So here I am with half an hour to spare, I'll just spew out some thoughts from an incident that occurred a couple of days ago. I was chatting with a science writer and unfurling my usual gripes about science journalism. Very few science writers are willing to tackle ideas originating out of biochemistry, molecular and cell biology. They would rather talk about 'omic research - you know "big biology" projects like the human genome project, ENCODE or the hap map. And when they write about subjects like genomic research, some journalist do a good job explaining the bare minimal basics (along…
This was just sent to me by an unnamed source at UCSF:
Over the last few years it has become increasing clear that gene expression is partially regulated at the mRNA level. What do I mean by that? In eukaryotic cells, the first step of gene expression occurs in the nucleus when regions of DNA are transcribed into RNA. These "transcripts" then encounter RNA binding proteins (RBPs), some which act to process the RNA into a mature message, others that simply bind the mRNA. The whole collection of RNA and its associated proteins is often referred to as the Ribonuclear Particle (RNP). The protein content will dictate whether the RNA is spliced,…
If you were flipping through the latest issue of Cell, you may have noticed an article entitled Tough Challenges for the Next NIH Director. Yes, way at the bottom that's yours truly making some remarks about the problems of postdoc-hood and how the next NIH director may have to rethink the academic pipeline. Feel free to leave your thoughts in the comment section.
Traditionally, gene expression patterns were seen as mostly dependent on transcription ... yes those nasty bits of DNA that seemed to be ignored by most "science journalists". But the picture that is emerging is that transcription is looking more and more sloppy, and this "sloppyness" is built into the system so that the act of transcription tends to influence the organization of that part of the genome, regardless of what is being transcribed. It also appears that processes upstream of transcription, (such as mRNA processing, mRNA export and translation) play a greater role in determining…
If you missed it, today's NY Times Science section has been dedicated to "The Gene" a concept invented 99 years ago by Wilhelm Johanssen. Overall, the articles were very good, however as a scientist who wants to explain basic concepts of molecular biology to the masses, I have a few problems. First, there is a misplacement of emphasis on how information flows from DNA to phenotype. The idea that the articles try to convey is that in the old model went along theses lines: DNA contains genes, each is copied into RNAs that are then translated into a certain type of protein ... and then presto…
After a hiatus, Nature has relaunch its Pub Nights, but this time there's a twist. Here's the email that I just got from my good fiend Anna Kushnir: What would your dream project in science be? Corie Lok, the editor of NNB and I would like to invite you to an informal evening of drinks and conversation about what science would be like if unconstrained by reality. Two speakers will address this question: Antoine van Oijen - Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School - Visualizing life at the molecular scale and Andreas Mershin - Center for Biomedical…
This weekend a group of postdocs and grad students got together for a spontaneous celebration. Yes, the economy is in the tank, job prospects for even us academics are looking worse, but over the past week we've all felt a sense of relief. To quote a cliché that has never felt more true, the nightmare is over. Perhaps now we could once again cherish what makes America so special for all of us. So there we were, Americans, Canadians, Germans, Portuguese, Chinese, and Japanese having a great time. We toasted to Obama and kissed an anti-American administration goodbye. You might be wondering,…
There are plenty of large mRNA agregates in cells. In the past few years, two of these structures have gained quite a bit of attention, Stress Granules (SGs) and Processing Bodies (PBs). mRNAs in SGs are loaded with 48S complex, which consists of the small ribosomal subunit, the cap binding complex (aka eiF4F) and the eIF3 complex. SGs are transient structures that are formed in cells experiencing stress such as arsenite, elevated temperatures and amino acid starvation. The key step in forming these structures is the inactivation of eIF2alpha, the protein that carries the initiator tRNA-…
The following was lifted from an email I sent to a friend yesterday. I've since modified it by incorporating David Brooks and Paul Krugman's columns as they clearly support my arguement that the framing wars have begun - it is a critical time and we must all continue the fight. OK here the email: As for Obama, the expectations are high, maybe too high. But politics is a constant battle. We progressives have won a major victory for now, but there's still more to do. We'll see if Obama makes the right moves to enact change, or if the whole thing collapses either due to the DLC, pressure from…
From confidential sources I have heard of at least two academic institutions, one in the Boston area and one on the West Coast, that have canceled their new faculty searches due to the current financial crisis. How widespread is the problem? We'll have to wait and see.
Just like a giant, well controlled, negative result right wing ideology has been repudiated. If I were a card-carrying member of the GOP, I would take a long look at the last 8 years, and a hard look at the demographics of this election. I won't reiterate my displeasure of libertarian fundamentalism with respect to the market, instead we'll be looking at what happened yesterday. Here are some eye popping numbers for you: In 2050 more than 50% of American will be a member of a racial minority group, be it Hispanic, Black or Asian. So how did they vote?Black: 95% Obama, 4% McCain Hispanic: 66…
C'mon you've all seen them. Here's one I just spotted in the most recent issue of Molecular Cell: Methed-Up FOXOs Can't In-Akt-ivate
OK this will hopefully be my last entry on the election - From Seed's endorsement of Obama to the comments of various bloggers on ScienceBlogs and elsewhere it is obvious where most scientists stand on the political spectrum, but why? Yes, it is true that most scientists I know are lefties when compared to the American political landscape. Is it that surprising that those who pursue a career in discovering deeper truths also tend to be slightly idealistic? But these statements neglect a deeper truth, this being the fundamental problem with American conservatism in 2008. In the past 30 years…
This is what happens when a politician gets advice from political operatives instead of professionals who have dedicated their lives to understanding the topic in question.
I have a second to blog - forgive me if it's full of typos (chances are, if you read this blog on a regular basis you're use to them) but it has been a while and I need to get back into the swing of things. Last week, Jonathan Weissman came over to Harvard Medical School. I had the opportunity not only to hear him talk but also to attend a dinner with Dr Weissman and a handful of fellow postdocs. The Weissman lab has perfected a particular type of science, one that combines high throughput technologies and small reductionalist biology. This approach is the future of biomolecular science. Let'…
The New York Times Editorial Board on Proposition 1: Courting Chaos in Massachusetts From NPR, Brian Lehrer interviews Naomi Klein. Also check out her latest book, The Shock Doctrine. And if you missed it here's Klein on the Colbert Report: Note trhat even Colbert is shocked by Klein's last line on the prison industrial complex. Thomas Frank, Columnist for the Wall Street Journal and author of What's the Matter with Kansas?, wrote an excellent expose on how right wing ideology drove the current wave of corruption in Washington. This new book is called The Wrecking Crew and I highly…
If you live in Massachusetts, one of the most important votes you'll be casting is for or against proposition 1. What is proposition 1? It's the right-wing libertarian delusion that the best government is no government. Written by that societal piranha, Grover Norquist, proposition 1 would cut the state income tax by half next year and eliminate it by the following year. Now let's get this straight, no one likes paying taxes, but running a state costs money. And in this financial climate where the state can expect less revenue from property taxes, sales taxes and income taxes, and when…
Last week was a big one for the Rapoport lab. Throughout my years here, I've come to realy apreciate how structure biology can realy lead to insight. In the latest issue of Nature, two papers describe how proteins are pumped out of cells by the SecA secretory protein. Background: You can divide proteins into three classes, those that stay inside the cell, those that are pumped out of the cell and those that must be incorporated into the membrane. The problem with the last two classes of proteins is that they must cross a membrane. This is accomplished by the translocon, a protein conducting…
A message from Marty Chalfie, winner of the 2008 Nobel Prize in Chemistry for the discovery of GFP: