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From DNA to proteins

August 30, 2011 1 comment

DNA is my latest fascination. So I am planning to do a few posts on the basics of DNA. Through this, I want to just get the basics across correctly, so that in future, we can talk about advanced topics like Genetic diseases, genetic therapy and stem cell research. More than with other posts, this series will be more of a self-learning exercise.

I assure you that what follows is very simple to understand, with just a little focus. The DNA is made up of 4 fundamental elements represented by the characters A, C, T and G. Each of the characters A, C, T and G represent 4 different molecules, called Adenine, Cytosine, Thymine and Guanine. These belong to a group of molecules called nucleotides. You don’t need to remember the names. But assume that these are the only letters of the genetic alphabet. In comparison, the English language has 26 letters in its alphabet.

The entire DNA is a sequence of these nucleotides A, C, T and G. Thus the entire instruction set needed to build our body is made of this alphabet. The important thing about the DNA is that it exists in a double strand. This is the picture that is most common in people’s minds when you talk of DNA. These strands are complementary, in the sense that if one strand has say A G G C T as its sequence, then the other strand will have the sequence T C C G A. That is all A’s are linked to T’s and vice-versa. Similarly all C’s are linked to G’s and vice-versa. Thus, whenever there is an A in one strand, the corresponding position in the other strand will be T. If it is C in one strand, the corresponding position would have a G. Thus, given any one strand you can say what the sequence of the other strand is. A and T form a pair, and similarly C and G form a pair. Given below explains the structure of the DNA. The shape, of course, is that of the famous double helix, like a coiled ribbon.

Structure of the double strands of DNA.

Now, a combination of three such nucleotides is called a codon. Thus C-T-A is a codon and T-T-A is another codon.These can be considered analogous to words in a language, like how R-E-D represents something and B-A-T represents something else. Of course the English language can have words of any length, whereas the genetic words have a fixed length of three.

The way English words come together to form meaningful sentences, the genetic words (the 3 letter codons) too, come together to form a meaningful string of codons. This string of codons is called a gene. Thus a gene is nothing but a string of codons. But what does the word “meaning” mean in genetics. What is the “meaning” of a gene?

We have all been taught that proteins are the building blocks of our body. That is, they are the fundamental elements that come together to build our body. But what is a protein? A protein is a sequence of molecules called amino acids joined together. There are many different amino acids present. Different amino acids are brought together to make a protein.

We can make the connection now. We saw that the gene is nothing but a string of codons, and the protein is a string of amino acids. The link must now be obvious. Each codon (the 3 letter combination) maps to an amino acid. Thus suppose, you have a gene that has codons C1 to C10, its “meaning” is a protein that has a string of amino acids AA1 to AA10, where C1 maps to AA1, C2 maps to AA2 and so on.

Let me add an important detail to this picture so that the picture becomes slightly more accurate. In the process of DNA getting converted to protein there is an intermediate type of molecule called RNA. It is the RNA that, so to say, reads the DNA and brings the correct amino acid for the codon read, into place, so that a sequence of such amino acids can form a single protein. An important difference between DNA and RNA is that instead of A being paired up with T, in the RNA, A is paired up with U (Uracil). That is, whenever there is an A on the DNA the corresponding position on the RNA is occupied by the nucleotide Uracil, represented by the alphabet U.

In fact, the mapping of different codons to Amino Acids, can be seen in this table.

A pictorial representation of what we discussed is given below.

The process of DNA getting converted into a protein

That is it for this time. It is good to take it slow. In the next post we will see where these genes reside in our body and how they are organised.

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The God FAQs – 1

August 15, 2011 3 comments

I clearly remember this incident from my growing years. This was the time when the serial Mahabharatha was going on in TV. My whole family, like many others, used to assemble in front of the TV for that one hour. In one of the episodes, Arjuna is teaching his son Abhimanyu, who is still in his mother’s womb, the art of breaking open and entering Chakravyuha (a war formation). But just as Arjuna completes teaching his son how to enter the formation, Krishna comes in, diverts Arjuna’s attention, and takes him away citing some reason. Years later, Abhimanyu is killed in war when he enters a Chakravyuha. That was because, though he was taught how to enter the formation, he was not taught how to come out of it.

