Notes from the Biomass (A Bioinformatics Blog)
A Bioinformatics Blog
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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. - Latter posts - comment spam
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. - Latter posts - further reading
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."
- Latter posts - Part 1
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. - Hard blogging scientists at work
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. - Alone down there
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. - Accessing sequence information by location
The three major DNA sequence repositories (Genbank, EMBL, and DDBJ) decided to include for a location identifier in 2005. You can now access EMBL via a map of the world.
Not that I think that it is highly useful as of now but it gives a birds eye view of things to come. - Scientific open source software
The market for most specialized science software is rather small, consequently the software is usually expensive. Many scientists even expect scientific software to be transparent (or downright free the younger they are) but how would one sustain a company in a niche market?
Dan Gezelter from the OpenScience project is facing the dilemma and summarizes the points that may have been made before but have never been solved.
Giving the software away for free and try to live off consulting is an approach that has been tried by the people involved in MySQL or WordPress with Automattic.com. However, the small market size will make it a very risky business - after all, grad students are always cheaper than any outside consultant, even if they would work for food and lodging. - More on high-profile papers on protein-protein interactions
The post on the interaction paper that I found peculiar due its stress on the "first analysis" received several comments by email and verbally. Several of them were rather disappointed with the paper in general and stressed that the body of interactions used for inferences was very small and that little novelty was described in general. However, I find nothing "wrong" with the paper and if the editors find it interesting, why shouldn't they publish it?
A similar paper by Zhong and Sternberg in Science this Friday might receive the same criticism - much of it has been seen previously in other organisms, there is little novelty in the methodology. The authors integrate transcription data and interaction data from several organisms and provide experimental evidence for their prediction. The approach is not different from strategies employed by in the String database (Disclaimer: done by my former lab) or work from Lee et al. that also appeared in Science and several others. One might want to comment on the lack of references but given the severe restrictions by the journals it is problematic to select the right ones.
Further in defense of it: The work by Zhong and Sternberg might not seem to be novel in the eyes of the pundits but it is probably of considerable interest for the C. elegans community.
Other memes that often go around with papers from your core expertise in prestigious journals: "This work should not be in Nature Genetics" and "I wonder how it got into Science". Maybe I am just getting older but I relax and think that if these works are accepted, my work has a better chance of getting published too. At the end of the day, good work is recognized in your field even if it is not published in Cell. There are just less people jealous people commenting - is that a bad thing?
Or as a collaborator recently put it: You can get away with publishing good work in mediocre journals but not publishing mediocre work. Focus on your work, not the impact factor accrued by other scientists.
[Note to self: Re-read every Friday until you really believe it] - The first analysis of the human interactome?
The analysis of the current data on protein-protein interactions described in human by TBK Gandhi et al in the March issue of Nature Genetics delivers a fair overview - solid but yielding little surprises. The authors compare human, yeast, fly and worm networks and verify a few transfers between species experimentally.
What struck me about the manuscript is the abstract which starts with:
We present the first analysis of the human proteome with regard to interactions between proteins.
Did the work by Lehner and Fraser not analyze human interactions - it is even cited? Many other publications analyzed aspects of the human interactome on many levels, e.g. work from text mining. There are works describing first glimpses into organisms that are not readily accessible for high-throughput methods. For instance, a recent computational analysis of Plasmodium falciparum does not claim to analyze the "interactome" but limits itself to prediction of new functions using protein-protein interactions.
Then again, every step to obtain a complete picture of biological data sets is oversold traditionally. The "complete human genome" was published about five times. There were only few experimental approaches to the problem of delivering a one-dimensional sequence. Given the complexity and the plethora of methods, the "complete human interactome" will be published a hundred times. - Annotated link list
A handful of noteworthy linksOther 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.
- Fractals in a petridish
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] - On the practice of using supplementary material for data
Gregory Petsko's editorial in Genome Biology compares the current practice of stuffing all data into tables and ill-formated text files as supplementary material and only giving an introduction and a discussion in the main paper with fighting a land war in Asia. I don't particularly like the analogy and the tone of the editorial in general but largely agree.
Currently, we attach complex data to a document style that is not much different from way science was communicated in 1950 despite advance in IT technology that make data sharing possible. However, we need to come up with better formats, not longer papers that include more data.
[Via Keats' telescope] - Vitamin-D mediates antimicrobial response
If you are but moderately involved in research in innate immunity and Toll like receptors, the Science paper by Philip T. Liu et al, led by Robert Modlin entitled Toll-Like Receptor Triggering of a Vitamin D-Mediated Human Antimicrobial Response will cross your path soon - in a journal club or on a coffee table conversation.
If your are just interested but have not been exposed to the questions of molecular biology in innate immunity, the publication is noteworthy as it reviews (and probably adds to) the challenges and controversies in the field of Toll like receptors (TLR) mediated signalling. TLRs are a *hot* class of molecules involved in recognition of pathogenic stimuli but are poorly understood given the amount of research they have been attracting.
The researchers focus on the known differences in the susceptibility of population groups to infections of Mycobacterium tuberculosis and on a particular group of TLR, the TLR 1 and 2 heterodimer. Tuberculosis was previously described to be influenced - amongst many other factors - by UV exposure which is involved in the production of vitamin D. The levels of skin melanin and consequently skin color limit the levels of UV light that reach lower regions of the skin where the vitamin is produced.
The hypothesis that vitamin D plays a role in the mediation of TLR signaling in the infection with Mycobacterium tuberculosis is experimentally augmented by showing that one of the key molecules, VDR is expressed upon stimulation with TLR-ligands in human monocytes. The differences in TLR between a caucasian and an afro-american group could be removed by adding the compound 25D3, a precursor to vitamin D, which suggests that it is directly involved in the signaling, not providing an overall benefit - the key finding of the study.
Finally, the authors argue that the some of differences in antimicrobial pathways of mice and humans might be explained by the nocturnal life style of the rodents, which relay TLR signals via nitric oxide instead of vitamin D.
Somehow, this sounds like it would be a good idea to spend some time in the sun to fight prevent infections. The work will be discussed in our lab for sure - if I learn some new insights from our experts, I'll comments it here.
[Links of interest to the article in The Scientist] - Fairy tales of actin tails
This Valentines Day greeting depicts Shigella flexneri (green) and its actin tails used to escape the phagosomes of macrophages[w]. Gullible people like me could think that the was a genuine finding - but it was photoshopped.
Following the stem cell fallout, journals are in the process of reviewing their publishing policies for scientific papers. Nature's is published in the current issue, including the requirement that all "enhancements" performed on the complete picture. I wonder whether such manipulations could be detected reliably and whether there are cases where image manipulation was the main route to a publication. My impression is
that the submission of a positive control as a confirming sample is the most travelled route in fraud.
[More on actin tails in Nature Reviews Microbiology[s]. Thanks for the picture, Sebastian!]
