44 posts tagged “science”
Today, the NIH announced that they are spending $27MM of your Recovery money on creating a social network for scientists in the biomedical research community. You can read about it here.
The goal is summed up as follows:
These Web-based initiatives will bring the power of Internet-based tools, as exemplified by social networking, to biomedical research. Modern technologies for communication and collaboration have the potential to enhance interdisciplinary research, enabling individuals to connect with each other and with resources — irrespective of location — to address challenges in new ways.
That’s very nice – but I wonder if this is really necessary? Frankly, most of the social networks among scientists that I know involve a couple of pints. And though I don’t want to be a Luddite, I wonder if it can be successful. Do I really need a social network to help me solve scientific problems of a common sort (Hey peeps, I’m out of ammonium sulfate, anyone in 92121 got any in da house?)?
Because I’ll tell you, the first thing that popped into my mind when I heard about this was two little letters: “I” and “P” as in Intellectual Property. The who “owns” what question is always a contentious issue that plagues researchers from the --- whose name gets to go on a paper, or whose name gets to go first on the paper questions on the academic side – to the industry ones of who had an intellectual contribution worthy to be on a patent to which organization owns the rights to this new discovery and can license it out to the highest bidder(s)? Can you imagine “Hey peeps, I’m looking to cure Parkinson’s Disease with this new compound I made, anyone got a validated preclinical animal model in da house?” Somehow I don’t think so.
I think this also raises the question of how many social networking sites do you really need? I have three that I can think of – Facebook, Vox and LinkedIn – which seem to adequately cover the personal and professional sides of life. I’ve eschewed Twitter because I think it only enforces America’s short-attention span problem. Though I did just get a GoogleWave test-account (thanks, DeWitte!) – and I’m not really sure how to classify that. So – is this new endeavor supposed to be a less “career networking” and more a "work networking" site than LinkedIn? Perhaps.
I’m sure being supported by the government, they’ll come up with some terrible name out of committee – NerdNet, Science Communication And Networking Tool (SCANT), Fritter? Maybe the social network itself should organize and name itself.
What do you guys think? Good idea, bad idea, I'm not a scientist so who the heck cares and I want my $27 mil back?
Now, if I asked any of you what the Central Dogma of Biology was you’d doubtlessly answer that of course that it’s that: (i) DNA replicates itself, (ii) DNA makes RNA, and (iii) RNA makes Protein.
And it’s been a good week for the old fundamentals, with the awarding of the Nobel Prize in Physiology and Medicine to the understanding of chromosomal telomeres and the Prize in Chemistry for the determination of the structure of the ribosome.
And I know, many of you are like --- pffft, dude, the Prize was awarded 50 YEARS AGO to Kornberg for the understanding of DNA Polymerase (step-i above). But as is often the case in biology that wasn’t the whole story. DNA Pol had a problem that while it does a swell job replicating DNA, it leaves raggedy ends of your chromosomes. In the good-bad scheme of things, this is BAD*. In the 1980s, folks realized that a) this doesn’t happen all that often and so b) there must be something that maintains chromosomal integrity. This “child-proof-cap” for your genetic material are telomeres and the enzyme telomerase, which finish the job and keep our chromosomes intact and happy.
But I have to say that as a structural biologist I was REALLY excited to hear that the Chemistry Prize went to the structure of the ribosome. You see, when I was in college and graduate school, we all learned that the ribosome, which is responsible for step-iii above is a huge 2-part complex of proteins and RNA – and it looked like this.
And so about a decade ago, several groups had figured out how to get crystals and good x-ray diffraction data** and were able to turn the picture above into this:
So rather than a vague understanding, we could see the intricate and subtle details of how this amazing piece of cellular machinery works. Also, because the first structures were of ribosomes from bacteria, we were able to see the places where important antibiotics bound and how they gummed up the works and killed bacteria.
When we first saw the structure of the ribosome, I remember having a lunchtime conversation with my colleagues about when they’d get the Nobel Prize for it. Turns out to be about 10 years, though I think I would have turned around and given it to them right then and there. I doubt I will ever cease to marvel at the beauty and complexity of biology.
*raggedy ends can lead to chromosomal degradation, errors in replication and all sorts of cellular unpleasantness.
** coincidentally (or not), one of the technological advances in crystallography about that time was the advent of CCD detectors – CCD technology won the Physics Prize this week, too.
