Notes from the Biomass

Notes from the biomass will continue at nftb.net.

My thanks to twoday.net, their service is recommended for everyone who is just starting to blog and doesn't want to be bogged down by administration of their own blog. However, at this point I need to move on and make use of more advanced software, most notably structured blogging.

A handful of noteworthy links

Other science blogs

• Science blogs - A blog network supported by Seed magazine, covering some 15 blogs

Blogs by editors of scientific journals

• Free Association - Nature Genetics
• Action Potential - Nature Neuroscience
• SciAm Observations- Scientific American

German blogs

• Spreeblick - No science here but influential on how to blog
• Riesenmaschine - Essential diversions
• Zeitwissen - Popular sciences blog

Meta

• Postgenomic - Tracking the life science blogs (covered previously)
• Technorati - The tracker of all things blog

Wikis

• BioWiki - An open wiki by the Ian Holmes lab (Berkeley)
• OpenWetWare A Wiki to share information between researchers in biological research. Covered here previously.
• Wikipedia - Obv.

So, according to the system biology et al. tag cloud that Kristofer posted, 'intelligent design' seems to be more important than 'genes' and 'computer' in what I try to avoid calling life science blogosphere. Can we have some other subject to bash please?

A nice essay about social bookmarking and spam - always felt uneasy about tagging to some extent.
[via Spreeblick ]

Half of my secondary blogroll, the rather mass compatible ones that I don't feel like emphasizing because everyone else does - Pharyngula, WorldMunger, Cognitive Daily and Uncertain Principles for instance - moved to scienceblogs.com, run by Seed magazine. Welcome to the sell out of the blogs.

I do understand why the individual bloggers went, given ease of hosting, professional help with web design and a broader platform of readers. On the other hand, the bloggers are now dragging Seed's shopping cart and there are not even statements about dependence on the farewell pages of the old blogs, e.g. Pharyngula or Uncertain Principles.
After all, Seed needs to make money and while they would not interfere with the content of the hosted blogs directly, let's wait until Seed publishes a somewhat fishy article that bloggers react to - And let's count how many links from scienceblogs go to the Seed news ticker in a few weeks. I found Seed rather shallow so far but I should give them some more time, they just started after all. Oddly enough, there are links from scienceblogs.com to Seedmagazine.com but no links pointing back.

This is a concentration of opinion and certainly a clever move for the magazine but bad for the overall independence of blogs. I would have preferred if the blogs would have introduced Adsense or the like on their pages to stay independent and spend the revenues on wine, hosting and song. You too can submit an application to Seed to have your blog hosted there - but whack some advertising to your pages, write a witty post about and keep your independence if you ask me.

Content armageddon - when the commercial forces finally battle the defenders of intellectual independence and creativity - is not due before web4.0 later this year. Scienceblogs is not a bad case of it either, just one that shows that bloggers are as likely to go the path of least resistance as everyone else. How dependent bloggers make themselves when joining these networks?

You can call me vain for linking to an overview of science blogs in Nature that mentions my views; Rolf Apweiler even considers bloggers as exhibitionists, so you'd have company.

Nature's feature explains the pros and cons of blogging in the sciences thoroughly, after I was somewhat discontent with Nature's coverage of Google Base last week. The article also reflects the opinion of many people on blogs as coffee room chats. I appreciate most things I picked up in lunch breaks and over coffees - and from blogs, much of it directly relevant to my work. And I don't want to think about the number of irrelevant, useless but peer-reviewed papers that I worked through. The number of valuable blogs (to every individual) is dwarfed by the number of irrelevant chatter out here but the same arguments can be applied to books or the scientific literature - it's only a platform after all.

Dear SVP of a Boston based PR company,

You are new in the email spamming business, aren't you? Otherwise you would have noticed that sending unsolicited email to bloggers is a mildly silly idea, even more so when signed personally by a "senior vice president". They can simply put the name of the company you would like to promote on their site together with defamatory statements (such as hires "PR companies to send unwanted emails"). Get that blogger issue from Forbes and tremble a little, I can't be asked to take any further actions here and won't even disclose your name here. You've got mail.

Roland

Looks like the biotech spammers are as inexperienced as the biotech spammees. And thank twoday.net for taking care of comment spam.

Generally, I don't like chain letters but the following survey that I picked up at Pharyngula, seems supportive of academic blogging, thus...

Overview:
The following survey is for bloggers who are actual or aspiring academics (thus including students). It takes the form of a go-meme to provide bloggers a strong incentive to join in: the 'Link List' means that you will receive links from all those who pick up the survey 'downstream' from you. The aim is to create open-source data about academic blogs that is publicly available for further analysis. Analysts can find the data by searching for the tracking identifier-code: "acb109m3m3". Further details, and eventual updates with results, can be found on the original posting:
http://pixnaps.blogspot.com/2005/09/academic-blog-survey.html

Instructions:
Simply copy and paste this post to your own blog, replacing my survey answers with your own, as appropriate, and adding your blog to the Link List.

Important (1) Your post must include the four sections: Overview, Instructions, Link List, and Survey. (2) Remember to link to every blog in the Link List. (3) For tracking purposes, your post must include the following code: acb109m3m3

Link List (or 'extended hat-tip'):
1. Philosophy, et cetera
2. Pharyngula
3. Notes from the Biomass
4. Add a link to your blog here

Survey:

Demographics
Age - 33
Gender - Male
Location - Berlin, Germany
Religion - None
Began blogging - October 2004
Academic field - Computational Biology
Academic position [tenured?] - group leader [no]

Approximate blog stats
Rate of posting - daily
Average no. hits - 80/day
Average no. comments - 1/day
Blog content - 80% academic, 0% political, 20% personal.

Other Questions
1) Do you blog under your real name? Why / why not?
- Yes. Anonymity is not for scientists that want to communicate.

2) Do colleagues or others in your department know that you blog? If so, has anyone reacted positively or negatively?
- Yes. Most colleagues seem rather puzzled about why one would do so.

3) Are you on the job market?
- No.

4) Do you mention your blog on your CV or other job application material?
- No. But there is link from my home page for those who are interested.

5) Has your blog been mentioned at all in interviews, tenure reviews, etc.? If so, provide details.
- n/a.

6) Why do you blog?
- Social software (and blogs) are (one) good way to foster scientific communication, particular across disciplines. Add general curiosity.

Two phrases dominate the label scientist use in bioinformatics. Couldn't the definitions people use for they "job descriptions" be labeled escapism?

• Bioinformatician - A scientist with a background in biology or biochemistry who stopped generating data himself
• Computational biologist - A computer scientist or physicist who happens to use biological data

Seriously - go to any conference, ask the participants for both their "label" and their background. I got 100% correct (sample size:2). Am I a biostatistician now?

Today, my hosting service recently enabled anonymous comments. They are now enabled on this blog also. One-click content but I thought I let you know.