apalazzo | March 6, 2008According to the latest issue of The Scientist.
Rankings for American institutions:
1 The J. David Gladstone Institutes, San Francisco, CA
2 National Jewish Medical and Research Center, Denver, CO
3 Sandia National Laboratories, Albuquerque, NM
4 Fred Hutchinson Cancer Research Center, Seattle, WA
5 M.D. Anderson Cancer Center, Houston TX
6 Genentech, South San Francisco, CA
7 Fox Chase Cancer Center, Philadelphia, PA
8 The Samuel Roberts Noble Foundation, Ardmore, OK
9 The Jackson Laboratory, Bar Harbor, ME
10 Sandia National Laboratories, Livermore, CA
11 US Environmental Protection Agency…
apalazzo | March 5, 2008Each row of colonies represents one yeast strain lacking one gene from the Saccharomyces cerevisiae genome. There are 8 rows per dish, and 550 dishes, resulting in 4400 strains. Saccharomyces cerevisiae has about 6000 coding genes. Strains lacking essential genes are not included for obvious reasons.
apalazzo | March 5, 2008I'm excited, baymate and I will be off to Radcliffe to attend a symposium entitled, The Origins of Life: The Earth, the Solar System, and Beyond.
In related news I learned from Corie that over the next year, Craig Venter will be a visiting scholar with Harvard's Origins of Life initiative.
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 | March 3, 2008Well this year will be known as the year that the LHC (Large Hadron Collider) at CERN was turned on. Will we find the Higgs Boson? Will we finally have data that supports Supersymmetry? For now enjoy these videos on the ATLAS detector:
ATLAS, A New HopeATLAS, The Particle Strikes Back (Part I)ATLAS, The Particle Strikes Back (Part II)
apalazzo | February 29, 2008As we correct for the earth's rotation by adding a leap day, I'll add an extra campus to this week's edition of Map That Campus. (Yes two for the price of one!)
Here's the first mystery campus:
And below the fold is the second mystery campus:
hint:Even
Possibilities unseen require
Some intelligence
Make undeniable observations, verify, explain
Can you see how all the clues fall into place? Leave your answers in the comment section.
apalazzo | February 27, 2008It's been a while ...
We'll start off with Science and Art: Design and the Elastic Mind at MoMA (NY Times article)
RPM at evolgen ponders about faculty members that blog. And now there are even journal editors that blog. In another post, RPM discusses the various phenotypes found in the typical audience attending the weekly departmental seminar.
We also have a pair from PhysioProf at DrugMonkey:Submit Your RO1 NowNew Fiscal Policy at the NIH FY2008 - Cuts in existing RO1s
You gotta love Sunil's great stories. In a recent post he tells a few tales about the giant scientific egos he has…
apalazzo | February 26, 2008I'll try to be there this time. From Corie:
Hi everyone,
The next Nature Network Boston-hosted pub night for local
scientists/researchers will be:
Thursday, February 28, 2008 at 6:30pm
Location:
Middlesex Lounge, 315 Mass. Ave, near Central Square on the Red Line
(also on the route of the M2 shuttle from Longwood)
For those of you new to NNB (http://network.nature.com/boston), the
networking website for Boston researchers, we host monthly informal
gatherings at a local pub for Boston-area scientists (including a few
Nature editors from Nature's Boston office) to meet, chat, and have a
drink…
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…
apalazzo | February 22, 2008Time for another mystery campus:
hint: Powering all life
I'll confirm that what must be shown over the weekend.
apalazzo | February 21, 2008Fundamentaly biology is about information. An evolving entity must be able to copy itself - it needs the information on how to make a copying machine and it needs to copy this information to its progenitors. Already you can see how this works.
INFORMATION => COPYING MACHINE => COPY INFORMATION
Of course it is much more complicated then that. Take step A (INFO => COPY MACHINE) how do you do that? Well there are other machines that will translate the INFO into MACHINE parts. This process lies at the core of biology, the transfer of information, which is stored in DNA and is coded by…
apalazzo | February 20, 2008Last night I rediscovered James Burke's Connections. Here is episode one.
(PS Yes there is a strange inadvertent 9/11 subtext - from the Twin Towers, danger in NYC, technology traps, the end of civilization, to even a potential airliner crash, which incidentally is flight 911, what else???? But since this series was aired in 1978, it is safe to say that these were all coincidences.) Below the fold you'll find the next five parts of this episode.
apalazzo | February 17, 2008As an outsider, I'm glad to hear all the new developments coming from those who study human behavior. It would seem from my ignorant, non-expert, outside-of-the-field perspective that there is a revolution going on. Many have abandoned the platonic view of thought, the juvenile Freudian view of motivation, and the idyllic view of the blank slate. What has replaced these ideas is the realization that the human brain is a product of evolution - our mental world was molded by our history. It is full of tools or what some refer to as modules - a language module, a moral module, a simulation (…
apalazzo | February 15, 2008(Yes I'm 2 days late, but I had to give journal club - which I postponed due to the grant - I finally presented this afternoon - the topic was all these paper describing transcrition profiles of the whole genome, I'll blog about the wonderful chaos in the transcription field some time soon)
Yes, Harvard goes open access (the vote was unanimous!)
Read it at the Boston Globe, the Scientist, the Harvard Crimson (again), The NY Times, A Blog Around the Clock, Open Access News (again again), and Effect Measure.
apalazzo | February 13, 2008Great posts by DrugMonkey and Dr. Free-Ride (part I and II).
It reminds me of a bit of advice given to a fellow postdoc by Dr. Richard Hynes - try to attend every seminar. I would also add that in my comparatively short science career I have found that conferences are great as well. You meet people, people meet you, you learn, you communicate, and you develop this type of long distance acquaintance. Over the years as a grad student I got to know quite a few of my peers in the cytoskeleton community, only to jump ship and enter the RNA community. Although I haven't been going to many…
apalazzo | February 12, 2008Harvard is to spearhead an Open Access Portal? We'll see after today's vote. From the NYTimes:
Publish or perish has long been the burden of every aspiring university professor. But the question the Harvard faculty will decide on Tuesday is whether to publish -- on the Web, at least -- free.
Faculty members are scheduled to vote on a measure that would permit Harvard to distribute their scholarship online, instead of signing exclusive agreements with scholarly journals that often have tiny readerships and high subscription costs.
Although the outcome of Tuesday's vote would apply only to…
apalazzo | February 12, 2008What a great day. The grant is done and now I can get back to the bench after about one month of tapping away at the keyboard.
Writing a K99, which uses the same format as an R01 (or the main NIH grant) plus a wee-bit more, is quite an experience.
Putting together a scientific manuscript for a journal is easy, all the data is at hand and your task is to convey to the reader the logic of the experiments and the implications of your results. But writing a grant is ... much harder.
In the methods, you've got to plan ahead in some coherent logical way. You've got to project the pitfalls, you've…
apalazzo | February 9, 2008I'm almost done with my grant. Yesterday I sent out a 95% completed version of my proposal to SPA (Sponsored Programs Administration - an organization that vets grants to make sure that there are no conflicts of interests and that all the proposed protocols treat human and vertebrate animals ethically - since my research uses tissue culture cells, this ain't a problem). Next I had to take care of all the other items I had been neglecting. Priority number two was the RNA Club. Here is the letter I sent out:
Hello All,
The next meeting of the New England RNA Club will take place Thursday,…