..:. Cracking My Vainpot .:..

My honeymoon period in Kansas City is officially over.

Actually, I want to divorce from it!

I'm stuck.

Stuck in a very hostile workplace.

Do i feel that my personal safety is at risk?

No, not yet.

But then again, neither did that yale student before she got murdered and then stufffed in her own lab.

I'm not scared.

I'm just upset.

Upset about colleagues who I've mistaken as friends.

I wonder if he slept well on that bed I drove 60 miles in the snow for him to buy.

I bet they're still drinking the same tea that they once served me like a special guest.

I'm upset that from now on, I will never make another real friend at work.

No wonder I can't stop looking at pictures of puppies.

10 years ago, I started my PhD in HIV immunology.

My department in Oxford was best known for its study on T cells that go around the body killing virus-infected cells. We have McMichael, Rowland-Jones, Phillips, Townsend, Hill, Cerundolo, Goulder, Klenerman, Screaton, Price, Sewell, Gallimore, Gao, Xu...

There was such a concentration of talents that I had no doubt if anybody was gonna give the world an HIV vaccine, we were.

One of the quirks about immunologists is that they either "believe" in antibodies or T cells. It's like a chicken and egg thing. Antibodies rid of the virus directly, but cytotoxic T lymphocytes (CTL) stop the body from producing them.

In the beginning, HIV researchers trumpeted the role of neutralizing anti-HIV antibodies. That hype lasted until infection studies in monkeys revealed that HIV can mutate to escape antibody control in merely 2 days.

It was devastating.

So the pendulum swung towards T cell-control of the virus. People in my department were treated like rock stars when CTL were found to be responsible for containing the initial spike in viral load during the acute phase of HIV infection.

One of my bosses discovered that HIV can also mutate to escape from T cell control, but that was interpreted as evidence for the efficiency of CTL in forcing the virus to evolve.

Back in 1999, everyone was in this blind "vaccination" mode, trying to induce better, faster, bigger CTL responses against HIV. To be fair, we really were THAT good. The Oxford "prime-boost" vaccination regime took over the world. The tetramer technology that we helped Mark Davis pioneered was a real revolution.

We won tens of millions of research grants, testing a whole basket of vaccines in mice, in monkeys, in the UK and in Africa. Even I had a patent.

Not only were we gonna cure AIDS, we were also eradicating Melanoma, TB and Malaria.

All at the same time! 

But at the back of our (my) head, however, the elephant in the room has never disappeared.

Everyone infected with HIV amount antibody and T cell responses against HIV. Left untreated, 99% of them die with those HIV-specific antibodies and T cells.

You may ask, so where is the evidence that CTL can protect against HIV from establishing an infection?

It must be somewhere!

It must be... in those small % of "long-term exposed uninfected" African prostitutes who got HIV everyday but remain healthy?!

It must be... in those gay couples where only one partner is infected?!

They must have some special immune system.

They must have some special T cells.

They must have some special antibodies.

They must have!

...

20 years. We've been searching for those special protective immune correlates for more than 20 years.

But nothing.

Nothing.

Well almost nothing.

They've found a handful of super antibodies that HIV can't escape from. But they don't explain everything and we don't know how to design vaccines that induce them.

* * *

Every year, immunologists all over the world convene to discuss progress.

I gate-crashed the Keystone meeting on HIV and immunology in Colorado earlier this week. I even did a YMCA with the wife of NIH's AIDS Vaccine Program Director.

But seeing my personal heros still hammering away at the same old thing after ten twenty years is truly heart-breaking.

I've followed their work since I was 17. I'd wait outside their office just to talk to them between conference calls. I wanted to work for them so much I had to pretend otherwise and rejected their first offer. I'd do ANYTHING to get them on my CV.

I even let them bleed me for white cells.

Now? Some switched to another virus, another disease. Others used the same technique screening for the same T cells, just on a slightly different scale or on a slightly different patient cohort.

Details.

More details.

On why we failed.

We have to.

THEY have to.

It's HIV.

"I think it was in 8th grade (14yo) when I first learned about evolution. I remember the teacher (a pastor) saying that if lizards get to live to 700 years old like they used to in the Bible, they'd become dinosaurs." - West Virginia

Went to Barnes & Noble the other day. Given the popularity of the new administration and how Obama has deliberately associated himself to the Abraham Lincoln, it came as no surprise that B&N has set up a special book stands in the atrium celecbrating the 200th birthday of the great abolitionist. But what about Darwin? The other greatest man ever lived who was born on the same day?!

Nothing.

One of the BEST popular science book written on evolution, Why Evoution Is True, has just been published in earlier this year. Guess how many copies they have.

One.

Well since evolution, the best idea in biology, doesn't seem to be well appreciated here in the midwest, I'd just do my own little celebration.

Darwin Stamps from the UK!!!

Aren't they beautiful?

Darwin himself assumes the 1st class slot, naturally. The galapagos islands, the finches, the turtoise, the lizards, etc, are all there as well.

Funny isn't it. Darwin is now such a hero in Britain that they've even put him on the 10 pound note.

Makes you wonder why it's slightly different across the pond.

Royal Mail: Special Darwin Stamps

http://pewforum.org/

48% for the US population? Two other polls have it at 14% and 39%... Oh well.

"So you believe in... monkeys?" a 21yo Kansan asked. 

Since then, I wanted to find out what children here really learn at school.

