Samurai Scientist

The Last Samurai

2010-08-19T00:00:00.000-07:00

Out with the old, in with the new. I've graduated, relocated, and switched to working on kidney stem cells. And as much as I've enjoyed writing this blog, it peaked a while back, and now it's time to mix it up a bit.

This blog is dividing - and neither of the daughter cells look exactly like the mother. Science News and Views will continue on Science Consulting, hopefully a communal effort between me and some friends from grad school. Interested in becoming a science consultant yourself? Please join our Facebook Group - we're looking for a few good nerds.

More of a left-brain person? I'm compartmentalizing my more philosophical musings into The Shmlag, a retro blog. While everyone else marches forward, I'm going to try to march backwards through the bustling crowd in search of my inner child. Should be fun.

But first, I want to give Samurai Scientist a proper send-off into the vast binary yonder. I've enjoyed writing this blog over the last year and a half, and hopefully you've enjoyed reading it. I've tried to convey the idea that science doesn't happen in a vacuum. There's a reality to it, a people, a culture, who are actually pretty fun to be around. Once you engage in all that, it enriches your life and becomes part of you.

Research, like life, is surely suffering. It's also purifying, clarifying, and enlightening. If you're going for a Ph.D., it helps to adopt the ethos of a samurai. You must master nature, force her to obey - it's like sorcery. And there are also obstacles you won't be able to overcome. It may be the hardest thing you ever do, but then few things worth doing are easy. The trick, as with everything else, is to stop worrying and enjoy the experiment.

And smile - don't forget to smile.

Necks 'n Hawks

2010-06-11T01:46:00.001-07:00

The top ten Google Search terms leading to my blog in the last 5 months (courtesy of Analytics). I find this remarkable.

A Peace Offering

2010-06-03T02:41:00.001-07:00

In light of recent current events, I thought it might be worth rerunning some of my posts about peace. These include Turkish Delight, A Giant Keg for Mankind, What Stands Between Us is Only Words, and Non-Violence and the Jedi.

http://www.samuraiscientist.blogspot.com/search/label/peace

Seeing Through God's Eyes

2010-05-26T14:42:00.000-07:00

One of the pleasures of studying the physical world is perspective. When you work with molecules long enough, you gain a sense of scale. It’s a little like being Neo at the end of The Matrix - you catch a glimpse of the millions of 1s and 0s that make up your daily life.

I was recently reminded of this at a no-kids night at the California Academy of Sciences. If you haven’t been, San Francisco has done a truly amazing job with both the CAS and the de Young art museum directly opposite. The museum night was magical, with low lights, a DJ, and wet bar – the perfect way to experience science.

By the time we made it to the IMAX Planetarium show, I was perfectly buzzed. We flew out and looked down on the planet Earth and the International Space Station, and I felt like I was there. I knew this was the closest I’d ever be to orbiting the Earth, and for a whole lot cheaper.

Then we flew out farther, so we could see the entire solar system, and paused to watch the planets in their rotational orbits. It’s quiet out there in deep space, peaceful, beautiful. As a molecular biologist, I’m used to thinking in terms of nanometers – not millions of light years. We flew out further, seeing nebulae and galaxies in infrared spectra, like looking through the eyes of God. After the show, we strolled through a night reef, watching jellies with four perfect rings of fluorescent pink pulsate rhythmically.

Sometimes it’s hard, as adults who have been-there-done-that, to find an emotional connection to the universe. But if we're going to do science, we may as well enjoy it. And in the right setting, knowledge can open our eyes to fresh perspectives, and help us rediscover the child-like wonder that inspired us in the first place.

Unsexy Science?

2010-05-18T07:57:00.000-07:00

Newsweek's cover story is "Desperately Seeking Cures: How the road from promising scientific breakthrough to real-world remedy has become all but a dead end." In it, Sharon Begley tries to break down the reasons we're all not living to 150 yet. Her main argument is that finding cures for disease is "unsexy." Unfortunately for an article about science, the article is thick on anecdotes but thin on statistics, and deteriorates into yet another Begley diatribe about how basic research fails to fill the public good.

First off, I take issue with the notion that curing disease is the only goal of the NIH or of academic science. Science actually shows that ~2/3 of human disease is self-inflicted, as the WHO points out: "Seven leading risk factors... account for almost 60% of all ill health in the Region." The NIH, correctly, takes a broad view of applied science: "NIH’s mission is to seek fundamental knowledge... to enhance health, lengthen life, and reduce the burdens of illness and disability." If you ask me, weapons and global warming are greater health threats than diseases caused by overeating.

While Begley claims disease is "unsexy," the reality is that the NIH pours money into medical school research campuses and every scientist has wet dreams about curing cancer. In fact, the last guy to run the NIH (Elias Zerhouni) was an MD who focused almost solely on translational stuff. Begley's argument boils down to a "lack of cures," but that's a loaded metric. As I've pointed out here before, testing a single cure can cost the same as 1,000 research labs per year. The $50b NIH budget just couldn't accomodate that, although we could fund it if we cut back our military. You want better cures? Pay scientists what they deserve.

From the article, it's clear that Begley (who holds only a B.A. and has never done research) thinks science is simple: find a drug, cure a disease. So she can't understand what's holding up the works. But what we've learned over time is that conventional small molecule therapeutics may not work for chronic disease. On the other hand, stem cell technologies and genomics are showing a lot of promise for curing disease. The system is by no means perfect, but I think in 50 years we will look back and realize that it was working, at least as much as we let it work.

Even a Caveman Should Know It

2010-05-11T22:56:00.000-07:00

The evolution wars are over. This may seem hard to believe, considering that 55% of Americans don't believe humans evolved. But behind the scenes there is growing a quiet revolution - of data. It used to be that the strongest evidence for evolution came from the fossil record, how whale nostrils turn into blowholes over millions of years. But now we've got a second, even better source: our genes.

Our genetic code is a biological history book, so long and convoluted that it takes millions of years to erase a single typo. And as we learn to read that book, we discover time and again that Darwin was right. A good example is the recent discovery that most humans share genetic markers with Neandertals (in other words, we dated them). When you compare our genomes to those of other animals, you can see the random changes that happened over time to differentiate our species. There are also special places in the genome that are protected from mutation called CpG islands, and we can tell how the rest of the genome has changed by comparing it to these special sections.

None of this is understood by the Young Earthers. One reason is that sciences continue to be woefully underrepresented in liberal arts curricula. The average American college graduate therefore has very little basic understanding of biology or any other science. Thanks to this institutionalized ignorance, the debates going on in newspapers today are based on data 20 years old - and are about as relevant. We are flapping our gums, spending energy and time, over questions that are already settled. If America is going to lead the world in the 21st century, we are going to have to do better than that.

Just another day in the life

2010-05-06T16:48:00.001-07:00

Wake up in the morning feeling not quite like P. Diddy, probably because it's 5AM and I'd stayed up late the night before toasting Cinco in the city. Stop by the lab, grab a double-shot of milk tea and 4L cold PBS, and I'm on the road to Modesto to pick up the pig brains for our lab tubulin prep (the second time I've done this in two weeks). The tunes run out after about 70 miles and all I get is some surprisingly on-message Christian rock and a pledge drive/classical music (Chopin's Heroic Polonaise, which reminded me of my Dad).

Got the brains, put 'em in cold PBS, drove back through SF morning traffic (2h), parked in front of my building with the parking pass my boss gave me. Wrote the Introduction, ate lunch, wrote most of the Discussion. My landlord calls and I'm discussing repairs with her as I walk back to the car and WTF?! Yellow envelope? THEY GAVE ME A PARKING TICKET! $75 buckaroos. Freaking city of B*****y. Get off the phone and I stare at this ticket for about 5 minutes and finally figure out it's because I forgot (in the dim light of 5AM) to scratch off the DAY OF THE WEEK! Yes, I'd successfully scratched off that it was May 6th but I forgot to also mention that it was THURSDAY today! For that they want to charge me seventy-five dollars!

Oh well. I hope the tubulin prep goes well. I'm taking a NAP.

The Anxiety Gene

2010-04-27T23:02:00.001-07:00

Fear is a very useful evolutionary trait. Species have survived for millions of years simply by running away at the slightest hint of a threat. Considering how useful fear can be, it comes as no surprise that mother nature occasionally deals out an overdose, which we humans recognize as anxiety, nervousness, or neurosis.

Animals can be neurotic, too. Just as humans bite their nails, some Dobermans have a nervous habit of chewing on their paws. A recent genomics study examined these paw-chewing Dobermans, and found that they tended to have a special version of one gene called CDH2. This appears to be a bona-fide behavior gene, a kind of holy grail in the field of behavioral genetics.

In humans as in dogs, inbreeding may permit neurosis genes to rise to the top and manifest themselves. For instance, I have been told that the Baba Nyonya, a group of Chinese-Malays who traditionally marry within the family, suffer from a high degree of mental illness among their females. Similarly, some researchers are studying whether certain neuroses are overrepresented among Ashkenazi Jews, thus explaining the ouvres of Woody Allen and Larry David.

Although fear might be useful from an evolutionary standpoint, too much of it can be crippling, and can even result in unnecessary violence. As Yoda put it, fear is the path to the dark side. Ultimately, neurosis/fear/anxiety are products of not only nature, but also nurture. We can't easily control our genes, but by diversifying our social interactions we can distinguish true enemies from those who exist only in our heads - a step towards a less anxious and less stressful life.

Birth/Death of My Facebook App

2010-03-28T09:00:00.000-07:00

This morning I'm talking with a friend in my lab about how LinkedIn sucks and I like using Facebook better. So it gets me thinking, why not write an application for Facebook that lets you display a 'professional' profile? That way you can add work contacts as Facebook friends without showing them your goofy personal profile.

I think about it some more and grow more and more enamored with the idea and in the afternoon I change my Facebook status to:

got a good idea for a facebook app - developers, ask me about it!

Maybe one of my programmer friends will want to help me with the project.

So now I'm at home bored after work after TV and I'm Googling how to write a facebook application and it's simple, all I have to do is download a Facebook application called Developer, learn a little PHP and bam - I've got a Facebook app! And in walks my computer-whiz housemate and I'm telling him my idea and how can we make it so when you Add friends in Facebook they go into one category or the other.

And I'm saying, See, really all we need is an alternative profile. You can already set up Facebook Lists so as soon as you Add a friend you can add them to the separate list for Work, which has its own privacy controls. So you don't need to rewrite Facebook to make a new kind of friend category. All you really need to do is replace the goofy profile you wrote with a professional profile for a certain list of people...

... of course, you could just post a slightly less goofier profile to begin with...

... Hmmmmmmm.

Can an Octopus change its spots?

2010-03-06T23:08:00.001-08:00

Last time we talked octopus, I showed you a classic vid of an octopus changing color. Watching Planet Earth the other night, I noticed a little squid embryo performing the same trick. It got me wondering: how do they DO that?

Well it turns out people have been studying this. Here's a cute video of a baby octopus embryo doing the camouflage dance:

The 'chromatophores' in the title are specialized skin/pigment cells that are the key to the whole thing. Watch starting at 0:18, where you see individual cells. Inside each cell is a spot of color, like a floating drop of ink; the cell changes color by spreading out the spherical, 3-D droplet into a 2-D hexagon that fills the entire cell.

Humans don't have chromatophores, so we can't change color. Yet.

Bird with the biggest playlist

2010-02-21T13:59:00.000-08:00

Things have been a bit busy lately but I wanted to share with you this incredible video of the lyre bird. Evolution has at least as much to do with impressing your date as it does with survival, and this bird does so by accumulating the biggest 'playlist' it can. Listen in as this male composes a love song which includes not only the calls of other birds, but also human machinery such as cameras and chain saws.

McCain Waxes Homophobic

2010-02-02T22:42:00.000-08:00

Gay rights are a litmus test for societal values. It is powerfully telling that our society has failed this test with flying colors. Our clergy - a den of infantilized fools who never took the message of Jesus, or Moses, into their hearts - continue to lead a pack of rudderless baby boomers off a cliff of fundamentalist nonsense that weakens us as a nation and divides us as a country. Denying gays equal citizenship and rights is terrible karma, a total failure of leadership, and I do believe it will come back to haunt us in the end.

There's no better example of this than John McCain, the man-who-would-(sell-his-soul-to-)be-president. 'Don't-ask-don't-tell' must be pretty awful if even old-fart military generals are speaking up against it, but John McCain is using the opportunity to score political points with the religiously befuddled. In an about-face, McCain claims it would be too disruptive to our armed forces to overturn don't-ask-don't-tell while they're busy bleeding us dry with two hopeless wars. So, he's decided to throw the gays under the bus.

The gay rights 'litmus test' is clearly divided along generational lines (see graphic below). The alter kockers think it's disgusting (McCain); the baby boomers are confused (Obama); and for the younger generation it's a no-brainer. But who is the politician for the younger generation? Where is our voice? If we do not lead, we cannot blame our elders for failing to have a clue.

I was blind but now I see

2010-02-01T19:12:00.001-08:00

It's easy to get caught up in the political tailwinds, but the truth is that politics rarely makes progress. Science, however, is constantly surprising me with its ability to power science fiction into science fact.

Take gene therapy. Fifteen years ago, the field seemed dead (some of its early adopters actually died, which did not help matters). Today? It's the future of medicine. Gene therapists have literally given sight to the blind, cured bubble boys (left), and most recently reversed beta thalassemia - and sickle cell anemia is not far behind.

The secret? Two words, my friend: Evo and Lution. Gene therapy works because the body selects for successful cells. The healthy cells - the ones with the good copy of the gene - outcompete the shitty ones mother nature dealt you. And your body is so highly optimized, even a small population of good cells is enough to keep the bad apples at bay.

So what's next for gene therapy? Well I'll put it to you this way: of the ~4,000 human diseases, only a few are currently treatable. As genomic data explodes, so will our understanding of the genetic basis of these diseases - and so will the cures. So in our lifetimes we can expect to see cures for Fanconi's anemia, Huntington's disease, polycystic kidney disease, and stubborn old cystic fibrosis, just to name a few. That is what scientists are bringing to society - but what is society bringing back? Only 39% of Americans believe in evolution. I wonder sometimes who we are busy saving.

Croak-ley

2010-01-20T16:19:00.000-08:00

Already the pundits are declaring the vote in Massachusetts a vote against health care. What nonsense! The Massholes already have health care, remember?

The reason the Dems lost is that they pitted an droning woman with zero charisma against a hot guy who posed in Playgirl. It's like going up against the Terminator, and throwing up the 90-pound weakling.

Oh wait, they already did that.

Also, the 'Pubs called in their special crack team of election-rousers. Those guys could get Californians to hate homosexuals. Oh wait, they already did that too.

In the long run, this one Senate seat ain't gonna matter much for health care. That will pass anyways, and if it doesn't I don't really care. I have a job, and anyways 2/3 of disease in this country is self-inflicted. The best health care plan is probably 'eat more fruit.'

I just hope the Dems have a better plan for Palin, 'cuz if that chick gets elected I'm moving to Paris.

Should web content be subsidized?

2010-01-17T07:52:00.000-08:00

TierneyLab addresses an old question, and comes up with an old solution. Here is my response:

John, you have a good idea but you aren't thinking big enough.

