Notes from the Biomass

Things to do when you're not blogging: Taking care of comment spam. After I revisited this site recently, I had questionable fun with several comments in German. They were just statements of admiration by Gotfrid and Hans and other namesakes of baddies from Die Harder Than You Can Possibly Imagine Reloaded, written within ten minutes. Still, there was a little lag time before I realized that they truly were spam and at first, I felt hurt. I do write in my second language, but mistaking it for German was a little much, even for a spammer - but there were no links to anything, so I suspected a funnyish prank. However, the earliest of six spam entries had the links that I was expecting. I am not sure whether others have had similar experiences, so it appears that the spammer enters several blunt, nice comments into the blog manually to obscure earlier link spam. There is an increase in this type of spam here. I was expecting that comments would not be indexed but I also realized that some of the spam on this blog that I had deleted was still accessible via Google.

Anyway, twoday.net was a good choice so far and at least I had never problems with automated spam as other blogs. I wonder when manual spam and silly comments will converge.

Why don't you turn to a book, read a comic or scientific paper? Some all time favourites that crossed my path recently.

A 120 page novel

Stanislaw Lem, one of my favorite authors died recently. As his best story (Experimenta Felicitologica) is not available in English - well read the Futurological Congress. Still excellent after the 5th time.

Evolutionists are the better demagogues

"Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision." by Dan Graur and William Martin.

Here's a motivating yet misleading excerpt:

In fact, we might ultimately be able to tell whether the human–chimpanzee divergence occurred on a Monday or not.

Promise to read the rebuttal too, will you?

The best graphic novel on the cheapest paper

The best story line to start reading Cerebus is Church and State.


"Cerebus will bless your baby and tell you a valuable story. You can get what you want and still not be happy about it."

365 days ago I started to blog about life sciences and bioinformatics in this spot - for one year. The experiment is over and I might review what has happened in the next couple of days in more details. However, I have decided to discontinue Notes from the Biomass in its current form.

A blog break hopefully gives me the opportunity to reconsider many things. Blogging takes time. It depends on your perception of the day whether it takes too much of it. I became pretty blog weary over the last couple of months and while there might have been one or two interesting posts, I was not overly happy with the quality and form for too long. In particular, the opportunity for serious scientific communication seemed less of an option than I had initially hoped for.

There will be a couple of posts coming here still but I will rather use other forms to use online communication. I'd rather comment on other sites and write longer articles and essays. Later, I might move finally run the Wordpress blog that I was aiming for for too long and resume but before that there will be some downtime.

So thanks for all the feedback so far.

The keywords Biology or Science in Technorati are dominated by popular science blogs, many of them discussing other topics ranging from politics to Harry Potter side by side. My preferences for this blog are different: I concentrate on sciene - bioinformatics and genomics - and mainly want to communicate with fellow scientists on special interest themes. There are a few blogs around that follow a similar setup, several in my blogroll.

Every once in a while, I was inclined to follow the trend to write a little manifesto for this style of blogging. I decided to focus on my content first and post the meta-content at a time when I think I have arrived at some stable point - which is yet to come.



It turns out that the hard bloggin' scienstist, a group of mostly German bloggers already came up with a manifesto, which includes several pieces that I had in mind. I am rather close to put the badge on this website. Just that "science is free speech" - it's a little more than that - feels a little too simplistic for the first paragraph.

The background of most of the founding scientists seems to be humanities and rather than life sciences or computer science. Many of the blogs are not very focussed on science yet but the manifesto comes closest to my approach to blogging as a scientist and is worth studying if you reflect on how to use your blog as a scientist.

Today, the Daily Transcript (a recent scienceblogs addition) lists the worst parts of scientific life. Somehow I cannot tune in the crying tonight - being a scientist of the best jobs I can think of on this planet. However, if your gel was empty, you can't find the bug in your own 3 lines of code and your arch-nemesis just published your good idea with sloppy and inconclusive data turn there to ensure that you're not alone in your misery. I'll join you tomorrow. Or some other day.