Kansas City is a funny place that trap both godless liberals, right-wing religious fanatics and everyone in between.

Kansas thrust into international spotlight in 2005 when the state board of education voted 6-4 to adopt a new set of "science standards" that marginalized the theory of evolution. Those stupid "intelligent design" lazy fuckers redefined science, paving the way to slip God into science classroom through the backdoor (something that Texas is now trying to do).

So it felt kinda unreal and exciting to celebrate the bicentenary of Darwin's birthday here in KC at the Linda Hall Library today.

We were late for the cake, but did make it to the discussion session.

I half-expected some uninvited insane bible-thumping Jesus freaks screaming in tongues, and there was one.

But it was a brave greying school teacher who captured my attention, and here's what she said. 

"I'm a school teacher in Shawnee (Kansas). I teach general science to 14 year olds. There're lots of Bible literalists in our district. The kids believe in whatever their parents told them and would openly challenge me every time I talk about evolution or genetics."

"They're very well versed. If you tell them about fossils, they'd just say that God put them there to fool them."

"They'd say they're not animals and would totally take the class down that road. I can't debate with 14 year olds in class. Very often I'd just have to stop the conversation. I hope one day they'll think back and realized that yeah, we actually HAVE taught them science."

"Fortunately, the district board is very firm about the curriculum and book banning. We've always been able to strike a balance in our library collection because of our incredible librarians."

"In fact, every year we have a ban-book-day called "Right to Read"."

[This post is a salute to her and all the defenders of science and reason.]

Darwin celebration: full house at the Linda Hall Library, Kansas City

Why Mark Twain?

a) He's from Missouri b) a contemporary of Charles Darwin c) he rocks!

Man has been here 32,000 years. That it took a hundred million years to prepare the world for him is proof that that is what it was done for. I suppose it is. I dunno.

If the Eiffel tower were now representing the world's age, the skin of paint on the pinnacle-knob at its summit would represent man's share of that age; & anybody would perceive that that skin was what the tower was built for. I reckon they would. I dunno.

- "Was the World Made for Man?"

I believe our Heavenly Father invented man because he was disappointed in the monkey.

- Mark Twain in Eruption

It now seems plain to me that that theory ought to be vacated in favor of a new and truer one...the Descent of Man from the Higher Animals.

- "The Lowest Animal"

Evolution is a blind giant who rolls a snowball down a hill. The ball is made of flakes--circumstances. They contribute to the mass without knowing it. They adhere without intention, and without foreseeing what is to result. When they see the result they marvel at the monster ball and wonder how the contriving of it came to be originally thought out and planned. Whereas there was no such planning, there was only a law: the ball once started, all the circumstances that happened to lie in its path would help to build it, in spite of themselves. 

- "The Secret History of Eddypus"

This morning, my boss told me to get 3ml of sperm and boil it for 10 min. We then incubate it overnight with some yeasts which should (hopefully) turn green in the next couple of days.

I'd do anything for science. But no, I didn't use mine.

:-P

Congratulations to Steven Chu the new Secretary of Energy in the Obama administration. Having a scientist in a position of power is like putting facts and logic before profits. Should he survive all the politics, Hope is on it's way for the planet!

"I was following this as an interested citizen. And it became more and more apparent to me that the dangers, the potential risks of climate change were looking like they were more and more likely, and that ... as a scientist, a responsible scientist, you really have to think of what you can do to help with this problem."

[NPR: Nobel Winner Chu To Land Top Energy Post]

* * *

Watching this 2004 video of Dr Chu tracing his career path is heart warming in so many levels. As a scientist, I appreciate that he truly understands our challenge to be novel and our desire to be inspired. As a Chinese, the way he described his childhood reminded me of my own and how my father tried to instill in me bits of the old Chinese culture that no longer exist. What's more, he was born in Missouri!

"One of the highest things you can aspire to is to be a scholar for scholarship sake."

"A good scientist is their worst critic. They're always trying to prove themselves wrong, which is hard."

"In science once you announce something, first everybody tells you that you're wrong, then they tell you it's trivial, and then you're not the first to discover it." 

"Science is really about describing the way the universe works... You have to have a natural curiosity for that... a really driven curiosity, you want to know the answer, and with that curiosity you have comes with a certain doggedness, because there will be setbacks, you will be discouraged, things aren't gonna work, you're gonna have troubles understanding them, things are hard to understand the first time."

Grad students @ Berkeley's Dpt of Molecular + Cellular Biology Presents:- 

What has a cucumber got in common with you and me?



Not that much, I thought. Well ok. All living organisms share the same DNA, using genetic codes that are almost identical. But still... cucumber!?

One good thing about studying biology is that everyday it reminds you how narrow-minded people are.

Time to take a closer look at the 1st revolutionary concept in biology, the cell.

It turns out that the epithelial cell layer that covers the surface of a cucumber look exactly like, for instance, the ones line our gut or those on the wing of a fruit fly.


Although these cells can have different number of sides, most are hexagonal.

Just like in cucumber, you can tell which of your epithelial cells will divide next simply by their shapes.

As these cells age, triangles will become a square, and then, a pentagon, hexagon, etc.

Thanks to some eccentric mathematicians, we now know that heptagonal and octagonal epithelial cells are most likely to divide, whether it's in human being, fruit fly or the humble cucumber :)

The significance of this? Give it another 20 years!