Instead of having the government run a micropayment system to charge consumers, take all the money that the government wastes (the 40-50% of our federal budget that is siphoned off to the military) and establish it as a fund for artists and reporters. You can slice up the pie based on the number of hits each author/artist receives. In this way, society still has its free information, and the contributors have a guaranteed incentive to generate fresh content.

This ain't undergrad, it's as real as it gets

2009-12-12T15:34:00.001-08:00

From the 2009 MCB Follies comes this parody of the Lonely Island's "I'm on a Boat." What's your favorite lyric?

Why Boston

2009-12-01T20:00:00.000-08:00

Excerpt from the ridiculously long NIH postdoc fellowship application I'm writing (this is a case where government has definitely gotten too large):

The _________ lab is the perfect environment for me, for several reasons. Translating basic research knowledge into societal well-being and progress is important to me. Having gained much already from the ivory tower, I now seek a lab that will expose me to medical doctors and clinical environments and human patients. I am very interested in stem cells and regenerative medicine, and the _________ lab is leading the fore in this field and part of the __________ Stem Cell Institute, the top regenerative medicine body in the field. I am interested in kidney tissue biology as it relates to several fields – polycystic kidney disease, epithelial-mesenchymal transitions, aging, differentiation, etc. – and the ________ Unit at ______________ has a tremendously high concentration of high-caliber nephrology researchers. The surrounding city of Boston will be a completely new academic network to connect to and learn from, and features powerful potential collaborators within a few blocks of our lab. These reasons convinced me to pull up stakes from my very comfortable and congenial surroundings in Berkeley and move to what I see as the most exciting place to be in research today.

I know, I know. Can't end a phrase with a preposition. I know.

Revenge is sweet

2009-11-16T23:43:00.000-08:00

About 6 months ago, I commented on a medical blog that possibly - just possibly - we were overtreating for breast cancer. After all, it was possible that some tumors came and went without us even knowing about it. I suggested that we needed some negative controls for breast cancer, and that it wasn't a bad idea to let some patients opt out of masectomies and see what happens.

I was laughed off the blog. My scientific credentials and ethical values were challenged. The comments were very reactionary, not very scientific.

Six months later, and my how things have changed. The phenomenon I predicted was borne out in major studies. I heard doctors talking about it on NPR. Now, in recognition of these new findings, it looks like the recommended age for mammography may soon change from 40 to 50.

A lot of bloggers call themselves "skeptics" because they dare to mock other peoples' beliefs. But that's not what science is about. Science is about creativity and challenge, not biology-textbook dogma. It's about thinking outside of the box. From that perspective, I daresay some of these science bloggers could learn a thing or two from the people they are mocking.

Talkin' politics

2009-10-25T00:05:00.000-07:00

Hi [Samurai],

Being that you are one of the most politically liberal people I'm in contact with, and I believe you to be intellectually honest, I'm curious how you would respond to this: Warmongers or Peacemakers: Who will scorch the earth?

Granted it's from a conservative source, but it seems to raise some very convincing points.

Also: WIKI - Prisoner's_dilemma Prisoner's dilemma & Obama

The arguments raised by the above cause the current approaches to relations with other countries, both by the US and Israel, to trouble me greatly.

(If you aren't yet interested in a political discussion, ignore this...)

----------------

Hey [Friend in Israel], thanks for the e-mail, I appreciate your genuine interest. I do try to be intellectually honest.

So far, I've listened only to the first video (about Hitler, WWII). I think these arguments do hold some water. In particular, I agree with the speaker's central thesis - that diplomacy frequently fails to bring peace. However, I think the speaker is not sufficiently critical of war, which often fails as well (often at tremendous cost).

... The main problem with the video is that it only considers only two options: diplomacy (by politicians), or war. Neither option is very effective in my opinion. This is characteristic of Western thought these days - very polarized, not very creative.

There is a third option - one that has been largely forgotten even by the left. That option is non-violent resistance. It is the way of Ghandi and Martin Luther King, both of whom led tremendously successful social movements post-WW2. Non-violence does not mean non-action. It means active protest without resorting to violence. In theory, this helps you win the enemy's hearts and minds by getting them to think and respect you. If you are interested in learning how it works, I suggest you read two books:

1. The Autobiography of Martin Luther King Jr., by Clayborne Carson
--this is a collection of MLK's writings and speeches, chronicling his civil rights days through his opposition to Vietnam

2. Ghandi: an Autobiography; the Story of My Experiments With Truth
--penned by Ghandi himself, it goes into depth about his early upbringing and his philosophies of non-violence and experimentation

A common denominator to these two fellows is that they were raised very religious, although in two different faiths, and both men drew from their faiths to arrive at the principle of non-violence. I can relate to this; when I memorized Pirkei Avot over ten years ago, the many sayings about peace, wisdom, and relationships planted the seeds of this philosophy in my mind, well before I read any of the above.

I think there are other ways to wage peace besides non-violent resistance, but you really have to get creative. This creativity is what's missing from our leaders these days. I do not trust them one lick - they are old fools, and one is worse than the next. I would not follow them into battle, or rely on them to make peace through diplomatic means.

Hope this gives you something to think about! Let me know if you have any specific responses to what I've said. Take care and always fun to talk politics with you.
Samurai

PS Have you ever seen Watchmen? Or read the graphic novel? It gets into a lot of these questions. You might like where it ends up.

How To Create 10,000,000 Jobs

2009-10-21T20:31:00.000-07:00

President Obama, here's a little back-of-the-envelope calculation for you:

~1~ Monthly wage for a security guard = $2,000.

~2~ Cost/month of our wars in Iraq+Afghanistan =
$20,000,000,000. (Yes, that many zeroes.)

~3~ Number of security guards this could employ instead =
$20,000,000,000/$2,000 = 10,000,000.

Economy crisis, solved.

On the Origin of (Four) Species

2009-10-01T08:28:00.000-07:00

“Nothing in biology makes sense except in the light of evolution.”
– theistic evolutionist Theodosius Dobzhansky

A corollary might be, “Nothing in religion makes sense except in the light of history!” Religions evolve and develop over time, just like organisms. For instance, take the ‘four species’ of Sukkot: palm (lulav), citron (etrog), myrtle (hadas), and willow (arava). The Bible speaks of “taking” these species before building a Sukkah/hut, but does not explain what to do with them:

מ וּלְקַחְתֶּם לָכֶם בַּיּוֹם הָרִאשׁוֹן, פְּרִי עֵץ הָדָר כַּפֹּת תְּמָרִים, וַעֲנַף עֵץ-עָבֹת, וְעַרְבֵי-נָחַל; וּשְׂמַחְתֶּם, לִפְנֵי יְהוָה אֱלֹהֵיכֶם--שִׁבְעַת יָמִים.	40 And ye shall take you on the first day the fruit of goodly trees, branches of palm-trees, and boughs of thick trees, and willows of the brook, and ye shall rejoice before the LORD your God seven days.
מא וְחַגֹּתֶם אֹתוֹ חַג לַיהוָה, שִׁבְעַת יָמִים בַּשָּׁנָה: חֻקַּת עוֹלָם לְדֹרֹתֵיכֶם, בַּחֹדֶשׁ הַשְּׁבִיעִי תָּחֹגּוּ אֹתוֹ.	41 And ye shall keep it a feast unto the LORD seven days in the year; it is a statute for ever in your generations; ye shall keep it in the seventh month.
מב בַּסֻּכֹּת תֵּשְׁבוּ, שִׁבְעַת יָמִים; כָּל-הָאֶזְרָח, בְּיִשְׂרָאֵל, יֵשְׁבוּ, בַּסֻּכֹּת.	42 Ye shall dwell in booths seven days; all that are home-born in Israel shall dwell in booths;
מג לְמַעַן, יֵדְעוּ דֹרֹתֵיכֶם, כִּי בַסֻּכּוֹת הוֹשַׁבְתִּי אֶת-בְּנֵי יִשְׂרָאֵל, בְּהוֹצִיאִי אוֹתָם מֵאֶרֶץ מִצְרָיִם: אֲנִי, יְהוָה אֱלֹהֵיכֶם.	43 that your generations may know that I made the children of Israel to dwell in booths, when I brought them out of the land of Egypt: I am the LORD your God.

What does it mean to “take” the species? It's unclear. Luckily, they are mentioned again in the days of Ezra (Neh. Ch. 8):

יד וַיִּמְצְאוּ, כָּתוּב בַּתּוֹרָה: אֲשֶׁר צִוָּה יְהוָה בְּיַד-מֹשֶׁה, אֲשֶׁר יֵשְׁבוּ בְנֵי-יִשְׂרָאֵל בַּסֻּכּוֹת בֶּחָג בַּחֹדֶשׁ הַשְּׁבִיעִי.	14 And they found written in the Law, how that the LORD had commanded by Moses, that the children of Israel should dwell in booths in the feast of the seventh month;
טו וַאֲשֶׁר יַשְׁמִיעוּ, וְיַעֲבִירוּ קוֹל בְּכָל-עָרֵיהֶם וּבִירוּשָׁלִַם לֵאמֹר--צְאוּ הָהָר וְהָבִיאוּ עֲלֵי-זַיִת וַעֲלֵי-עֵץ שֶׁמֶן, וַעֲלֵי הֲדַס וַעֲלֵי תְמָרִים וַעֲלֵי עֵץ עָבֹת: לַעֲשֹׂת סֻכֹּת, כַּכָּתוּב. {פ}	15 and that they should publish and proclaim in all their cities, and in Jerusalem, saying: 'Go forth unto the mount, and fetch olive branches, and branches of wild olive, and myrtle branches, and palm branches, and branches of thick trees, to make booths, as it is written.'
טז וַיֵּצְאוּ הָעָם, וַיָּבִיאוּ, וַיַּעֲשׂוּ לָהֶם סֻכּוֹת אִישׁ עַל-גַּגּוֹ וּבְחַצְרֹתֵיהֶם, וּבְחַצְרוֹת בֵּית הָאֱלֹהִים--וּבִרְחוֹב שַׁעַר הַמַּיִם, וּבִרְחוֹב שַׁעַר אֶפְרָיִם.	16 So the people went forth, and brought them, and made themselves booths, every one upon the roof of his house, and in their courts, and in the courts of the house of God, and in the broad place of the water gate, and in the broad place of the gate of Ephraim.
יז וַיַּעֲשׂוּ כָל-הַקָּהָל הַשָּׁבִים מִן-הַשְּׁבִי סֻכּוֹת, וַיֵּשְׁבוּ בַסֻּכּוֹת--כִּי לֹא-עָשׂוּ מִימֵי יֵשׁוּעַ בִּן-נוּן כֵּן בְּנֵי יִשְׂרָאֵל, עַד הַיּוֹם הַהוּא; וַתְּהִי שִׂמְחָה, גְּדוֹלָה מְאֹד.	17 And all the congregation of them that were come back out of the captivity made booths, and dwelt in the booths; for since the days of Joshua the son of Nun unto that day had not the children of Israel done so. And there was very great gladness.

Note that by this time (~450 BCE) the exiled Israelites had forgotten what was written in the Bible or how to keep Sukkot. They appear to have interpreted the Bible’s command to “take” the four species as

“take them… and use them to build a Sukkah!”

To this day, all Jews build their Sukkah using plant materials.

However, the tradition of the “four species” has evolved again since then. By the Rabbinic era, a different interpretation had taken root:

“take them… and bundle them!”

It’s not clear how this tradition of bundling and shaking the four species during prayers arose, but it seems to have happened during the second Temple period (500 BCE-70CE; see Mishna Sukkah 3:8). Perhaps when the Israelites rediscovered Sukkot (in Ezra's day), they were not sure whether the Bible meant “take them… and use them to build a Sukkah!” or “take them… and bundle them!” Karaite Jews today follow the first interpretation (mentioned in Nehemiah), while Rabbanites follow the second (mentioned in the Mishna).

Some people may not like tracing the history of religious traditions, but for me it’s the only way to understand and appreciate them! I’m a scientist, and religions are like living organisms - they can only be understood in the context of their evolutionary history.

Curing color blindness, and color vision

2009-09-22T23:57:00.000-07:00

My two color-blind brothers will be heartened to learn that scientists recently used gene therapy to cure color blindness in adult monkeys. After being injected with a corrected gene, the monkeys' brains rewired and learned to correctly distinguish red from green. If the research translates to apes like us, there's a good chance my brothers will see green and red before the end of their lifetimes.

Turning to color blindness of a different sort, I recently had an interesting facebook conversation about the hidden hand of race in our society. I was not alone amongst my friends (or the media/politicians) in detecting a hint of racism in the GOP of late. From the "fiery latina" bullshit that surrounded the Sotomayor hearings (white males are the victims of racism!) to Joe Wilson's shameful "You lie!", there's something more than a healthy fear of socialism going on around here.

Most agreed, but one friend felt I'd mistaken partisan politics for racism, and certainly it's difficult to prove. After all, no one wants to be a racist, and even fewer want to be labeled one. In this emotionally charged arena, science is really our best hope of understanding what is really going on. As another friend pointed out, there is a burgeoning field of research on implicit racism, which distinguishes between overt racism and less conscious racism and predicts that people with implicit biases act equally in cut and dry situations, but act very biasedly in ambiguous situations.

One set of recent experiments showed that people pause just a fraction of a second longer before identifying opposite-race faces as friendly. Other research has revealed that schoolchildren have a tendency to self-segregate, suggesting that racism is to some extent a natural tendency (the tribe instinct?). There's some great stuff about this in a recent Newsweek cover story, including this hilarious excerpt about an experiment observing classroom children:

It being December, the teachers had decided to read to their classes 'Twas the Night B'fore Christmas... As the teachers began reading, the kids were excited by the book's depiction of a family waiting for Santa to come. A few children, however, quietly fidgeted. They seemed puzzled that this storybook was different: in this one, it was a black family all snug in their beds.

Then there was the famed clatter on the roof. The children leaned in to get their first view of Santa and the sleigh as Johnson turned the page—

And they saw that Santa was black.

"He's black!" gasped a white little girl.

A white boy exclaimed, "I thought he was white!"

Immediately, the children began to chatter about the stunning development. At the ripe old ages of 6 and 7, the children had no doubt that there was a Real Santa. Of that they were absolutely sure. But suddenly there was this huge question mark. Could Santa be black? And if so, what did that mean?

Now replace the word "Santa" with "President," and you begin to get the idea!

It may yet prove easier to cure color blindness in our eyes than to unlearn "color vision" in our hearts. But if there's a cure to this societal disease, it lies in every next generation. We have to talk to our children, integrate them socially, and be honest about our own implicit biases - when in doubt, letting science be our guide.

Johns Hopkins Samurai

2009-09-18T11:02:00.000-07:00

I wouldn't be much of a samurai if I didn't mention the stoppage of a would-be burglar by a Johns Hopkins student wielding a samurai sword. Many geeks (me included) own a sword as a reminder of their own undeniable bushido. After the frightening murder of Annie Le, the Johns Hopkins Samurai is a revenge of the nerds. The burglar had it coming!

