Wednesday, April 7, 2010

Are recombination random events?

If they are and not because of an existing signal, we should expect the following :

If e.coli is infected by two bacteriophage one functional other not functional, the plague forming unit formed in a given time will be less than when e.coli is infected by only functional bacteriophage (same titer as used in previous experiment). It is because unnecessary recombination event forming some non-functional virus.

Monday, April 5, 2010

What is spin of an electron?

Spin is a quantum number. Quantum number is used to define the state of an electron in an atom.

Quantum numbers:
  1. Principle quantum number indicates distance of the electron from the nucleus
  2. Azimothal quantum number indicates angular momentum of the electron orbiting.
  3. When electron orbits in the orbital it creates a magnetic field which is expressed by magnetic quantum number.
  4. Spin quantum number is an intrinsic magnetic field which arise from the spinning of the electron on it's own axis.
Things written above can't be taken literally. It's only poor analogy drawn between quantum and classical mechanics. From classical theory and experiment we know that moving charge (macroscopic) produce magnetic field. Charge is a fundamental property of matter, there is no question about it's existence. Now the question is whether it is true for fundamental particles like electron or proton. Do moving electron produce magnetic field? I think it does. Because magnetic field is a fundamental thing, if it is not produced by some fundamental action it can't arise at all. From that we can be sure that moving electron must produce magnetic field.

But there is a difficulty in saying that the spin of electron arise from rotating on it's own axis. To produce observed magnetic moment the equatorial region of the electron must rotate at speed more than that of light. And another point that electron don't spin in classical sense is that - to complete a period or make a complete revolution it must rotate 4 pi radian as opposed to 2 pi.

So here are the safe things to say -
1 . Electron has two magnetic field separate from each other.
2. One is associated with the shape of orbital and other is intrinsic.
3. Both of the them are quantized,
4. Spin quantum number can only take two values - +1/2 and -1/2.
5. Electrons in the same orbital must have different spin quantum number.
6. Because spin quantum number can take only two values associated magnetic moment has also two values. If set in a magnetic field it can either align with or against the magnetic field but can't do otherwise (say align in a direction 60 degree with the magnetic field). I don't know the answer why??

Sunday, April 4, 2010

amplification of signal (biological signals)

Fire: Fire is an example of one sort of amplification. Naively amplification of heat, we give a little heat and it get's amplified. Heat is one kind of energy so it's wrong to say amplification of energy. We can think of it as one kind of signal amplification. The existence of fire indicates the existence of initial activation energy. Flammable substances are systems for amplifying a signal namely activation energy. Initial activation energy may be very low to notice but it is transformed to fire which contain large amount of things and light to be noticed.
Production of fire involves chain reaction as shown below.
















In every step the energy released is not completely used in transforming substrate to product, the extra energy is added as the reaction goes on and it gets hot and bright.

Enzymes: Enzymes transform one type of substance to other. One enzyme molecule can easily transform a large amount of substances. This is one sort of amplification.


In biological system one excited enzyme molecule can transform thousands of other molecule in small time. This way signal which excite or activate a single molecule can be amplified. Fire usually amplifies in uncontrolled way but biological signal amplification is controlled.

Finding optimum solution

Enzyme catalysis:
Specificity is about binding. When we say that an enzyme is exclusively specific to a particular substrate it only binds with that substrate and in a sense repel other substances. For being strictly specific correct form of binding must be strictly necessary for catalysis.
This specificity will also result in strong binding. There is a problem with strong binding because if so after the reaction or chemical transformation, product will not easily leave the enzyme and make it available for new substrate. This will slow the actual rate of transformation of substrates. So good enzymes should give only marginal time for reaction to occur and release the product. This is about enzyme affinity for substrate which is directly related to binding. Strong binding (high specificity) will oppose quick release.
Rate of transformation inside the enzyme is also a function of binding. Releasing is also a function of binding. If they were separate event one would say that for a good enzyme, the binding affinity for substrate (of an enzyme) will be such that to match the average time of transformation.
But the reality is that rate and binding affinity is not independent from each other so that they can move freely to be adjusted to an optimum. They are connected - changing binding affinity inconsiderately can effect rate. Rate is not only dependent on substrate binding but also with the binding with transitional state, so there may be ways in which we can change binding affinity still not changing the rate.

Thursday, April 1, 2010

vomitting

There is a place in brain called vomiting center.
Why an organism would like to kick out ingested food?
Because the food may contain poison, pathogen etc.

There may be several signals which tells the brain that the food contain harmful material, then the brain send a signal to vomit.

spinning also induce vomiting. Why?
May be there are some harmful thing which cause the brain to feel spining , that's why spinning feeling is interpretted as harmful thing inside the stomach (I just speculate).