Rosh Hashanah

I went to the evening service of the “Worship and Study” Minyan at Harvard Hillel. The service was a bit uncomfortable for me, as it’s essentially the Conservative interpretation, to which I’m still unaccustomed. Whenever there’s Hebrew happening I am usually lost in unfamiliar text, thrown off by slight variants in the prayers, or trying to learn a new tune amidst a tone-deaf cacophony. I miss Cantor Silverman from Westport playing folk-pop on a carbon-fiber electroacoustic.

Nonetheless, the service was great thanks to a truly wonderful sermon by Rabbi Norman Janis. I can’t do it justice in summary, but his surprising thesis was: “Rosh HaShanah and Yom Kippur are not Jewish holidays.”. The argument is that Passover, Chanukah, and all the other Jewish holidays commemorate some event in the history (“biblical or post-biblical”) of the Jews. Rosh HaShanah has nothing to do with Jews; it’s just a celebration of all creation … and as if to emphasize this point, the bible passages we read on this day are a litany of instances in which God bestows blessings upon non-Jews (even sworn enemies of the Jews), and in which non-Jews act righteously and crucially.

In other words, Rosh HaShanah is the day for Jews to celebrate Everything, including Everyone Else. So happy birthday to the world, and whoever you are you’re probably awesome.

P.S. My favorite quote definitely has to be from Amos 9.7:
“Are ye not as children of the Ethiopians unto me, O children of Israel? saith the LORD. Have not I brought up Israel out of the land of Egypt? and the Philistines from Caphtor, and the Syrians from Kir?” Note that in modern English the Hebrew for “Philistine” might instead be translated as “Palestinian”.

Advice

I’ve just come back from my second Dissertation Advisory Committee meeting, and I did indeed receive some excellent advice and feedback. One item unanimously agreed item stands out: I need to at least attempt to use my system in a Real Living Creature, rather than the poor man’s animatronics I’ve been using so far.

I think it’s at least a little bit funny that the standard question I get asked, in reference to the dissertation, is “Can you see the light at the end of the tunnel?”.

Ram scoop

My physiology lecture yesterday was especially entertaining, filled with off-topic anecdotes like “You don’t need a blood system to survive” (under ideal conditions, for about 4 months, for certain definitions of “blood system”).

I think my favorite concerned the lungs of birds. It turns out that unlike the lungs of reptiles and mammals, who breathe in and then breathe back out, birds have flow-through lungs, with exits in the nostrils that are often separate from the inflowing bronchi. This means that, in flight, a bird can open its mouth and drive air through its lungs, powered by the kinetic energy of its own mass, without the need for a diaphragm. Bar-headed geese use this system to fly over the Himalayas in a single day, performing strenuous aerobic work at altitudes that would kill most humans.

Robert Bussard would be proud.

Present

Lots of presentations, no time for weblog. Today was a presentation for my Physiology class, on a topic about which I knew next to nothing (thank goodness for expert friends). Next week is my Dissertation Advisory Committee meeting, a progress review of everything I’ve done in 2011. The week after is a presentation of my whole project so far to the whole of Harvard Biophysics, students and faculty.

One cool thing I learned while preparing this presentation: whole-genome sequencing is now about $9,500 retail, and prices are still falling fast.

Among many other things, that means if I ever have children, they’ll probably be sequenced before they’re born.

Above average

I went to a birthday party today and returned with a gift bag consisting of 17 freshly dug potatoes, weighing at least 10 pounds and representing only a small fraction of the potatoes that were present. This might be more potatoes than I have cumulatively owned ever.

Potato recipes will be appreciated.

Switch

In New York City last weekend I walked several times past this building:
33 Thomas Street December 1991
The building is known as 33 Thomas St.. The Wikipedia article calls it “an extreme example of the Brutalist architectural style”, which seems like a perfect description to me. You have to walk by at the tail end of dusk, and crane your neck to search for the top, to realize how imposing this building is. Its windowless granite faces are folded into geometric forms but unbroken save for rows of massive cooling ducts. By height, it would be 9th tallest building in Boston, or a sinister mechanical match to the Washington Monument.