But 's/he had it coming' is double-edged sword. I'm sure there were more than a few animal-rights activists who said exactly that about Annie Le, who did experiments with mice. The next attack on scientists may come from these nutjobs, who might be inspired to copycat. So if you work in a lab, it's worth taking a few extra precautions. Myself? I'm bringing my samurai sword to the lab.

When Scientists Murder

2009-09-16T19:33:00.000-07:00

The evidence in the Annie Le murder case now points clearly at animal-care technician Raymond Clark. He met with Annie the day she died. He was in and out of the building 10 times that day, including after hours. He failed a lie-detector test. And he had defense wounds all over his body.

My reaction to all this is sadness. When I first heard about the murder, I was sure it was someone from outside the building. I was reluctant to believe that a researcher could kill a fellow scientist, sure enough to bet on it. I was wrong.

Science for me has a moral component, a character-building component. That's why I call this blog Samurai Scientist. But it also teaches us to avoid prejudice and to investigate carefully based on all the facts. In retrospect, there's no shortage of assholes and anti-socials in the scientific community. The guy who murdered a call girl off Craigslist was a doctor.

I don't know if this tragedy could have been prevented. Nobody thought Raymond was capable of murder. The bottom line is that people are not what they seem. You do not have all the data. What they show you is only what they want you to see. Tread carefully.

Yale student murdered in the lab

2009-09-13T23:30:00.000-07:00

In a tragic end to a 5-day mystery, the body of missing pharmacology doctoral student Annie Le was found today in her lab building at Yale. It was supposed to be her wedding day. The case strikes a cord with me because Annie reminds me of many of the excellent students here in NorCal, where she also grew up.

According to police, the body “was found behind the wall in something called a chase, which is a space that carries utilities from one floor to another.” She was last seen on security camera entering the building Tuesday during daylight hours. Some bloody clothes found earlier in ceiling tiles did not match her attire and may belong to the murderer. It might be some creep from the New Haven ghetto, although the fact that the body was so cleverly hidden suggests some prior knowledge of the building.

Many campuses are in dangerous areas, where land is cheap. Our lab building (in a major research university) is routinely infiltrated by criminals, who wander the halls looking for laptops to swipe. After two laptops were stolen within a week, I e-mailed the campus police chief, whose force was spending 90% time waging war on tree-sitters. She ignored me. Only after I sent a campus newspaper reporter to the department and raised a ruckus among co-workers did we get any response. The building is now locked down after hours, but anyone can come in during the day and hang around. Not long ago, I ran into a suspicious person after hours, posing as a scientist. I confronted him, asked what he was doing, requested an ID, and told him to leave when he refused to produce one. On his way out I called the police and he was arrested as he fled the building. (Several of my colleagues have had similar confrontations, sometimes retrieving their laptops in exchange for letting the thieves go.)

If New Haven is anything like our campus, it is possible Annie ran into a similar situation but was not so lucky. The perpetrator may have cased the building all day and noticed the chase at some point, then returned to use it after the murder. He may have even visited the building before and stalked Annie. I hope police and administrators at universities everywhere take note of this case, as well as the largely-forgotten Virginia Tech massacre, and seriously reassess their security priorities. There are more dangerous things out there in this world than tree-sitters.

Towers of Miscommunication

2009-09-11T00:00:00.000-07:00

ד וַיֹּאמְרוּ הָבָה נִבְנֶה-לָּנוּ עִיר, וּמִגְדָּל וְרֹאשׁוֹ בַשָּׁמַיִם, וְנַעֲשֶׂה-לָּנוּ, שֵׁם: פֶּן-נָפוּץ, עַל-פְּנֵי כָל-הָאָרֶץ.	4 And they said: 'Come, let us build us a city, and a tower, with its top in heaven, and let us make us a name; lest we be scattered abroad upon the face of the whole earth.'
ו וַיֹּאמֶר יְהוָה, הֵן עַם אֶחָד וְשָׂפָה אַחַת לְכֻלָּם, וְזֶה, הַחִלָּם לַעֲשׂוֹת; וְעַתָּה לֹא-יִבָּצֵר מֵהֶם, כֹּל אֲשֶׁר יָזְמוּ לַעֲשׂוֹת.	6 ... And the LORD said: 'Behold, they are one people, and they have all one language; and this is what they begin to do; and now nothing will be withholden from them, which they purpose to do.
ז הָבָה, נֵרְדָה, וְנָבְלָה שָׁם, שְׂפָתָם--אֲשֶׁר לֹא יִשְׁמְעוּ, אִישׁ שְׂפַת רֵעֵהוּ.	7 Come, let us go down, and there confound their language, that they may not understand one another's speech.'
ח וַיָּפֶץ יְהוָה אֹתָם מִשָּׁם, עַל-פְּנֵי כָל-הָאָרֶץ; וַיַּחְדְּלוּ, לִבְנֹת הָעִיר.	8 So the LORD scattered them abroad from thence upon the face of all the earth; and they left off to build the city.

Mankind commits no sin here. Rather, it is God who feels threatened by a unified mankind, for whom the sky is literally the limit. To curb humanity's potential, God purposely puts a stumbling block in its way: language.

Today we face global challenges: ecological and economic disasters, pollution, poverty, hunger, and disease. United, it is within our power to solve these problems. And yet we spend our time quibbling over matters of 'language', allowing cultural, racial, and religious differences to divide us, even to the point of war.

The same irony applies to our country, America. As Thomas Friedman puts it, we have a one-party democracy - because the second party refuses to cooperate! We are the richest, most powerful country in history, yet we can't even get health care reform through Congress. China, on the other hand, has a government which, although corrupt, is unified. And her people are unified. While we're wasting money on wars nobody cares about, they're quietly cornering the green energy market.

The first step to ending our 2,500 year curse is to realize that we are all brothers, all in the same boat, and that we are stronger together than we could possibly be apart. After that, the sky's the limit.

They Might Be Scientists

2009-09-09T17:01:00.000-07:00

Kids' music is where its at these days for quirky, creative rockers They Might Be Giants. Enjoy these vids from their new album, "Here Comes Science."

Is Van Jones a 9/11 "truther"?

2009-09-08T10:02:00.001-07:00

On the recent resignation of politician-activist Van Jones, by Rabbi Michael Lerner of Tikkun Magazine (you can read the whole article here):

Right-wingers pounced on [Van Jones] for a speech in which he allegedly called Right-wingers assholes, though he used the same word to describe himself and the Left. But what gave them a supposedly clinching argument was that he signed a statement calling for an objective investigation of 9/11. Look below to see what it really said—not what the media claimed.

... As to how Jones could have signed the statement below, let me make clear that neither he nor I, who also signed the statement, signed something accusing Bush of being directly involved in 9/11. I did authorize my name to be used to call for an investigation of the claims of those who deny the official story of 9/11.

I am now and was then an agnostic about what actually happened to make 9/11 possible, but do agree with those who say that there are enough inconsistencies and problems with the official story to warrant an impartial investigation by people not connected to the government of the US and not bound by political considerations. I think that such an investigation would be a great advantage to everyone.

I have often found myself surrounded by people obsessed with 9/11 and acting in ways that I would call "nut cases" because they are so sure that they know not only what I agree with--namely that the inconsistencies deserve further investigation-- but also what I disagree with, namely that there is a prima facie reason to believe that President Bush had concrete prior knowledge of an attack on the US and for political reasons allowed it to happen. Frankly, I don't believe that one bit, but that is one of the reasons why I'd like to see an impartial investigation by people who have no political stake in the outcome of that investigation,and with the power to subpoena all relevant documents. Such an investigation could once and for all put these paranoid types to rest or at least silence them. So that is why I signed the call.

What the Right did, with the help of the 9/11 "truthers," was to distort the intention of at least some of us who were asked to sign the statement. The "truthers" published that statement with their own speculations of the role of Bush, and the way that it appears on their website makes it possible for someone to imagine that the signatories to the statement were all agreeing to their framing--and that is simply not true. Conversely, the Right used that deceptive form of publicity by the "truthers" to affirm something that Van Jones and others made clear we never intended to sign, namely the claim that Bush was knowingly involved. ( One reason I don't believe Bush was part of 9/11: it was too well executed for that bungler to have been involved. Even Cheney seemed incapable of pulling off a serious military move, much less something that would have required the coordination and secrecy to make 9/11 happen, and then keep secret the involvement of others for the next eight years.. Though it worked very much in favor of their militarist policies, they were far too incompetent to have made it happen. )

I was asked to sign a letter which I was told had four demands:

As Americans of conscience, we ask for four things:

An immediate investigation by New York Attorney General Eliot Spitzer

Immediate investigation in Congressional Hearings.

Media attention to scrutinize and investigate the evidence.

The formation of a truly independent citizens-based inquiry.

I did not authorize my name to be used for all the other stuff that I now see was included surrounding the letter, namely the sponsors of that 911truth.org, and would not have had I been aware that all that stuff was presented in ways that suggested that I agreed with it, and though I do recognize a few of the people I'd consider "nut cases" among the list of signatories, my guess is that most of those who signed were, like me, unaware of the context in which our names would appear.

Freudian Strip?

2009-09-06T10:06:00.001-07:00

Quote from today's WSJ article on legal prostitution of Asian women in Rhode Island (italics mine):

Medical student Philip Markoff was indicted... on charges of killing a woman at an upscale Boston hotel who had advertised on the "exotic services" section of Craigslist.

The section of Craiglist was actually called "erotic services."

Tim Gunn is Iron Man

2009-08-19T23:43:00.001-07:00

Maybe there's hope for us yet.

Really Beautiful People

2009-08-16T09:12:00.000-07:00

The cast and set of Mad Men (3rd season starts tonight on AMC) are so good looking, I always come away feeling like I've got to install ivory handles on all my sinks. A short (spoiler-free) intro to the show's main characters so you can jump right in:

Betty Draper (left) - Don's sweet, elegant, gorgeous 1950's housewife. She lives only to serve.

Roger Sterling (below left) - good-natured heir to the agency, knows how to laugh and enjoy life.

Joan Holloway (front left) - sultry, stylish alpha secretary. When this redhead smiles, she gives Betty a run for her money.

Don Draper (center) - Mad Men's Ayn Rand-ian protagonist. The perfect man, he simply lives with no strings attached.

Peggy Olson (front right) - the agency's ambitious, creepy new girl. She's got more balls than the boys.

Pete Campbell (far right) - Mad Men's villain. Spoiled brat, alternatively admiring and jealous of Don.

Tune in to see watch these beautiful people every Sunday at 10PM/9C. Your eyes (and sinks) will thank you for it!

A shortcut to curing human disease

2009-08-11T23:00:00.000-07:00

Last time we discussed the crazy high costs of sponsoring clinical trials. What you may not realize, however, is that there's a shortcut to making medical advances - the medical "innovation".

"Medical innovations" is what surgeons call trying out new techniques on patients. It's important to keep in mind here the difference between medicine and research. As a recent Science article explains:

... What are the hallmarks of aninnovative stem cell–based medical intervention? To answerthis question, we have to clarify the central difference betweenresearch, as carried out in a clinical trial process, and medicalinnovation. As explained in the seminal U.S. research ethicsdocument, the Belmont Report, research aims at scientificallygeneralizable results (not patient care), whereas the goal ofmedical innovation is the benefit of the individual patient. Because of these disparate aims, the regulatoryrequirements for clinical research do not serve as a propersurrogate for the ethical standards appropriate for attemptsat medically innovative therapies. In short, the ethicsof medical innovation is the ethics of patient care, not research.

There is potential here for a cheapie shortcut towards curing human disease. Basic research funding is cheap and gives us detailed, scientific information. Medical innovations are cheap and let us test potential cures. If we can establish lines of communication between the two (plus reasonable ethical guidelines for their application), perhaps we can circumvent the need for prohibitively expensive clinical trials - and discover some new cures in the process.

Health Care or Don't Care?

2009-08-09T14:15:00.000-07:00

A friend of mine at lab - socially liberal, fiscally conservative - has been trying to decide his views on the public health care option. He wrote this and forwarded it to all his friends. -SS

This is the link to an extremely interesting, and disturbing interview by Bill Moyers of Wendell Potter, a former CEO of Cigna, one of the largest insurance companies in the country. I highly recommend watching it to become much more informed about the issue, whether you are a democrat or republican.

http://www.pbs.org/moyers/journal/07312009/watch.html

(SS: here's a snippet...)

I personally was a bit on the fence for the public option. For those of you who don't know me, I am socially liberal, but fiscally conservative. Government waste and bureaucracy are huge problems in our country, and we can't just create programs simply because they would be nice to have. On the other hand, health insurance companies have an insane amount of bureaucracy, and the system they have is designed to make people give up and just accept whatever they are told.

This interview is not some rhetoric from a democrat or republican congressman spewing party dogma. This is a former chief executive from the insurance industry, who knows the ins and outs of the business. It is very informative. If you don't have the time to watch the 30 minute interview, let me highlight a few points.

1. The insurance companies are terrified of a public option above all other things. It will remove their oligopoly.

2. The insurance companies are proposing to eliminate pre-existing conditions denials of coverage because they don't like them. They are the ones who created the pre-existing condition denials. No one is forcing them to do that. Why haven't they eliminated them before? According to Wendell Potter, they won't. Once the reform talk is over, they'll continue their current practice.

3. The companies want status quo. They are making lots of money currently and will do whatever it take to kill any legislation.

4. He outlines the methods in which the companies eliminate insurance for those that they aren't making a profit off of.

5. In the 1980's, 95% of premiums went to pay for care. Now that % is down in the eighty percentiles. The rest is either insurance bureaucracy or profit.

6. Wall Street gives insurance companies better rankings the less they spend on their members.

7. One of the media statements the insurance lobby has put forth is that "you don't want a government bureaucrat coming between you and your doctor." Well, right now you have a Wall Street bureaucrat doing just that.

8. The insurance companies want everyone to have insurance. Not out of the goodness of their hearts, but because it means more premiums for them.

There are many other points that come across. If you can spare the time, I implore you to watch this.

Why isn't my disease cured yet?And then there's the cost.

2009-08-05T22:47:00.000-07:00

the long therapy "pipeline" starts with broad basic research

I want to get back to this question of curing diseases. In a way, Palin/Chavez/Begley are right: the academic community (like most sectors of our society) could do more relevant work. It's not that fruit flies and worms are useless - after all, breakthroughs like RNA interference, which cures cancer in animal models, emerged from such model systems. But research without grounding can turn into an intellectual "random walk," mental masturbation that rewards scientists for playing it safe. For biology to be relevant, we must avoid such distractions and focus on the big questions, using systems great and small.

Curing disease is a noble goal, but the fiscal and legal barriers are formidable. People are not lab rats, and thus experimental medicine requires an M.D. and carries serious legal/professional/ethical considerations. Remember Jesse Gelsinger's death, and the lawsuit that followed? That killed the field of gene therapy. And then there's the cost. Funding a biotech through a clinical trial costs ~500 million dollars - enough money to fund 1,000 academic research labs. (The FDA requires the doctors to take extremely detailed notes on each patient's progress, which takes up hundreds of billing-hours.) Most of these trials fail, and even successful drugs are often recalled when side effects are identified.

