Notes from the Biomass (A Bioinformatics Blog)

Last post

spitshine — 2006-07-16T10:56:00Z

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.

Stubborn

spitshine — 2006-07-07T08:55:21Z

OK, you got me. While technically not blogging at the moment, I should at least respond to your requests.

Ideas that I do support and I had in mind where with giving credit and communicating your work in beyond what is required to give you credits. We can go through the items individually, let's start at No.1.

"1. I believe that science is about freedom of speech."
While freedom of speech (or the right to express your ideas) is vital to science, you can't equate the two.
There is the "scientific method", which people more skilled in these arts have written tomes about, which could be summarized to state what science is about.

Certainly, I would not start the manifesto with that note.

Greetings from another HBS-founder (media-ocean.de).

"...which...

freshjive — 2006-06-15T18:06:13Z

Greetings from another HBS-founder (media-ocean.de).

"...which includes several pieces that I had in mind.."

Why don't you share what you had it mind and we can get a discussion going. Help us improve and extend the manifesto! :-)

HBS manifesto will be updated

020200 — 2006-06-15T16:13:24Z

Hi there!

I am one of the hard blogging scientsts.

We are about to enhance the manifesto. The current Version is 0.1 and we will continue updating the manifesto, since we have also scientists in house who research about blogs.

greetings!

Martin / 020200

Latter posts - comment spam

spitshine — 2006-04-29T16:45:00Z

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.

...perfect for the retreat tomorrow
Sounds great! I will make a proposal...

Konrad (anonymous) — 2006-04-25T11:34:53Z

...perfect for the retreat tomorrow
Sounds great! I will make a proposal to have a Powerpoint Karaoke session at our biocomputing retreat tomorrow. Cheers.

schade, I always liked to read your stuff, old friend. But I can perfetly understand...

vertikalist (anonymous) — 2006-04-25T11:28:40Z

schade, I always liked to read your stuff, old friend. But I can perfetly understand that you want to take a break. Wondering what you are going to do with your spare time now...

The free time

spitshine — 2006-04-10T21:13:48Z

Good question - actually, it feels like there is no additional free time. Guess I squeezed blogging just in. However, I really think a lot less about what to blog etc. Let's see.

On the way out

spitshine — 2006-04-10T21:08:15Z

Ahem, yes thanks but this blog on is on its way out. Visiting from time to time might be, ahem, optimistic.

schade

vertikalist (anonymous) — 2006-04-10T12:14:24Z

schade, I always liked to read your stuff, old friend. But I can perfetly understand that you want to take a break. Wondering what you are going to do with your spare time now...

Hello

Andrew Sun (anonymous) — 2006-04-08T14:38:36Z

I'm considering starting a blog on scientific literacy in English. Although the purpose is somewhat different from yours that aims for communication within academic collegues, blogs on science rather than 'politics and Harry Potter', as a whole, are of a limited number. I'm glad to know this blog and will drop in from time to time.

Thanks for the flowers

spitshine — 2006-04-03T17:46:36Z

Have to admit that the break does me well so far. Was a little surprise to myself when I decided to change/pause/stop last week. Does me well though...

Latter posts - further reading

spitshine — 2006-04-03T17:34:40Z

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 humanchimpanzee 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."

Enjoy the break

Neil (anonymous) — 2006-03-30T13:23:04Z

Blogging is an odd activity. I know what you mean by blog weariness, the feeling that you should try to post regularly, wondering whether it's a good use of your time, worrying if you don't feel that you have something to say.

I'm not convinced that a personal blog is the best forum for serious scientific discussion. If you try to "popularise" it in a certain writing style or by adding non-science topics, you're extending the readership to a non-specialist audience. On the other hand if you keep it very serious and focused on research, you'll only have a small audience :). Community blogs work a little better in this regard.

I think everyone has their own personal perception of what a blog is for and why they blog. For me, it's just a place where I can note things of interest that I've seen or read or sometimes just offload some mental baggage at the end of a long day. I'm not trying to be a great communicator and I don't really expect anyone else to read it, but if someone occasionally finds something of interest, well then that's great. In other words, I don't think it's worth getting too serious or concerned if a blog isn't working for you. Take a break, try to figure out what you want from science communication and try it out.

Don't stay away for long

Pedro Beltrao (anonymous) — 2006-03-30T08:33:45Z

You can't stop really :), who do I link to then ? Its too hard to find people actually blogging on science related topics (intelligent design bashing does not count).

