Direct evidence to Dawkin's selfish gene

The biophysics department here at Hopkins had invited Dr. Alexander Van Oudenaarden from MIT physics to give a student invited seminar. I was a bit familiar with his work through my junior thesis. He is trying to understand noise and random behavior of cellular signaling pathways through experiments and computer simulations.

The talk had a lot of good things, but what caught my attention the most was a topic I could directly relate to the heading of the post. In our cells (except mine!) , or in any other eucaryotic cell there is a signaling pathway called the GAL switch. When the cell is put in an environment which lacks any other nutrients except galactose (which is a kind of sugar present in milk) the GAL switch operates and produces carriers which help the transport of galactose from outside of the cell in the cytoplasm (inside of the cell). I genetically lack that system and that's why I cannot consume milk which is a major source of galactose.

Suppose we start with a bunch of cells which at time t = 0 do not have the machinary to transport galactose in. We then supply galactose to this culture. What we expect to find and do find is that the internal GAL switch starts functioning and builds up the transport machines which take the galactose in. This makes a lot of evolutionary sense, that to a given change in environment, the cells are able to cope up accordingly. (case A)

Now suppose we start with a bunch of cells which at t = 0 already have the machinery present to transport galactose in. And suppose now we put this culture in a solution where there is a lot of galactose (case B) or there is no galactose (case C), what we would expect is that the cells would continue living with their existing machines in case B and that they would shut off the factory of transporting galactose in case C (since there is none in the environment).

Counter intuitively what we find experimentally is that in case A, there will be some cells which do not produce the machinery, in case B there will be some cells which shut off their machines and in case C, there will be some cells which will keep on maintaining the machines though they are rendered useless. This phenomena is no accident and is a persistent feature of the culture. It is counter intuitive because the cells which are going against the popular vote are eventually going to die because of their apparently stupid decision. If the organism were to evolve such that the selfish unit of evolution were the individual itself, this kind of suicide does not make much sense.

Cleverly when the experiments were performed in a medium/solution where the concentration of external galactose was changed in time, the lab found that this suicidal behavior makes a lot of sense for the gene! During evolution of the yeast, the species was exposed to a time varying environment the nature of which we surely don't know. The gene's way of predicting the future environment or differently put, the gene's way of coping up with random changes in the future environment was to produce individuals of all kinds some of which are unsuitable for the current environment (but might be suitable for the future). By maintaining a population which has some members which are suitable for the present and some members which are not, the gene ensures that for any reasonable change outside of the cells the species as a whole is not wiped out. In other words (I suppose) the gene makes sure that it does not follow a path to extinction by maintaining a pool of suicidal members (who potentially may cope better with random change in the environment in the future).

I thought this is a direct evidence to the selfish gene rather than a selfish individual or a selfish species. And that made me happy :-) This is a direct evidence because neither selfish individual nor selfish species hypothesis can explain this kind of a behavior.

And to conclude, it is important to give some definitions as I understand them. By selfish X (X = gene, individual, species) we understand that X is the unit which will try to survive in case of competition by perhaps eliminating other members of X. For example in case of food shortage, a selfish individual theory would imply that individuals will kill each other to survive so that they can acquire sufficient amount of the limited resource for themselves, a selfish species on the other hand would perhaps imply that humans would kill off other animal and plant species so that they don't have any competition for food resources. The most counter intuitive selfish gene would imply that individuals would take actions in such a way that individual genes are retained in further generations.

Pacman

In an academic discussion (hmph!), it was pointed out that Lysozyme is equivalent to Packman in it's job. It' lyses ie. cuts and kills proteins when they are vulnurable to attack. It also turns out that they are isomorphic in shape as well.

Mistakes. Some more

I've realized that it's no fun committing the same mistakes again and again without learning the lesson. Now I am not even mad at myself, I am just bored of going through the same process again :-) Hopefully next time, I'll make a different ones.

Purushottam

Communication breakdown

A typical conversation in the land of plenty amongst the students will go as follows. The matter of the conversation as we show below is not important but the recurrence of certain motifs is.

I'm like, I went to like this bar last night, and the bartender was
like, the skirt is awesome, and I was like blushing. And it's like, we
are like with fake id's so it's like scary to go in such places and I
was like all daring and it's like it was like awesome.

What it means:

Dash dash dash like dash dash dash like dash dash dash dash dash dash dash dash like dash dash dash dash dash dash like dash dash dash dash like dash dash like dash dash dash dash dash dash like dash dash dash dash dash dash dash dash like dash dash dash dash dash like dash dash like dash.

The theory:

Because this kind (the first of the paragraphs) of conversations are frequent in universities, researchers were lead to believe that there exists a deeper pattern in them. It was soon proposed out that the original pseudo-English conversation is actually a Morse-code with everything other than the revered word like being determined as redundancy in the information packet travel. This theory is now finding a wide spread acceptance amongst the scientific community.