As a country, we are smart enough and rich enough to overcome these barriers if we want to. Health-related research funding is less than 5% of what we spend on the military, so each F-22 we cut is another clinical trial we can sponsor. But those trials shouldn't come at the cost of basic research that helps us understand how biology works. The problem is not the 1% of people doing basic research - it's the 99% of people that just don't care. As science journalist Henry Fountain recently put it, Our mass culture is just not that interested in hearing about it. But if we want better therapies, we need to encourage biologists to make those big discoveries, chase those big unknowns.

UPDATE 8/6: Jim Watson just weighed in on this issue from the perspective of the war on cancer. For once, he doesn't sound crazy.

Next: Cutting the cost of new cures.

How to avoid neck strain

2009-08-01T23:32:00.000-07:00

I wrote my entire thesis on this laptop without neck strain!

You'll recall that earlier this year I was getting a lot of stiff necks, and these started when I began writing a lot of papers on my laptop. So when it came time to write my thesis, I modified my desktop setup. I raised the height of the laptop (in the pic above, I just used my backpack) and plugged in a separate keyboard/mouse. This provided an extra degree of freedom for my neck and shoulders, and allowed me to spend several weeks pecking away without getting a stiff neck.

I bring it up because it's hard enough to write a thesis without a stiff neck!

... a giant keg for mankind?

2009-07-30T23:35:00.000-07:00

Not long ago, I blogged about Obama's commitment to world peace. A lofty goal, but not one that most of us can impact directly. But before long, Obama himself became embroiled in a little war of words about a certain white police officer arresting a certain black professor in his kitchen - a conflict decidedly more down-to-Earth.

Obama's solution? "Let me buy you a beer." And in less than a week, they were all together, Obama, Crowley, Gates, and even Joe Biden, hanging out on the white house lawn with brewskies.

Some may dismiss this as a publicity stunt, but I think Obama is making a point about how to resolve our differences. It's human nature to be sucked into interpersonal drama, especially when someone offends our brain's delicate sense of 'identity'. But go out for beers, and something else kicks in: suddenly, you're buddies. Something deep within our psyches identifies friends emotionally, through shared social interactions, and such interactions are a shortcut to peace.

In other words, a beer's a hell of a lot cheaper than a lawsuit - and a lot more fun.

Did Michael Jackson's doctor KILL him?

2009-07-30T00:00:00.000-07:00

What's clear is that Mikey's personal physician gave him a heavy anesthetic the night before he died. What isn't clear is whether he ever woke up in the morning. The drug in question (propofol) is quite dangerous and is usually only administered in hospitals, because it can cause breathing problems.

Granted, Mikey had issues. But he was not overweight or diabetic, and appeared in decent shape compared to other big stars. His sudden heart attack at 50 was unexpected, and now we know why. He might have lived another 20 years at least - had this douchebag with an MD not poisoned him!

(And don't even get me started on the cosmetic surgery that made him look like an alien. Some doctor did that to him, too.)

The physician's rule is "First, do no harm," and I wish every vocation had such noble priorities. But I find it strange to hear physician-scientists on the web constantly criticizing alternative medicine but never thinking to question the dangers of their own profession. Jackson's death is a reminder that medical technology is a double-edged sword. Physician, heal thyself!

How Cells Break Up

2009-07-28T22:19:00.000-07:00

Here's a 10-minute time elapse movie I made of a growing frog embryo. You can't see the edges of the cells, only their DNA. Most cells have round nuclei, but some are dividing. Can you see the dividing cells? Does anything about the division process surprise you?

Busby Berkeley Dreams

2009-07-26T23:46:00.000-07:00

A hauntingly beautiful song by Magnetic Fields; the elegant, black-and-white vid captures the simple essence of the melody.

What's in our wallet?

2009-07-24T10:48:00.000-07:00

This is the budget President Bush requested from Congress for 2009 (from Wikipedia; the legend reads clockwise). I unable to find an accurate pie chart of actual 2009 Congressional appropriations, since these tend to 'omit' the war on terror.

Since America runs a deficit, the money for this will come from Americans who are just entering the workforce. It is obvious to me that our generation cannot afford to pay for all this and survive. My question for you is, what do we really need in this budget? What would you cut?

Is cancer incurable?

2009-07-23T08:04:00.000-07:00

All of the livers above are from the same strain of mouse, which develops liver cancer. The livers on the right are from mice injected with virus that expresses a special microRNA that is usually lost in liver cancers. The livers on the left are from mice that were injected with a control virus. The animals were injected with the virus at the time when their livers had already developed small tumors, and then sacrificed for autopsy 8 weeks later. The same issue of Cell features another article about a microRNA that prevents breast cancer metastasis.

Despite their power, microRNAs are pretty new, and were discovered only through basic research:

The first microRNA was discovered in 1993, in worms. It took seven years for the second one to be found, also in worms, but then the floodgates burst.

Funny Science

2009-07-19T16:33:00.000-07:00

Researchers Quietly Chuckling at Placebo Group

Studies Show Alternative Medicine Ineffective (American Voices)

Nice lead-in to our discussion about clinical trials!

Why isn't my disease cured yet? The problem.

2009-07-15T23:18:00.001-07:00

Sharon Begley - Newsweek's science editor - recently wrote an op-ed which blames academic science for "slowing" the search for cures. This comes on the heels of her cover story last year which says we've lost the war on cancer by funding a bunch of ivory-tower academics who "never met a signaling pathway they didn't like."

Begley's not alone. Last year, Sarah Palin made headlines by complaining about a grant for biological research on fruit flies. (Some folks later pointed out that fruit flies had actually taught us a lot about birth defects, one of Palin's champion causes.) On the opposite side of the political spectrum, left-wing strongman Hugo Chavez of Venezuela recently blasted academic scientists for working on 'obscure projects' and told them to start doing something useful with their lives.

When Palin and Chavez (and Begley) say the same thing, it's time to start listening. Is there something to all this? Is academic research too ivory tower? Is that why there are so many diseases that are not being cured - because we are too busy curing diseases in worms? I'll post my thoughts on this important question in follow-up posts. What do you think?

We are all radiologists

2009-07-14T22:19:00.000-07:00

Convo with labmates J & B, one of whom is headed to med school:

SS: So J, what kind of doctor are you gonna be?

J: I don't know yet. Maybe a pediatrician.

SS: Are there any specialties that let you enjoy life? Y'know, go golfing every once in a while?

B: Radiologists. Those guys have the life.

J: Yeah, but radiologists can be outsourced.

SS: Surgeons can be outsourced, too. Pretty soon they'll have robots doing that job, and ours.

B: True. We are all radiologists.

Blow it out your hole, Roberts!

2009-07-13T22:28:00.000-07:00

Kudos to Charles Siebert for writing a wonderful article about whales for the New York Times rag. Siebert has previously covered other highly social and self-aware animals, such as elephants and chimpanzees, and he was interviewed yesterday on Fresh Air. There's a wonderful moment when Siebert starts talking about how, through research, we are beginning to appreciate the aliens right here on Earth, whose cultures are no less intricate than our own.

Boo-hiss to John Roberts and the United States Supreme Court for supporting Navy war games which terrify and kill endangered whales. Apparently Roberts thinks it's uber-important that we give our subs a lot of target practice... unfortunately, all they're blasting out of the water is a bunch of friendly whales.

Black Cab

2009-07-13T10:37:00.000-07:00

I always play this funny Jens Lekman song when experiments don't work. It helps me laugh at the failure and move on to something new.

Perfecting Pinchas (answers)

2009-07-10T14:50:00.000-07:00

Ruth Cuddleth with Boaz, from Avi Katz's Alien Maidens in the Bible series

Last time, I posed two questions: What was Zimri's sin, and on what legal grounds did Pinchas (Phineas) assassinate him? In the comments, my brother took up the challenge:

from the pesukim themselves it seems that the sin was worshiping Baal Peor, which had something to do with the girls of Midyan; seemingly being that they seduced the Israelites to worship their G-d. (Which is not at all far from the Midrashic interpretation of the sin, beside the whole Kanaim Pogine Bo part.)

Bravo! I came to the same conclusion. The Moabites and Midianites (led by Balak and Bal'aam) conspired to send girls over to Israel to trick them into worshipping idolatry (v. 18 here, more explicit in 31:16). Contrary to the midrash, the big sin of P'or - what kindled God's wrath - was idolatry, not fornication. Zimri's sin was either worshiping idols, or encouraging idolatry publicly.

According to the translation you provided the line 'vehoka osam' means to hang the leaders, which would set a legal precedence for Pinchas to kill Zimri.

Excellent - I think that's exactly right. At the start of this mess, God instructed Moses to "impale the leaders of the tribe opposite the sun (v. 4)," i.e. to make a public example out of them. Note that Moses actually disobeys this order and instead instructs the judges to "kill those involved in the sin." No wonder the plague didn't stop! Indeed, it is only when Phineas actually stabs an elder to death in public - as God had originally demanded - that the plague relents.

The rest, as they say, is commentary... go and learn! Shabbat Shalom.

Perfecting Pinchas

2009-07-09T01:02:00.000-07:00

Phineas Slays the Celebrants, from Avi Katz's Alien Maidens in the Bible series

My brother recently blogged about the Biblical tale of Pinchas (Phineas) and Zimri (Numbers 25). In school, I was taught a midrashic interpretation of this story: Zimri sinned by engaging in public sex with a gentile woman, and Pinchas had a secret tradition that such behavior was grounds for assassination. But this is only a midrash - let's take a look at what the Torah actually says. Based solely on this passage, what do you think Zimri's sin was? (Hint: what was the role of Midianite women?) On what legal grounds does Pinchas assassinate an Israelite leader in cold blood? I'll post answers next time.

א וַיֵּשֶׁב יִשְׂרָאֵל, בַּשִּׁטִּים; וַיָּחֶל הָעָם, לִזְנוֹת אֶל-בְּנוֹת מוֹאָב. ב וַתִּקְרֶאןָ לָעָם, לְזִבְחֵי אֱלֹהֵיהֶן; וַיֹּאכַל הָעָם, וַיִּשְׁתַּחֲווּ לֵאלֹהֵיהֶן. ג וַיִּצָּמֶד יִשְׂרָאֵל, לְבַעַל פְּעוֹר; וַיִּחַר-אַף יְהוָה, בְּיִשְׂרָאֵל. ד וַיֹּאמֶר יְהוָה אֶל-מֹשֶׁה, קַח אֶת-כָּל-רָאשֵׁי הָעָם, וְהוֹקַע אוֹתָם לַיהוָה, נֶגֶד הַשָּׁמֶשׁ; וְיָשֹׁב חֲרוֹן אַף-יְהוָה, מִיִּשְׂרָאֵל. ה וַיֹּאמֶר מֹשֶׁה, אֶל-שֹׁפְטֵי יִשְׂרָאֵל: הִרְגוּ אִישׁ אֲנָשָׁיו, הַנִּצְמָדִים לְבַעַל פְּעוֹר. ו וְהִנֵּה אִישׁ מִבְּנֵי יִשְׂרָאֵל בָּא, וַיַּקְרֵב אֶל-אֶחָיו אֶת-הַמִּדְיָנִית, לְעֵינֵי מֹשֶׁה, וּלְעֵינֵי כָּל-עֲדַת בְּנֵי-יִשְׂרָאֵל; וְהֵמָּה בֹכִים, פֶּתַח אֹהֶל מוֹעֵד. ז וַיַּרְא, פִּינְחָס בֶּן-אֶלְעָזָר, בֶּן-אַהֲרֹן, הַכֹּהֵן; וַיָּקָם מִתּוֹךְ הָעֵדָה, וַיִּקַּח רֹמַח בְּיָדוֹ. ח וַיָּבֹא אַחַר אִישׁ-יִשְׂרָאֵל אֶל-הַקֻּבָּה, וַיִּדְקֹר אֶת-שְׁנֵיהֶם--אֵת אִישׁ יִשְׂרָאֵל, וְאֶת-הָאִשָּׁה אֶל-קֳבָתָהּ; וַתֵּעָצַר, הַמַּגֵּפָה, מֵעַל, בְּנֵי יִשְׂרָאֵל. ט וַיִּהְיוּ, הַמֵּתִים בַּמַּגֵּפָה--אַרְבָּעָה וְעֶשְׂרִים, אָלֶף

יד ...וְשֵׁם אִישׁ יִשְׂרָאֵל הַמֻּכֶּה, אֲשֶׁר הֻכָּה אֶת-הַמִּדְיָנִית--זִמְרִי, בֶּן-סָלוּא: נְשִׂיא בֵית-אָב, לַשִּׁמְעֹנִי. טו וְשֵׁם הָאִשָּׁה הַמֻּכָּה הַמִּדְיָנִית, כָּזְבִּי בַת-צוּר: רֹאשׁ אֻמּוֹת בֵּית-אָב בְּמִדְיָן, הוּא. ...{פ}טז וַיְדַבֵּר יְהוָה, אֶל-מֹשֶׁה לֵּאמֹר. יז צָרוֹר, אֶת-הַמִּדְיָנִים; וְהִכִּיתֶם, אוֹתָם. יח כִּי צֹרְרִים הֵם לָכֶם, בְּנִכְלֵיהֶם אֲשֶׁר-נִכְּלוּ לָכֶם עַל-דְּבַר-פְּעוֹר; וְעַל-דְּבַר כָּזְבִּי בַת-נְשִׂיא מִדְיָן, אֲחֹתָם, הַמֻּכָּה בְיוֹם-הַמַּגֵּפָה, עַל-דְּבַר-פְּעוֹר.

1 And Israel abode in Shittim, and the people began to commit harlotry with the daughters of Moab. 2 And they called the people unto the sacrifices of their gods; and the people did eat, and bowed down to their gods. 3 And Israel joined himself unto the Baal of Peor; and the anger of the LORD was kindled against Israel. 4 And the LORD said unto Moses: 'Take all the chiefs of the people, and hang them up unto the LORD in face of the sun, that the fierce anger of the LORD may turn away from Israel.' 5 And Moses said unto the judges of Israel: 'Slay ye every one his men that have joined themselves unto the Baal of Peor.' 6 And, behold, one of the children of Israel came and brought unto his brethren a Midianitish woman in the sight of Moses, and in the sight of all the congregation of the children of Israel, while they were weeping at the door of the tent of meeting. 7 And when Phinehas, the son of Eleazar, the son of Aaron the priest, saw it, he rose up from the midst of the congregation, and took a spear in his hand. 8 And he went after the man of Israel into the chamber, and thrust both of them through, the man of Israel, and the woman through her belly. So the plague was stayed from the children of Israel. 9 And those that died by the plague were twenty and four thousand. {P}

... 14 Now the name of the man of Israel that was slain, who was slain with the Midianitish woman, was Zimri, the son of Salu, a prince of a fathers' house among the Simeonites. 15 And the name of the Midianitish woman that was slain was Cozbi, the daughter of Zur; he was head of the people of a fathers' house in Midian. {P} ... 16 And the LORD spoke unto Moses, saying: 17 'Harass the Midianites, and smite them; 18 for they harass you, by their wiles wherewith they have beguiled you in the matter of Peor, and in the matter of Cozbi, the daughter of the prince of Midian, their sister, who was slain on the day of the plague in the matter of Peor.'