Thanks for a year of good reading

Stew (anonymous) — 2006-03-29T21:20:42Z

Sorry to hear that you're winding down the blog for a while. I've very much enjoyed reading it over the past few months, and it sets a high standard for bioinformatics blogs in general: I think you've done a great job. Hope your blog holiday isn't too long...

In any case, thanks for a year of good reading.

Latter posts - Part 1

spitshine — 2006-03-29T19:51:04Z

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.

Why opting for fraud?

spitshine — 2006-01-11T20:58:41Z

My most dangerous idea was voiced earlier on this blog:

It appears frightening simple to found a scientific career on fabricated results alone - and to get away with it. Most of the scientists that were uncovered doing fraud did very foolish mistakes. More recently, Derek Lowe at In the pipeline wondered how one can actually live under the specter of being an imposter. I largely agree with his analysis of the situation but somehow do understand why you can opt for fraud instead of taking a real risk of failing rather than being uncovered.

There is an enormous pressure on scientists to succeed. You only have limited to time to succeed in a risky business, either because your contract is running out or because of competition. Do you want to be a third class researcher or an underachieving ivy league alumni - or a successful imposter? The emotional burden seems comparable. You should even have a lot fun if you take that road to hell (which seems like a stairway to limbo from down here - limbo ain't so bad, eh?).

Besides that, science is build on trust and I have no sympathy for anyone who opts for fraud rather than accepting the risk. The internet is a bad place to be sarcastic, I know. Don't consider the following advice to ensure your scientific career without being overly dependent on research results as a real.

Start as soon as you get your own lab to keep things in control. Grad school is too early (you'll graduate anyway, getting in is the difficult end). You can try enhancing your results as a Postdoc but don't push it, there are still people who don't like you and are too close to you. Once you have the lab to yourself, go all in.

Work on the forefront in a challenging area that is just too difficult yet boring for others to get in just to check some one else's results. Make sure you collaborate with a clinician that provides you who with whatever odd sample you might need. Don't worry, there is nothing an MD wouldn't do to get his name on a paper. Perform cross-disciplinary studies, employing expensive equipement on precious sample - who will ever repeat it?

In that respect, cell biology is be a good field, the findings are of great impact yet research is difficult and results are somewhat fishy in general. Gel and microscopy pictures are easy to fabricate. Most scientific institutions have site licenses for Photoshop and they all use it before publication anyway. Just use it creatively!

Don't forget some bioinformatics or statistics mumbo jumbo. The anoraks make excellent collaborators as they are not interested in the experimental procedures in the first place, and a call for more experimental data should not pose a problem right? Besides, there is so much data on the web that one could resubmit. Get one statistician to apply noise to it (build a model...) and another one to analyze it. No worries, they don't talk to each other anyway. The human interactome can be constructed from yeast and and worm interactions and 8000 random pairs of proteins at no sweat and you'd even beat existing technologies. Always leave room for further improvements in your next ground breaking work.

You should appear like a real scientist before you become a great one - make sure you are only somewhat successful, stay modest, you get the press coverage when you go down. Don't go to a different fields for publishing every month as a single author. You have all the time in the world, if you know you can do it.

Stem cell research might be a good call again in a few years after the field will recover a from the fallout of Dr. Hwang. He was an amateur anyway (but wore nice ties). Your data must be waterproof - only beginners ever re-use the same picture. It should not be too difficult to redo all the controls in different concentrations (and no samples).

Peer review won't stop you. The reviewers got to decide whether the work is believable and of significant interest, not whether it is true. You can always perform the experiments that the reviewers want - what else could they ask for ever anyway? Just make sure you don't resubmit too soon or declare that the results were sitting on your desk, you just did not include them for clarity.

The difficult part in science is coming up with an original idea anyway - and they all know what results they want to see. Make them happy. If you can come up with an original idea, you've *done* all the hard work. Instead, work on your nimbus. Make sure your Powerpoint presentations look convincing before the publication to spur some talk in the field.

Hire some bright yet dependent people - visa issues are a great handle to keep your personnel on track. To get the right mix, hire some bloke from your home country, who is a hopeless scientist (and knows about it) but brings your good mood to the lab and can act as a bully. He might not even notice what you are up to and praise you as a God (get some satisfaction out of it, after all you gave up the opportunity in commercial enterprises to do good to society).

Go down in style! Wait until you have achieved tenure to ensure maximum damage for the institution you work for - that'll also maximize the press coverage (watch your wardrobe). The wife or the daughter of the dean, preferably both, should be involved in some way. You can still call it an attempt to show the world how leaky the system really is. Write a book about it, laugh at them - these things sell well. You don't even have to face financial consequences - it's all tax payers money anyway - your money, right? And everyone is going to read your blog finally (please, please-please-please link here - promised?)

