Friday, November 28, 2008

Molecular and Cellular Videos (External Link)

OK, I thought I'd keep my blog mostly about only my projects but sometimes one runs across something really cool and blogging about it increases its Google score. My friend Eric Siegel at NY Hall of Science sent me this link to large collection of nice molecular and cellular animation videos.

I love videos like this. That said, I do have a very big complaint about the non-simulations (most of them) -- they make molecules appear to be intelligent agents. Molecules do not make deliberate choices; they do not see a complex forming and then think to themselves: "Hey, I think I'll whiz over there and insert myself into that growing structure!" For example, see the microtubule growth in Inner Life.

It is completely understandable that the animators of these videos have a hard time capturing the reality of molecules because the velocities at which things happen at the nano-scale are extremely difficult to comprehend and thus it is hard to create these animation without resorting to the "cheat" of "deliberateness". Unfortunately this cheat creates a major confusion -- I know because I remember being confused! In Segan's wonderful Cosmos series, there was an animation of DNA polymerase with its reagents all flying across the screen to assemble themselves into a growing polymer. I distinctly remember as a nine-year-old thinking: "How do the parts know where to go?" No one told me that 1) that's a great question and 2) they don't.

Here's the way animators to create these effects. They place the pieces of the model together in their final configuration and then they tell the animation program to fling all these pieces away in random directions with random tumbles. Then they simply play the animation backwards to create the effect of the individual molecules assembling themselves into the formation (that's the easy way to do it anyway). It creates the lovely assembling effect but it is a lie -- a very, very interesting lie.

Think about it -- in order for the animators to make it look like the molecules know what they're doing they have to run time backwards. That isn't merely a statement about animation -- it affords a deep insight into thermodynamics. Things which "know what they're doing" are, in effect, "running time backwards". Getting your head around this idea is the key to understanding what life is, why perpetual motion is impossible, and failing to understand it is central to many misconceptions especially among creationists.

Molecules don't know where they are going. They just thrash around randomly due to collisions. The sum of all that motion is what we call "heat" -- more heat, more violent thrashing around. If you were to put some molecules in a little pile they would bounce off each other spreading out into a more diffuse pile. Why should they spread out and not stay put or even compact themselves tighter? Because, as long as they aren't interacting with each other (we'll come back to this case) there are a lot more ways to be spread-out than there are to be compact. Scientist call this by weird name "entropy" -- it's the second law of thermodynamics: entropy (spread-out-ness) is always increasing. It's an idea that's so simple and yet so profound. Why is it true? Nobody knows; that said, try to imagine what the world would be like if it were false.

Suppose that molecules spontaneously created little ordered piles without interacting (again, we'll come back to interaction case). Those little piles are information. In other words, you could look at them and say: "Hey, there's a little pile there that shouldn't be -- since they aren't interacting they should have spread out, thus, something must have put them there." And then what? What are these little piles of spontaneous information forming? Are they spelling out Shakespeare? Or drawing a picture of a cat? Or writing out a cryptic secret that we can't read? See, it's nonsense; you can't turn it around. When you try to imagine a world that doesn't spread-out spontaneously then you end up with a world where information spontaneously appears out of nowhere and such a world would be indistinguishable from one where time was running backwards. In other words, the concepts of time and increasing entropy are the same concept.

Here's another way to think about it. Suppose that you had a tiny ball in a tube trap. Say the ball can be on either side of the tube: left or right. If the ball and tube are not interacting in some biased way then there's just as much chance that you'll find the ball on the left as the right side. Say you tried to use this tube as a memory device with the position of the ball meaning different things. You reach in and move the ball to the left side and then shut the trap and hand it to over to a friend who examines it. You shouldn't be surprised that when they open it they are just as likely to see the ball on the right as the left. This is a terrible memory device! The reader of the information might as well have just flipped a coin instead of relying on this thing to remember what you entered. How would you fix this? You'd have to glue the ball in place somehow to prevent it from moving. So, how would you glue it? There's lot of ways, you could introduce a chemical bond that stuck the ball and tube together or you could jam in a plug or lots of other clever contraptions. But every way of "gluing" will have the same requirement: it will need an investment of energy. In other words, an investment of energy is the same thing as information. If you see a pile of energy laying around somewhere then you know that such a pile potentially holds information (what that information encodes or means, that's a totally different question). And vice-versa, if you know some information then it must be that case that energy was invested to make it known. The two concepts -- information and free-energy -- are the same concept! And this explains why you can't build a perpetual motion machine. If you could then it would be creating information out of nowhere which is the same thing as time running backwards. Or, to put it another way, if you do build a perpetual motion machine then (just try) to stay the hell away from it because that thing is running time backwards!

