Transitions, transitions

Quite a few things happened while I was away. If you’re interested, here’s not so short summary of my internet hiatus:

Research area

I think I’m done with bioinformatics. My current research area seems to be located somewhere between systems biology, theoretical biology and information/complex systems theory. I hope to build on Dawkins work, deal with emergence in biology and study subtle effects in biological systems. While I’m not sure if I will have anything interesting to show ever, I don’t have energy to do yet another project which involves programming/web interfaces/dealing with data/annotations/modelling etc. I’m done with analytics, time for synthesis :).


Last year I wrote a post dreaming about small non-profit contract research organisation. This model of Research-as-a-Service has materialized in a virtual research institute which we have finally launched few days ago (materialized in something virtual, sign of times? 😉 ). The setup is quite simple – the institute gets a project (or applies for such) and then it searches for researchers/institutions/freelancers which are willing to subcontract parts of the project. We have outsourced not only research part, even money gathering (writing grants, etc.) is done by external company. The setup is quite flexible and pretty transparent – for example, we may represent somebody’s rights, but no intellectual property is owned by the institute. Why such institution? We become a single point of contact for a large and diverse group of scientists, which are willing to do some research for real money but don’t have time and energy to hunt for gigs by themselves. While I have an academic job, I’m in the middle of transition from being a freelancer, to being a jobs provider for freelance scientists. More on that in some other post.

Open science

I plan to spend way more time on advocating open science (all of its flavors), but… in Polish. This step is out of large frustration that even prominent figures in Polish science have no idea about changes in the science internet-aware researchers are watching and creating. Knowledge about even basic things like Open Access is dramatically low in Poland (a number of people here equals OA with low quality publications which have not been peer-reviewed). With few friends, we have a number of projects in the pipeline (for example, we hope to launch a nation-wide, created by professionals  promotional campaign – bilboards, TV commercials etc. – for open science). If any of these actually works, I will let you know if we have any measureable success 😉 .

Labels, labels

Robert Anton Wilson tells a nice story in his book Prometheus Rising:

William James, father of American psychology, tells of meeting an old lady who told him the Earth rested on the back of a huge

“But, my dear lady,” Professor James asked, as politely aspossible, “what holds up the turtle?”
“Ah,” she said, “that’s easy. He is standing on the back of another turtle.”
“Oh, I see,” said Professor James, still being polite. “But would you be so good as to tell me what holds up the second turtle?”
“It’s no use, Professor,” said the old lady, realizing he was trying to lead her into a logical trap. “It’s turtles-turtles-turtles, all the way!”

Another story is a comment from my advisor about putting my real research plans in some proposal (he supports these plans):

The most likely a reaction from reviewers will be something like this: “Nice start, some decent papers, PhD looks good. And then he got crazy.”

I feel like screaming “Labels, labels, labels, all the way!” when facing stiff schemas of what scientists “is” or what artists “is” etc. It’s a hard task by itself to integrate multiple passions and multiple interests into a coherent structure. I don’t need another set of issues because of labels people attach to seemingly creative professions. But limiting myself only to topics consistent with the image of an online scientist became even more frustrating. Therefore expect that this blog (or any other venue I choose to express myself) is going to become a lot more diverse in topics and form.

1 Comment

Posted by on October 28, 2009 in Comments, Research, Science and Art


Open Science: a step towards Open Innovation

Open Innovation is a catchy phrase, but I don’t think we are that close to it, as many people claim. Innocentive, InnovationXchange or NineSigma operate in the very small market, and this market does not seem to grow as fast as we would wish. Innocentive posted some statistics as of 2nd of June, 2009, so given these numbers and amount of open challenges, it’s safe to assume that as of today, around total of 1000 challenges were posted and ca. half of them were awarded. If you compare that numbers with almost 200 0000 patents issued only by US Patent Office in 2006, it gives a clear picture of the size of the market open innovation crowdsourcing companies (edit: as Jean-Claude points out in the FriendFeed comment, Innocentive and the other two companies mentioned earlier are rather crowdsourcing, not “open innovation” companies) are operating in. There are plenty of reasons why OI did not yet become mainstream (too many to list) and for that to happen, there are two important steps that we need to make first.