I am not claiming any kind of expertise on Mahabharatha, and as usual there are many versions of the story floating around. But anyway, that is not relevant to why I brought it up. I remember that after the episode was over, one of my family members (I don’t remember who, but I think it was one of my uncles) explained to me, that the reason for this is that since Abhimanyu is perfect in all other respects, he cannot be killed in any other manner, and if he becomes undefeatable, he will live forever. And Krishna, for some reason, did not want this. And so he “cleverly” drags Arjuna away at the crucial moment, so that Abhimanyu does not get the complete knowledge. This strategy of Krishna, ensures that Abhimanyu is killed in the war. I was aghast at hearing this and started crying (remember I was only 8 or 9 years old then). I just could not digest the fact that Krishna, who is considered a god, could be so mean. I continued crying for some time and created quite a scene. I also could not understand how everybody else could go on with their lives, when such an injustice has been meted out right in front of our eyes. (My mental faculties were at such a stage then, that, I once asked my father, whether all those who were killed in the war scenes, actually died, and if so, why they agreed to act in those scenes at all, in the first place. I knew, the actors were not really the characters they played, but I thought that the scenes were really enacted). The reason why I recollect this funny incident now is that, to the extent that I can remember, this was the first time I questioned the infallibility of God.

I don’t know when exactly I stopped believing in a god, but I remember that even in my 11th or 12th standard, I was an atheist, and clearly recollect using that very word to describe myself, even though I was aware of the word agnostic. That atheism continues till date, and in the last 4-5 years, I have looked at the various arguments for and against the existence of god and realized that the existence of a god is next to impossible. It is not often, that the topic of religion/atheism comes up for discussion with friends. But from the few times this has come up, I can see some questions being repeated and so I thought, it would be good to make a list of FAQs. The idea is that, different people have varying degrees of belief in god. In many cases, they continue their belief in god, because they feel they have good arguments for their belief. But those points of view might not have been honed by active discussion or reading the various pro and con arguments. I don’t blame any of them, since on many important issues in this world, I don’t have a well-thought out opinion. And even on Atheism, I could be wrong (That is theoretically possible, but in my opinion unlikely). But to me this is an important and interesting question. The idea of this post is to make people think through their religious beliefs and other related ideas. Not all of these questions are directly about the existence of god, though many of them are. But all of them are in some way linked to the divine.

1. Is not Agnosticism a better position than Atheism?

This is a common question. The argument goes something like this. “I agree we cannot prove god exists, but neither can we prove that god does not exist. So we should wait till some evidence comes up. Till then I am going to be agnostic about god” The problem with this argument is quite simple. It can be seen easily by substituting the word “god” with “Harry Potter” or “Superman” or “Shaktimaan”. Let me help you. “I agree we cannot prove Harry Potter exists, but neither can we prove that Harry Potter does not exist. So we should wait till some evidence comes up. Till then I am going to be agnostic about Harry Potter”.

Do you see what is wrong with it? Being agnostic sounds like the middle-ground reasonable position. Such a position suggests that there is a 50% chance of god’s existence and non-existence. But if you think closely, that is not how we evaluate probability in daily life. When somebody says he was Mohandas Gandhi in his previous birth, or that he is Tipu Sultan’s reincarnation, you don’t give him a 50% probability that he is right. You will laugh at him. And that is the correct way to react. We cannot assign 50% probability to all claims (Is there a 50% chance that Ramar Pillai created Petrol from herbs?). As long as there is no evidence, the claim is as good as being false. Proving a negative is not possible. You cannot prove that I do not have a miniature invisible elephant in my pocket. Only if some positive evidence exists for some claim, can that be considered reasonable. Just because some claim is not disproved does not mean it deserves credibility. So the next time somebody tells you she is an agnostic, ask her what she thinks about Santa Claus? Is she agnostic about that, and waiting for evidence on that too, or would she say she doesn’t believe in Santa Claus.

2. If a god does not exist, how did the universe come into existence?

This argument seems to firmly establish the existence of a god. But it only seems. It comes from the idea that something cannot come out of nothing. So, if this universe exists it must have come from somewhere or something, and that something is god. Let us momentarily agree that something cannot come out of nothing (though that is not true as can be seen in this post). So it could be argued that the Universe was created by God. At least, she/he/it initiated the Big Bang. But will it not lead to the question of how that god came into existence? As somebody who is not ready to believe that the Universe could have existed on its own, how does the same person assume that god can exist on its own?

So how do we solve the question of how god came into existence? Should we postulate a next level of god, say Super-god, who creates god, who in turn creates the universe. We can keep doing this, and there does not seem to be any end to this kind of backward chaining. So is this an impossible question to answer?