Cleaning Lady

2009-07-07T23:23:00.000-07:00

She called me her professor,

though I was only seven then –
cleaning, washing, making beds,
she spoke in broken English.

I was only seven then,
I helped her learn to read;
she taught us games in broken speech,
we were her only children.

I tried to help her read, but still
she couldn’t understand. And soon
we weren’t children, didn’t need
her silly Polish games.

We mocked her, couldn’t understand
her broken English, crooked teeth;
“The stupid Pollack’s fault again,”
blaming her for everything:

the missing pen or broken lamp,
those teenage years were full of hate.
We blamed her for our own mistakes –
I led my siblings on.

Those teenage years were full of hate,
and where was she to run?
One night I led in the attack,
so cruel the words I said. . .

but where was she to run? Ten years
of cleaning, washing, making beds –
“I used,” she said with angry tears,
“to call you my professor.”

Hope for wallflowers everywhere

2009-07-06T00:37:00.000-07:00

OK, I'll admit it, I listen to Jordin Sparks. I know she's no Michael Jackson, and her simplistic lyrics are occasionally cringeworthy, but she's a guilty pleasure, OK? OK? Why do I always have to defend myself around you! Sheesh!

"Shy boy" is about every nerd's dream of being picked up by a cool girl. It has been lovingly set to video by someone who is apparently a super geek.

Moonwalkin'

2009-06-27T23:27:00.000-07:00

In college, my friends and I entertained ourselves by watching old Michael Jackson clips. We marveled together with the audience to his first live moonwalk, 25 years ago:

The man was an unworldly dancer, a true artist. "Smooth Criminal" is my all-time favorite music video, a witch's brew of speakeasy noir, Jackie-Chan-esque choreography, and mind-bending zombie funk:

When I go to the club - which isn't very often, these days - I try to channel a little Michael Jackson. His jerky, frenetic movements fit my dance style, which started with tap dance lessons many years ago.

Goodbye, Michael. Rest in peace. Thanks for pushing the envelope. Thanks for taking us to the moon. You were right, enjoy yourself, it's later than you think. That's something we can all learn from.

Turkish Delight

2009-06-22T23:54:00.000-07:00

My friend E recently invited me over for dinner with her parents, who were in town from Istanbul. I grabbed a bottle of Mendocino Pinot Noir Grape Juice ($12.95 at the neighborhood wine store), plucked a huge lemon from the tree in front of my house, and headed over on an empty stomach. E is a great cook, and let me tell you, the food was delicious. The first course was a lentil soup, amazing taste, I'd never had anything like it. While we were sipping, E let slip to her family that I was Jewish. E's father -- a short, mustached fellow with serious brown eyes -- got very excited about this.

E's dad informed me that there were many Jews in Istanbul. Apparently, the late, great Ottoman Empire had taken in the Jews when they were chased out of Spain by the inquisitors. "Yes, there are many, how do you say, hahams in Turkey," E chimed in. E's father, himself a civil engineer, had recently read a biography of Einstein ("He was religious!") and was greatly impressed. He taught me that inshallah is the Arabic equivalent of im yirtzeh HaShem, gave me a blessing that I should have good luck in my career, and offered to host me and show me around if I ever visited Istanbul. He was very friendly in his somber way and I didn't detect a trace of anti-Semitism in the man. (With his three daughters and his sister at the table, I think he was just happy to have another guy around.)

We retired to the living room, where we sat together on the couch and broke open the grape juice. "Nice color," E's dad complimented, holding his shot glass up to the light (the Pinot Noir grape gives a deep red color, not the dark purple of the concord grapes). We drank the sweet, cool juice with a twist of the lemon I had brought, a wild California lemon with a large rind. "The lemon tree in my garden tastes the same," E's father reminisced. Then E served up flan with caramel. It held together perfectly and had a clean, just-sweet-enough finish. It was one of the best desserts I have had in my entire life. I reminded her husband, a friendly PhD who makes microchips for a cell phone company, that he's a lucky man.

Only once did the Israel/Palestine issue come up (or as E's father malaproposed, the "Isra-el/Phili-stines"). He was opining about how our two cultures had so much in common. "You and I are cousins!" he exclaimed, squeezing my shoulder. "So why are our peoples at war?"

I had a flash. "Sometimes we fight most with members of our own family."

E's father nodded and smiled, his dark eyes flashing. "I understand what you said. I understand."

The Dirtiest Word in America

2009-06-21T00:44:00.000-07:00

A guest post from an erudite and intelligent friend. -SS

I’m a fundamentalist. There I said it. Phew…What a relief coming out of the closet. Perhaps the last taboo in America, I finally have the courage to admit it. Don’t look at me like I just said a dirty word. Carlin’s seven words may now lack shock value, but this word elicits fear, scorn, and even hate. Why do Americans consider me an abomination?

Fundamentalism threatens Americans not because of any particular ideology but due to the tendency of fundamentalists to want to impose their beliefs at all costs on everyone else. In fact, Americans can care less what I think about anything as long as I don’t expect anything from them. The problem is that fundamentalists are so convinced of their views that they want to eliminate any dissenting opinions from the national discourse. Americans do not want anyone dictating morality to them even from amongst their own ideologues.

In our efforts to avoid fundamentalism at all costs, Americans have unfortunately swung to a dangerous opposite extreme. Complete apathy for what my neighbor believes or how he conducts himself in the privacy of his own home permeates our culture. As long as our fellow citizen does not impose his beliefs on us, our only interest in his life is voyeuristic status update watching. We simply do not care how his beliefs affect him or how his actions affect his family as long as he stays on his side of the fence. The questions I ask myself are -

Can we create a society in which people have the passion in their beliefs like a fundamentalist, yet respect other views?

On the other hand can we advocate freedom and pluralism yet educate concern for what our neighbor thinks and does, even when it does not affect us?

I’m convinced that I’m right about this but I am still anxious to hear what you think. You are entitled to your opinion but I reserve the right to be concerned that your views are bad for you even if they are not bad for America. So please don’t stare at me because you think I’m an abomination. Join me as we form a line for the care bear stare - because fundamentalists care and that is not a dirty word the last time I checked.

Ubirr

2009-06-16T23:22:00.000-07:00

In the cliffs of Ubirr, in Kakadu National Park, we found an art gallery of the ancients. There the aborigines had painted sacred images of the animals that surrounded them and kept them fed - the wallaby, the long-necked turtle, the great fish barramundi. The figures lived on ceilings of high, jutting sandstone, which protected them from the elements and had preserved them for millenia. They were crudely stylized, stick-figured, skeletal, brimming with the rawness of the surrounding wilderness.

We hiked up further to the top of the enscarpment, where I looked out over all the Arnhemland, the wetland plain which still belonged to the aborigine. The land ran a gradient from yellow to deep green as it approached a sparkling blue billabong in the distance. The wind blew gently in my face, and two green parrots flew by, breaking the silence. This was a place of peace, a spiritual place - it was easy to understand why the aborigines chose it for their visions.

I remembered suddenly a scene from Survivor:The Australian Outback, that show's most brutal second season. Throughout it all was Colby, a ruggedly good-looking Texan who pulled his team to safety and then survived their slings and arrows by winning the last five immunity challenges. On the final day, Colby painted a wooden idol symbolic of his ordeal and carried it to the top of the highest cliff he could find. He wore a look of solemn indifference as he tossed his idol over the precipice, tossing away his experience even as it became a part of him, traversing from being the person he had been to the person he had now become.

Obama, Respect, and Peace

2009-06-04T23:00:00.000-07:00

Back when I was campaigning for Obama, I called a member of the family who is a prominent rabbi and Jewish political emissary. He expressed reservations about Obama, particularly on Israel. "What I want to know," he told me, "is what Obama is actually going to do if he's elected."

"What's he going to do?" I replied, "He's going to bring world peace, that's what he's going to do!"

I think the bigness of that vision caught the rabbi off guard. He laughed, and it was a good laugh, a delighted laugh. He was silent for a moment, and finally replied, "Well, I hope you are right."

Today in Cairo, Obama made a gesture towards that world peace I was talking about. You can watch it here:

I noticed that the audience gave its biggest applause whenever Obama referenced something from Arab culture. This reinforces a suspicion I've had for a long time that what the Arab world really wants is respect and recognition. There is something to be said for encountering other cultures by visiting, learning, and absorbing - so many of our biases arise from the neighborhoods in which we live. In terms of Israel/Palestine, you'd be surprised how far a good apology might go towards regaining trust.

The weakest part of the speech to me was the part about nuclear weapons. It is the height of hypocrisy for the leader of a country with >2,000 nuclear warheads to deny the rights of another country, even an imperfect country, to have even one. Obama, the States, and Israel ought to put their money where their mouth is - either toss your own nuclear weapons into the sea, all of them, or acknowledge that fact that every nation has an equal "right to bear arms." (The only reason Obama doesn't do that is the political reality that a nuclear Iran is simply not in the limited strategic interests of the United States.)

World peace may seem like a lofty goal, but it's also the most important thing humanity can achieve. The opportunity is here today, right now. Herzl once said, Im tirzu, ain zo agada - if you will it, it is no fantasy. It's time to take that vision, and make it bigger.

Nature's Most Amazing Event

2009-06-01T19:53:00.000-07:00

High-def film makes for some freaking amazing wildlife photography. Watch as this school of herring becomes trapped between two flocks of birds - one underwater and one at the surface - setting the table for a much bigger predator.

The full program, Nature's Most Amazing Events, aired on Discovery Channel last weekend. It points out the irony that whales, the world's largest animals, depend primarily on teeny-tiny plankton and crustaceans to survive. These in turn depend on precise oceanic water conditions and temperatures.

Gearing up for Darwin and Nature's Way

2009-05-31T12:57:00.001-07:00

I'm going to Australia! On Wednesday morning, for a week and a half, with a friend. It's winter in Oz, so we'll be visiting the more tropical Northern Territory. We'll rent a car in the port city of Darwin (what could be more appropriate for a naturalist?), then drive the "Nature's Way" itinerary, which includes several days in Kakadu National Park. Kakadu is the Yosemite Valley of Australia, with gorgeous waterfalls and billabongs, and is home to abundant wallabies and crocodiles. The park is also a center of Aboriginal culture, featuring rock-art galleries that have been preserved for thousands of years.

I watch a lot of Survivor-type shows (currently hooked on Out of the Wild), so I'm excited about the prospect of camping in the Australian bush. My girlfriend and I are both adventurous types, and we've never camped together before. I set up my little tent on my deck just to make sure it had all the pieces (pictured above). I'll also bring a Coleman propane stove, a pot and pan, beans and franks, an air mattress, blankets, lantern, binoculars... am I forgetting anything?

Science tattoos!

2009-05-28T08:31:00.000-07:00

Discover's Carl Zimmer seems to have realized that his biggest impact in 2+ years of blogging is the Emporium of Science Tattoos. He's put a link to the Emporium on his homepage. The tats are interesting because they show the human side of science workers, the love and devotion they have for their trade. A labmate of mine has a science tat on each ankle, one a little frog and another a DNA double-helix. Personally, I like this anglerfish. What's your favorite science tat?

Why I'm not 'Orthoprax'

2009-05-26T10:11:00.000-07:00

[Hillel] said: What is hateful to you do not do to your fellow man; this is the entire Torah, the rest is explanation - go and learn. (BT Shabbat 31a)

I've never been so disappointed in our 'democracy.' The majority-Republican California Supreme Court just upheld Proposition 8, a discriminatory and religious Constitutional amendment banning gay marriage. It's bad enough we have a bunch of religious lawyers out there making unconstitutional laws - we need judges, too? This is a bitter disappointment, a complete failure of democracy and freedom, and it's the religious peoples' fault, especially their leaders.

It's not the first time I've run up against this issue. For years, I was "Orthoprax" - meaning I kept Orthodox Jewish halakha and kept my mouth shut about what I knew about it. A turning point came when I helped organize, for our college Hillel, a community discussion of the film Trembling Before G-d, which documents gay and lesbian Orthodox Jews. I faced bitter opposition from wet-behind-the-ears community members and ultra-Orthodox rabbis who keep their wives behind closed doors. These rabbis should have been sponsoring the event - not opposing it!

We had the event, and it was successful, but the experience raised doubts in my mind about the Orthoprax approach. Once you get beyond "absolute truth" (which I discovered was nonsense after three years of intensive study in Israel), organized religion is really a bunch of organizations. The Orthodox Union does not support gays - why should I support them? Why donate money and time to an institution that I don't believe in and don't agree with? Why participate in a conspiracy of silence just so rabbis could continue to abuse the Torah?

Some 'religious' institutions do get it right. One of these is Progressive Jewish Alliance. I danced at their huppa on the steps of San Francisco City Hall for the first state-recognized gay marriages, before Prop 8. But these organizations are a drop in the bucket, and we could accomplish the same thing without the religious angle. As support for gay marriage grows, I am sure other religious organizations will begin to catch up. But I'm not sure I want any part of it.

Here are some pics of those weddings at City Hall. I will always remember it as a sweet day.

That's one gay huppa!

Free Ben and Jerry's - yum!

May 2009 CA Supreme Court majority opinion

True Grit

2009-05-24T11:44:00.001-07:00

איזה הוא גיבור--הכובש את יצרו, שנאמר "טוב ארך אפיים, מגיבור" (משלי טז,לב
Who is strong? He who conquers his desires, as it says (Ecc. 16:32), "The patient man is better than the warrior, [and he who rules his emotions than the conquerer of a city]" (Avot 4:1)

The hullaballoo over waterboarding in the media raises an interesting question over the efficacy of torture and when it should be authorized (if ever). Waterboarding is basically a political smokescreen; you can rest assured that America tortures, although we prefer to offshore it rather than get our own hands dirty.

In this interview, interrogator Matthew Alexander explains that making friends with the captives is actually a more effective means of getting information out of them than torture. As the old aphorism goes, you catch more flies with honey:

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If we'd be better off taking these guys out to dinner, why do we torture them? Well, some of it is simply anger-letting - it's easier to knock them around than pal up to them, emotionally. Another big chunk of it is historical - torture has been so ingrained in us, we've forgotten that other (more effective) methods might exist. Unfortunately, we are in real danger and true strength is required - and that means overcoming our instincts and using our brains.

The Science of Qigong

2009-05-21T23:20:00.000-07:00

בן זומא אומר, איזה הוא חכם--הלמד מכל אדם
Ben Zoma says: Who is wise? He who learns from every man. (Avot 4:1)

Many American science bloggers are obsessed with disproving Chinese medicine, but good science is about data, not ideology. The jury is still out on Chinese medicine, as well as many conventional Western medical therapies, simply because experiments on people are prohibitively expensive and as a society we prefer to spend our money elsewhere (mostly guns). In fact, studies have vindicated certain alternative therapies, such as acupuncture for back pain, which is why they are covered by health insurance plans here in CA.

I've learned to keep an open mind about what's possible in the physical world. For this week's Fun Science Friday, I'll introduce you to John Chang, a master of the ancient Chinese art of Qigong. While I am dubious about his ability to light fires with his hands, I am intrigued by the possibility of sending electric shocks through the body. Brain and nerve cells throughout the body are inherently electric, and signal through instantaneous changes in voltage. With enough practice, it seems possible that a human being could focus these voltages to release energy or heat, like an electric eel.

