Wednesday, August 31, 2011

Crowd science

First of all, the two problems being addressed...

1) Great ideas are created when several small ideas come together. The
inability to keep up with a wide variety of research will lower the
chances of small ideas coming together. We're having trouble keeping
up with publications in just our own field, so imagine what all useful
discoveries we might be missing from other fields, especially those
obscure journals which might be hiding fragments of a great discovery.

2) Currently, if a curious high school student wants to learn more
about ongoing research, they would have to start reading review papers
or something like that -- this is not very inviting. No wonder the gap
between researchers and public is growing. The current mode of doing research requires a person to go through the PhD 4-6 year ritual. A self-motivated individual does not have sufficient material to become a self-motivated scientist. Even worse, a scientist who wants to cross from one field to another also needs a cross several large barriers.

And now, the solution...

An online game. Imagine a role-playing game where you walk around on
the earth (google earth-like interface with a person walking on it).
As your character walks through regions of the globe, you will see
little signs pop up indicating where the research labs are. There will
also be signs for "schools" (described later). When you click on a
research lab, you see comic strips of up-to-date research -- that's
right, comic strip of what each post-doc, graduate student, and
faculty did that day or any other day. You will also see the data
(graphs, tables, etc.) below each block of the comic strip.

Each comic strip is one line. It starts with a 'mission statement'
(objective or hypothesis) and ends with a concluding statement.
Conclusions can include emoticons, of course. Everything between those
two sentences describes what was was done using pictures and short
descriptions. The comic strips would describe procedures like miniprep
and PCR or even computational steps like parameter fitting. The player
can hover over the comic strip and find "schools" that teach those
concepts. E.g. I would hover over "PCR" step and see several schools
located across the globe that teach what PCR is, with ratings for each
school. Clicking on the schools takes me to online lessons (videos,
etc.) that teach those concepts. Schools with high ratings might even
make money from ads (incentive).

Ok, so now you ask how will these comic strips be generated... with
the Comic Maker of course! Each research lab participating in this
game can download a software called Comic Maker. Comic Maker comes
with hundreds of comic blocks representing some basic procedures. Each comic block can be generates by combining those basic blocks. It will have an easy drag-n-drop interface for creating a pipeline and attaching data to each step of the pipeline. The researcher must start a pipeline using a 'mission statement' and end it using some conclusion, even something as simple as :-( or just a few key words.

More fun stuff: researchers can announce "quests", which are open
problems that they are unable to resolve. Gamers can get involved in
quests. These players have to gather facts from other labs across the
world and generate some solution. They can request the researcher to
perform new experiments for them if they need more data. Similarly,
gamers can create novel hypotheses by collecting results from several
pipelines and present them to researchers.

One key question is: how does this reward the scientists who are in universities? Mainly, the reward is visibility, which is in many cases a big reward. Making research visible is a key for doing good research, and most researchers understand this obvious fact. Of course, placing results in this online game might interfere with the current "publications" approach. The workaround for that problem is simple: just place this in the game after they are published.

That's it. Hopefully that was a fun read. I think it can can be done.
Imagine spending your weekend looking at comics of what everyone is
going at Berkeley instead of going through the procedure section of a
paper. Of course, there will be nice search features, like "find me
everyone who is doing XYZ", where "XYZ" is some sequence of

Friday, August 19, 2011

Information vs information carrier

Suppose I write the word "Mango" using pen and paper. Then, suppose I wrote the same word using a chalk and blackboard. It is obvious that I am conveying the same information. The instrument used to convey that information is hardly relevant.

If this analogy can be applied to biological systems, then it is misleading to study physical aspects of signaling separately. Whether the signaling is via transcription factors, enzymes, RNA molecules, small metabolites, or DNA structure, there may not be any relevance with the content of the information that is being delivered by those molecular interactions. Similarly, between-cell communication may not be related to the type of signaling (paracrine, endocrine, quorum sensing, etc.). It might even be possible that the information encoded by molecular interactions is no different that information encoded by cellular interactions.

In summary, it is possible that information in biological systems might come to light if we study the patterns and ignore the physical components that create those patterns. At the same time, the physical aspects are not completely irrelevant. One would not write a book using chalk and blackboard, so the physical aspects of the instruments do restrict the type of information that can be conveyed.

Wednesday, August 10, 2011

Cell density based effects

In videos such as the one below, the cells in the middle have smaller size and therefore, there are more cells per unit area. This means that the concentration of molecules inside those cells might be different from the concentration of molecules in the cells at the outer boundaries. Suppose the cells have multiple stable states; in such cases, concentration differences can trigger state changes, causing different behavior of the cells based on their location in the colony.

Colonies where density is not equally distributed might use this fact (density dependent state change) to create different roles within the colony. Maybe the state of the cells at the center governs certain aspects of the colony and the state of the cells at the edges governs some other aspect of the colony. Even if evolution has not used this observation as a design strategy, it does not limit us from using the density difference as a design strategy for creating diversity within a population.