lab life
apalazzo | July 20, 2006From The Scientist: Public Concern for Private Funding.
More money generally means more science, and vice versa. But the source of the money - whether from public or industry well-springs - may be as important in determining the type of research that gets funded as well as the direction that research may take. During the last several years, the percentage of industry funding relative to public funding has grown (see Box). For example, industry funding of clinical trials rose from $4.0 billion in 1994 to $14.2 billion in 2003 (in real terms) while federal proportions devoted to basic and…
apalazzo | July 19, 2006I just read an EXCELLENT opinion in the July 6th edition of Nature, Illuminating the black box. Note to biologists: submissions to Nature should contain complete descriptions of materials and reagents used.
Sounds familiar? I've complained about it before.
From the Nature article:
This journal aims to publish papers that are not only interesting and thought-provoking, but reproducible and useful. In order to do this, novel materials and reagents need to be carefully described and readily available to interested scientists.
That might seem obvious. But despite the efforts of our editors and…
apalazzo | July 4, 2006Yesterday, while driving up to Ipswich to spend the day at Crane beach and watch the see the annual July 3rd Fireworks, a group of us gabbed about the transient nature of being an academic.
Living from place to place, moving until you are in your late 30s, an academic is expected to travel and see the world. You live in various places; experience the day to day hustle of different cities, towns and often countries. You absorb the local customs, the ideas, the history. You attempt to form relationships with coworkers ... but in the end it's all very transient.
I've made many good friends…
apalazzo | June 28, 2006Here's a tale from the lab.
Today we had an interesting discussion. It started off with PBS and ended up on the topic of understanding the principles behind much of the protocols used in a lab.
It all started when a rotation student asked if there was a lab stock of PBS (phosphate buffered saline), a common buffer used in the lab. Another postdoc informed the student that there wasn't a lab stock and she did not have any at the moment. The student had to either get some from another lab member or make the solution from scratch. Five minutes latter he showed up with a small packet of powder,…
apalazzo | June 27, 2006I've got lab meeting in 5 mins. Here's some stuff I've read in the blog-o-sphere recently.
From Coturnix, DarkSide interviews Sean Carrol on DailyKos about the Big Bang, Dark Matter, Dark Energy and String Theory.
Next up ... Ode to the ... pocket protector? From M. William Lensch's blog:
The pocket protector was once an icon indicating a technical education, perhaps THE icon. They were tiny vinyl billboards not only proclaiming to the world that you knew important things but also which brand of reagents you preferred (my own vintage specimen says "STP", my dad was a mechanic).
The pocket…
apalazzo | June 22, 2006For those of you not in the biomedical sciences, you may not be aware of the coming crises. Right now aspiring postdocs and new independent investigators are involved in a war of attrition when it comes to funding.
How did this happen?
Well as the NIH budget grew in the 1990s, PIs simply used the funding to hire more postdocs. Postdoc salaries were (and are) obscenely low and thus many Americans refused to enter science. However, the supply of potential postdocs was (and is) high due to the large number of foreigners in science. This is the reason that much of the scientific establishment in…
apalazzo | June 21, 2006Over the last month, many things have been happening in the world of scientific publishing. Nature is trying something new, and they are having a public debate about how to alter the review process. PLoS is pushing ahead with a new type of publishing platform, PLoS ONE. And they are blogging about it. Now Cell has started an online comment section. Similar to ArXiv.org that displays trackbacks, and to the suggestion left at Nature's peer review blog that articles should be publicly debate both before and after they have been published, Cell is providing a public posting area so that…
apalazzo | June 14, 2006(via The Scientific Activist, Evolving Thoughts)
First came PLoS, then PLoS ONE, now PLoS blogs
A blog? Here's their mission:
... to give an insider's view of the latest developments at PLoS. To keep it simple, we've divided the content into two tracks:
Publishing
Enter a discussion of our latest e-publishing initiatives.
Technology
Enter a debate surrounding our new open access 2.0 platform.
Here is an exerpt from one of the first entries:
This is the first post from me on the PLoS Blog. My name is Liz and you can check out my background here.
While preparing to launch this project, a…
apalazzo | June 14, 2006Part of the problem with Science is the verification process. From the outside looking in, you may guess that there is a quick and easy solution ... data should be reproduced by others. In the end scientists should be concerned with the facts.
Alejandro Rivero comments on my entry on being scooped:
What do you mean by "Being scooped"? If the paper that comes out coincides with your research, that is good, shouldn't it be?. If it proofs that your research line is a failure, then really your work has been useless.
In response to my entry on Nature's new and experimental Peer review system,…
apalazzo | June 8, 2006I was alerted to the fact that strange things are happening at Nature Magazine.
From the Nature website:
Peer review is the bedrock of scientific publication (for Nature's position on peer review, see our Guide to Authors). It is widely considered essential for improving submitted papers and enhancing the credentials of scientists as well as those of the journals in which they choose to publish.
