Sunday, November 4, 2012

The ideal biofuel company...

The ideal biofuels company would not use giant farm land to produce large amounts of fuel for everyone. Rather, the company would sell barrels to people. People can put any compost-able items (left over food, paper, maybe human waste, etc) into the barrel. The microbes and/or other chemicals in the barrel would convert these items to fuel, making people self-sufficient. Of course, people who do not have a back yard would probably have less material; for these people, the company can sell fuel made from waster matter that is purchased from other people who have excess waste.
The big question is regarding efficiency - whether waste material from individual homes would provide sufficient fuel. But even if it provides a certain fraction of the fuel requirement, that is still a significant step. 

Friday, October 12, 2012

Analogy for Cancer as a Systemic Disease

Lets think of a multi-cellular organism (i.e. humans) as a small city, a society, of individual cell citizens. When the citizens of a society feel a strong sense of unity and like to interact with one another, the chance of someone becoming malicious is small. Any malicious person is likely to get caught because the members of the society have a high rate of interaction; members who interact in an unhealthy way would be identified quickly. On the contrary, in a system where individuals are isolated, it is quite easy for a malicious individual to remain hidden and carry out their plans.

Carrying over the analogy to the human body, the "malicious citizen" is the cancerous cell. It is not an invader but a member of the system. Now the question is: what creates a sense of "unity", or high level of interaction, in a multicellular system? This question is difficult to answer even for a human society - what creates a sense of unity in a society? The answer might lie in vague concepts such as culture, language, values, or beliefs. These are abstract concepts. Concepts such as culture cannot be written into books; they evolve; they form spontaneously and are not designed by humans.

So the task is to identify what constitutes the "culture" of a multicellular organism. My imagination tells me that the answer might lies with wave-like patterns within the body - heartbeat, breathing, hormone cycles - that affect almost all the cells in the body. The fact that these phenomena are oscillations allows cells to synchronize, or resonate, with those patterns. Multiple waves can combine to form more interesting patterns. Cells resonating with this pattern might be in similar physiological states, and therefore, those cells might interact with one another more. More interaction creates a healthier "society".

If the above hypothesis is true, the way to heal a large number of illnesses lies in identifying patterns of global phenomena such as breath, blood flow, hormone cycles, and especially how they interact with one another to form more information-rich wave pattern(s). Then, we can identify how various cells change states in response to this global pattern.

In some sense, malicious members of a society are like indicators of the society's overall health. In an unhealthy society, more individuals would feel less inhibited to harm one another. In this sense, the malicious members ensure that an unhealthy society falls apart, giving way to a new, healthier, society. Cancer might serve a similar purpose. A body where the overall unity is weak is perhaps dangerous to the larger ecosystem. Cancer ensures that such a system falls apart.

Analogy connecting Proteins to Words in a language

While analogies can be dangerously inaccurate at times, they can also be invaluable in other cases. Therefore, they are worth considering (with open-minded skepticism). So, here is an analogy of molecular biology research...

There are 26 alphabets in the English language and 20 amino acids (maybe more) in biological systems. Combination of these basic alphabets can be used to constructs hundreds of thousands of words, and similarly, combinations of amino acids can be used to create numerous different protein molecules. However, both are retrained in some way. For example, when constructing a new word, we will probably not create something like "qxtrpeeoo", because it is not speakable. Similarly, when making protein molecules, stitching together random amino acids would not produce a stable molecule in its environment. So, there is some similarities.

Now, lets try performing some "experiments" on words in a similar way that we do experiments in biological systems. Lets try a "kockout" experiment. We will remove the word "grocery" from all text in a city. We might see that traffic patterns have changes because people are trying to find grocery stores. After a few weeks, people adjust to the situation, so the traffic patterns settle. So, from this observation, what might we conclude about the role of "grocery" in society? Consider a different experiment in which part of a word, e.g. prefix or suffix, is removed or a different part is added. What type of conclusions would we reach by observing the consequence of such changes?

So what is a different approach to learning the meaning of words? I do not have an obvious answer, but following the above analogy, one might look at how babies learn language. First, they usually learn words that refer to real objects, such as "light" or "fan" or "mom". Applying this analogy to proteins, it might be reasonable to start with proteins that directly interact with the environment, e.g. binds metals or other environmental signals (i.e. objects outside the internal language of the cell). Moving from the word "light" to the meaning of a sentence such as "the light is on" or something more intricate such as "please turn the light on" is a much larger step because here the word "on" is entirely context dependent. The same word would mean something entirely different in a different sentence. It is possible that some proteins, specifically those involved in internal signal processing of the cell, are entirely context dependent. Consider the difference in the response when someone asks "is the light on" vs "light is on" vs "turn the light on". All of these involve "light" and "on", but the response of the listener is quite different in each case.

Tuesday, August 21, 2012

Distributed research...(again)

Imagine if we have two things:
1. public research labs such as the BioCurious in many cities
2. free software system for uploading pictures, data, etc. from experiments

Then, a situation such as this can be possible:
- person A starts an experiment on day 1
- person B comes to the same lab, looks up what remains to be done for the experiment and performs the remaining steps on day 2
- person A comes back and uploads pictures of the results, e.g. gels, plates
- person C, located across the world, sees the pictures, analyzes them, and uploads the analyzed data
- person D, watching the experiment from some other location, makes some insightful observations
- and for the sake of practical benefits, persons A-D, having demonstrated their caliber, get recruited to an excellent university/company.

Saturday, August 4, 2012

Environmental sensing by the collective

Imagine if everyone who scoops up a cup of sand, lake, or ocean and submits it to a local repository gets some money in return. Why? Well, the local repository would process the microbial population and make it available to the public. Companies can analyze this data and predict changes in climate, spreading of potential parasites, etc.

Further, rather than analyzing microbes, it might be even more informative to analyze bacteriophages. First, they are more diverse than bacteria. Second, phages generally switch between dormant and virulent states based on environmental factors, hence providing an additional source of information.

Monday, February 6, 2012

The wet-lab machine


Scientific literature is openly available to anyone who wants to read them. However, "open" does not mean much if no one can understand them. Molecular biology protocols fall in this category. If you are not a molecular biologist, you will probably have no idea what the "methods" section of a molecular biology journal paper is talking about.

Possible solution:

The Incredible Machine is a nice game that is fun and intellectually challenging. For how complex the scenarios are, the interface and visualization make the game relatively simple to learn. 

I wonder if an interface like the incredible machine can be used to explain wet-lab procedures. Of course, the minute details would not be illustrated, but one of the issues with wet-lab at present is that there are only protocols. There are no higher-level 'big picture' explanations, which are necessary for someone who is trying to learn how to do wet-lab. In some sense, there is nothing equivalent of a pseudo-code.

Imagine supplementing the "methods" section of a journal paper with a cartoon animation similar to the Incredible Machine - how much more education value would it add to the journal paper! Further, imagine a repository of Incredible-Machine-line animations explaining the overall ideas behind wet-lab protocols.