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.

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.

The wet-lab machine

Problem:

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. 

Perfect class project for teaching science

Imagine a class project where the students have to find a few failed experiments (or experiments with confusing results) and develop hypothesis on possible explanations. Of course, some of them might be human error, but that is the part of the challenge of the assignment -- to develop reasons why that is the likely explanation.

I don't think this assignment is possible at present. Why? Below are my reasons, although I am sure there are many more.

1) There are a few journals of negative results, but I think they probably capture only a very small fraction of the number of failed experiments [in biological sciences as a whole].

2) EVEN IF all the failed results were published, how would a student navigate through them. Usually, understanding the nature of a failure is far far more difficult that understanding a successful experiment, because the pieces of a successful experiment make a coherent story. For a failed experiment, an expert in the field is often required to hypothesize potential explanations.

3) Failures MAY very often relate to each other. I, personally, think that most failed experiments can be attributed to a combination of human error and actual biological issues. If this is true, then looking at any single failed experiment is meaningless (sort of obvious). Finding "patterns" amongst thousands of failed experiments is practically impossible via the traditional journal-reading process.

Possible solutions (ambitious):

I believe that the human eye is extremely efficient in finding patterns, and therefore, it is necessary to leverage the visual + intuition capabilities of human researchers in order to make sense out of failed results.

A class project means that this task needs to be accomplished by non-experts. I think a framework that combines education + research + visual representation of results can by-pass this problem. In other words, provide ways to educate a student about a method when presenting the results from that method. If such a framework can be created, the boundary between education and research may become vague, which might be quite remarkable.

Implications:

The traditional test-based system for selecting students is bound to miss several great minds who have the potential to solve many unresolved mysteries in science. If an infrastructure can be constructed where anyone can educate themselves and connect research results efficiently, there is a possibility that various geniuses around the world will be able to utilize their potential and service the community. The opportunity to circumvent the traditional test and money-based avenue to higher-education should provide an incentive for students around the world to try to do science on the side.

Leave "pheromone trails" on research articles

What if there was a way to leave a "trail" (like ants) whenever researchers jump from one research article to another and find the connection very interesting. As more researchers walk the same path, the "pheromone" along that trail becomes stronger. This would provide a nice way of linking interesting research articles together, highlighting interesting patterns in the network of related research papers.

A dynamical systems analogy of society

Lets consider individuals in a human society as monomers. These monomers can interact in different ways to form larger complexes, with each complex having different functional capabilities. The reason why monomers might come together may be different. For example, in a modern company of workers, the monomers come together because of money - the salary provides the attractive force that brings the monomers together to form a larger cluster. Families are formed due to a different form of attractive force. Friends circle and so on have a different (maybe similar) force. Non-profit organizations or other occupations that are not motivated by salary (i.e. intrinsic reward based systems) attract monomers for an entirely different reason. I think this type of attractive force forms a larger variety of complexes, many of which interact more closely with the world outside human society (based on a few observations).

Now, lets consider society as a system with multiple stable states. Each stable state is defined by the types of complexes that exist in that state. For example, in one stable state, all the complexes are formed by salary-driven forces. In another stable state, the salary-driven forces are weak and therefore, intrinsic-reward forces are responsible for forming complexes. In another stable state, perhaps other forces are responsible for the complex formation. The question is: what causes these systems, i.e. societies, to shift from one state to another?

Yet another perspective on evolution

Consider this possibly true scenario:
---
Virus X lives inside 10% of the human population. It has integrated itself into the human genome, as many viruses do. It gets activated during the lifetime of a human and it exists the human body through the mouth and nose It is only able to invade other humans with specific proteins, which happens to be the same 10% of the population. In addition, this virus is also able to invade 10% of dogs and cats.
---
In the above situation, the virus X serves as a channel for DNA exchange. In other words, it is possible to build a "family tree" based on this virus. It is another a family tree based on a different means of reproduction. In normal reproduction, we do not reproduce our entire selves. Rather, some part of us is reproduced. Virus X is also reproducing a small part of us, and therefore, it is just like normal reproduction.

We think of the "tree of life" as a tree with lots of horizontal transfers. What if all these horizontal transfers actually form another tree of life, a tree that uses a different means of reproduction. Why limit to viruses? Microbes in our body are part of us. If microbes are mutating and being carried between species, then they, too, can be a means of reproducing a part of us. In summary, there might be several means by which we reproduce specific aspects of "us". Each of these means of reproduction can be used as a basis for building a different "tree of life". All these trees intersect.

So what is a species? It is basically a way of categorizing individuals. Just like there are different ways to classify books (e.g. language, subject, readers), there are different ways of classifying individuals. Each individual belongs in multiple species -- one for each type of reproduction process that affects the individual. We are all part of more than one species. So why do we give the regular form of reproduction so much importance? It's because of the brain, of course. The brain is not the master of our body. It is one component of the body, and just like any other component, it has roles. The brain is designed to pay attention to certain types of reproduction. For humans, these types of reproduction include sexual reproduction and cultural (meme) reproduction and maybe some other ones. We should not let the role of the brain affect the reality, which is that all of these forms of reproduction contribute significantly to natural evolution.

Therefore, natural evolution is a process where multiple trees of life are expanding and interacting. Individuals sit at the intersection points of these trees.