Pure Biology
apalazzo | October 1, 2008This is the third year that I update this list of potential winners. A warning, the list is highly biased towards basic biomedical research. In addition, some of the prizes may be more appropriate for the Chemistry prize.
We'll start with my favorite, Membrane Traffic. This finding is one of the most basic discoveries in cell biology. The two obvious winners would be James Rothman and Randy Schekman.
Last year there was a rumor that intracellular signalling may win. Tony Hunter could get it for phospho-tyrosine, Tony Pawson for protein signalling domains, and Allan Hall for small G-protein…
apalazzo | September 15, 2008I've been neglecting science lately but I just wanted to point out that Victor Ambros, Gary Ruvkun and David Baulcombe just won the Lasker Award in Basic Sciences for their work on miRNAs, small non-coding RNAs that are encoded in the genome. These 19-23 nucleotide long RNAs regulate the stability, localization and translation of mRNAs and have been implicated in almost every biological process from stem cells, to cancer to development.
Ambrose and Ruvkin are well known for their work on miRNAs and worm development, while the lesser known Baulcombe made similar discoveries in plants. These…
apalazzo | August 12, 2008Sorry, I've been busy these past few days.
I want to respond to a comment posted by Dan and take this opportunity to broaden the discussion about how we use language to construct models.
Dan's concerns about information and life have been echoed by many out there, for example by John Wilkins. Can we use the term "information" when discussing life? Is there such a thing as "information"? Are these buzzwords without any deeper meaning?
What is lost in such an analysis is that all of our theories are infused with metaphors. These words and concepts help us to better understand the ideas and…
apalazzo | August 5, 2008
Here's an interesting micrograph of a nucleus lit up by fluorescent dextran. Besides the slightly darker areas (these are nucleoli - dense structures where ribosomes are manufactured), you'll note the small round blebs on the top of this dumbbell shaped nucleus. I run into cells like this once in a while, and I'm sure that others have seen similar nuclear morphologies, yet we still have no clue how such structures could form.
apalazzo | August 3, 2008Two weeks ago, an interesting commentary by Paul Nurse, came out in Nature.
The bottom line? We need to change how we study and understand cellular signaling cascades.
First, some background. Cellular function is governed by a network of protein interactions that act like an information processing device. These devices sense external inputs, such as cell signaling factors, pH, nutrient availability and temperature, and they regulate a vast number of different cellular responses such as changes in morphology, alterations in the metabolic state, the modulation of cell division, or the…
apalazzo | July 27, 2008Now that I have a good chunk of time where I'm not scheduled to run off to some distant land for vacation or to give some talk, I have decided to work extra hard. Right now I'm incubating my samples. This post is the result of me killing that time.
I want to bring up an article that appeared n WIRED over a month ago. I know, that's ancient history in the world of blogs, but it's an idea that pops up once in a while and it is common in certain young naive scientists. Let me just quote a passage from the article:
This is a world where massive amounts of data and applied mathematics replace…
apalazzo | June 4, 2008With the sequencing of the human genome, the public at large has been told that biologists now have a full picture of how life works. This is far from the truth. In this series of posts I'll try to outline what we don't know - in other words gaps in our knowledge.
Today we'll look at how proteins acquire sugar modifications, aka glycosylation.
Look at any eukaryotic cell and you'll notice that one of the main differences between it and its prokaryotic cousins is its elaborate systems of membranes and its complicated secretion machinery. Unlike prokaryotes, which inject secreted proteins…
apalazzo | June 2, 2008
I must say that the animators omitted many details, such as the RNA polymerase's c-terminal repeats, splicing, the assembly of an RNP, the workings of the nuclear pore complex, and the assembly of a translation initiation complex ... but WOW! We need more of these videos!
apalazzo | May 29, 2008OK this is an attempt to revive the blog. This entry is inspired by a talk given about a month ago by my mentor, Tom Rapoport. I hope that it will be the first of a series of posts where I ramble on about what we don't know. In each post I'll discuss a topic that remains mysterious. I'll try to point out what we don't fully comprehend and add my two cents. Today's topic will be organelle shape.
Look inside any eukaryotic cell and you'll lots of little membranous organelles whizzing around. These membranous structures play crucial roles in various cellular activities. Very often their shape…
apalazzo | May 11, 2008Friday I was supposed to meet up with Mike Springer from the Kirchner lab. At some point Mike and I had set up a collaboration in order to figure out what was so special about little regions of the genome that encode signal sequences. (To read more on my paper and what we did click here).
