Friday, August 26, 2011

Should evolution be taught in schools?

I almost cried watching the Miss USA contestants address whether evolution should be taught in schools. The predominant answer are "No!" and "Children should be exposed to all belief systems and theories about how life arose." Because, of course, "Students should be knowledged about different options."

Why teach only two sides of the creation story? The world may have hatched out of an egg! So I guess biology class will soon become mythology class.

Personal favorites: California, Indiana, Kentucky, Maryland, Nevada (OK, I kind of <3 New Mexico!), and what is Miss Washington even saying?

Note: Candidates are in alphabetical order by state if you want to hit the highlights.

After you've seen all you can stomach of the first video, watch the parody!

Wednesday, August 24, 2011

White privilege

I enthusiastically agreed to go with my husband to an a capella gospel concert at the church he attended as a child. I love a capella, I love gospel. It's gonna be great!

Then, as I looked at the Facebook event page, I thought, "I wonder if I'll be the only white person there..." Then I realized that the converse is my husband's situation at least 80% of his life, if not more. And I kept my mouth shut.

Tuesday, August 23, 2011

I heart our tech

Subtitle: "How I ended up doing surgery with a shoe-cover on my head."

Our tech/lab manager type person is away this week. Our tech is a 20-something who didn't get into pharmacy school and makes beer in his parents' basement. I didn't like him at first. But he is astonishingly long-suffering and good-natured, and even though I don't think he gives a darn about the science we do, everything always runs smoothly.

But, as previously stated, he is away. So is one of the other grad students and our research assistant is sick. Thus, I am somehow in charge. In charge of ordering. In charge of the frogs. In charge of making my own solutions and electrodes. And stuck with frog surgery.

So, I go up to anesthetize the frog. This rarely works in the time-frame described in our protocol. 45 minutes later the frog is still kicking. At an hour it's not. But then I flip it over, and I can see it's throat pulsing. Back in the anesthetic. Meanwhile, my surgery suite reservation is running out of time. (N.B.: I did not reserve the suite, our blessed lab manager did, I didn't even know we needed to reserve it!). Finally, the frog is out. I realize I have no gauze for dabbing blood. I figure, oh well, I'll just deal. I start the surgery.

As soon as I start extracting eggs, the person who had the surgery room reserved starting 5 minutes before pokes her head in. I say I need 15 more minutes, she says no problem, she'll use a different room. It's all good. Then I go to stitch the frog back up. I swear to goodness, that thing had HIDDEN the other side of the muscle layer (it could have been all the blood that I couldn't mop up sans gauze). I was stressing. My new (very professional hair) was in my face and sticky. This is because I had no hairnet (they're not required in this situation, but are helpful for hair restraint). For some reason, the little supply station on this floor was out of hair nets. Finally, in extreme frustration, I leave the suite in search of a hair retainer. The little supply station is just outside the door. I grab a shoe cover and stick it over my head and return to fishing around for the muscle layer. When I eventually put the frog back together and start hauling all my supplies (and the frog) back to where they belong, I get strange looks in the hall. This is when I realize I still have a bright blue, waterproof shoe-cover on my head.

Thank heavens he's only gone a week. I will remember to be extra-nice to him when he comes back (until I forget).

Thursday, August 18, 2011

Race bias in science funding

It's a fairly well accepted fact that there are pipeline issues in getting racial minorities into STEM (Science, Technology, Engineering and Math) careers in the US. But it turns out that even once you get there, there are still hurdles.

A recent study published in Science (see the News and Views here) found that black PhDs have lower R01 funding rates than any other ethnic group (they note that there was also a disparity in NSF funding). While there are (due to the above mentioned pipeline issues) many fewer black applicants, 29% of white applicants were funded, 25% of Asian applicants were funded and only 16% of black applicants were funded. When only US citizens are included (to minimize language barrier bias), the funding gap between Asian and white applicants disappears, but the funding rate for black applicants was still 10% lower.

Why the disparity? They controlled for as many variables as possible (training, publication record, etc), but the gap remained. One theory was that better mentoring allowed whites and Asians to submit higher quality applications, but one would then expect a lower funding success rate for Hispanic applicants as well, but this was not observed.

Obviously, the NIH is working to determine what is causing this gap so that it can be closed. Reviewers do not have access to information about an applicant's ethnicity, but perhaps it is being inferred from the name, location, or college attended. My personal guess is that there's a bit of an old-boys-club effect going on, in addition to other factors such as not having access to high-quality mentoring and grant-writing training in their early career.

PS - There are also programs that try to address the minority pipeline issues by supporting STEM students from a very young age with high-quality mentoring and research opportunities. I recently became aware of the extremely rigorous physician-scientist training program, and there are many others.

Wednesday, August 10, 2011


This seems to be entirely accurate at all levels with which I am familiar (click to enlarge).

Had some viewing problems, hopefully fixed. If you still can't see it, try clicking here.

Tuesday, August 2, 2011

This guy is cooler than me

He DIY'd a scanning electron microscope! And just yesterday I was lamenting the state of science education, cuz I'm pretty sure no teenagers today could figure out how to build a nuclear reactor in their backyard. (Not that kids should use their science-smarts to build nuclear reactors, of course.)

Engineering HIV resistance

You may have heard in the news of people who are “immune” to HIV. This is because in order to infect cells, HIV needs to bind to a primary cell-surface receptor called CD4 and a co-receptor. HIV can use two kinds of co-receptors, CXCR4 and CCR5; X4 strains use only CXCR4, R5 strains use only CCR5 and X4R5 strains can use either one.  Some people are born with a mutation in the CCR5 receptor that makes it unrecognizable to HIV. This means that they’re not susceptible to infection from R5 viruses, but could still get HIV from X4 or X4R5 viruses.

Can we use a similar strategy to treat/prevent HIV infection? Maybe. There is a drug on the market (maraviroc) that blocks CCR5 so that HIV can’t recognize it. While this drug slows down infection, it usually comes back. First, because there is now a selective pressure for proliferation of any X4 or X4R5 viruses the patient might be harboring.  Second, because in some cases the virus mutates to recognize even the blocked receptor. (HIV has very little proofreading, so mutations accumulate very rapidly. One talk I went to estimated that every base is mutated to every other base every day in every patient.)

What if we could find a way to block both receptors at once in such a way that the virus couldn’t mutate to recognize them? Enter the zinc finger nucleases (ZFNs)!

ZFNs are engineered enzymes that use a zinc-finger domain to bind to a targeted DNA sequence and an endonuclease cleavage domain to cut the DNA at the binding site. The cleavage domains often need to function as dimers, so to edit DNA you need a pair of ZFNs that bind to adjacent regions. ZFNs can be used to edit genes, since after they cut DNA, it will be stuck back together in a process called non-homologous end joining (NHEJ) which will induce insertions or deletions that make the gene non-functional.

Scientists have tried this in cell cultures and found that they can indeed use ZFNs to edit both CCR5 and CXCR4 and these edited cells are resistant to HIV infection. Even more promisingly, this strategy also protects humanized mice which are immunodeficient mice that have human CD4+ T cells engrafted into them. When a portion of the T-cells are ZFN-edited, the mice show significant reduction in viral load and edited T-cells can be recovered, suggesting that they have a selective advantage.

Currently, clinical trials are underway. In these trials, a sample of CD+ T-cells is removed from the patient and edited with ZFNs and returned to the body. The hope is that these cells will create a virus-resistant reservoir that will preserve immune function. Of course, this therapy only applies to CD4+ T-cells and these cells won’t live forever, but extending immune function may prevent opportunistic infections and progression to AIDS in HIV infected patients.

ZFNs are already used for editing in a variety of research applications and scientists believe they show promise as a therapy for a variety of single-gene diseases.  Maybe ZFN editing will one day allow me to have permanently blue hair! I can only hope.


Alas, I have been too long absent. Seriously, my poor neglected blog, I haven't forgotten you.

I came back from vacation just in time to revise a paper, draft another paper and resubmit my F31. After all that serious science-writing, I couldn't summon the willpower to do more than whimper about science.

Now, however, various entities are casting their blood-curdling gaze upon my other work, so I have time to write here again. Cool science is on its way!