So, when you’re a young chemist you have to take classes in all the various versions of chemistry – analytical, organic, inorganic, physical, biochemistry are the “typical” way that the field is broken up.
And one of the first things you learn in Physical Chemistry, is Atomic Theory. That molecules are made up of atoms. Atoms, in turn, are composed of a nucleus (where the protons and neutrons reside) and an electron cloud. Atoms bond to one another (to make molecules) by sharing their electron clouds.
Most of this work was done in the 19th and early 20th century (for the past century, most work has been on subatomic particles), which is pretty remarkable, given the lack of sophisticated instrumentation available at that time. But atomic and molecular theory has stood the test of time because (as you’d suppose) experimental support continues to support the conclusion that matter forms up this way.
As students, we’d draw molecules as lines, or balls and sticks – approximations of the way atoms are bonded to one another. We’d draw the shape of different electronic orbitals --- “s” orbitals are spheres, “p” orbitals are like squashed dumbbells. Why? Well, again, that’s what the math and thousands of indirect experiments made you conclude. As a student, you just sort of accepted it and moved on – after all, this stuff was old news.
Well – even though I went on and became an organic biochemist type, there was plenty of work going on in the P-chem world – especially in microscopy. And two papers that came out in the last month demonstrate how.
The first is a paper from a group at IBM Zurich that imaged – down to single atoms – a small organic molecule – pentacene. The picture shows a typical ball and stick diagram of pentacene and below it is ACTUAL PENTACENE. Not a structure you deduce based on disparate data. That’s IT. Right there.
Not to be outdone, another group has figured out a way to image the electron clouds of individual atoms. And here, the images look just like the ones I had to draw on Chem111 tests.
Amazing.
Now, I guess I shouldn’t be surprised that these molecules and electron orbitals look like “they’re supposed to” – as I said, there’s a couple of centuries of data to back it up. But to see it – not just deduce it – is remarkable to me.
We don't see things as they are, we see things as we are. -Anais Nin.
Last week, the Pew Research Center published the results of a survey of several thousand Americans on the perception of science in this country – half were professional scientists, half were not (i.e. the public).
First the good news. People like science and think that it’s had a positive effect on society (84%) – woo hoo! Scientists (the folks that have produced all that good stuff) rank pretty high too – only losing out to the military and teachers. Not so bad.
Which is funny – because Americans have a bit of inferiority complex about the science produced here. If you judge by literature citations, research budget, and Nobel Prizes, science in the US is still the champ --- and 90% of American scientists put it at or near the top. The general public? 17% of Americans said that US scientific achievements were tops. Whoa. I’m starting to feel a bit like chopped liver over here. I’d love to know who folks thought was doing and producing more. Hrmph.
The division between professional scientists and the public was very clear in a couple of high-profile questions – and the one that staggered and depressed me the most was, of course, evolution. Nine out of 10 scientists agreed that animals (including you and me) arose from natural processes. The public? 32%. Seriously? How do we get to that point?
If you go to a doctor that says that he’s concluded from your test results that you have appendicitis, and the second opinion says agrees, and the third, and the fourth and so on --- I doubt 2 out of 3 people would disregard them.
For what it’s worth, I don’t believe in evolution either. I don’t have to – based on the mountain of geological, archaeological, genetic and biological evidence, I conclude it is the explanation that best fits the data. Show me one that does so better, and I’ll support that. This is why I think St Thomas the Apostle should be the patron saint of scientists.
Clearly though, a sizable majority of Americans are participating in willful ignorance and/or have been drawn into the misinformation and hyperbole around “Intelligent Design”. I know it’s difficult when facts are contrary to certain worldviews – but the Earth is no longer the center of the Universe, and it’s no longer flat. And we are biological organisms that play by the same rules as all the others that have come before us.
And we have the added bonus of having brains smart enough to perceive that.
I saw a recent blog post about how the American Chemical Society was going to phase out hard copies of the journals that they produce – going strictly online in the future.
Now, this has probably been coming for a while – I’d say >95% of the journal articles I read in the last five years have been acquired by downloading the PDF version and printing it out locally. A decade or so ago (and before that), you would most likely be photocopying a paper out of a journal by hand in the chemistry library.