I could hardly guess its mysterious purpose, so I looked it up … and in fact, the building is a switch, a massive monolithic machine whose sole purpose is to redirect incoming signals immediately to their intended destination. It’s connected to myriad subterranean copper and fiber-optic cables, originally routing telephone calls but now arbitrary data. If the scale of this doesn’t inspire awe, then you haven’t considered the capacity of a building’s worth of single-mode fiber.

On the way home I walked by the James Farley Post Office:
Manhattan New York City 2009 PD 20091129 065
The building is immense and gleaming, spanning two city blocks and featuring the largest colonnade ever built. At its peak it was open to process mail 24 hours a day, 7 days a week. It’s surrounded by a moat wider than most city streets, maybe just to show off that it extends as far below ground as above. As I walked by, I realized: this thing is also a switch, a great machine only slightly less automated than the network routers that have made it obsolete.

The coup de grâce, though, happened when I walked around the post office to reveal this perspective:
Acela nearing 9th Av jeh
Sixteen lines of heavy rail run directly under the post office. The grand switch of the paper age sits directly above an underground railyard, which is itself a packet switch for rolling steel.

Beats

The average human heart beats 3 billion times in a lifetime. There are 7 billion people on planet earth. So if you saw a photo of a different person with every heartbeat, in a lifetime you would see a bit less than half of all the people there are.

This is actually more heartbeats, and comparatively fewer people, than I was expecting.

Not Invented There

This month’s issue of the Harvard Medical School magazine has a perfectly nice article describing a recent publication co-authored by some HMS researchers on the Ebola infection pathway. The article, and the discovery, are excellent:

“This research identifies a critical cellular protein that the Ebola virus needs to cause infection and disease,” explained Whelan, who is also co-director of the HMS Program in Virology. “The discovery also improves chances that drugs can be developed that directly combat Ebola infections.” … there are no available vaccines or anti-viral drugs that can fight the infections.

This reflects the conventional wisdom about how drug development works. A laboratory at an institution like Harvard, almost invariably funded by the National Institutes of Health (in this case by a combination of many NIH grants, and a few grants from other governments as well) discover a “promising target”. Big Pharma then swoops in, hires a few of the researchers, and starts in on the massively expensive process of discovering a molecule that exerts the desired effect on the biomolecule, i.e. a drug.

The noteworthy thing, then, is buried near the end of the article:

The team identified a novel small molecule that inhibits Ebola virus entry into cells by more than 99 percent.
The team then used the inhibitor as a probe to investigate the Ebola infection pathway and found that the inhibitor targeted NPC1.

In this case, the publication not only names a target; it also describes a drug that has the right effect and blocks the virus. This is big: independent university research labs, with budgets that are tiny in comparison to the pharmaceutical companies’, can discover a viable drug candidate (now in animal trials). It represents a paradigm shift that leaves Big Pharma with nowhere to stand.

Oh … one more thing (from this article):

…a patent application has been filed covering compositions of compounds and their use to treat Ebola and related infections.
… covering the host factor targets NCP1 and HOPS, and for the two therapeutic leads imipramine and U18666A as treatments for Ebola infection. … Another patent is held by the Whitehead Institute that covers the genetic screening technology platform.

So although the government has been funding this research effort for over 10 years, the positive results are now a monopoly that will enrich a handful of private individuals and organizations. This is particularly egregious in the case of the patent on imipramine, a drug that has been known and approved for other purposes for over 50 years.

Meet the new boss, same as the old boss.

3 nights

This is my third night in New York. I’ve stayed with a different friend or relative each night, which has been great both to spend time with as many people as possible and to avoid wearing out my welcome.

The conference has been fun, although the inevitably broken conference wi-fi made keeping track of VoiceLab responsibilities a bit stressful. It’s been great to be able to listen to discussions between the developers of Firefox, Safari, Chrome, and Opera, not to mention Ogg and WebM, all in one room.

Today, 10 years after the attacks three block south, the organizers were faced with a challenge to find an appropriate presentation. I think they made a great choice by having Brewster Kahle and Tracey Jacquith present an astounding new page showing the 20 largest television channels’ coverage of the attacks and their aftermath, in a way that can be referenced and quoted for analysis and journalism.

I made a pilgrimage of sorts to the World Trade Center this evening. There’s not much to see (they’ve carefully screened off the view down to save the surprise for tomorrow’s grand opening of the memorial) but the new construction is huge and impossible to hide. The process has taken an impossibly long time, but the results look very good.