In any case Mike had emailed me that Alex van Oudenaarden was giving a Systems Biology "Theory Lunch" and that he had to postpone our lunch. Having heard Alex once before and being impressed, I decided to check it out.
It was one of the best seminars I've attended in quite a while.
Now I'm not going to give…
apalazzo | April 14, 2008Sorry, posts will be few and far between. I need to do some experiments.
Here's a nice giant cell with gobs of ER.
apalazzo | April 2, 2008In the previous two parts I've described how cell biologists (and scientists in related fields) began to uncover the causes of cancer. Today I'll wrap things up with a recent discovery that goes full circle. But first lets have a recap and an expansion on some key points.
I started this series of posts by describing the Warburg effect. This was first described by Otto Warburg about 100 years ago and led to the golden age of research into metabolism. Here's a summary of the principle as described in one of the papers that I'll be covering today:
Otto Warburg noted that tumour cells, unlike…
apalazzo | March 25, 2008George Daley dicussed the results of that incredible Lin-28 paper on NPR's Talk of the Nation. Click here to listen.
apalazzo | March 25, 2008Here's a micrograph that I snapped way back in December 2004.
This is a picture of a mouse fibroblasts, a cell type found in connective tissue. The chocolate chip like circles are cells' nuclei where DNA is stored. The chips in each cookie, are nucleoli where ribosomes are manufactured. I took this micrograph in the middle of a microinjection experiment because I notice the heart shaped nucleolus (actually it looks like 3 nucleoli that are in close proximity) and just had to record this freakish event.
apalazzo | March 24, 2008Last past week was incredible. A slew of very important papers stemming from basic science and having deep impacts on cancer and stem cells came out in Nature and Science. Both stories came from labs here at Harvard Medical School, and everyone's been talking about both papers. The first story is complicated - but I wanted to use it to give a history of one aspect of cancer research. I have already written a two part intro into the topic (here and here). The other story, which was presented at last week's New England RNA Data Club, is now available online, I'll sum up the incredible discovery…
apalazzo | March 21, 2008Last time I told you about how the view of cancer switched from the perspective of metabolism to oncogenes. Today we'll see how recent developments have placed the spotlight back on metabolic pathways.
I'll begin this tale with a quote from a review written by Andrew M Arshama and Thomas P Neufeld:
The TOR (target of rapamycin) signaling pathway has been the subject of a 30-year-long reverse engineering project, beginning in the 1970s when the macrocyclic lactone antifungal compound rapamycin was purified from soil bacteria found on the Pacific island of Rapa Nui, famous for its moai (giant…
apalazzo | March 17, 2008One of the biggest stories over the last decade was how metabolism taught researchers new lessons on cancer.
Say what?
Here is a brief history lesson on how cancer was viewed by cell biologists over the last hundred years. Today I'll talk about how our views changed from metabolism to oncogenes, tomorrow (or the day after) I'll close the loop by explaining how metabolism came back into the picture.
About 100 years ago the famous German biochemist, Otto Warburg, thought that the way to understand cancer was through metabolism. Unlike normal cells, which broke down sugar using oxidative…
apalazzo | March 4, 2008So in previous posts I've written:
How to think about biology, Life is full of machines and Life and information. I guess I'm on some philosophy of Biological study kick.
Now I'll put the pieces of the puzzle and talk about what those proteins encode in the typical mammalian organism. This will go a long way to explaining how these machines promote what has been called evolvability. But what is evolvability? Here I am using the term as the ease of which a system can evolve phenotypically in response to natural selection. Going back to my first essay, I had emphasized the idea that the…
apalazzo | February 25, 2008John Wilikins has a post on my last couple of entries:
In a couple of posts, Scibling Alex Palazzo of The Daily Transcript has given two quite distinct views of what biology is about: information, and mechanism. In the first he argues that what is needed to build organisms is information, and in the second that biology is about machines, things that do work. I want to say that he is wrong about the first and right about the second, and moreover that they are contradictory ways of looking at the living world.
So why does Wilkins have a problem with a discussion equating information with life?…
apalazzo | February 24, 2008Ken Miller thinks that life scientists should reclaim the word design.
I was going to write the followup to "How to think about biology" post, but instead I'll pick up on the ideas being floated by Miller that scientists should take back the word design from pseudoscientists (discussed at Pharyngula, Evolving Thoughts and Gregg Laden's blog). But instead of design, I think that we life scientists should reclaim the idea that life is the product of machines.
Now of course I'm exaggerating a bit. The word "machine" is used everywhere within molecular biology, biochemistry and other related…