Safir Merchant.
The Johns Hopkins University

(Communicated by Purushottam Dixit)

I don't belong here

When you are walking on the road, on a normal day sometimes there is a strong burst of realization that you don't belong here in this place at this time doing this. For the past 3-4 months in here, I haven't even got close to anything of that sort at all :-)

A B argument

An AB argument is a conversation between two people PD and VK which proceeds as shown below:

VK : A
PD : B
VK : A
PD : B
VK : A
PD : B

.. ad infinitum (or till one of them gives up)

If VK is replaced by AM, PD always looses the AB argument. The essence of the conversation is that VK claims A is true while PD claims B is true where B<==> ~A (or !A) and both of them want the other to believe that what they believe is true is the truth. Do not take this construct lightly for its triviality, this has been proved to be a useful model for explaining adamant people.

Recently I had to perform a technical survey, all the scientists were people who have achieved a significant amount of discovery (some of them Nobel laureates) and all the papers I read were either in Nature or in Science. And the argument goes like this:

RM: S4 linker moves 20 angstrom
RH: S4 linker does not move 20 angstrom
RM: See results from XYZ experiment, S4 linker moves 20 angstrom
RH: See results from XYZ (the same XYZ as above) experiment, the S4 linker does not move 20 angstrom

They continue this way for every other aspect of the problem. There are around 5-10 aspects to the problem and each of them results in atleast 10-20 Science or Nature papers.

The end of the AB argument as told above comes only when t --> infinity or one of them gives up. The giving up has been observed within 30 minutes with probability 1 when the mode of conversation is speaking in front of each other. But we believe that it is really difficult to observe the giving up phenomena when the mode of communication is writing up 1 page papers in Science or Nature. Thus a more evolved type of argument is needed to to settle the issue.

The Johns Hopkins University

The Gillman Hall and quadrilateral

If you ever happen to visit Johns Hopkins and wonder why all buildings are small, here's the reason. (Though the university disclaimer denies it) It has become a convention that no building should be taller than the Gilman hall (Mr. Gilman was the first president) and the Gilman hall should be visible from the North Charles street.

A cafe near a university

I was sitting at a cafe, and a guy is impressing a girl by telling her the Russell's paradox. Then he moved onto Godel's incompleteness theorem. The girl was completely awestruck. Then a french man came for some help with wireless net and we talked about the paradox and then life.

Also, when you wake up and go to work or whatever that you are meant to do. Do you feel that you are not meant to be there and all this is going on is wrong? For the last few days, I am feeling exactly the opposite about graduate school.

:)

ps: I realized that I have issues with pens. Can't work with bad pens, simply can't.

Thus in livejournal language, the mood can be described as cheerful and the music, without doubt the beatles.

Piano and PDEs

The story goes back to a conversation between me and analytique de maximus, Lothar. "Which instrument do you like the most Purushottam?", He asked. "Piano", I answered quickly. Though I played only guitar, piano was my favorite always. " And why is that?", he insisted. Why one likes anything is a different issue altogether and I am not going to dwell into that here. Important to this context was the answer I gave. "I like the pure sound, the notes, without mircrotones, not like violin, piano has a definite sound". I was able to satisfy his ultra-inquisitive mind with this. I was relieved for that.

Some years later, that is today, I was sitting in in my PDE class. And the prof. was teaching something about wave equation. It's not that I hate it or something. Being the geek I am, I was enjoying the mathematical aesthetics in the problem. Now, I am going to write something which you might not understand or like, but it's a graduate course and never mind :)

In the wave equation, the initial conditions on time are the initial velocity and the initial displacement on the string. The string is assumed to be bolted at the two ends so that given a displacement, it vibrates periodically. The solution generally is a fourier series, each term representing a definite mode of vibration of the string. If we solve a problem where the initial velocity is zero while the initial displacement is finite and linear, we find that the fourier coefficients die down as 1/n^2. While in the initial velocity (no displacement) case, the fourier coefficients die down as 1/n^4. Even this part was enough interesting for me. But then, the professor started talking about piano.

In a piano, sounds are produced by pressing the keys which in turn results in a small hammer striking the string. Hence an initial velocity is given to the string problem. While playing a guitar, you pluck the string and give it an initial displacement. But since in an initial velocity problem the coefficient which are nothing but the amplitude, decrease rapidly, the higher overtones of the frequency are not heard, while the higher overtones are powerful in guitar and what we hear is a mixture of frequencies. That is why a piano sounds pure and single frequency and the guitar doesn't.

Math is beautiful in her own right. But then you can see her in nature, and in things you love and then it feels like adding more stars in her crown.