BioSec 2012: Luc

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Random Thoughts

Cell signalling

Chemistry vs Photonics, Electric, Sound

Chemical signalling allows the signal to carry methods of transformation (essentially code) in addition to communicating state.

Thought Experiments

What sort of emergence could we evolve from a dynamic system comprised of little computers that were essentially something akin to battery powered RFID / smartcards with limited wireless range and had interfaces for connecting themselves together for closer interactions.


IKKB protein and the reversal of insulin resistance

Programming Atoms

Is it engineering or programming?

'Simple' building blocks coming together to create complex interactions


Extensible, Reused, Re-factored, Re-appropriated, Hijacked

Contaminate, Corrupt, Desecrate, Mutate, Profane, Taint, Tarnish.

Life seems without qualms to re-appropriate pieces for completely different tasks.


I think I'm going to end this tangent here.


Photons are absorbed when they correspond to the difference in energy between two different possible electron states. Observed colours are the inverse of the objects ability to absorb photons.

Light can cause physical deformations in molecular structures. An excited electron will have an orbital that allows it to bond with the second nucleus in a way that requires more energy (is stretched)

Simple organisms seem to be hard-wired to respond to stimuli in predictable manners. Instead, humans get things like desire and impulses that can, to a certain extent, be overridden. The fact that we're significantly less hard-wired, where instead, we come pre-programmed to learn, this is a big deal.

Is the creation of silicon-based computational devices the practice round for when we start playing with carbon?


Life seems to exist to promote its existence.

Dynamic, yet stable. Homoeostasis.

Stable yet evolving.

Cells are the smallest unit that we consider holding the gestalt that we call life.

Organelles are highly structured and almost appear to be appropriated forms of life, yet we do not consider them life?

What would a computer program look like if its primary design goal was to survive indefinitely as an individual? As a species? If a computer program propagated autonomously over the network, would that be considered the individual or the species?

It's hard not to wander into personal philosophies. As a theist, I find the order of this humblingly incomprehensible emergence to be divinely inspiring. However, I readily admit that the Atheists have just as good a reason to stand where they do.


The death of code

I remember that we came to this insight over a decent chunk of class time, but there are two major pieces that stuck with me. The first part was expressing my frustration with software, games in particular, though GAIM / Pidgin was another non-game example, where I felt that community contribution wasn't welcome. In the cases I lamented, software had been released with some really good ideas, but had ultimately been lost to history / obsolescence because for whatever reason the primary authors did not want to relinquish control to the community of users. The end result being that once the authors moved on, the users moved on simply because once they had extracted the available value from the software, there was no sense dreaming about possible new value, there was no hope of it ever being implemented.

Through those lamentations, but slightly after that, I remember collectively deciding that programs could be imbued with life, and what that meant was that people were actively working on them, dreaming up new possibilities and implementing them, while fixing the negative aspects. Live code is worked on. Live code is code that is intimately understood. Live code that is actively being made more useful, pleasurable. Once code is left, it stagnates, and finally dies slowly as those that were involved in its creation lose their intimacy.

Examples of the effects of community support on software:

Vampire: The Masquerade - Bloodlines. This is both an example of death and life through the community. This was the swan song for Troika Games. Shortly after it was released the development studio went bankrupt. The end result is a game that is riddled with bugs but with a really engaging game underneath. And lots of content that was almost included but not quite. As far as I could tell, the only two official patches didn't do much at fixing the underlying issues. But, Wesp5, a member of the gaming community, took it upon themselves to hack around and see what they could do and if one were to look up the state the game is in after applying the unofficial patch, you will find a much more refined game.

The Saboteur: Another swan song, this time from Pandemic studios. The game was released, the studio was closed, the game had some really interesting ideas but was also riddled with bugs, plus it had problems running on certain AMD GPUs. A couple minor patches were released but the game itself never got further than RTM and any dreams of improvement will never become a reality.

Mirror's Edge: This one was prime territory for mods. A 3d platformer centred around parkour, This game was prime territory for mods. But no tools were included to allow users to do that not to mention that the copy protection on the version distributed on physical media actively killed the in-game character under certain conditions. This game was almost lost when someone discovered that one could use an editor from another unreal engine 3 based game to modify map files resulting in some amount of custom map creation, but to get them running is a hack and requires replacing an existing map with the custom version.

Half Life: Released SDK, begets Counter-Strike, Day of Defeat.

The Elder Scrolls: Each release has a tool kit that lets users create new content. Morrowind, released in 2002, is still played today. Oblivion actively played at least until the release of Skyrim, six years later.

Minecraft. Both as the re-incarnation Infiniminer and as the result of massive community participation that made it what it is today.

Quake 3: GPLed source results in many derivatives.

Second Life: Only what the users made of it.

Actively Forgetting

When change happens, the default result is that the change is permanent. If change needs to be reversed in some manner, something has to work actively work against that change to return the environment to its original condition.

Everything Else

Want new functionality? Assimilate it.

The creation of lots of little programs that do one thing well provides a rich ecosystem for programs to organize into more complex structures and amalgamate into distinct bigger units.

Biological process are rarely binary. Much more analog, operating over a continuous range where "more active" and "less active" make a lot more sense than "on" and "off"