And if they don't catch you? Switch into a new field immediately after getting tenure, hire some good postdocs that do good work for you finally. Or don't switch, they can even show that you are a visionary, not an imposter. The world of science is yours, take your piece, you deserve it. Only desperate people found companies to rip off investors. Found a lab!

Hard blogging scientists at work

spitshine — 2006-03-22T13:53:35Z

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

spitshine — 2006-03-15T17:30:43Z

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.

Can you make a good program with just a handful of people?

spitshine — 2006-03-14T17:04:52Z

Widely used software products - say, Microsoft Word or its FOSS equivalents tend to have a long history, a large userbase and many programmers - and interface designers.
Scientific software developmens teams are much smaller despite data that is often more complex. Commercial developments needs to compete with scientific hacks on Pareto distributed ground. I don't think that a better user interface, higher standards and better support deliver the competitive edge in this particular market.

N.B. We should really have this conversation over at the OpenScience site. The second part of series has just been released.

Accessing sequence information by location

spitshine — 2006-03-14T16:38:51Z

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.

Perceived value

Deepak (anonymous) — 2006-03-14T15:02:32Z

It depends on what you need. In much of the informatics space, the end user usually has enough savvy to work with open source software (and free software can be a little rought about the edges, since it is free). This is especially true for software to generate data. I still think that the software to analyze and visualize data is not that trivial, which is why analysis packages do cost money. Stew is also right. There are too many packages doing to same thing, which always brings the value down

In the physical modeling space, the software is not trivial to write (even many of the academic packages are not free). How much should they cost? It boils down to the value people get out of it and the business model around it. I do think that the services model will gain ground, at least in industry. I fail to see how it will be that successful in an academic environment, where grad students and postdocs come cheap.

In the end it boils down to this "what am I getting out of it?". I also think that usability expectations have changed a lot over the years, especially as more and more non-domain experts use software and are less willing to jump through hoops.

Expecting scientific software to be free

Stew (anonymous) — 2006-03-14T09:52:59Z

I don't know about scientific software in general (EndNote etc. probably clean up) but I can't think of any current genetics software packages that are complex, user friendly or unique enough to warrant a great deal of expenditure - programs tied to specific pieces of hardware excepted. There always seem to be in-house or comparatively rough around the edges (but free) open source alternative solutions.

Perhaps the most obvious solution to making money from scientific software is "make it good enough for people to be willing to pay for it". Pricing realistically for individual researchers, not just that big pharma bulk licencsing department, might also help.

Scientific open source software

spitshine — 2006-03-13T06:39:40Z

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.

We might agree more on the subject than you might have understood from my post. I...

spitshine — 2006-03-11T19:10:35Z

We might agree more on the subject than you might have understood from my post. I don't want to got through the text line by line if you allow (and promise to express myself more clearly from here on).

However, my reference to the C. elegans community might nicely map to your notion of the difference between methodology and biology. And I would agree that more worm geneticists would start to exploit the interactions available from the Zhong paper than from a web site that is not focussed on C. elegans.

There is no agreed standard on what signifies great scientific work - a clever idea, 10 person years of hard, targeted lab work, or a lucky finding? We could disqualify almost every work for lack of one or the other.

Thanks for speaking up.

I enjoy your blog, but I think you're being unfair on this one, Spitshine. The...

Sean Eddy (anonymous) — 2006-03-11T14:57:26Z

I enjoy your blog, but I think you're being unfair on this one, Spitshine. The Zhong and Sternberg paper is about genetic interactions (not protein-protein interaction), and it's in a multicellular model system (not yeast). If you think it's not novel because the overall technique doesn't seem novel, I'd argue you're losing sight of the difference between progress in biology versus progress in methodology! I reviewed the Zhong paper, and as a computational biologist, my initial reaction to the methodology was much the same as yours -- but then I looked at the results harder, from the perspective of a worm geneticist, and my feelings were much different. I think it's a nice step forward.

Annotated link list

spitshine — 2006-03-05T21:03:15Z

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

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.

More on high-profile papers on protein-protein interactions

spitshine — 2006-03-10T18:06:07Z

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 format is not the problem

spitshine — 2006-03-10T17:22:19Z

The text files not the problem for the supplementary data, it ist rather the way there are tied into the manuscript.

The problem with the web interface lies in the long time commitment and that it often does not really help people in navigating the data. A tab separated file for Excel or a database might be the much better choice in many cases.

Besides, one would not be able to track the hot molecule that one is working on. If you happen to access a site of lab that scan their log files for it ...