The stunning of images of simple bacteria growing in stunning patterns crossed my browser several times last week. Explore the astounding Sociofiction blog, one of the sources and other references from Pruned.

[via Kottke.org]

The following blogs have been in my blogroll for some time - I'd like to point them out anyway. While it shows that they started recently, all of them have potential to contribute to the blogosphere and arrive in the magic middle.

Nature erratum is my preference amongst the grad student blogs that uses anonymity to reflect on the process, hence other PhD students might get the most out of it. The advice to fedex your application (and hopefully its positive results) are worth following up.

The initial reason to read Blogging the biotech revolution by "Francis Crick" was to make fun of it, I have to confess - that combination was just too much. However, the content - mostly conference coverage - reads well versed and I hope to see more of it.

Unlike the two above, Deepakh Sing has no intentions of hiding himself in anonymity at business|bytes|genes|molecules. His rather playful blog connects nanotechnology and bioninformatics in a unique way.
[Thanks for the link, Robin]

The main shortcoming of the above blogs is the small number of posts per time - I can only advise to continue.

Most mashups suck fail to deliver suck - aggregating feeds from other authors by subject and placing google ads around them is the despicable and brainless end of web2.0. Postgenomic.com is one of notable exceptions, released by Stew (of Flags & Lollipops fame) that delivers information for science bloggers that you won't get out of your RSS reader easily, such as statistics on cited publication and an aggregation of meeting reports (pretty close to what I had dreamed of). It's still in the making and might be more alpha than beta but certainly not gaga. Tres cool!

[More explanations at F&L]

Old Nodalpoint has always been more than a multiuser blog and recently polished its forums. Incidentally, my recent search for useful discussion groups on bioinformatics subjects turned out to be futile again. Now I hope that Nodalpoints user base will ensure the quality of the posts. There is really not much point to discuss the same subject in every science blogs in solipsism.

The concept of hypertext needs little introduction - its simplicity is immediately obvious to novice users of the internet. However, one aspect of hypertext remains problematic: How do you describe the link target without breaking the text flow? The use of placing the link on a 'here' after a short description fell from grace quickly.
People advocate the explicit description of the link but that is no solution if you want to link from text that is styled as in a book or paper magazine. Some sites (e.g. Wikipedia) use icons to show that links refer to external pages. Many commercial publishers only link within their own publications and contain links to external pages in yucky boxes, together with a disclaimer that they have nothing to do with the content, thus completely splitting text and links.

For a blog, this is usually not an option. However, Notes from the Biomass often links to content that need to be identified for users: Links to sites requiring subscription - mostly scientific papers, and links to German content. Both types of links annoy me quite a bit when I find them on other sites but I am also appalled by the ugly insertions of '(Subscription required)' or '(Danger, German language)', hence I found myself constantly violating my own ideas on how to write for the web.

At first, I developed little icons that could be inserted after the link. Little flags to indicate the language were surprisingly difficult to choose, after all, German is an official language in Switzerland as well as parts of Belgium and I have even less desires in littering my blog with German flags. Locks or toll barriers, indicating links to content requiring subscriptions or one time paid access, are difficult to identify, let alone that I am not a Photoshop gimp.

After some thinking I invented just a simple code of letters and place to explanation in the sidebar of this blog.

[en] - Target page in English (usually omited, only to be used if there are ambiguities)
[f] - Free access (default, again for disambiguation only)
[de] - Target page is in German
[i] - Internal link - link to other posts at Notes from the Biomass
[p] - Paywall - This link might require paid access - news papers such as the New York Times often restrict access to subscribers or individual paid access after several days.
[r] - Free registstration required (I think these sites are on the decline - but just in case, you can try bugmenot.com if you don't want to give away your personal details)
[s] - Subscription required (Many scientific journals)
[w] - Wikipedia

It still does not solve the problem of where to place the link in a given sentence but I hope it's a start. I restyled some of my recent posts accordingly - let me know what you think of the idea.