Open Science must become mainstream

I’ve been advocating Open Science for some time and I’m following Open Science luminaries for much, much longer. At some point it hit me that Open Science in its fullest form is not an issue that scientists can truly solve by themselves. Open Science crosses domain of Science – it’s an issue for Science, Politics and Business. We should experiment with various ways the research is done, collaborate openly, attempt to invent new business models to fund science and spread “open” meme as much we can. However, the real deal will be made between people in power from these three domains. Why this is necessary to achieve that before we may fully innovate in the open? Because in this step we will sort out all the problems we have today with intellectual property and technology transfer (both being not efficient enough for today’s standards). I cannot envision that happening in other domain – we are paid to collaborate and test ideas. This community is able to hit every major obstacle to “open” in a very short time. And once we have these obstacles removed there’s a next step:

Working models of Open Science should be tested outside of Science

In other words I postulate that whatever solutions work in domain of Science, these should be tested outside of it, in other domains. Not vice versa. Principles of Open Source software did not prove to be useful in open drug development (see Joerg’s post on the topic). Crowdsourcing will not advance quantum physics. Not all aspects of collective intelligence are working in Science. We simply need to invent working solutions within the domain first, and then test them in other domains, such as art or engineering. This step will provide another set of protocols, changes and adjustments that will allow seekers and solvers (to use Innocentive’s nomenclature) to work efficiently together crossing every domain.

Open Innovation is not a single step

I may be proved wrong by some genius that will solve Open Innovation proovedissues in a single brilliant step, but so far I believe that we need more than one to achieve this goal. And it is important to recognize that Open Science is a great opportunity to come closer to it. The sooner we realize it, the better.

Reblog this post [with Zemanta]

Posted by on July 2, 2009 in Comments, open-science


Tags: , , , , ,

Visual analysis in not only about seeing

I’ve just sumbled across this short video on work of Turkish artist Esref Armagan, born blind, who nonetheless paints and draws. I will let you draw your own conclusions – mine are briefly expressed in the title of this post.

Hat tip Mayer Spivack.

Reblog this post [with Zemanta]Update: if you cannot see video embedded, here’s a link.
Comments Off on Visual analysis in not only about seeing

Posted by on June 29, 2009 in Comments


Tags: , ,

All 2.0 – an attempt to connect disciplines

All 2.0Last year I bought a domain name Initially I had an idea to launch a huge portal around “2.0” meme – essentially tracking changes in communication methods across various areas. I wanted to quit science and start a consulting career in helping people to communicate more efficiently (new channels and tools, efficient visual communication, etc.). However, a market for such services in Poland is nonexistent, and I didn’t have a mood for relocation, so I’ve turned to other opportunities (and as effect, I’ve stayed in science). Neverthess, I still had a domain but no clear idea what to use it for.

So, with only a little time left, the next option I took was a tracker/aggregator. In theory, once done, it didn’t need much maintenance. There’s quite a lot of services for such purpose out there, but they didn’t necessarily allowed for certain things I wanted to have, so I had to code my own script. As I didn’t have much time, the resulting site is a little rough (it cannot compete with wonderful sites Euan is coding, such as recently released preview of Streamosphere). However, you should get an idea what I’m aiming for. Currently it tracks blog posts and conversations in areas of Science 2.0, Health 2.0 and Culture 2.0 (with Enterprise and Government to follow). Because within these types I sort all entries by date, I had to remove some bloggers from “Key People” list, as their high-speed blogging did not allow others to appear in the box at all. 🙂

At this stage, the set of sources is far from perfect – outside of science, conversations seem to be highly homogenous. When I improve the sources (maybe will use Twitter and custom FriendFeed searches), I plan to add some kind of visual summary to the tracked conversations to see if I can find some patterns that will let me establish a connection between disciplines. Let’s see…

While I was collecting links, I’ve found one interesting thing: you can find people interested in these three areas both over at FriendFeed and over at Twine. However, it seems that only scientists are actively talking with each other at these services – where are other groups storing their discussions?


Posted by on June 28, 2009 in bioinformatics


Open Science, what is your message?

It recently occured to me that maybe Open Science could be marketed more efficiently by simplyfying its messages and better targeting. I often find it difficult to convince scientists to support the idea, because Open Science idea does not seem to solve their problems. Western scientists have the main problem: not enough money – the rest are just details (I will be happy to be proven wrong, but I constantly notice that majority of scientists will happily play in the current academic system as long there’s enough money for their research). How about having the main message of OS movement along the lines of “Open Science = Cheaper Less Expensive Science”  (that’s something that Jean-Claude and Cameron say for some time)? I know that we don’t have enough evidence to say so, but on the other hand nobody seems to care that there are better measurements of scientific productivity than impact factor (and have some evidence for that).

Simple message – but also better targeting

Such message is not going to resonate at places that have much more significant problems than lack of money. To me, there are several places in the world that suffer from other issue – isolation. Thomas Erren in his short commentary on Phil’s Bourne “Ten simple rule for getting published” cites Rosalyn Yalow, a Nobel prize laureate:

… I am in full sympathy with rejecting papers from unknown authors working in unknown institutions. How does one know that the data are not fabricated? … on the average, the work of established investigators in good institutions is more likely to have had prior review from competent peers and associates even before reaching the journal.

