nodalpoint.org - Microbiology - Comments

writing style

chris — Fri, 23 Dec 2005 13:25:37 -0500

I'm a big fan of these sorts of articles. The best writing usually tells a story: a continuous narrative for some reason resonates deeply with the human mind and allows us to absorb information and place things into perspective. It's an old trick, going back to the legends and parables of the ancient worlds of Gilgamesh and Homer.

One of the things we often miss when reading/writing a scientific paper is this narrative: the introduction should at least set the scene, but in truth so many scientists are so poor at writing that their papers become garbled and abstruse, even for other experts in their field.

Maybe we should all try to tell stories in our next papers?

A huge parts list

PedroBeltrao — Sun, 08 Aug 2004 11:56:11 -0400

I specially like the idea of using the minimal genome (still a work in progress) to determine in high throughput fashion the function of the huge gene list that he will produce. Imagine the potential of such a parts list, combined with the ability to quickly assemble and test. It is a kind of "what do you want to build today".

I don't really know how he plans to get the function for the genes, since most proteins work within systems and not in isolation. Maybe something like rescue of function by adding, in the minimal genome, random combinations of the genes he finds.

Sometimes his actions seem like - do it first, think about it later - but anyway it looks fun :).

Data availability

Greg — Sun, 08 Aug 2004 05:36:24 -0400

No matter how much you may loathe J. Craig Venter, you must admit that sailing around the world in your personal luxury research vessel is amazingly cool. Back in the real world, Mr. Venter is making all the data collected from the expedition available for download.

the origin of sars

Anonymous — Fri, 13 Jun 2003 13:09:36 -0400

Despite a lot of hypothesis about the origin of sars indeed that their is a speculation that sars of the unimprtant coronavirus group in medicine could be originated in medical virology laboratories in countries which they have immense facility in creating gene maipulations or as a viral mutant or further more due to change in the ecology of viruses specially in heavily populated countries

Reference

chris — Tue, 27 May 2003 03:55:35 -0400

Sorry about that. Pubmed hadn't cited it yet when I posted. It's the Lancet, Volume 361, Number 9371 24 May 2003. Can't find in PubMed.And, fwiw, a pubmed search (via hubmed)on the man himself (bio note: he was a student and collaborator of Fred Hoyle's -- hence panspermia). Notice a theme to his papers?

In context...

Neil — Mon, 26 May 2003 23:28:58 -0400

Is there a link to the Lancet story? This has captured the imagination of the press of course; see Yahoo News for a brief story. A lot of media outlets are making the error of saying "Scientists say...", as if we speak with one voice. It should be pointed out that the main proponent is Chandra Wickramasinghe, who is a big fan of "life from space", panspermia etc. in general and a fairly controversial character.

Or...

Neil — Thu, 22 May 2003 02:24:01 -0400

...a well thought-out markup language ;-)

Idle query - what mechanisms are there in XML for binary data, like images? My only experience is in SQL where rather than store binary files in the database (immense storage/memory requirements ensue), a link to the file location is normally used.

It would be more useful

Greg — Wed, 21 May 2003 08:16:19 -0400

if I could download the data in a suitable XML format :)

lab monkeys

chris — Wed, 21 May 2003 04:34:17 -0400

Agreed. Like any problem, there are two sides to this one. Bosses very often just get students to repeat and repeat experiments, especially if the boss is busy and/or has many students. That means less hands-on supervision is required. The student must bear the brunt of this one, though -- at the end of the day, it's your project, and your time. An hour's worth of research or planning or troubleshooting (ie thought) can save days/weeks/months of repeating the same old experiment, again and again and again. Most people have no one to blame but themselves if they turn into lab monkeys.

Relieve the tedium

Neil — Mon, 19 May 2003 20:20:08 -0400

Maybe not rocket science, but definitely useful. It strikes me that a lot of "science" consists of students wasting their time doing incredibly tedious experiments (i.e. running gels) which must have been done countless times all over the world. Provided protocols are standardised and performed well, why not rely on another source?