Random theories/observations/thoughts about life

Here I list some random thoughts and ideas (categorised!) I have about various things in this universe. Most or all of it is pure speculation. I love to think and when I think this is what I come up with. Many of these are tongue-in-cheek. Some of these will grown and become part of my regular pseudointellectual essays collection.


Self replication, emergence, evolution, self evolution, and sentience

My first set of thoughts on this topic have been collated into this essay.

Electron acceptor enzymes mediating disulphide bond formation in proteins

First, the title explains the reason for this note. Second, these proteins have also been called chaperones (the publications are there if you UTSE). Third, a little factual information: From the definitive Molecular Biology of the Cell by Alberts et al. textbook: "The most abundant substance of the living cell is water. It accounts for about 70% of a cell's weight..." [For the record, 26% are macromolecules.]

This is some abstract "cell". Depending on the type of the cell, the amount of water would be different. I believe blood cells have the most amount of water and sperm cells have the least. Some cells are extremely small (and have about the same amount of genetic material) and some are extremely large. Disulphide proteins are present everywhere. Molecules in a cell exist under very crowded conditions (and at different stages!). So the percentage of water in a "cell" is such a widely varying figure that it explains the presence of electron acceptor enzymes (such case DsbA) in certain cells---it guarantees folding!

Proteins are robust folders

It is readily obvious why most proteins' three-dimensional structure is generally encoded by the amino acid sequence alone. This is because proteins have been evolved to fold under very different conditions as organisms became more complex. For example, some cells have a lot of water and others have little. Consider also that proteins have the property of being functional across species that exist in different environments (thanks again to evolution) it makes sense that the sequences that have evolved are robust folders under many different conditions.

Thus there is a set of extrema where proteins will no longer fold, but within a certain range, the folding and the stability of the protein will be relatively the same. Since the folding process itself may be chaotic, it's only in terms of the overall general pathway and structure that the folding will be similar. (In other words, this is not to dismiss the effect of the environment on protein folding.)

Molecular chaperonins that lower the activation energy required to cross the transition state barrier, and those that permit a misfolded protein to refold (to a lesser degree), do indeed violate the view that the amino acid sequence alone is responsible for the three-dimensional structure, but this is a means of additional control of the folding process by the organism.

The marble and the volcano analogy of protein folding

Analogies are generally flawed and I try to avoid them generally, but I like this one a lot. This is how I view protein folding: imagine you have been given a set of marbles (in constant jiggling motion) and you're standing on the edge of the top of a very high volcano. You place the marbles on the edge. Under a relatively broad range of certain conditions the marble will roll off the edge and fall into the volcano. The surface of the volcano is fairly rugged and not completely even, but generally most marbles are designed such that they complement the surface of the volcano and roll down in about the same length. In other words, most marbles will start rolling, hit a few obstacles and go over them until they finally reach the bottom where they continue to move around. Some marbles may not be smooth and frictionless and therefore might get stuck on the rugged surface (where a "normal" marble wouldn't) every once in a while. In this case, another marble must come along and nudge it a bit so it gets free and continue its rolling. In other cases, there might be spots on the surface that are really hard to cross and a marble's path might take it so it's in front of those spots. In these cases also, a second marble would be necessary to bump the first marble so it goes across the barrier in front of it (and continue its rolling).

While each marble takes a similar amount of time to get to the bottom (the surface is sloped, the force of gravity is constant, the marbles are designed in this manner), with the exception of those few marbles requiring help, the path a given marble takes, even if it's released from extremely similar conditions will be expontentially different.

The set of marbles are the proteins we see in nature. The slope of the volcano is the time (y) coordinate. The conditions that the marbles roll into the volcano are the range of physiological conditions. The surface of the volcano describes the folding and energetic landscapes of a protein. The design of marbles to complement the surface of the volcano is the biological evolutionary process. The bottom of the volcano represents the various states of a folded protein, including its functional states.

Marbles that get stuck on the rugged surface because of their own lack of smoothness and because of the surface are proteins that need chaperonins to fold up, and marbles that help the stuck marbles are the chaperonins themselves. The chaotic process of protein folding and its sensitive dependence to the environment are exemplified by the different pathways a marble can take to get to the bottom, but get to the bottom it usually does (and in about the same time).


Sucessive upgrades in relationships

When you go out with a member of the attractive sex, the other person tries to make you look in their eyes. Since we're all conditioned by society as to what looks "good", you will probably end up looking better and will be able to attract more members of the attractive sex, thus giving you better choices for an "upgrade". When you upgrade, the process will repeat. The incremental benefit with each upgrade will be marginal. However, if you stop upgrading or stop being in a relationship for a while, you'll soon end up right back at square one.

So nerdy they are hip

Think of coolness measured as points on the circumference of a circle. Zero coolness (complete nerd) is right next to 359 coolness (completely hip). Achieving complete nerdiness is probably a lot easier than achieving complete hipness. So if you make it a point to get very very close to complete nerdiness, you might end up fooling people into thinking you're extremely hip (like the band Devo :).

So stupid they are genius

Same as above, using a circle for measuring intelligence. Zero intelligence (complete studidity) is right next to 359 intelligence (genius). Achieving complete stupidity is probably a lot easier than becoming a genius... So if you make it a point to get very very close to complete stupidity... you get the idea. (Note this circular idea can be applied to almost any sort of measurement.)

Girls pay more attention to lyrics than boys

For reasons I can't quite fathom, my observation is that girls in general pay more attention to lyrics in rock/pop songs than boys do (who care more about music).

Pseudointellectual ramblings || Ram Samudrala || me@ram.org