And it’s just only one side of isolation – there are many more. So, maybe in such places the message of OS should be along the lines of “Open Science = Connected Science” (following one of Deepak’s blog themes), explaining that openness creates connection through which knowledge, experience and recognition can flow both ways?


Posted by on June 22, 2009 in bioinformatics


Dreaming about bio-spreadsheet

One of the often occuring task in my work is to present results of an analysis in some kind of table. I have used for such purpose quite a number of approaches, starting from generating simple HTML file, through fetching of SQL data into table stored in a wiki, up to using Rails. One of the dreams I have recently is a web-based spreadsheet that would allow me to apply some specific piece of code over every row/column and show resulting table.

ScreenshotA simple mockup is shown above. In this example, a code:

print " <img src="{column_1}_bio_r_250.jpg>"

… iterated over first column containing PDB codes, would substitute these codes with an image of a protein from PDB server.

In other words I dream about simple (single file would be the best – I like the approach Sinatra framework is taking) web-based programmable spreadsheet. Something like Resolver One, but simpler. Is there anything like that available?


Posted by on May 19, 2009 in bioinformatics, Software


Science 2.0 – introduction and perspectives for Poland

This is more-or-less transcript of Science 2.0 based on a presentation I gave on conference on open science organized in Warsaw earlier this month. Please remember that it’s not meant to be a general introduction to S2.0 – it was prepared for mixed audience and focused on perspectives for Poland.

Science 2.0 is a concept describing new forms of communication between scientists. Communication has been the essence of science; research become meaningful only after confronting results with the scientific community. So far it was thought that peer-reviewed publication is the best communication channel we had so far. New internet technologies had changed this picture – not by replacing the “best” channel, but by showing that the concept of “the best” covers only small part of a communication spectrum. We knew that already, but we keep forgetting: people didn’t stop calling each other after email had appeared – these two services complement each other. And in the same way many of new communication channels complement peer-reviewed publication.

Collaboration, exchanging information and confronting research results in 2.0 era have two important attributes in which they differ from traditional models: openness and communication time. Exploration towards increased openness and shorter communication time happens already in publishing industry (via Open Access movement and experiments with alternative/shorter ways of peer-review). However I wanted to say few words about experiments that go little or quite a lot beyond publication.

I have chosen My Experiment as an example of an important step towards openness because it’s probably the least radical idea you can find in modern Science 2.0 world. This service provides a virtual research environment in which the main focus is put on sharing scientific workflows. One of the use cases may be sharing a precise diagram of the “methods” sections from experimental (including bioinformatics analyses) publications. Small step towards openness towards other scientists – we can make it easier for others to understand what we did in a particular paper.

And while we can open towards other scientists we can also open towards non-experts. FoldIt is a game in which people from all over the world compete in improving structural models of proteins. There’s no deep knowledge required – a brief tutorial contains essential introduction to the topic and exercises testing if user understands some basic concepts. Playing the game does not contribute directly to the science, but helps in improving protein structure prediction software and in understanding protein folding. Two other examples of non-expert participation in science are Annotathon and Spectral Game. These are servers that combine “required” and “useful”, that is combine teaching and data annotation. Both servers aim at enhancing learning process and at the same time use crowdsourcing approach to curate data – metagenome sequences in first case and chemistry spectra in the second.


What about shorter communication time? The image above combines various data visualization techniques based on the Second Life platform. While Second Life was first sold to scientists as a conference platform, it turned out it’s not very useful for such purpose – but scientists stayed for SL’s very good visualization capabilities. How many times instead of explaining via email/phone some concept to a colleague, you said “come here, I’ll show you”? SL allows to prepare interactive visualizations of chemical structures, genomes, proteins or multidimensional data and as such, to communicate some difficult concepts faster than via other channels.

Last year’s ISMB conference became a major step towards new approaches in conference reporting. A few scientists that happened to be bloggers and users of a life streaming service called FriendFeed decided to report in real time from the conference. Their effort was followed by a number of people, including even the ones that were already on the conference. I’ve seen my colleagues creating an account on FriendFeed (which they sadly abandoned shortly after) only to follow this report. It is still available in permanent, searchable archive over at FriendFeed and resulted in an interesting publication. Life streaming service wasn’t designed strictly for conference reporting and similarly, virtual world platform wasn’t designed strictly for data visualization. But it obviously doesn’t matter to us, as long as it works. slajd13

