

Stick a cape on that man and call him a super hero. That’s got to be a serious rush.

The earliest sunset is here!

Every year this time I am compelled to point out the day in December with the earliest sunset. Where I live, that day is December 9th, which means I am now safely on the far side of the solstitial crepuscular cusp. Since I’m not an early riser, that means I’ll be seeing a little more of the sun every day from now until next summer. That, in my opinion, is worth a stiff drink and some seasonal good cheer.

sunset.png

I refer you to analemma.com if you’re puzzled as to why the earliest sunset does not coincide with the solstice. Celebrating the earliest sunset is a nicely localized tradition, since (unlike the solstice itself) the day varies dramatically depending on your latitude. Speaking of analemmas, APOD recently featured this lovely animation of the sun’s seasonal progress over New Jersey.

Also, in news astronomical, I’m glad to report that my Sky Clock is back in business again. The data source I use to locate the planets, ephemeris.com, was offline for a while, but it’s healthy again. I made an animation to show how the Sky Clock changes over one day, one month, and one year. Below is the animation for a year. Notice the arm-like lines that indicate sunrise and sunset. You can see them closing like a caliper in late December before releasing us for another year. Thank goodness.

one-year-05.gif