I am fascinated by the origins of life.  I love entertaining ideas about where this all came from, and why and what is subjective experience?  Is conscious experience really just an inevitable expression of the brain and free-will is just an illusion as Daniel Dennet suggests, or is it an essential ingredient in defining self-organising systems as Christopher Langan says ( My own interpretation of the his mad...?? genius ), or is it a waste of mental energy thinking insight could be gleaned from the unknowable.

Anyways, if you're on board so far I'd like to say that I'm particularly fascinated by Pilobolus fungus.  The first time I saw Pilobolus fungus on BBC documentary 'Life' I was just in awe.  How does such a thing achieve such complexity?  Especially since fungi came before cellular life..  so interesting.  

So one day while at work I came up with a proposed computer simulation that could  ~kinda~ simulate the life cycle of Pilobolus fungus.  I'm going to be making up a whole lot here and I'm going to make a lot of erroneous assumptions about the complexity of cells.  I'm hoping someone who knows what they're talking about can show me the errors in logic.

When I talk of 'system' I mean the actual Pilobolus fungus, o.k I'll try my best to convey the idea:
- Within the fungus is DNA containing instructions/chemical bonds which have developed in complexity over the many iterations of the self-organising system.  Through inevitable external/environmental  interactions, the fungal spore synthesises and facilitates the processing of billions of chemical bonds resulting in RNA.  Through similar processes mentioned in the previous sentence Protein bonds begin to fill the system.  O.k, this is where I just simplify the hell out of this idea, so the system creates protein A, B, C, D and E.  Each Protein has a bonding-potential given the right external conditions.  At first the single spore develops a disproportionate amount of Protein A, which is good because protein A is responsible for cellular division ( hyphae ).  Mean while Proteins B through E just slowly build up in concentration.  Eventually the concentration of Protein B reaches a point where it's forced to develop an equilibrium with it's surrounding environment (thanks to maybe sunlight, moisture, dryness, nitrogen...) as a result a new type of structure emerges ( stalk ).  Perhaps with the addition of the stalk a new set of environmental conditions allow for protein C to begin doing its bonds to achieve an equilibrium and develops the ( cap ).  Now the cap happens to have an elastic component to it.  As moisture is pushed to the extremities of the system the concentration of protein D builds up and creates a sort of one-way valve/gate, and moisture begins to accumulate within the cap.  Eventually the whole system develops an equilibrium with its external environment and an equilibrium within itself.  Once this state is achieved the system begins to self-germinate ( or it begins to foster the creation of spores within the system ).  These spores are pushed to the extremities of the system and are trapped behind the one-way gate.  Eventually the cap bursts.  Protein E does nothing significant during this iteration.-

What do you think?

I know next to nothing about Pilobolus, but if you are interested in how life achieves complexity then I would recommend reading some Dawkins as a grounding to how it all works - 'the selfish gene' and 'the blind watchmaker'.

I really don't know the extent of your biology knowledge, but imo there are 2 big aspects to get a grasp of - evolution and genetics (which Dawkins is a good introduction to, and there are more advanced books by e.g. Matt Ridley). The other is development and complexity arising from simple rules, and understanding that something apparently complex (e.g. a tree) can be built by simpler branching etc rules (have a look at Conway's 'game of life' cellular automaton for an example). Even things like human organs tend to be built in the same way - see for example the similarity in the branching in the lungs with the structure of a tree. It is a means to increase the surface area to volume ratio for gas exchange. 

I'm not super familiar with the specifics of development of any particular organism, but a lot of work has been done on simple organisms like fruit flies to understand how they are built, you could read about this to see how things like limbs and specialisation can happen. As you read about evolution you will read about how most of the organisms today are built from a few body plans / phyla, and share a lot of their blueprint. I just finished reading 'wonderful life' by Stephen J Gould, which aside from being a little rambling and overlong, suggests that during the first explosion of multicellular life there were far more bodyplans being experimented on by mother nature, and whether by random accident or better design, just a few of them won out and form the basis for later life on earth.

As to creating models, go for it, maybe even start with simpler models than Pilobolus. You can even add genetics to your model and let nature 'select' the best version of your species. Or even compete 2 or more species against each other if you want to make things interesting, or have predator prey interactions.

This is all assuming you are not a religious fruitcake, of course, in which case, forget all this, and just accept that everything was created by the flying spaghetti monster, waving his noodly appendages.

Matt Ridley hey?  I'll have to give him a read.  Is there as specific book by Dawkins you'd recommend?  I'm familiar with Conway's 'game of life'.  It's interesting all the different forms that can perpetuate within the 'game of life' by simply following a few simple rules.  I kinda imagine that's how evolution works too.  

On 27/06/2017 at 5:59 AM, lawnjelly said:

This is all assuming you are not a religious fruitcake, of course, in which case, forget all this, and just accept that everything was created by the flying spaghetti monster, waving his noodly appendages.

FSM?  hahaha, well philosophically you might consider me nuts .  What do you make of free-will and subjective experience?  I personally think they are integral to the universe, but just how and why is unknown.  What is known is that it allows us to observe.

You may find reading about self-replicating robots, and self-organizing robots of interest. It's not biological, but it does touch how a system can make itself fit for a purpose.

Of course, there is also the concern about the day when robots become more smarter than us. What will happen? It seems it's unlikely to end well for us though.

9 hours ago, Awoken said:

Matt Ridley hey?  I'll have to give him a read.  Is there as specific book by Dawkins you'd recommend?  I'm familiar with Conway's 'game of life'.  It's interesting all the different forms that can perpetuate within the 'game of life' by simply following a few simple rules.  I kinda imagine that's how evolution works too.  

Curse this mammalian brain, it's actually Mark Ridley, I think it was just titled 'Evolution' but I had it as a textbook on a 3rd year genetics course 20 years ago. There are probably many other great more recent books.

For Dawkins I'd recommend Selfish Gene, then Blind Watchmaker. They are his earlier books but did very well, the later ones often rehash the same points. After all the principles involved haven't changed, although I'm pretty sure there's been a lot of breakthroughs in stuff like epigenetics since I studied it.

4 hours ago, Alberth said:

You may find reading about self-replicating robots, and self-organizing robots of interest. It's not biological, but it does touch how a system can make itself fit for a purpose.

Of course, there is also the concern about the day when robots become more smarter than us. What will happen? It seems it's unlikely to end well for us though.

Spot on, I was going to mention this in my first post. There's a lot of programmers experimenting with genetic type methods / selection to evolve artificial life / methods of locomotion in physics simulations, things like that. It may not be biological but the principles involved are exactly the same.

This kind of thing for locomotion: 

9 hours ago, Awoken said:

FSM?  hahaha, well philosophically you might consider me nuts .  What do you make of free-will and subjective experience?  I personally think they are integral to the universe, but just how and why is unknown.  What is known is that it allows us to observe.

Well 'free will' I'd just say is a fancy name for the decision making process our brains do all the time (and most other organisms more complex than say, a fly). I don't really know anything about subjective experience..
 

On 01/07/2017 at 3:31 AM, lawnjelly said:

I don't really know anything about subjective experience..
 

Yeah well.... neither do I.