But you may ask: where is “science” in “science 2.0”, as these examples are not necessarily about doing research. And while I could provide some examples of using new communication channels in day-to-day work, I think it’s more important to tell you about people who test boundary conditions of communication spectrum in their research. In 2006 Jean-Claude Bradley coined a phrase “open notebook science” which means conducting research using publicly available, immediately updated laboratory notebook. Despite obvious disadvantages of such approach (competition, scooping etc.) he is quite successful in terms of getting grants, publishing his results and so on. A number of people followed his approach with smaller or bigger modifications and it is argued that ONS enables more effective collaboration and more effective (no repeated experiments) science. Is that true? Quite probably, but it’s important to recognize that Science 2.0 is not only about better communication. As Jean-Claude mentions is his talks, all these experiments are parts of a bigger process, a change in a way science is done. The outcome of Science 2.0 is not going to be limited to complementary channels to peer-reviewed publications – the more important part will be rules, formats and standards for communication between machines, not scientists. Those who think that removing scientists from scientific process is not going to happen all that soon, I would like to point to a recent publication in Nature presenting Adam, a robot that independently discovers scientific knowledge. While Adam seems to be an equivalent of a junior lab assistant (or a postdoc as some say) and is definitely too expensive to consider as your cheap lab workforce replacement, it’s a quite significant step towards automatising of many elements of scientific process.

There’s another aspect of Science 2.0 that is usually skipped in many articles. A screenshot I’ve shown you contains my conversation with Cameron Neylon over at FriendFeed in April 2008 and was presented in many talks on open science since then. The reason was clear – FriendFeed wasn’t designed to start scientific collaborations and this was the first example of such kind. However what is usually not said is the fact that I wouldn’t answer anonymous request. The reason I did a model for Cameron’s grant was that I subscribed to his feed before so I actually could see the request. However, I didn’t subscribe to Cameron because I knew his professional profile – I didn’t even know his affiliation then (and barely remember today). The reason I subscribed to Cameron was that I somehow “knew” him, this is I read his blog, I commented on it and he commented on mine, etc.


An important part of Science 2.0 is the fact that it has human face. In other words, through participation in online communities we become living persons, instead of anonymous scientists hiding behind publication list.

Why does it matter? Looking at Science 2.0 from perspective of a young scientists working in Poland, this aspect of Science 2.0 becomes a game changer. Poland has ca. 30 times less money in available grants than UK (according to calculation of the UK research budget by Duncan Hull). In biology, which is a very expensive field, it simply means that we have a hard time competing with other countries. And while that fact matters less on the country scale, it matters a lot at a level of individual researchers, because it closes many career opportunities.slajd20

This is not an example, this is a comparison of two real people I know, that finished their PhDs about the same time. The first was from a major Polish institute, the second from a major European one. And while impact factor is a poor measure of their research outcome, it’s exactly what a head of a lab both would apply to will see: few publications, not that impressive vs lots of publications, all in good journals. With research budget Poland has it’s hard to compete with Western Europe and even the EU money will not change that situation in a matter of days, because we also lack experience in spending money. While the system slowly transforms, young Polish scientists have already a way to fill this gap – by Science 2.0, or more precisely by participation in online scientific conversations. There’s no currently easier way to show that poor publication record does not equal poor skills.

And the last aspect of Science 2.0 I want to talk about today comes from the fact that I’ve just became a lecturer at the University of Warsaw. There’s another gap we must fill, this is between current research and lectures we give today. It is a hard task as the amount of knowledge doubles faster and faster. To adopt to such speed the structure of the university courses must change – or instead, we let the students to take care of the gaps. They can easily follow current research and decide what is important to learn by having an access to real-time scientific conversation, by participation in Science 2.0. It’s not an easy road, but at least it will allow them to learn important concepts long before we come up with an idea to teach these concepts.

Consider such example: a group of students from Department of Biology of University of Warsaw participated in 2008 in IGEM, International Genetically Engineered Machine competition. This is a part of a new field, called synthetic biology. This field is fresh and somehow still controversial and these are not the only reasons why not all universities in world have synthetic biology courses. University of Warsaw doesn’t have it either – but it didn’t stop these students, and they plan to participate in IGEM again this year. However, synthetic biology, as many emerging fields today, is done in the open. Scientific conversations are open. Ideas and thoughts are open. And students can learn from it before we organize these thoughts into textbooks.

The last slide shows a community of life scientists I’m a part of. These are not only scientists – there are librarians, science communicators, editors from scientific journals, people working in biotech industry or even people without direct connection to science. These people with diverse skills and background create a 24h a day, all year long online conference. Ability to interact with them and to learn from them was among biggest privileges I had in recent years. And even if this is the least visible aspect of Science 2.0, it’s the most important one and the main reason for my participation in online communities. Thank you.

Reblog this post [with Zemanta]

Posted by on May 18, 2009 in Community


Tags: , , , , , ,