Archive for December, 2007

Hot Portal Action

Published by Mr. Gunn on December 15, 2007 0 Comments

Two big portal plays recently: Scirus Topic pages and Google Knols. I don’t know if this is related to the recent Wikipedia infighting brouhaha, but it’s certainly timely. Wikipedia is great for what it is, but we do need something that takes and authority into account.

Of course, no one’s calling these new efforts portals, because that would be way too 1.0, but it’s what they are. A single comprehensive destination site, just like Facebook et. al are portals. One single place to go for people to whom the open web is too big and scary. There’s something to be said for that, as it allows the and authority that wikipedia and the web as a whole don’t have, but readers of this blog will know that I’m a fan of decentralization and distribution. My blog is where I create content, and the nexus of my social network. Of course, because the web is open, it automatically includes all these closed efforts, and ideally, will interlink them.

The commentary on “Defining Pluripotency in Human Cells” is up at the Niche.

Published by Mr. Gunn on December 13, 2007 0 Comments

Featuring commentary on their previous article by Peter Andrews, Shinya Yamanaka, Paul Tesar, and William Gunn(aka yours truly).

I really like Paul Tesar’s idea of a “pluripotency score”, because it’s just this kind of multi-factorial definition we’ll need to really nail down just exactly what pluripotency is.

What’s New in Pubmed? Nothing!

Published by Mr. Gunn on December 5, 2007 3 Comments

There’s a long-standing problem with trying to follow the literature on MSCs. The more proper name is “multipotent stromal cells“, whereas the name many people still use is “mesenchymal stem cells”. There’s also plenty of literature, on what is presumably the same cells, that uses “marrow stromal cells”.

To try to get around this problem in the past, I used the MeSH Browser to find the preferred term for relevant categories, searched on that, and created a feed from those results. That quit working about a month ago. According to the feed for “Multipotent Stem Cells”[mh] OR “Adult Stem Cells”[mh] OR “Mesenchymal Stem Cells”[mh], nothing is new since the first week of November. I see today there’s an announcement from about their update to MeSH for 2008, so I’m guessing there may be some connection between the two.

In the new hierarchy, multipotent , mesenchymal , and adult are all under as distinct categories. Multipotent is defined as “specialized stem cells that are committed to give rise to cells that have a particular function” whereas mesenchymal is defined as “Cells that can develop into distinct mesenchymal tissue” and Adult is defined as “Cells with high proliferative and self renewal capacities derived from adults.” I don’t know how they derived these categories, but clearly they aren’t non-overlapping categories.

Here’s what I get when I run various queries:

MeSH no MeSH
mesenchymal 2180 3386
multipotent 708 857
Adult 261 642
all 3 with AND 3 6
all 3 with OR 3025 4671
difference of OR and summed individual results: 124 214

So both MeSH and keyword queries lose some results when combined, and though MeSH queries lose less, they lose less of a smaller set that doesn’t contain as up-to-date results. I guess I’ll have to subscribe to each feed separately, or maybe mash them together with Yahoo Pipes or something.

YourSci.com is pretty slick

Published by Mr. Gunn on December 5, 2007 2 Comments

Yoursci.com is a 2.0 project along the lines of OpenWetWare, but with a little tighter focus. They’ve got a section for contributing a project, and protocol section, and what I particularly like, a negative data section.

Content contribution and tool making kinda trade off one another, but all too often the cycle breaks not because the tool isn’t functional, but because it’s ugly. YourSci.com is pretty, looks functional, and it just so happens that I have some information they’re looking for.

A good intro to microarray technology

Published by Mr. Gunn on December 4, 2007 0 Comments

A set of video clips illustrating the technology behind a DNA microarray. This is also a good example of the use of video in , leaving the focus on the process and not the reporter.

A couple reasons why columnists should be very careful when they opine about science.

Published by Mr. Gunn on December 4, 2007 0 Comments

Even active scientists often make mistakes when they comment on fields outside their expertise. In a recent example not involving a crackpot theory of quantum consciousness or intelligent design, Charles Krauthammer, an columnist for the Washington Post with a background in psychiatry, writes: Continue reading ‘A couple reasons why columnists should be very careful when they opine about science.’

The Personal Genome project website is live.

Published by Mr. Gunn on December 3, 2007 0 Comments

The Personal Genome Project aims to collect the genetic information of 100,000 people. According to Misha Angrist, one of the first ten volunteers, the cost to them will be about $1000, and it will cover the “exome”, or the protein-coding sequence of all 22,000+ known genes. This is still a tiny fraction of the total genome, though it’s significantly greater detail than the ~650000+ SNPs covered by 23andme for the same amount of money. More significantly, the PGP’s mission is to provide a benefit to society through research, whereas 23andme is for personal curiosity and there’s no explicit research infrastructure. Users of either service may find it useful to consult with a genetic counselor, such as DNA Direct or a service such as IMD, covered under some insurance plans. Fellow blogger Dr. Hsien-Hsien Lei is affiliated with DNA Direct.

More coverage here:
Genomics: Being Well Informed
Geek Doctor: Life as a Healthcare CIO
GenomeBoy.com
Full Disclosure
The Personal Genome Project
The PGP Blog