Doesn’t matter how big
the A or a are
that’s just a point
for Hardy and Weinberg

One stream
where the frog sings
strangely like a bird
Sit and humid, daytime

I sat and waited, got you
Now rush, run and show me
A sequence of colours that
might mean something

Oh, I know I put them
on a tree, made by bits
and pixels like
the first one

Like the next one,
and the next, that
might be like the previous
or the last one on this
line.

How can you make a position on something you don’t understand?
How can you say something won’t work when all you know if it is from a couple of Google queries?
I understand from your blog post that you have a short attention span and are not willing to spend much time researching ideas, but just because you have reached the end of the amount of time you are willing to spend on understanding doesn’t mean that you are reached the point at which you are read to judge that concept.

Apparently, my writing is pretty bad, or your reading comprehension is pretty bad (but I’m betting on the first in Vegas). I know what Open Science/Research is, but the graduate student down the hall does not, and he or she has many other important things than “waste time with the hell of OS/R”. I don’t have a short attention span, but the grad student down the hall might have, who knows. eh? And I’m not judging the concept, I have a very clear idea of what the “concept” is, I just think it won’t fly, at least now.

Egon pitches in:

I think you can approach Open Science from various angles. The OpenScience project (where Jmol originated!) comes from an angle that OpenSource tools is an important step in making the data analysis in science reproducibility, and people sometimes seem to forget that data analysis is science too.

On the other hand, data discovery can be seen as the first step where science should open up. This is closer to the Open Notebook Science things.

I understand your confusion. Doing science involves many steps, and if you have no clue where to start doing science, it won’t work. Similarly, if you have no clue where to start making your Science Open, you won’t get it to work either. But that does not mean, it cannot work at all.

Nice introduction, and hoping that your further analysis may trigger some thoughts on why Open Science can work.

Yes, there is confusion, and I agree the Open Source software is an important step. I have seen many cases of closed source software hindering data analysis because you don’t know what’s going on. Many people out there don’t know, don’t want to know or don’t have time to learn about Open Science and they’ll sure get confused if they search for resources. The lack of a centralized, useful and with a nice user interface resource (website, application whatever) makes difficult to anyone to start.

Rajarshi also wants to comment:

I’ve always thought of Open Science as a social process rather than a technical process (though it has technical aspects). From that point of view, the lack of a central repo of information, is certainly a bottleneck, but I doubt it’s a deal-killer. In the absence of such a repo, the ideas behind Open Science will just take longer to diffuse.

Indeed, it’s a social process, never technical. And no, as he pointed, is not a deal-killer, but it helps make the process slower, which is the conclusion I would like to have included in the post, or at least make the reader conclude that. If it’s social, why not take advantage of the so-called WEb2.0 (another thing that I don’t believe, just a clever name to sell books - or whatever they sell on the web these days).

Next time, I will tell a short story of an open science blog. That was when I started thinking “If is it open, why some stuff is closed (or not shown)?”

1. What is your blog about?

Anything that I wish I had done and willing to do. Also there are interviews (I want to do more!).

2. What will you never write about?

Confidential stuff, anything that is very personal or people do not want to publicize. Send me a message if you want to know the latest gossip in Bioinformatics.

3. Have you ever considered leaving science?

Nope, but sometimes I have the feeling that I would like to be a airplane pilot.

4. What would you do instead?

Airplane pilot? F1 mechanic?

5. What do you think will science blogging be like in 5 years?

Oh boy, I dunno. Ask me in five years, if I’m still around.

6. What is the most extraordinary thing that happened to you because of blogging?

Extraordinary? Nothing. If you call extraordinary befriending someone, than I can say that is. Being able to feel part of a community, that’s a good one.

7. Did you write a blog post or comment you later regretted?

Nope.

8. When did you first learn about science blogging?

Nodalpoint was the catalyst. I knew about blogging for quite sometime, but Maddox influenced me not to, until I found out Nodalpoint.

9. What do your colleagues at work say about your blogging?

“What blog?”

10. Extra credit: are you able to write an entry to your blog that takes the form of a poem about your research?

Yes. If you want to read it, leave a comment. If I get 20 comments, I will post it.

As a “lay open scientist/researcher”, I decided to enter the belly of the beast, and the easiest way to do that was googling. Nice. Open and science returned me 98,500,000 links. Looks good. “Open science” returned a “mere” 200,000. What is the first search result? This one. Looks exactly what I needed. Let’s check the about page …

The OpenScience project is dedicated to writing and releasing free and Open Source scientific software. We are a group of scientists, mathematicians and engineers who want to encourage a collaborative environment in which science can be pursued by anyone who is inspired to discover something new about the natural world.

Ah, open source software. Nope, not what I wanted (yes, I want open source software especially in science, but it’s not what I want right now).

