Drawing parallels between Genetic Biology as a Software Engineering Problem

[Mellinia]

I came across this perspective when I realize using the CRISPR gene editing technology in the context of synthetic biology is basically doing code/DLL injection. In another way of seeing it, it is akin to installing chrome extensions (though this isn't really accurate because chrome extensions requires explicit permission, but this will be an easier example to use than a computer virus) to add or modify functionality of chrome. Chrome extensions are able to modify and monitor everything you do in the browser, and with what genes we have designed and inserted into the genetic host, we can do something similar.

This got me thinking if a new perspective can be drawn to solve biology problems. Computer engineers design one of the most resilient and precise systems known to man (This may sound like a joke to you, but you will realize that the reason why your car and airplanes all work as expected with all the programs in them is because of the effort the engineers made to make them secure and resilient). No matter how much you hammer away or abuse your computer, you don't expect all the billions and trillions of electronic parts to just give up on you. Hospital systems, rocket systems, these are all systems resilient to failure. Modern software OS-s has integrity checks, auto-repair and security schemes designed to protect the information in your computer and prevent all the extra programs you install from going on a rampage. Some times there will be failures, but we can expect the program to be better the next time a security patch rolls out. I do not mention UI/UX because this is pretty subjective, but security systems in of itself it something to behold.

There are many parallels that can be drawn from both our human body and computer systems (including the network systems all the way to kernel software). For example, protein networks/reaction chains can be thought of computer ABIs and program flow processes. One can hook onto them by hijacking one part of the flow. In bio systems it would be gene injection as mentioned at the start of this post and in software it can be DLL injection.

Take for example, cancer. I know cancer is a bit too complex to be taken as an example, but it is also one of the easiest, IMO to illustrate this. I will skip a lot of details because being nit-picky will only stifle the discussion. Cancer has two main high-level problems : the cancer genetic mutation and the cancer micro-environment. The cancer genetic mutation by external factors can be thought in terms of software memory corruption, which can be caused by a faulty installed program or accidental memory rewriting by another program. In modern software, this is mitigated by integrity checks and auto-repair systems where the system just copy-pasts working environments. If this doesn't work, software engineers can opt to do in-memory patching of the faulty software. In biological terms, integrity checks are performed by our immune system, who also deletes faulty programs/cells.  The immune system is also capable of killing cancer cells. However, there is another factor in preventing this, which is the cancer micro-environment.

In a summary, the cancer tumor covers itself in a mesh of normal cells, creates an acidic environment and creates interstitial pressure. This is a major design problem that a lot of cancer medicine has to solve in drug delivery. In terms of computer engineering, the corrupted program has barricaded itself behind a locked segment of memory, where high level programs cannot reach (user privileges), where it also faces resistance from the corrupted program which overwrites and shifts its memory footprint dynamically. The easiest way software engineers deal with this is to nuke the memory segment: deleting it from memory. We also do this with cancer tumors by removing the tumour directly. However, the cancer cells / corrupted programs, might still survive within the body. Computers typically have scanning programs that check through all of the memory. These programs are more commonly known as anti-viruses. However, our body does not have a proper full body scan that checks every cell except the over-worked WBCs.

Essentially we have developed a highly scalable solution for our computers, why can't we do the same thing for our body, like developing new antivirus programs for our favourite OS-s.

Having said all this, I would like to extend this perspective by working with people from both biology and computer engineering fields in suggesting new places where this perspective will help, and spark a new discussion about this.

[naitche]

I've found very similar when looking at the 'culture' of the kennel Clubs via their written constitution, mission statement and rules to explain the the overall mess dog breeding Culture is in and the lack of 'environmental support' for breeders, and values of breeders.

And wondering how to begin. Because it does work, and has implications ( very sure ) for any ongoing, identified,  biological construct.

Not so much new, but a different perspective.The basis being that an 'identified subject, or 'identity' is the environment for all it contains. held together by the homogeneous traits of common purpose/belief of self. What that identified subject is based on.

It allows broad but what looks to me like very accurate predictions.

The Mission statement of most Pedigree Dog registries is often headed with the statement that (basically) Dogs not bred to the pedigree protocols laid out as conditions of membership will not be recognised.  There was an environment set up create more favourable conditions to support Dog breeders.  But with that statement, they don't recognise dog breeders, they recognise only the limitations of their own identity.

They don't recognise their environment- what they were founded on. Purpose and responsibility are lost as they discredit their environment  (dog breeders) in favour of the Pedigree.  A pedigree represents a 'Standard' An environmental condition. Limitation.  The value in dogs does not lie in the pedigree. The show ring.  It lies in Dogs bred to respond to the needs of their natural environment in all its diverse conditions, and the natural environment for Domestic Dogs is Humanity. Dogs bred in the environments they contribute to, for the value they offer. not a narrow environment driven by how predictably they conform to the conditions of the 'standard' environment.

The K.C culture that has dominated  for over 150 yrs does not recognise   the diversity that could allow a viable response to the conditions of their environment and not the response that their environment demands.They don't recognise their environment- What they were founded on. 

If we consider everything not of our 'self', our environment,  then how we 'identify our selves' in our environment has great bearing on how we will be excepted or rejected by it. Environmental conditions of humanity, or the 'Human condition'  become sex, colour, race , religion, marriage. All are conditions of the human environment or the 'body' of our human identity. Are we part of it, or not? Are there conditions on our acceptance in that identity and and are we meeting them? Or maybe  lowering expectations .

Environment is the space we are given and the conditions that gave rise to our existence We can  add value to that space through our ability to respond, our response -ability to it, or try to shape conditions to be so narrow and predictable responses become fixed. Denying an  ability to respond in any other  way. A narrowly defined identity is not diverse. it is anti diversity and  unable to respond to changing conditions.

 

Edited February 16, 2018 by naitche

[naitche]

It does make it hard to know what science discipline this belongs to since it includes language, (re; the messages an identity is operating on) physics, biology, belief etc. seems a very unifying concept of multiple fields.

The best analogy I can think of is to view an identified subject as as a biological body. The belief of 'self ' or foundation of that identity can be viewed from the same perspective as the selected genetics of a biological entity.

[naitche]

Viewing an identified subject as the environment for all it contains also allows for a greater understanding of  the form, nuance  and interactions between environmental expectation, demand, acceptance and rejection and the role of response and recognition.

The properties of environment as a space, and of realising possibility and potential within an identified space.

 

Recognition as a 'part' of some thing is not the same as acceptance and there are demonstrable effects that those terms should not be interchanged in  social or cultural constructs.

Social or cultural constructs can be viewed as as diverse parts working together to a common intent.

Recognition of parts of the whole allows them to work together while maintaining independent response and can only be achieved through familiarity.

Expectation is set by  familiarity. Demonstration shows possibility and potential and is maximised by diversity.

Acceptance implies a complete responsibility with out  allowing for independent  action of  parts.

Less autonomy or 'free will' if you like. Less  diversity of response recognised to ultimately be accepted.

 

Edited February 18, 2018 by naitche