Laser Protein Flashlight Blackout!

2009-05-15T00:00:00.000-07:00

The weird pyramid you see in this movie is a cluster of DNA, about 1 % of a millimeter in diameter. The DNA itself is invisible (black), but it's coated with thousands of fluorescent DNA-binding proteins that I genetically engineered. You can think of these proteins as each having a tiny little flashlight; when they all bind to the DNA, they make it shine bright white. A second or so into the film, I zap the top region of the cluster with a highly focused laser beam. The proteins are still there, but the laser permanently disables their flashlights, resulting in a blackout over the zapped region:

You'll notice that this blackout is quite short - in fact, it's more like a brownout. How are the flashlights returning? The key is to understand that these flashlight-bearing proteins are not permanently bound to DNA. They are constantly coming on and off, too fast for the eye to see. In our case, the zapped proteins with dead flashlights are quickly being replaced by fresh proteins with functional flashlights. Using this method, we can measure the on/off rate of these proteins on DNA. This graph tracks the brightness of a zapped (blue) and an unzapped (olive) region over time; it takes about 30 seconds to fully replace all the proteins in the zapped region:

Your body may look stable, but experiments like this demonstrate that there is constant motion inside every cell, much faster than the eye can see. These experiments are also really fun because you get to fire a laser at a cell - it's kind of like playing a video game, only tinier and real.

E.O. Wilson's War

2009-05-13T00:45:00.000-07:00

הלל אומר, הוי כתלמידיו של אהרון--אוהב שלום ורודף שלום,

אוהב את הברייות ומקרבן לתורה

Hillel says: Be like the students of Aaron, loving peace and chasing peace,

loving other people and bringing them closer to Torah. (Avot 1:12)

Pulitzer Prize-winning biologist E.O. Wilson is passionate about biodiversity. The multitude of plant and animal species is not only beautiful, but also holds secrets to combating human disease. In the 1990s, Wilson became concerned that industrialization of the world's most biodiverse zones, such as Madagascar, was threatening thousands of species. But his efforts to raise awareness were frustrated by the political climate, in which any environmental cause was linked with liberal politics and rejected by the right. Wilson's response? He wrote a book, The Creation, which reached out to religious groups to cooperate with scientists in order to save endangered species. In a recent interview on NPR, he described his thought process (skip to 18:50):

I said to myself, it's something obvious, you know we're not going to really get a lot of movement until the people arebehind it. Then, who are the people? This is a religious country... the Evangelicals, I grew up among them, that's what I was, when I was a kid in the South, ~42 % of Americans are Evangelicals. Why not find a way to form an alliance? And the only way to do that was to extend the hand of friendship, sincerely, to show some respect, to show that scientists don't really disrespect them, at least in terms of what we could all accomplish together. And so I wrote the book The Creation, in which I did this, and asked for their help.

... I believe this is the right way to proceed: Let's put all this stuff we've been fighting about - evolution and traditional Judeo-Christian or Abrahamic religious beliefs - can we put that aside for a moment, and fuss about it later, and meet on common ground... to talk about something that is transcendent.

Note the Obama-esque pragmatism of this approach. It's very realistic (read, scientific). To succeed as a modern-day Noah, Wilson knew he'd have to come down from the ivory tower and start speaking the peoples' language. As a result, both sides have moved a small step closer to one another - and to saving Earth's precious biodiversity.

A Very Karaite Lag B'Omer

2009-05-11T22:14:00.000-07:00

Think today is the 33rd day of the Omer? You must be a "Rabbanite," who counts the Omer from the second day of Passover. But if you're a Karaite, you take the Bible as literally as possible – so when it says you count from "the morrow of the Sabbath," you always start counting on a Sunday.*

Around the time of Christ, this difference caused a huge rift between Rabbanite and Karaite Jews. But these days, many Jews have not even heard of Shavuot. In such times, wouldn't it be wise to broaden our horizons a little and welcome the Karaites into the greater Jewish community... even if they celebrate Shavuot a little later in the week?

The thriving Karaite community in San Francisco recently celebrated a major milestone: a Karaite conversion ceremony, the first since 1465. Browsing online, I found this interview with the Karaite rabbi, Joe Pessah. To me, the most interesting stuff is what he says about interacting, and intermarrying, with Rabbanites. This could be the start of something big, the mending of a rift that has festered for far too long.

I am reminded of a mishna every Jew should know:

בית שמאי מתירין את הצרות לאחין, ובית הלל אוסרין. חלצו--בית שמאי פוסלין מן הכהונה, ובית הלל מכשירין; נתייבמו--בית שמאי מכשירין, ובית הלל פוסלין. אף על פי שאלו פוסלין ואלו מכשירין, אלו אוסרין ואלו מתירין--לא נמנעו בית שמאי מלישא נשים מבית הלל, ולא בית הלל מבית שמאי. וכל הטהרות והטומאות שהיו אלו מטהרין ואלו מטמאין, לא נמנעו עושין טהרות אלו על גב אלו

Beth Shammai permit the [rival wives] to the surviving brothers, and Beth Hillel prohibit them... Though these forbade what the others permitted, and these regarded as ineligible what the others declared eligible, Beth Shammai nevertheless did not refrain from marrying women from Beth Hillel, nor did Beth Hillel refrain from marrying women from Beth Shammai. [Similarly...] neither of them abstained from using the utensils of the others for the preparation of food that was ritually clean. (Y'vamot 1:4)

Amen.

*The intricacies of the debate are far too boring to go into here. All interested parties should start with Leviticus 23:9-21 and Joshua 5:11. The interested Rabbanite should proceed to the Babylonian Talmud (Menahot 65a-66aa); the interested Karaite to the Korner. The Modern Orthodox movement has prompted much more in-depth learning of Hebrew Bible, and this has re-opened a very interesting debate about literal (p'shat) vs. exegetical (d'rash) understanding of the Torah. Historically, a chasm has developed between Orthodox Jews and the Karaites and Samaritans. Perhaps this newfound appreciation of "p'shat" will lead back to a reunification of sorts.

Lebron's mom, the natural juice

2009-05-10T09:12:00.000-07:00

When Lebron first came into the league a few years ago, I was shocked at how BIG he was for an 18 year old. I have to admit, the first thing that came to my mind is that this kid must be juicing. But over the years, I've come to realize that King James doesn't need performance-enhancing drugs. He was born with a far more formidable competitive advantage: his mother Gloria.

Gloria is fearless, and Lebron's biggest fan. Last year in the playoffs, she almost decked Paul Pierce after he flagrantly fouled her son to stop an easy basket (luckily, Kevin Garnett was there to calm her down):

Lebron's response: Momma, sit down!

Now, she may not look like much standing next to these NBA all-stars, but Gloria's tall, buff, and aggressive - traits Lebron seems to have inherited. Looking at the kid, I suspect she fed him some pretty big breakfasts, too. It wasn't easy for Gloria to raise Lebron - his dad was a deadbeat, and at times she had to send her son to live with another family. But despite all the instability, Lebron always knew there was one person out there who always had his back. With a mother like that, who needs steroids?

Here are some of King James' most amazing plays this year - he was named league MVP a few days ago. Happy Mothers Day!

Just don't call it a "Borg Arm"

2009-05-08T00:54:00.000-07:00

TGIF! Amputees are not a fun topic, but "Luke Arms" like the one shown here promise to give them a piece of their lives back. Skip to 1:30 to watch the arm in action; it takes only a few hours of practice before an amputee can perform simple tasks.

The Commencement Speech That Never Was

2009-05-05T00:01:00.000-07:00

Well, my commencement speech was turned down in favor of a classmate's. But that doesn't mean I can't give the speech right here... on my blog!

Esteemed professors, ladies and gentlemen, and fellow classmates,

As we stand here today, it’s hard not to look back at the bright-eyed, bushy-tailed young students we were when we entered graduate school, 5, 6, or even 8 years ago. And if you’re like me, you can’t help but ask yourself: “What was I thinking?!” And yet, that is where the growth is. The fact that we can look back and see ourselves so far away is a reminder of how far we’ve come, each and every one of us.

My first year in graduate school, a professor told me, “In science, there’s a lot of delayed gratification.” At the time, I didn’t know what he was talking about. But today, I think every single one of us standing up here can appreciate the wisdom in those words. In science, a single experiment can take months, or even years. And you don’t know how it’s going to turn out! When you’re in the trenches, it’s only natural to question why you signed up for this mission in the first place.

But if you’re standing here today, it means you’ve learned to deal with that kind of uncertainty. You’ve learned to stop worrying and enjoy the experiment – discovered that it’s the process, not the destination, that counts. And once you realize that, you can’t help but feel grateful for the tremendous privilege we’ve enjoyed these last few years. We have gotten paid to do what we love. We have been able to play with molecules the way a child plays with tinkertoys, taking the pieces apart, putting them back together, or perhaps trying to build them into something new entirely. Yes, it has been very hard work. But precisely because it’s so challenging – precisely because it’s so uncertain – there’s a sense of adventure about every single experiment, and a pride we feel when we see the results.

So sing with me now:

"You can’t always get what you wa-ant.

You can’t always get what you wa-ant.

But if you try sometimes,

You just might find,

You get what you need!"

Congratulations class of 2009!

"I decided not to finish my thesis"

2009-05-02T23:40:00.000-07:00

שוב יום אחד לפני מיתתך
"Repent one day before you die." --Avot 2:13

In a recent comic strip, scientist-cum-cartoonist Jorge Cham explains in naked pink why the war on cancer won't be won anytime soon. Along the way, he wrestles with the insignificance of both art and science in the face of life-threatening disease. In the final panels of this poignant piece, he describes being approached at a booksigning by a chemo patient:

What if you were diagnosed with cancer? If you only had six months to live? How would you change your life?

And why aren't you doing that right now?

--

Me worry about swine flu? When pigs fly

2009-04-29T22:08:00.001-07:00

I'm always thrilled the one week a year when a science story grabs top headlines (always infection-related). But this swine flu scare has me flummoxed.

Here's the thing: there are definitely dangerous flu viruses out there. Every year, flu virus gets a little more resistant to antivirals like tamiflu. And we can't predict how a flu is going to behave. Remember that avian flu that wiped out millions in 1918? Well, it's still around - in freezers - someone sequenced that little bugger's genome, and guess what? It looked just like any other flu virus.

So yeah, there are some dangerous viruses out there. But this year's swine flu doesn't appear one of them. First off, most of the cases are turning out to be pretty mild. Second, unlike a lot of the flus out there, this strain is actually susceptible to common antivirals. I keep hearing on the news about how many people have died this year of swine flu. But the important number is how many people died of it last year, when no one bothered to check. For all we know, the mortalities this year are baseline.

One last thing. That 1918 Spanish flu was a bird flu. If you really want to spread a virus, use a bird. The damn things travel all over the world. Swine, on the other hand, are fat, lazy creatures. They don't have wings. So unless you're working on a hog farm, you probably have nothing to worry about. (Those folks who died lived next to a big pig farm... in Mexico City, which ain't exactly the cleanest place in the world to begin with.)

So here's what I think. Are lots of people going to die of swine flu in shitty parts of the world this year?

Yes, because those places don't have good hygiene or medicine anyways, and we don't care enough about the people living there to do anything about it.

Is swine flu the result of overcrowding and shoddy practices on animal farms?

You betcha! Just like the MRSA flesh-eating superbug.

Am I going to worry about swine flu?

... When pigs fly.

Should Jedi torture?

2009-04-27T00:00:00.000-07:00

There's probably no greater contemporary commentary on the futility of war than LucasArts' Star Wars: Clone Wars saga. What could possibly be more futile than a war between a droid army and a clone army? The whole thing is orchestrated by a Sith puppet-master with no interest in either side winning, but rather in wreaking chaos, weakening his enemies, and consolidating personal power. In envisioning the Clone Wars, Lucas has brought our generation a story more complex and relevant than the simple good-versus-evil semantic of the original trilogy.

In the trenches of the Clone Wars are the famous knights of the Jedi order. Their training has prepared them to keep a cool head, but they're only humanoid, and they've never been involved in a conflict this big or this scary. Try as they might, they can't help being sucked in by the murky business of war. In this scene, a younger Jedi makes a strong case to her mentor in favor of bullying a prisoner for information. The mentor stops her - "Terror is not a weapon the Jedi use," she says - but here, as later in the episode, the question of whose judgment is correct remains unresolved.

Pull the slider to 4:00 for some hot Jedi torture

The greatest example of how war corrupts, of course, is the star of the show - Anakin Skywalker, well on his way to becoming Darth Vader. Anakin's in over his head, and his emotions are beginning to strain even as his reputation grows (cartoon Anakin is actually a better actor than Hayden Christensen). It's impossible to imagine that this powerful Jedi's experiences in the Clone Wars played no role in his turning to the Dark Side. On the contrary - his exposure to violence, anger, frustration, and power were just what Palpatine had in mind.

It is... unfortunate... that Clone Wars has not been more popular with the American public. Perhaps it was the hackneyed dialogue of the prequels, or the complicated plot, or perhaps the message of the Clone Wars was simply not what the audience was expecting to hear (I'd have missed it myself had my brother, a Star Wars expert, not pointed it out to me after The Phantom Menace). But there are real wars out there, and universal challenges, and our generation is inheriting them. I am concerned that America is still thinking in terms of good versus evil, black and white, us versus them. We would do much better to heed the harsh lessons of the Clone Wars: that all war is costly, and we often do not recognize the real menace until we taste his lightsaber. And of course, sometimes that menace is us.

At least he's not a girly man

2009-04-26T09:09:00.000-07:00

He's been a par governor at best (remember that failed special election?), he's foreign-born, and the Republican base hates him. But that's all water under the bridge. The GOP needs a fresh face, and the movie star's their only hope. Look for Arnie to run for President in 2012.

Arnold, I've got a better idea: Flip. Become a Dem, we could use a man like you. After a short stint as a CA Representative, you could run for Prez in 2016 and *not* have to take on an incumbent Barack Hussein Obama.

Oh, and lose the ring.

--

Fun Green Science Friday: How to grow an avocado plant

2009-04-24T00:52:00.000-07:00

I'm growing an avocado tree! I learned this trick from my mom when I was a kid. Basically, next time you eat an avocado, save the pit, stick 3 toothpicks in it, and rest it on top of a cup of water as described here. Put it on the kitchen windowsill. If your avocado pit is killer like mine, pretty soon you will have crazy roots and a plant like the one shown at left. (Change the water every couple of days. If you don't see anything after a week, start over with a fresh pit! Not all 'cados are created equal.)

Here's a pic of the gnarly roots from mine. You can see how the seed is now split in two after a few weeks of growth:

And doesn't my avocado tree look cool in this engraved pot I found lying around the garden?

Bottom line, this is a fun and easy nature activity that both kids and adults can enjoy. Happy planting!

Polluted clouds, silver lining (An Earth Day meditation)

2009-04-22T13:30:00.000-07:00

Something amazing is happening.

We are all in it together. We are all in the same boat.

