Molecular Visualisations of DNA [video]

And then in terms of the biology itself, you will run into things that we might think of as "complications" but which are actually for the sake of redundancy/fault tolerance, etc.

I remember watching a series of biology videos where a particular messaging pathway was explained. It had at least 5 or 6 proteins. But then the lecturer described that by having so many proteins in the chain, the messaging is exponential. So what initially might seem like a complex way of sending messages is actually an amplifier!

Complexity is something that can be clearly defined in terms of probabilities and hence measurable. If it's stated that these complex (made of {large number of} parts) molecules _work together_ with these others complex (also very large) molecules, than this all process, in order for it to fulfill a function, requires a set of very specific values for very specific parameters.

This is measurable complexity. And if one says that in time evolution will solve a problem, you can make the liaison with the complexity of the process through the probability of its occurrence.

For example, do you like your lungs? They work pretty well, right? But how long can you hold your breath under water? Obviously cetaceans have much better lungs that humans, but that's because our lungs are just good enough for running around on a savannah. If we were forced to dive to incredible depths to search for our food, we'd need to evolve better lungs, as the cetaceans have done.

Before the dolphins get to smug, though, they don't have the best lungs either. The title of best lungs goes to the birds. Whereas all other air breathing animals have bidirectional flow in their lungs, birds have evolved a system of continuous unidirectional flow. Turns out that bidirectional flow is not good enough at high altitudes with an extremely high metabolic rate.

As for what makes Biology and Medicine difficult, I think the answer is: time. That is, aside from dealing with systems composed of more moving parts than physics or chemistry, biology is also less open to direct manipulation and experiments take, on average, much longer for the amount of information gained. Eventually, though, I don't doubt that we will understand biology as well as we understand the other two. At the moment we're in the "alchemy" stage of biological research. We have a sense that there are units of action and rules governing these units, but we don't know what those units are or how they interact. A rock you dig up from the ground is, also, a rather complex system difficult to understand until you have knowledge of chemicals, molecules, bonding, etc. We just need to figure out what the "atoms" of biology are.

Often complexity would come at a cost though, and evolution would automatically end up optimizing for it. Such costs may include energy costs, vulnerability to faults/diseases, etc. With such elaborate mechanisms for DNA wrapping, replication, etc., I wonder how much cost junk DNA brings to the system (vs. benefits in terms of fault-tolerance and evolution).

[1] http://en.wikipedia.org/wiki/Junk_DNA#Junk_DNA

[2] I am not making any assertion here about the percentage of junk DNA in the human genome, and am unqualified to do so.

Of course, in order to proceed in a meaningful way this conversation we should first establish what exactly complexity and optimization means, in this context.

So if you feel like it, please share a specific example.

Think about all the school, high-school and even college visualizations showing the organelles f.e. just hanging there pinned into place. Between them wast areas of ... what?

Now look around you. What do you see? Maybe the furniture of you room resp. office... now wave your hand in front of your eyes (nooo, they are not laughing AT you ;) ... did you feel the interaction of the molecules "in the air" with those of your skin? They are filling the gap between us and the things we are capable to perceive with our eyes...

The "invisible" content of these gaps is interacting with the visible parts. At molecular levels those invisible elements contribute hugely to the non-deterministic, non-lego like snappiness, to the "random walk" way of things working out.

This kind of insight I think should be replacing the "deterministic machinery" view when describing and picturing molecular and micro-biological processes.

Visualizations by Dr. David S. Goodsell present this kind of ideas in a fascinating way.

(you can stop waving your hand now ;)

And in doing so makes another sewing machine.

Life is awesomely complex stuff.

At the same, even as a biophysicist, I think these animations are superb learning tools. Those beautifully rendered animations actually describe the mechanism in far greater detail than, say, textbook diagrams. One should just be aware that fluctuations dominate at these scales.

Molecular biology is like entering the rabbit whole.