But, like any process, peer review requires occasional scrutiny and assessement. Has the Internet bought new opportunities for journals to manage peer review more imaginatively or by different means…
apalazzo | June 7, 2006Last night we were invited to celebrate the launching of Nature Publishing Group's Network Boston at the Museum of Science here in Boston.
What, you may ask, is Network Boston? It was described as a new digital community center for scientists in the Boston/Cambridge area. Another description would be the academic version of myspace. If all goes well other network sites will open in the near future.
Scientists can post their profile (photo, interests, publications etc. click here to see mine), form community groups (such as an RNAi discussion group), look for jobs in academia and industry (…
apalazzo | May 30, 2006I haven't been blogging that much recently ... well to be honest I've had too much work to do.
But as time goes on my ability to cope with the rich experience of daily lab life requires me to rant every so often. So here is today's rant.
There are two approaches to small biology, studying molecules and studying processes. Stay away from the molecule-centric approach!
What do I mean by that?
An easy trap for biologists to fall into is to latch on to their favorite protein and attempt to explain how it functions within the context of a cell. This methodology can sometimes lead to advances,…
apalazzo | May 27, 2006Hi Folks,
Sorry for the delay. It's been a busy week for me. Being swamped with work, the Daily Transcript was ignored. I've thought about it all this week ... life writing a blog and living the life of a postdoc. It's stressful. I enjoy both however the combination does not leave enough time in the day for other ESSENTIAL activities. From this point on I will be limiting myself to 3-4 posts per week. With the number of excellent blogs covering the big ticket science items, my blog will be refocused on NON-media items ... such as the life of a postdoc, comments about the machinations of…
apalazzo | May 19, 2006About two weeks ago I wrote an entry on what I hated about scientific journals. I intentionally did not include the issue of public access to publicly financed research, but it came up in the comment section. Interestingly Maxine, an editor at Nature, replied:
On the access problem mentioned here in the comments -- can't speak for other publishers but institutions almost always have site-license access to Nature which gives complete online access.
Nature ran a debate on this topic a while back which is free-access and can be see at:http://www.nature.com/nature/focus/accessdebate/index.html…
apalazzo | May 19, 2006Good news from RPM:
I just got word that the House of Representatives passed the FY2007 Budget Resolution which includes an amendment that ensures that all programs within the Labor, Health and Human Services and Education Appropriations bill will be funded at FY2006 levels, including a 2% increase for inflation. This will mean the NIH budget will receive a $600 million increase. It is not the $7 billion proposed increase that passed in the Senate, but it's better than nothing.
To read more and to read a from the Genetics Society of America, see his latest post.
apalazzo | May 15, 2006You got a love blog entries that start like this ... "there are two types of scientists"
Yes I know I do it too. But categorizing is what the human mind does best and so in this vein I'll present to you "Robots and Independent Thinkers"
A friend from Columbia told me about this particular type of division of grad students and postdocs.
Robots do what they are told.
Independent thinkers do what they want regardless of what they are told.
The question is, if you were a Principle Investigator, which would you prefer? When current postdocs were asked this question they responded "independent…
apalazzo | May 12, 2006Well a good friend of mine is starting a virtual journal club, Science Sampler. We'll be 3 to 5 contributors and the entries will be about articles from the current scientific literature. From the website:
We read them so you don't have to!!! Comments on recent works in Cell Biology, from the cytoskeleton to membranes. And we also read yeast papers...
So far there are two articles reviewed on the site, including a review of the same STED microscopy paper that I wrote about a couple of weeks ago.
The format of this virtual journal club will be based on the 5 minute men, a club at Columbia U.…
apalazzo | May 11, 2006I missed this. From the March edition of the Scientist. The top 10 in North America:
1. The J. David Gladstone Institutes, San Francisco
2. Fred Hutchinson Cancer Research Center, Seattle
3. US Environment Protection Agency, Research Triangle Park, NC
4. Emory University, Atlantic, GA
5. National Institute of Environmental Health Sciences, Research Triangle Park, NC
6. Fox Chase Cancer Center, Philadelphia
7. National Institute of Diabetes & Digestive & Kidney Diseases, NIH, Bethesda, MD
8. Wadsworth Center, Albany, NY
9. Dalhousie University, Halifax, Nova Scotia
10. USDA…
apalazzo | May 10, 2006Blogs = web+log. I started writing one to force myself to write. Although each entry is stored out there in the either of the net, blogs tend to be transient creatures. But how about all those great entries those that are read for a week then ignored?
Well in my "About" section I've now included a list of such posts ... the Essential Transcripts.
Enjoy.
apalazzo | May 6, 2006OK now time for some real blogging (I.e. rant).
Things I hate about journal publications.
1) Supplementary Data. You see a neat paper, you downloaded of the website and then as you go through the text you bump into "see supplementary data". Now I don't really mind this, however I hate that journals do not append the data to the end of the pdf file. Now I understand not everyone wants the hard copy of 2345 two hybrid reactions, but for most cases the 2 or 3 supplemental figures are crucial. It drives me mad. I get a paper emailed to me and half the data is missing! What is worse is if the…