It doesn't matter whether you register Democrat or Republican. Whether you are capitalist or communist.

It is as the Buddha said. We are all connected.

For years they have tried to stifle the truth. And yet it has a way of shining through - in scientific journals, at international conferences.

Smoke from our factories in China is turning the snowcaps gray.

Marlins caught today are only a third of the size they were in the 50's.

The rise in ocean temperature and acidity is causing algae to flourish, and choking our coral reefs.

The ancient Hebrews knew this. They called for a Sabbatical every 7 years, to let the land rest.

"Go forth and multiply" - we have done this. "Conquer the Earth's creatures" - we have done

this.

But we forgot to tend the Garden.

The Native Americans knew this. They respected fellow creatures as equals, and used every part of the buffalo.

But we have ignored these teachings, and we have suffered for it.

The Big Three automakers are filing Chapter 11. Huge lots full of gas guzzlers, never to be sold.

Japanese cars, based on the Kyoto protocol, are selling like hotcakes all around the globe.

We are addicted to oil. If those prices rise again, it will send us spiraling into a Depression.

The good news is, the world is finally beginning to take these problems seriously.

Thanks to Al Gore and the IPCC, who won the 2007 Nobel Prize.

Good riddance to George W. Bush, who did his utmost to silence the scientific community.

It's a shame America is a follower, not a leader in this effort. Par for the course lately.

But our environment does not belong to any country, creed, or government. It is bigger than that, more real, and more important.

It doesn't even belong to our species.

It is as the Buddha said. We are all connected.

In this age of racial/religious/political diversity, humankind's greatest challenge is to realize that we are all in the same boat.

And it's an ark.

Climate change is bringing that awareness. Where philosophy has failed, reality is turning heads.

That's the silver lining on our polluted clouds this Earth Day.

Origin of the Chicago Black Hawks

2009-04-20T22:31:00.000-07:00

I've always thought that the Blackhawks was a cool team name. I never imagined the story behind it.

From Bury My Heart at Wounded Knee:

When white settlers began streaming into the Illinois country after the War of 1812, the Sauks and Foxes fled across the Mississippi. A subordinate chief, Black Hawk, refused to retreat. He created an alliance with the Winnebagos, Pattawotamies, and Kickapoos, and declared war against the new settlements. A band of Winnebagos, who accepted a white soldier chief's bribe of twenty horses and a hundred dollars, betrayed Black Hawk, and he was captured in 1832. He was taken East for imprisonment and display to the curious. After he died in 1838, the governor of the recently created Iowa Territory obtained Black Hawk's skeleton and kept it on view in his office.

Interestingly, from Wikipedia:

In 1986, while going through the team's records, someone discovered the team's original NHL contract, and found that the name "Blackhawks" was printed as a compound word as opposed to two separate words ("Black Hawks") which was the way most sources had been printing it for 60 years and as the team had always officially listed it. The name officially became "Chicago Blackhawks" from that point on.

Playing "Uncle Darwin"

2009-04-19T08:30:00.000-07:00

I usually try to pick up some toys for my nephews well in advance of my visits. I was all prepared to give them a wooden rubber-band gun and a slingshot, which I picked up on my travels for a couple of bucks. But wouldn't you know it, I went in to lab before my flight and forgot to pack the toys. What's a scientist uncle to do?

Improvise, of course.

Truth is, there are lots of nifty "toys" just lying around the lab. I remembered making 'potions' of random liquids as a child, so I grabbed a bagful of little plastic test tubes and several of these little plastic dounces (think mortar and pestle). I demo'd it for my nephews (4 and 6) and got them excited about the idea. I suggested smashing up bugs, but both children objected on ethical grounds. Instead, we picked petals from flowers and plants of different colors and "extracted" the colored juice. The older nephew, who is quite the budding young naturalist, started a little zoo of bugs in test tubes - he even caught a baby praying mantis! It was a lot of fun and confirmed my suspicions that science is a little like playtime for adults.

Failed priorities in a Tracy church community

2009-04-12T09:00:00.000-07:00

Note: since I first wrote this, new details have come to light. Rape with an instrument has been added to the charges against Melissa Huckaby, and police have revealed that Sandra died inside the church.

After a short inquiry, police in nearby Tracy have arrested mother and Sunday-school teacher Melissa Huckaby for the kidnapping and murder of 8-year old Sandra Cantu (left). If Melissa is indeed the killer - and the police sound pretty darn sure - there is an irony here. California is a state where a religious coalition of priests, rabbis, and pastors encouraged their flocks to ban gay marriage by popular vote, in the name of "protecting the family" and "protecting the kids." Everyone knows you can't trust those gays around children, right?

Well, here you have the pastor's granddaughter, herself a mother, charged with murdering a little girl. Turns out the greater threat to kids came from within the church and the "traditional family."

As the Bible says,

מְקוֹם הַמִּשְׁפָּט שָׁמָּה הָרֶשַׁע, וּמְקוֹם הַצֶּדֶק שָׁמָּה הָרָשַׁע

The place of judgment, that's where the evil is; the place of justice, that's where the evil is. (Eccl. 3:16)

The reality is that anybody can be a child abuser. Anybody can be a killer. It doesn't matter if they go to church. It doesn't matter if they're gay or straight, atheist or devout, single or married, kids or no kids. That's the great danger about child predators - you can't predict who they are. They always seem like nice, normal people.

If this is child abuse, it's not the first time. It's happened before, in Sunday school, at home (her 5-year old daughter is "rail thin and sick a lot"), wherever. 28-year old-mothers don't just suddenly murder a child out of the blue. This tragedy was a long time coming, and somebody knew about it, someone inside the church and/or the police department.

Our American society likes to flap its gums about wedge issues like gay marriage and abortion. But when it comes to really protecting our kids - our living children, not some ball of cells on a petri dish - we come up short. We trust our children to people who are untested and unqualified, because we go to the same church as them. When child predators arise in these low-security systems - and I've seen this happen more than once - the State lets them off on a plea bargain, and the clergy sweeps it under the rug to save face.

Truly, The place of judgment, that's where the evil is.

The sad truth is, politicians and clergy in this country don't really care about domestic abuse, or child abuse. It's just not a priority in American society. There's too much agreement on those issues, they're not polarizing enough. They're not interesting enough. So they distract us with backwards-thinking non-issues like gay marriage. But there's only so much time in the day. If your church is worried about two loving homosexuals, you can be sure it's overlooking something far more dangerous.

Don't even get me started about the all-important wars we send our young people out to die in. Stupidity to the infinite power.

An eight year old girl is dead.

Don't be fooled.

I'm Not One of Those Fancy College-Educated Doctors (Fun Science Friday)

2009-04-02T21:41:00.000-07:00

I totally get this guy.

"Back off, man. I'm a scientist."

2009-03-27T00:00:00.000-07:00

In TV and movies, science is often portrayed as lacking a sense of humor. A notable exception is Ghostbusters - a comedy about four scientists studying the paranormal. It features perhaps the coolest nerd of all time, Egon, as well as the unforgettable Peter Venkman - a scientist so jaded he can't even believe it when his research turns out to be real.

IMDB has assembled a list of memorable Ghostbusters quotes. Check it out, you will enjoy it. I'm going to cut and paste a few of my favorites here.

*****************************

Man at Elevator: What are you supposed to be, some kind of a cosmonaut?
Dr. Peter Venkman: No, we're exterminators. Someone saw a cockroach up on twelve.
Man at Elevator: That's gotta be some cockroach.
Dr. Peter Venkman: Bite your head off, man.

Dana Barrett: You know, you don't act like a scientist.
Dr. Peter Venkman: They're usually pretty stiff.
Dana Barrett: You're more like a game show host.

Janine Melnitz: You're very handy, I can tell. I bet you like to read a lot, too.
Dr. Egon Spengler: Print is dead.
Janine Melnitz: Oh, that's very fascinating to me. I read a lot myself. Some people think I'm too intellectual but I think it's a fabulous way to spend your spare time. I also play raquetball. Do you have any hobbies?
Dr. Egon Spengler: I collect spores, molds, and fungus.

Gozer: [after Ray orders her to re-locate] Are you a God?
[Ray looks at Peter, who nods]
Dr Ray Stantz: No.
Gozer: Then... DIE!
[Lightning flies from her fingers, driving the Ghostbusters to the edge of the roof and almost off; people below scream]
Winston Zeddemore: Ray, when someone asks you if you're a god, you say "YES"!

Dr. Peter Venkman: Ray has gone bye-bye, Egon... what've you got left?
Dr. Egon Spengler: Sorry, Venkman, I'm terrified beyond the capacity for rational thought.

Dr. Peter Venkman: Alice, I'm going to ask you a couple of standard questions, okay? Have you or any of your family been diagnosed schizophrenic? Mentally incompetent?
Librarian Alice: My uncle thought he was Saint Jerome.
Dr. Peter Venkman: I'd call that a big yes. Uh, are you habitually using drugs? Stimulants? Alcohol?
Librarian Alice: No.
Dr. Peter Venkman: No, no. Just asking. Are you, Alice, menstruating right now?
Library Administrator: What's has that got to do with it?
Dr. Peter Venkman: Back off, man. I'm a scientist.

Live Blogging "Genetics and Evolution of the Skeleton" Symposium at UC Berkeley

2009-03-26T08:53:00.000-07:00

I'm currently live blogging a symposium on the Genetics and Evolution of the Skeleton on twitter. Should be of interest to those who like stem cells, evolution, regenerative medicine.

Talks I'll probably be going to:

Craig Miller (UC Berkeley) - "Genetic analysis of development and evolution of the head skeleton"

Ophir Klein (UCSF) - "Long in the tooth: genetic regulation of stem cells in the mouse incisor"

Jackie Moustakas (UC Berkeley) - "Studies on the development of teeth in non-model organisms"

(afternoon:)

Rich Schneider (UCSF) - "Mesenchymal control of skeletogenesis during development and evolution"

Nadav Ahituv (UCSF) - "Characterization of regulatory elements leading to human limb malformation"

Ralph Marcucio (UCSF) - "Mechanisms that pattern the upper jaw"

Gabriela Loots (LLNL) - "Genetics of Van Buchem disease and role of sclerostin in limb morphogenesis"

Mike Sohaskey (UC Berkeley) - "JAWS coordinates chondrogenesis and synovial joint positioning: a disjointed tale of mouse skeletal development"

Bill Clemens (UC Berkeley) - "Evolution of the mammalian dentition: a 250 million year perspective"

Needles for needles? (Response to Orac comments)

2009-03-25T15:39:00.000-07:00

I don't know when this Orac fellow sleeps, but he is not only a research scientist and surgeon but also writes a well-researched blog on medicine/biology. Recently he wrote a post criticizing a Baltimore prison program sponsoring acupuncture as a drug addiction therapy for inmates, saying it's a waste of $40,000 since acupuncture has been discredited as an addiction therapy in most studies.

Here is what I commented:

An interesting post. I agree in some ways, disagree in others. Have you ever tried acupuncture, Orac? Some people swear by it.

I doubt acupuncture will have much of an effect on drug addiction, we agree there. But then what does? There is no cure for addiction, just like there's no magic bullet for cancer. We spend plenty more than $40,000 treating addiction with all kinds of therapies that might also not work. We also spend trillions making wars that don't make any sense. Are you as critical of those programs as you are of this one?

As a research scientist, I think it's not a terrible idea to try some "high risk" therapies - ones that might not work, but if they do there's a big payoff.

I got a lot of responses. I will reply to a few of these here so my readers can benefit from the discussion.

@Techskeptic,
oh sigh... There is a reason that randomized double-blind studies are used to determine the efficacy of therapies – personal experience is unreliable.

Although double-blind studies are perhaps our most rigorous test of therapies, they are not infallible. They provide no mechanism and often use small sample sizes. Human society is very diverse and it's difficult to control for different variables.

Personal experience is subjective, certainly, but it is still data. It's a valuable way of gaining insight into what is actually going on. I wouldn't be so quick to dismiss it. In fact, I'll bet most doctors use "personal experience" as their #1 diagnostic tool.

Please don’t tell us that your woo therapy worked because you felt better just after you were treated, unless you can explain why the improvement you experienced could not possibly be due to one of the following:

1. Placebo
2. Temporary mood improvements due to the personal nature of the treatment
3. Psychological investment of the patient in the success of the therapy...

I agree with your idea that we should try some high risk therapies. Its just that acupuncture is not one of them. Not only is it not an unknown, its been tested and tested for 30 years, and after initial confusion with placebo, its pretty damn clear that there is nothing else to support it.
First off, there was that Yale study that Orac mentioned in his post that suggested that acupuncture helps with cocaine addiction.

Second off, so what if it is placebo? We're talking about inmate drug addiction here. Even if it works by providing the inmates a little personal contact and love - shouldn't we take advantage of that? Maybe placebos work.
As for being critical of other things, like wars...total non-sequitur. Superman could come here and wipe out everyone in the state of Virginia and if Orac didn't bother to comment on that, it still wouldn't make acupuncture any more effective or useful.
The question is about our priorities in spending public funds. How can you talk about the ants if you ignore the elephant in the room? (sigh)
@Becca,
It's funny, I think a lot of Orac's previous acupuncture posts start with the mention that once upon a time, he thought there might be something to the whole 'acupuncture thing'. Not the business with energy flow and meridians, but that there might be some science behind 'being poked with needles makes one's head hurt less'.

Then he did some reading on it, looked at studies that compared acupuncture with being poked with non-needles in the wrong places, and noticed that they show the exact same result. That's a very good sign that the needles aren't doing much, and it's mostly in the heads of the people being poked (maybe not consciously in there, but in there).

Hey, a few years ago I'd have been totally dismissive of acupuncture. But after 6 years in California, well... there's something in the water out here :)

FYI, acupuncture and Chinese medical treatments are covered in your health insurance out here. They are practiced by licensed professionals. One of my housemates just passed her boards, she works side-by-side with a very successful MD.

As for the therapy being "mostly in the heads of the people being poked" -- see my reply to TechSkeptic above.

@Pareidolius,
I tried acupuncture when I was a believer in such things. I swore it up and down that it worked. It had to, it was expensive. Once I had awakened to what a gullible slave to woo I had become, I saw that acupuncture was really not any more effective than a good nap... The same was true for bodywork, reiki, and other assorted woo I used to swear by. Now I just go lie down or talk to someone I love or pet the dog or, well, you get the picture. Science works. Woo is wishful thinking.

I loved your story. This personal experience may be subjective, but it's still data.

I think some of these inmates might not have a dog to pet, or a loved one to talk to. Acupuncture may be beneficial for their health, possibly to help them relax, possibly as a placebo. I don't think it will cure their drug addiction. But who knows, maybe it couldn't hurt.

That's all the comments I feel like replying to right now. I got work to do. Science, y'know.

Live Blogging the UC Berkeley "Systems Cell Biology" Symposium

2009-03-24T15:50:00.001-07:00

I'm currently live blogging what's left of this informative symposium on "systems cell biology" on Twitter. Systems biology is an attempt to get "big picture" information on complex biological phenomena. Cell biology is the study of basic cellular processes, like eating and dividing. Scheduled speakers:

Lucas Pelkmans, UTH Zurich: Population context predicts activity in human cells

Ulrike Eggert, Harvard Medical School: A combined chemical genetic/RNAi approach: new tools to study cell division

Charlie Boone, Univ. of Toronto: Integrating high-throughput yeast genetics and high content screening

Jonathan Weissman, UCSF: Biology without basis: functional insights from high-resolution genetic interaction maps

Tune in!

