Proposed change to Biological Sciences

As I was doing my PhD, I started to question most of what I learned from molecular biology textbooks. I noticed similar trends in other PhDs. It is not that the textbooks are incorrect, but intuitively, I think most people who are educated in biological sciences "sense" that something very fundamental is missing in our knowledge of biological systems. Systems-based approaches tried to address some of the defects of looking at individual molecules in isolation. However, even then, the fractal-like complexity of biological systems make it extremely difficult for us to understand how it is "working". And perhaps that itself is the flaw in our thought process. How do our thoughts and emotions "work"? How to relationships between people "work"? The word "work" is probably not the right choice for these questions. An adaptive, highly responsive, and intelligent system does not work in one defined way - rather, it changes based on the thing that it is interacting with. 

It is arguable that "intelligence" (let's keep that word loosely defined), like evolution and adaptability, is a quality of most, if not all, biological systems. Intelligence of an entity can only be observed if we can communicate with it. We humans have difficulty communicating properly with other humans; it is fair to assume that we are very poor in communicating with other biological systems. In this case, it is possible that there are highly intelligent (again, loose definition of intelligence) systems all around us and within our bodies. By "highly intelligent", I mean that they are comparable to human tool-making intelligence, but in a different context. 

If we look as nature's biochemistry of cells and the human body through the perspective that they are all intelligent systems (like aliens), then it is not a matter of understanding how they work, but rather how we can communicate with them. These systems are more than capable to solving problems - from health to environmental problems. Humans need to communicate with them. Biological sciences should be an effort to communicate, not to understand these systems in the same way that we understand mechanical human-constructed devices. When I smell a flower, what is it communicating and what is the conversation that I should start in order to become friends with that plant?

Role of humans in a world with super-intelligence

 There are conversations about AI reaching the so-called "super intelligent" level, at which point it will (1) become a much better inventor than humans, (2) keep improving itself, and (3) quickly learn to do everything that humans can, except for the things that require a biological body.  

If this super-intelligent system is truly intelligent, it would realize that humans would be unhappy without a purpose-driven life style. It would create instability. Additionally, this super-intelligence would realize that humans serve a very important purpose - they are the bridge between the biological world and the silicon-based intelligence. Humans have forgotten what all they have in common with animals - the deeper feelings that are shared with all living things. While non-biological entities may learn to "feel" in their own way, biological feelings will still be different. The feeling humans share with other living things are also the source of real wisdom and human-to-human connection. The super-intelligence will realize this and propose the creation of spaces, much like national parks, where humans live with nature and each other in a purpose-driven setting, allowing them to re-discover the value of being human. 

Trust in Synthetic Biology

The concept of trust with respect to synthetic biology has enormous economic importance. Lack of trust can cause people and governments to block an entire division of research, such as GMOs in some parts of the world. Similarly, synthetic biology related companies that have lost their reputation can have great difficulty releasing an honest product. Consider other products, such as an electronic device. Such products are often tested by unbiased individuals; the reviews generated by these unbiased individuals is trusted by the general public. By using such third-party reviewers, who share their testing methods openly, a product is able to gain trust on its own.

The review process for biological or chemical products is different. The processes of assessing safety and effectiveness of medicines, farm-related products, and various chemicals for every-day use are often hidden in publications that are normally difficult to understand by the users. Websites that target the general public often rely of vague concepts rather than specific facts. What if biologically engineered products had a review process that is open.

"Open" is not a matter of exposing the raw results of experiments. Open must allow other individuals to repeat the tests and contribute their results. Open must also mean that honest efforts have been made in order to make the information understandable by as many people as possible. Open access to scientific publications does not mean that the knowledge is open because those publications are generally written for domain experts. Further, publications do not guarantee that the experiments are reproducible. In order to address the problem presented in the first paragraph of this blog, open-science needs to invent a new method of sharing information.

Additionally, trust is often strengthened when both sides are involved. If customers of a product participate, even remotely, in the testing of the product, their trust, through a feeling of ownership, is likely to increase. For example, suppose some of the customers utilize open labs in order to conduct some of the verification experiments. It would cause the customers to feel a bit closer to the product.

Morning Dew

Morning dew hanging from the railing of a balcony - I looked at them for a while. As I noticed the details, it was only natural to think about the geometric shape created by the droplets and the Poisson distribution of the droplets along the rail. Someone versed in music might imagine a song. A poet might invent a new poem. All are expressions of appreciation of morning dew. There is a feeling associated with this appreciation of nature. When I have this feeling, I cannot imagine how science or art can exist without that feeling. It is simply the foundation for science or art. Science education that does not exercise this feeling is education without the foundation of science.

Cancer cells might be Creative

I have heard a few times that human beings are comparable to cancer (not a positive view, sorry) in the sense that humans: (1) drain resources from the other members of an ecosystem, (2) grow at a disproportionately high rate when compared to fellow animals, and (3) cause ecosystems to malfunction due to the previous two behaviors.
It can also be argued that human beings have their advantage due to the combination of a creative brain and social skills. Physically, human beings are hardly a match for most other animals. So, taking this analogy back to cancerous cells, would be appropriate to say that cancer cells have a sort of "creativity" that is lacking in other cells. Just as a "better" brain is defined by the amount of information it can process, it is arguable that cancer cells process more information than other well differentiated cells, partly because cancer cells can perform a myriad of functions.  

Synthetic Biology vs natural biodiversity

A constant worry in the environmental front of synthetic biology is its influence on natural biodiversity and natural systems in general. Synthetic biology products are human-made things, no more natural than buildings, radio, or television. If this is the case, the question about environment is not solely related to synthetic biology but engineering as a whole. Human constructions - buildings, roads, night lights, irrigation, dams, etc. - have probably affected natural systems significantly. Synthetic biology is another item on this long list; perhaps humans were much less careful about natural systems when they first started engineering buildings or dams. After witnessing the slow decrease of natural landscape, perhaps humans have become more cautious about consequences of engineered products. The question on how to safeguard natural systems from engineered biological systems is perhaps a starting point to the question about how to safeguard natural systems against any engineered system.

rules in biological systems

Researchers are often surprised when we find organisms that break the 'rules' of living systems. These rules include commonly observed phenomena such as amino acid codes, conserved metabolic pathways, etc. Considering the unplanned nature of evolution, it should be surprising that such rules actually exist. It should feel more logical when rules are broken.Well, lets consider other places where we find 'rules'. Human societies have rules, and even though every person has different interests and tastes. People agree on the rules because what is gained from following the rules is probably greater than the gain from breaking the rules (in general). Similarly, perhaps rules exist in living systems because there is sufficient gain - better exchange of information between organisms, better 'modularity' in evolution, role for viral-mediated horizontal gene transfer, etc. Now, the question to ask is - what does it mean when organisms break the roles? Perhaps they belong to a different society with a different 'culture', or perhaps they are lone explorers who do not want to interact with the rest of the system.