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.

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
procedures.

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.

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.

Unnoticed evolution of humans

1) Suppose that the microbial community living inside us have a sufficiently long relationship with our own cells such that the microbes have an important role in a large majority of physiological functions, not just digestion.

2) As human societies have evolved, the variety of microbes that live in our environment have undoubtedly changed. Once humans wandered grasslands on bare-foot and ate raw food without even washing them. Now we buy processed food from supermarkets and even walk inside our houses with socks. The result is that the community of microbes that interact with and enter/exit our bodies has changed.

Combining (1) and (2) above leads to the possibility that the human physiology has indeed changed of the past several centuries, even though the change the human phenotype "appears" unchanged. The extent of evolution depends on the extent to which the microbial communities influence human physiology. If there are long-distance signaling molecules that are released by microbes which enter the blood and if the microbes are capable of receiving our signals, then...