Fresh Fathers: Pre-ramble

2009-03-23T00:00:00.000-07:00

During my first year in

Israel after high school

, I decided to memorize the mishna. Like a Tanna of old, I wandered the streets of Jerusalem, silently repeating the little tidbits of case law and pithy sayings. Did you know that the word mishna means “that which is repeated”? And when you repeat something long enough, a little bit of it trickles down into your soul.

The book that truly stuck with me was Pirkei Avot, or the Book of Fathers. Memorizing Avot was a transformative experience - it blew my mind. The book is abstract and philosophical in nature, quite different from the case law that characterizes most early Rabbinic writings. It opened my heart to many of the values I still cherish today.

I'd like to revisit Avot, here on Samurai Scientist and/or Twitter, over the coming weeks. Traditionally, the book is studied during the seven weeks between Passover and Shavuot, so this is a good time to start. Avot lends itself easily to blog format - the pithy sayings are short and open-ended, a springboard for discussion. I hope you'll chime in.

What stands between us is only words

2009-03-21T21:30:00.000-07:00

I'm damn proud of you people.

Maybe I don't say it enough. Definitely I don't say it enough. But it's true.

We may have different opinions, you and I. We may see life from two different points of view. But that doesn't matter. What matters is, you're an amazing person.

It's easy to get bogged down in politics, religion, ideology, etc. There's something in our crocodile mind that identifies ourselves with "truth" and perceives everything else as a threat. And yet what separates us is only words, only ideas. We have much more in common than we ever could have apart.

The way to overcome these barriers is through human communication. Face-to-face if possible, over the telephone or the internet if necessary. Seeing each other, hearing each others' voice, has a way of easing our fears. Of reminding us that we are all just human beings, each of us with an intricate life, dealing with challenges as best we can.

When we talk to each other, when we see each other, when we touch each other, I do not need to understand you, and you do not need to understand me. We only need to be in each other's presence, to accept one another, to spend time together. Then our monkey minds, always racing with thoughts and fears, is quieted. For isn't rejection our greatest fear? And if we're sitting together, then we are not being rejected.

So when I think of my family and my friends, this is what I think: I'm proud of you. You are amazing people. I learn from each of you. We may not always agree, and that's natural. That's to be expected. But let's not let it stand in the way of appreciating each other, just as we are.

Be Amazing!

2009-03-20T00:00:00.000-07:00

Thanks to the Avanator for tipping me off to this superviral video.

Back-of-the-envelope ~Can coffee give me cancer?

2009-03-18T06:00:00.000-07:00

The jury is still out on whether caffeine is bad for your health. However, caffeine has been proven to block the body's DNA damage repair pathway, which protects us from mutations. This means that a high enough dose of caffeine should theoretically be carcinogenic - a fact that cost/benefit analyses of caffeine such as this article frequently fail to mention. So is the amount of caffeine in a cup of coffee enough to block DNA repair? Let's crunch the numbers in our very first back-of-the-envelope calculation:

~1~ The molecular weight of caffeine is 194, or ~200. So a 1 M concentration of caffeine is ~200 g/L.

~2~ Caffeine starts inhibiting DNA repair in cells at ~1 mM concentration in the surrounding fluid (blood, in our case). 1 mM = 1 M/1000 = 200 g/L/1000 = 200 mg/L.

~3~ The average cup of coffee contains 100 mg caffeine. Upon ingestion, this is diluted into your ~5 L of blood. Assuming 100% retention of the compound, caffeine's final concentration in your bloodstream is 100 mg/5 L = 20 mg/L. This is about ten times less than the active concentration of caffeine calculated in step 2.

So according to this back-of-the-envelope calculation, a single cup of coffee is unlikely to generate bloodstream caffeine concentrations that would inhibit DNA repair. Ten cups of coffee, however, might certainly be dangerous, and some energy drinks contain nearly this much. In addition, it is possible that daily consumption of caffeine has a cumulative effect.

Note: I am not a medical doctor, and this is not meant to be medical advice.

It's Called EpMotion

2009-03-13T03:00:00.000-07:00

This music video combines elements from two previous Fun Science Fridays: an automated robot, and a researcher as intelligent as she is beautiful. Enjoy!

Is Obama behind the times on stem cells?

2009-03-10T03:14:00.000-07:00

He's so eloquent, I'll just let him say it.

Political opponents reacted by calling Obama "behind the times" on stem cells. After all, there are now ways of making ES cells without destroying embryos:

If you listen closely to Obama, you'll realize that he knows this, too. But he also realizes that Bush's opposition to ES cell research was a symbolic gesture - fueled by anti-abortion ideology, not science. By overturning the Bush ban, Obama is laying down his own criterion for science policy - that it should be guided by facts, and not ideology.

What are the facts? The embryos used to derive embryonic stem cells are tiny balls of about 100 cells, without sensory organs or circulatory systems. Our society is willing to discard them for the sake of IVF, just to give parents their own biological child instead of adopting. Certainly, we should be willing to discard them for the sake of research which may cure untreatable diseases. The destruction of adult farm animals, just so we can enjoy the pleasure of eating their meat, poses a far greater ethical dilemma than embryonic stem cell research.

Watch this

2009-03-10T00:30:00.000-07:00

What I'm about to say may constitute comic-book heresy, but Watchmen the movie is better than Watchmen the book. The director has managed to pick the best, most exciting parts of the graphic novel and edited out the boring stuff (Tales of the Black Freighter, anyone?). And whereas the art in the Watchmen comic always struck me as too sterile, the movie's visuals are stylish, emotional, and even set to music.

If you've never read the comic, it's set in an alternate reality where there were a couple of superhero teams: the Minutemen (1950s), and their successors the Watchmen (1970s). Both teams eventually disbanded, due to political pressure. This alternate history is depicted in the gorgeous opening montage (set to Dylan's Times They Are A-Changin'). The story focuses on the living members of the Watchmen, one of whom has recently been murdered. It takes place around 1985, but there are a lot of flashbacks, so keep that in mind while you're watching.

Rumor has it that Alan Moore, creator of Watchmen, took his name off the movie halfway through production over creative differences. I'm not sure what his problem was, seeing as the film is remarkably loyal to the comic. Most scenes are so similar that I'd swear they used the graphic novel as storyboards. The performances are excellent, especially Jackie Earle Haley (Rorschach) and Jeffrey Dean Morgan (the Comedian). Watchmen is a long book, with a lot of little stories and big ideas. Turning it into a film is no easy task. Yet they managed it without diminishing the individual characters or bungling the plot. Alan Moore set out to blow up comic book cliches and raise questions about human nature, and the movie stays true to that. Looking at the final product, I think he'd be proud.

Beats the hell out of V for Vendetta, anyways.

The science of Bible study

2009-03-07T13:08:00.000-08:00

Science is a state of mind which has always been natural to me. A good example of this is religious studies. I went to religious elementary and high schools, and even spent three years in Israel studying in a Rabbinical college. These schools took a fundamentalist, rather than liberal, approach to classical Jewish texts. As I gathered expertise in these texts, however, I discovered the critical approach on my own. It flowed naturally to me from the source texts themselves, being the simplest and most rational explanation of their historical development.

I say "the simplest and most rational" because there are other ways to interpret religious texts. Text study is not an exact science. If you want to, you can explain a text in a hundred different ways. The way you understand any document depends on your own expertise and your own bias. Even if you think your explanation is the correct one, it is difficult to prove it.

I mention "expertise" because it is only through labored study of primary source-texts that one can hope to find the truth. There is a science to text study, and it emerges the more you learn. If your mind is pattern-oriented, as mine is, it will figure things out on its own. Each type of text is its own world - you can be a total expert in Shulchan Arukh (a 16th century Jewish legal code), but that doesn't make you knowledgeable about the Hebrew Bible in any way.

If you are interested in understanding religious texts properly, keep an open mind. Discard any commentaries, beyond what is required to translate. Start with the Bible itself - it is the foundation on which everything else is built, and also remarkably interesting in its own right. I used to memorize Bible verses - I memorized about half of the Pentateuch as a student - and this is a powerful way of developing expertise. If you don't have time to memorize, simply read ten verses a day until you finish the book of Genesis. Don't get hung up on understanding every verse, as some verses will take you years to understand. Skip the geneologies if you wish, the main thing is to keep going and cover ground. As you do so, the Bible will offer up its secrets, and you will be amazed at what it actually says.

Fun Science Friday: Lab Lit

2009-03-06T09:11:00.000-08:00

Cell recently reviewed Experimental Heart, a new novel by cell biologist Jennifer Rohn. I found this description to be strangely hilarious:

The protagonist and narrator, Andy, is a successful but somewhat hapless postdoc in a famous cell and molecular biology lab in contemporary London: successful because he's just published a paper in Cell, hapless because for a variety of reasons he chooses to spend all his time in the lab. His carefully restricted life starts to unwind when he encounters a glamorous biotech researcher, Gina, who is as smart as she is beautiful. Their love story (this IS a love story) unfolds against the background of their respective research into cell signaling in cancer and virus-based vaccines. It features all the usual competitive scuffles of academia, where reputations and careers are at stake, as well as a sly look at the biotech industry, where money and time are key drivers in the quest for cures. Nothing appears to be simple or straightforward in their worlds, and once their hearts get hooked, the story takes off.

A hapless postdoc, a biotech researcher as smart as she is beautiful, and all the usual competitive scuffles of academia. What more could you desire for a Sunday afternoon? Seriously, though, Cell gave it an excellent review, and Amazonians agree (five out of seven five-star ratings). I may have to order it myself.

Octopus Crimes and Misdemeanors

2009-03-02T20:39:00.000-08:00

The LA Times reports that a two-spotted octopus succeeded in redirecting her tank's flow valve onto the floor of the Santa Monica Pier aquarium, flooding the neighboring exhibits. Note the timing: "Judging by the size of the flood, [aquarium personell] estimated that the water flowed for about 10 hours before the first staff member... showed up for work." To pull this off, the octopus would have had to wait until everyone went home, and then complete her redirection of the water flow sometime before midnight.

This reminds me of a mind-blowing story I once heard from a labmate of mine, who used to work at the Monterey Bay aquarium. They had this beautiful petting-zoo tidepool display, where kids could come and touch starfish and sea cucumbers and the like. But every couple of days, an invertebrate from the tidepool would disappear. They figured the thief must be working at night, so finally they put the tidepool under video surveillance to catch him or her in the act.

When they checked the tapes, they caught their thief: an octopus living in a display tank opposite the tidepool. Every night, this wise guy would wait till everyone went home, then squeeze his way out of the top of his tank. He'd climb carefully down the side of his tank and walk over to the tidepool display, where he'd find himself a tasty, defenseless snack. The octopus knew that if he stayed in the tidepool display too long, he'd get busted, so he made sure to get back to his tank before any of the humans showed up in the morning.

While we're on the topic, have you seen this amazing video of an octopus in camouflage? Watch as the diver, David Gallo, approaches very slowly, until finally the octopus decides he's been spotted and opts for plan B.

Fun Science Friday: Future Shock!

2009-02-26T00:15:00.000-08:00

In honor of Mardi Gras, let's usher in Fun Science Friday one day early. This week the subject is robots - military robots. Quicker than you can say "Clone Wars," here comes the Daily Show's Samantha Bee, courtesy of Hulu.com.

Roger Cohen on Iran's Jews

2009-02-23T18:26:00.000-08:00

Roger Cohen, one of the New York Time's conservative op-ed columnists, had a nice piece about Iran's Jews in yesterday's paper. Iranian political and religious leaders make a lot of anti-Israeli and anti-Semitic comments, which make a lot of American and Israeli Jews fearful and angry. Yet it seems that the Jews who actually live in Iran basically blow off the rhetoric, and blame Israel for the recent Gaza invasion.

I'm not sure these Iranian Jews are sophisticated, as Cohen suggests, or naive. But either way, I think this is an interesting example of how our geographic neighborhood influences our seemingly objective interpretation of reality.

Fun Science Friday: Salmon Sperm DNA

2009-02-20T08:29:00.000-08:00

In the tradition of keeping science fun, I'm going to start posting along that theme on Fridays. There's no better place to start than this crank call a friend of mine placed to a biotech company (and made a video to match the conversation). The company rep (who posted the vid) claims he was playing along... as if.

Science activism: Darwin's other legacy

2009-02-12T00:00:00.000-08:00

A post in honor of Darwin Day.

A new biography named Darwin's Sacred Cause suggests, rather audaciously, that the great naturalist's theory of evolution was motivated in part by his documented hatred of black slavery. I submit that there is a relationship between abolitionism and naturalism, but I'm not convinced it's a causal relationship. Instead, I see science and morality as chicken-and-egg, indistinguishable, with one nourishing the other and both springing from a common fountain.

I feel this thread in my own life. I am not only a naturalist, but also a deeply idealistic person. Both characteristics spring from something deep within me: a healthy respect for intelligence and reason, a strong sense of fairness and justice, and an irreverent refusal to take someone else's word on anything, no matter who they are. To me, Reason will always be King - and when Reason is disrespected, it needs to be corrected. This absolutism, this intellectual boldness, stands at the core of both my scientific and ethical principles.

Just as Darwin hated slavery, I hate prejudice with a passion. My own sense of justice has been informed by Jewish texts, just as Darwin's abolitionism was informed by love-thy-neighbor Christianity. Yet I have been bitterly disappointed by today's religious leaders, who - by actively and vocally opposing gay rights - have actually stood in the way of that simplest and most central of ethical principles, Do as to others as you would have done unto you. Organized religion has failed to see the ethical forest for the ritual trees, and has left a generation starving for moral clarity.

The old Jewish saying goes, Where there are no men, strive to be a man. As scientists, we have an opportunity today to continue Darwin's forgotten legacy - science activism. We cannot afford to let clergy, politicians, or even social scientists be the sole arbiters of ethical behavior. We must strive to apply our passion for truth beyond the sterile environment of the laboratory, into the broader sphere of political and social action. Nor is it enough to simply stand at a distance and take cheap shots at the failed philosophies of others. For who is free from sin? As Einstein and Darwin learned the hard way, science can bring harm as easily as health. We alone decide how this power is used. Let us plan wisely, for the road to hell is paved with good intentions.

It doesn't matter what cause you decide to take up - whether it's the environment, endangered species, human origins, or the threat of biological weapons, you will find that science has something to say about it. It is something that society needs to hear. It is something that no one else can say but you.

--

Demetri Martin's funny data

2009-02-09T15:05:00.001-08:00

There's a LOT of funny data out there, but only Demetri Martin's is supposed to be funny. I love his flip chart routine, a sort of fractured fairy tales version of scientific illustrations. His deadpan delivery reminds my brother of Zach Galifianakis and my father of Steven Wright.

Martin's got a new show called "Important Things" premiering on Comedy Central this Wednesday night. I plan on checking it out, because laughter really IS the best medicine.