No. To see why, let us look at an example. Suppose you are dropped off a space ship on some far away planet. You are all alone and you start going around the planet. There you see a small shapeless pebble, a spherical stone and an intricately crafted pendant. You will naturally assume that the pebble was the result of natural processes, but that the pendant was created by some sort of intelligence. On the question of the spherical stone, you will be in two minds. You do that because, you see that the pebble is not complicated, the pendant is complicated, and the spherical stone is somewhere in between. Thus, the more complicated a thing is the less probable it is of being the result of natural processes.

Now apply this logic to god and the early universe. Our universe, at the beginning was a very simple one. It was small, and mostly uniform (except for occasional disturbances in its uniformity, which supposedly is the starting point of today’s galaxies). Now consider god. It is an intelligent being, capable of imagining what the result of the big bang would be and the ability to create the big bang. It is also capable of seeing into future and calculating all the consequences of its actions.

At this point you would agree that the early universe is far less complicated, than a thinking all-knowing god. Thus there is a high probability that the universe is a result of natural processes (like the pebble), whereas, the god, like the pendant, needs a lot of explanation. Thus, in the end, it turns out that the universe, which we feel needs an explanation, actually needs much less explaining than the god, who is brought up to explain the universe. In case of any other two things, such an argument might sound like a joke.

A: I just don’t understand how a mountain came into existence. I think it must have been the result of some natural process.

B: Oh no. See how the mountain is shaped in a nice conical way. It serves the purpose of bringing rainfall to one side. It also serves as a landmark. I know how the mountain arose. There is this computer software, which reads the minds of all the people in the world, and finds their requirements. Based on these requirements, it decided that a mountain has to be built. It then prepared a design. This design is read by a hardware controlling program which is connected to a lot of machines, and actually built the mountain.

A: Oh is it!! (Scratching her head). Then how did the software and hardware technologies come into existence?

B: Oh that is easy. The software and Hardware technologies are timeless, eternal, and have been there forever. So that does not need an explanation.

Would you agree with that logic? Not me.

This is the first of a multi-part post. More questions in the coming parts. Meanwhile, let the discussion continue in the comments.

Here is the second part.

Categories: General, Skepticism Tags: , ,

Are we really free?

August 6, 2011 11 comments

Ok. If you seriously think about this, it might give you sleepless nights. I am talking about the question of whether we really have free will. A Google search for “define freewill” gives me this definition.

Noun: The power of acting without the constraint of necessity or fate; the ability to act at one’s own discretion.

Free will essentially means the ability to choose from choices. This is something we do daily. Whether to get up from bed or not, whether to get up now or 5 minutes later, whether to brush your teeth and then look at the newspaper or to do it the other way round, what to make for breakfast, what to wear, which bus to take to work, whether to take the stairs or the lift and so on. We keep making choices every second of every minute of every hour of every day.

Or that is how it seems to us. My purpose of this post is to make you think about this. Are we really choosing? Or is it only that it seems we are, but we actually are not. It could be that even though your brain thinks it had a choice, it really did not have any. Is it possible that given that exact situation, you could not really have chosen anything else but what you have chosen?

If the previous paragraph was too abstract, consider this scenario. On August 5th 2011, at 1.00 PM, you are at an ice-cream shop where you have a choice of flavours you can choose from. You decide to go for the chocolate ice cream at 1.01 PM. Now let us do the thought experiment. Imagine, that by some mechanism, you were again at the ice cream shop on the same day August 5th 2011 and at the same time 1.00 PM. You again have a choice. There is no difference in the way the universe was the first time and the second time. Is it possible that on the second attempt, you would choose a different flavour? Could you have, for instance, chosen the strawberry flavour, instead of the chocolate flavour, the second time?

That is really the crux of the question. Could you have chosen otherwise, given that everything else in the universe is the same? Now that we have understood what the question is, let us proceed.

It might seem a stupid question. You might say “Of course, I choose. I could have definitely gone for the strawberry flavour, but I decided to go for chocolate, since I felt like it. I consciously chose”. That is what we would all feel. But if you look at those words used, closely, you will see that we talk about decisions, feelings, consciousness etc. But where do these things come from? The decisions and feelings are a result of the brain reacting in some specific manner to a given set of stimuli. Consciousness too, as argued earlier, is nothing but the result of the physical processes in the brain. Our brain is like a computer, but vastly more complex. But all said and done, it is a machine.