Let’s check the second search result: http://en.wikipedia.org/wiki/Open_research. Wikipedia, nice, good (second) place to start. OK, some definitions

the central theme of open research is to make clear accounts of the methodology, along with data and results extracted therefrom, freely available via the internet. This permits a massively distributed collaboration.

Great. But, even though the Wikipedia entry is open and anyone can edit it and add information, it’s not enough to feed my will to learn about open science. Knowing a bit about Wikipedia (remember I am a lay open scientist here and computers are not my forte), I go to the external links section and get the first one: OpenResearch.org. Yes! that’s what I was looking for.

OpenResearch.org is a “a semantic Wiki aiming to collect scientific meta-data such as about calls for papers, tools, journals etc.” Great … wait what? A semantic what to collect what? I don’t know nothing (yes, double negative, my native language is no English, but I guess you guessed that, right?) about wikis, there’s Wikipedia, but wiki?

I go to the page and I don’t know where to start. There are so many links, so many pages, and I don’t know how to navigate this messy webpage and I don’t have time to learn. Let’s get the second link on Open Research entry on Wikipedia: Philoptima, Open Research Marketplace & Community. Just a sec, isn’t Open Research to be open to anyone interested, why do we need a market place for it? Ok, maybe I try some other time, because now I have to get back to do some research so I can get it in the open …

–

I think you guessed what is the moral of the story: there is no central repository of information about open research. I have to dig deeper, waste time, and if I already have a constrained schedule, I won’t do that. If I didn’t know the open science advocates, I will never have heard of some of their sites. Don’t expect a large group of people to make a huge effort to learn about it, what do they have to do to join the “next revolution”, how to navigate an horrible wiki user interface (much less learn how to edit it). And don’t let me started on collaborating online, sharing files, connecting to other computers, etc, etc (that’s another post).

I’m not here to suggest anything to the open scientists, just point out what is wrong and why it will be a failure for some time to come. I may be wrong, but that’s easier than being right.Technorati Tags: open science, open research, failure, series, long, wiki?

1. create an efficient informatics support for the institution - yes, that’s true. At McMaster we had in the lab a informatics guy, that not only was able to administrate our small cluster but to advise on a number of things we needed. Problem: they were understaffed. So, let’s create an IT department, not only to administrate things, but to educate people and have bioinformaticians, chemoinformaticians, whatever-science-field-ician. I don’t want these guys doing science or competing for grants, I want this as a service and a competent one.
2. As an addition to our recently suggested IT-do-it-all department, let’s have a group of artists working on creating figures for papers, either hand drawing for those guys in morphology, or creating the latest visualization of nanotubes to those guys in nanoscience. OF course this should be a specialized group, with people from different areas working on streamlining graphical production for faculty and staff.
3. A science related marketing department, with PR people that actually know that molecular biology, quantum physics, paleontology is. MB is more than using micropipettes (yes, news reporters have a fetish with micropipettes, so everytime I see one talking about “genetics engineering” on TV, I tend to check the pipette brand the guys are using). After all science is done with mostly public money, and I bet there a bunch of geek kids interested in learning more and more. NBA is not for everyone (below 6″).
4. There are not enough positions? Let’s create new ranks. There are people out there that don’t want to be a PI, but don’t want to be post-docs for 10 years. There are people out there that don’t care if they are first in a publication or third, as long as he or she knows the contribution they gave to the research. Creating the above departments/services, it will be simple to create these new positions.

I might have more steps, but my spare time is short today. Maybe there is no money, or political will to do these kind of things, but I didn’t promise anything.

Next time, I will pitch in the oil crisis and Middle-East peace process. Prepare yourselves.

In Flanders fields the poppies blow
Between the crosses, row on row,
That mark our place; and in the sky
The larks, still bravely singing, fly.
Scarce heard amid the guns below.

We are the dead. Short days ago
We lived, felt dawn, saw sunset glow
Loved, and were loved, and now we lie
In Flanders fields.

Take up our quarrel with the foe:
To you from failing hands we throw
The torch; be yours to hold it high.
If ye break faith with us who die
We shall not sleep, though poppies grow
In Flanders fields.

The original is here and the crooks are here.

Compare.

list updated daily/weekly/monthly/yearly

I bet he is a molecular biologist now and found some genes related to baldness.

It’s only downhill from here

Image by ! *S4N7Y* ! via Flickr

It seems that it is based on Qt, and a good point (maybe the only one) is that the program is cross-platform. I decided to give it a go and import around 700 PDFs that I have in one directory (I’m using it on Vista). It has been almost an hour already and the import hasn’t ended, and it is using one core of my AMD CPU. Process Lasso already lowered its priority 10 times, because it is taking too much cycles. For read a PDF file?

Yep, uninstalling it soon. And not recommending it at all. I will keep using Citeulike, Zotero and the like.