And this gets us back to life. If it is the case that things can't spontaneously assemble then how can there be living things which are made from spontaneously assembled molecules? The fact that life is so information rich, is this evidence that something made the investment of free-energy? Yes. Shall we call this investor of free energy some sort or god or spirit or vitalistic force? That's a reasonable question, and I've seen this argument in creationist literature, but the answer is: no.

This gets us back to the videos and what's wrong with them. The videos make it appear that molecules "know" what they are doing. The seem to "know" that they should fly through space and attach themselves to some cool growing nano-machine. But they don't. What they do instead is much more interesting. They bounce all over the place without knowing squat. Why don't the spread out? They do, but they are held inside of a bag -- the cell -- which keeps them contained. When they bounce around they accidentally find molecular partners with whom they interact. This is very different than what I described before with the ball in the trap where we assumed that there was no interaction. Now, there is interaction -- they stick like glue. As described, such gluing requires energy. Where does the energy come from? It is pumped into the cell from the outside. And when the interactions break, that energy is released at higher entropy (time moving forward) and that entropy is pumped outside of the cell to keep it from poisoning the inside. Living things are devices that invest free-energy from their environment to temporarily increase the information inside of the cell. This is only possible because they have access to the free-energy; no free-energy, no life. By the way, there’s lot's of things do this, not just life. For example, a whirlpool is a pretty clearly defined "thing" that it is possible because free-energy in the form of rushing water gets trapped into a shape that then dissipates the entropy out the bottom. Whirlpools, and living things, are not "things" in the sense that they are persistent collections of molecules -- they are things in the sense that they are persistent patterns of molecules -- the molecules themselves just pass right through.

What makes life really interesting and different from a whirlpool is that it is a self-contained computational device that stores the changeable instructions to copy itself. A whirlpool's pattern is created by the external circumstances around it -- the pattern of the rocks and the waterfall. In contrast, living things internalize the "circumstances" that build them (the DNA, the proteins, etc) thus living things can be viewed as a single package that makes decisions and evolves as a computational whole. The magic of living things is that no individual part (the molecules) "knows" what it's doing (my problem with these videos) yet the ensemble does "know" what it's doing! When we casually look at a living thing we can't easily track the energy flux in and the entropy flux out and thus living things appear unique, as if they were running time backwards -- exactly the trick the animators use to make the (wrong) animations. Ha!


Stephen Uzzo said...

Hi Zack, Eric Passed on a link to your comments. Thanks for this, and I agree with everything you’re saying, except I would clarify one thing. Evolution doesn’t forget. While time does not go backward, the complex molecules that represent the interacting aspects of cells have been created through many repetitions of the same structures over and over again from an existing complex set of conditions (I guess you could call this computation, cells make great computers, even though brains make lousy ones!), that evolve over time through random changes introduced to those structures and interactions. Increasingly, we are realizing that these chemical configurations and reactions have hierarchical structures that are composed of repeated substructures put together in a limited set of ways. In other words, a network. I would conjecture that it would be more accurate to say that there are random changes to the structures that result in evolution, but the structures themselves have very specific configurations and reaction modalities that have been repeated through the eons. So while it might not be intentional, it is not random either, it is structured or patterned because of doing it so much over so long a period of time. Evolution tunes these interactions and streamlines them. The interactions that are retained are likely more effective and require less energy or intermediate steps than those that might have been filtered out because they led to a less successful or effective living processes. Without this filtering process, and without the ability to retain and tune existing processes, evolution would barely exist, if at all. So when we talk about entropy in terms of complex interactions within cells, it is my belief that we need to temper it with the notion of complex structures than have favored certain kinds of interactions over billions of years and have the preconditions and structures in place to improve the effectiveness of those interactions that lead to more successful organisms. So while video clips of depolymerizing microtubules may deploy stupid human tricks like backward explosions, life deploys its own tricks, some of which might not look like the video clip, but which may appear intentional because life is a creature of habit!

Carl Batt said...

It is what I call the hand of god. Because it is an external force that makes everything right. It is not tolerable for things not to work or to take so long as to bore the viewer. Because of the speed the only thing acceptable is to have everything fall into place guided by an invisible hand. In fact it is mass confusion only guided slightly by a small but finite set of interactions that are promoted at a molecular level. The nuances only making a difference because the number of pieces on the board. In the case of these videos, they are appealing because they are instructional and in the end it all comes out as predicted.