The chemistry library. There’s an institution that is probably going to be as rare as a Blockbuster Video store in the next few years. It’s weird to think that they’re obsolete (though my own practice suggested it) because I spent a lot of time in them as a student and young scientist. UNC had a good one (it’s no longer there) that was the epicenter of both learning (Do you have the latest issue of Nature?) and grad-student personal drama (Do you know who I saw Steve sitting with in the library!?!? You’ll never believe it!).
I suppose like all things, even scientific communication changes. I remember making the BIG change from slides (that you shot yourself!) to PowerPoint presentations. And today, I came across a series of videos from a group at the University of California at Davis about food safety (which is very important in the summer, don’cha know).
I’m not exactly sure why Frodo (or is that Sam?) is the “protagonist” or why our heroes are so mad about getting food poisoning that they go after him. I mean, I don’t think he meant to do it!
So, when I was a young scientist, I didn’t work on drug targets or diseases or anything remotely seen as practical. I worked in a fairly esoteric field – protein folding and protein stability. Why? Well, because I thought it was cool. No, really.
Anyway, everyone outside of certain parts of Kansas and Louisiana knows that DNA is the genetic material that makes us what we are. However, DNA is BORING. It sits in the nucleus under essentially cellular lock and key. How come? Well, mostly because it’s so important that you don’t want it out in the cellular milieu because it could get damaged. And in the good-bad scheme of things, that’s bad. So, DNA does what any good manager does, it delegates. And it delegates nearly all the cell’s to-do list to proteins.
Proteins are long chains of amino acids that fold into three-dimensional structures in the cell. This structure dictates what they “do”: whether it’s be an enzyme, a receptor, a structural component, a messenger, and so forth. In the 1970s, it was shown that proteins could reversibly fold and unfold – but the “whys” and “hows” of that were still a mystery.
So – I worked on some of that. Why some proteins folded more readily than others and what made some more stable than others (those two were not always correlated). But what was it good for my wise mother would ask me? And I’d tell her, “Errrr, well Mom, it helps our understanding of biophysics and blah blah woof woof…” until her eyes glazed over. Later, I became disenchanted with the “academic” aspect of protein folding studies and moved onto real-world drug discovery and got into anti-infectives and endocrinology.
Guess what? As it turns out over the next decade or so protein folding (or mistakes in it) have been implicated mechanistically in several diseases – including Alzheimer’s Disease, cystic fibrosis, mad-cow like diseases and even some cancers.
Today, I came across a paper in which scientists in San Antonio examined differences in the behavior in proteins between mice and bats. Why mice and bats? Well – no offense to pigeons – bats are essentially rats-with-wings and genetically very similar. One difference is that bats live a lot longer than mice.
As it turns out, proteins from bats are more resistant to oxidative damage than their murine counterparts (oxidation is linked to age-dependent damage and disease) and their protein folds are more stable, too.
Go figure. Rather than blather on to my mom about biochemistry and biophysics, I could have told her I was working on the Holy Grail of biology: Longevity. In essence, the Fountain of Youth!
Oh – and guess where the bats from that study live? Florida.
It probably comes as little surprise to many of you, but I’ve always liked the Alfred Hitchcock movie “The Birds”. In it, the avian population around Bodega Bay begin acting a little oddly. Pretty soon, they all flock to put the hurt on the human population for no apparent reason.*
Well – a new paper coming out in the Proceedings of the National Academy of Sciences puts an interesting twist on bird behavior. In an experiment carried out on the campus of the University of Florida, local mockingbirds were capable of recognizing individual human beings on day-to-day basis, make a “threat assessment” of them and carry out flushing and harassing activities on individuals. Pretty amazing.
Better yet, in the experiment, different people walked near a mockingbird nest. Some would touch the nest (very threatening behavior). After repeating these actions for a couple of days, the parent mockingbirds would preemptively flush and attempt to drive away the “aggressive” persons, while more or less ignoring the literally thousands of student passers-by. The flushing was not dependent on the clothes worn or on the direction of the approach. The mockingbirds learned who the offenders were after – get this – two approaches.
So, as you’re hanging out in your back yard, think about this. You may not be able to tell one finch or cardinal from another, but watch out. They know who you are and where you live. So be nice!
*Today, you’d argue they’d banded together to fight off natural habitat destruction, but in the 1960s, it was okay not to have a reason. They just did. And it was freaky.
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