Look at it this way. The fact that you chose chocolate ice cream, could have depended, for example, on the following facts

  1. You had chocolate sometime back in the same shop, and you liked it very much
  2. That previous time, your friend took you there for you to have a first taste of that ice cream.
  3. Today your wife wanted to have an ice cream and made that suggestion which made you come to the shop, in the first place.
  4. She saw an ad for it in the newspaper that day morning.
  5. The weather was hot and so you felt an ice cream could do you some good
  6. The ice cream shop could have put the chocolate ice cream closest to the place from where you are standing and thus you were tempted
  7. Or (if you are like me), you would have bought it since there was some discount on the Chocolate flavour

And so on. There could have been a thousand causes, which would have led you to that decision. If you say that none of this mattered, and that the only reason you had chocolate ice cream was because you felt like it, even that “feeling like it” would be the result of the weather, what food you had in the morning, what you overheard some colleagues discussing yesterday and so on. You can continue this all the way back to the big bang of the universe. It is for this reason that free-will is dicey.

Why do we think we make a choice, if we don’t think the computer makes a choice? What is that we have extra that the computer does not have? The computer too behaves differently each time it starts up. Take the browser for example. It shows me my favourites, that I added previously. It gives me a list of websites I visited in the previous session. It takes in any updates it has installed in the meantime, and its behaviour depends on many such factors. But given the exact inputs, it should behave exactly the same way. Granted, that the number of stimuli that our brain takes in is almost infinitely too many. But just because it is complex, does not mean it has freewill. Going by that logic, the stock market should have free will.

Let me give you some examples to support this notion that free-will is an illusion. There is a certain parasitic fungus which infects an ant, enters its body and reaches its brain. Once there, it manipulates its brain in such a way that the ant, instead of hiding under the grass, when sheep come to graze, actually does the opposite by climbing up to the top end of a blade of grass, thus making it susceptible to be eaten by the sheep. The ant does not gain anything from it. It only loses its life. But the fungus gains everything (that is why it is called a parasite). The fungus then enters the sheep to continue with its next phase of life, this time being a parasite to the sheep. Here is a similar fungus, doing a similar thing, but for a different purpose. There are numerous examples of such parasites.

Looking at those examples, you won’t really say that the ants really chose what they did, would you? They were forced by the fungi. But if brain can be manipulated to make the ant do something else than what it would have normally done, what meaning does it hold, to say that the ants really make a choice in the normal uninfected scenario?

If you think ants should not be compared to humans (though I wonder why not), here is an article that completely shatters our myths of culpability. This article, shows, that what we think are voluntary decisions, are not really so. To quote a striking part from the article.

Take the 2000 case of a 40-year-old man we’ll call Alex, whose sexual preferences suddenly began to transform. He developed an interest in child pornography—and not just a little interest, but an overwhelming one. He poured his time into child-pornography Web sites and magazines. He also solicited prostitution at a massage parlor, something he said he had never previously done. He reported later that he’d wanted to stop, but “the pleasure principle overrode” his restraint. He worked to hide his acts, but subtle sexual advances toward his prepubescent stepdaughter alarmed his wife, who soon discovered his collection of child pornography. He was removed from his house, found guilty of child molestation, and sentenced to rehabilitation in lieu of prison. In the rehabilitation program, he made inappropriate sexual advances toward the staff and other clients, and was expelled and routed toward prison.

At the same time, Alex was complaining of worsening headaches. The night before he was to report for prison sentencing, he couldn’t stand the pain anymore, and took himself to the emergency room. He underwent a brain scan, which revealed a massive tumor in his orbitofrontal cortex. Neurosurgeons removed the tumor. Alex’s sexual appetite returned to normal.

The year after the brain surgery, his pedophilic behavior began to return. The neuro-radiologist discovered that a portion of the tumor had been missed in the surgery and was regrowing—and Alex went back under the knife. After the removal of the remaining tumor, his behavior again returned to normal.

The article goes on to the question of whether people can be held responsible for what they do. If nobody has free-will, in what sense can we say that somebody is guilty of something. Can he just say that his brain made him do that, and that he (in whatever sense) did not actually choose anything? Was he not anymore culpable than an air-conditioner that has a short-circuit which triggers a fire, thereby killing a couple of people? After all, neither had a choice given the circumstances. But then, they are even tougher questions, which we are not talking about today.

Coming back to the topic, looking at such examples, how do we say we have free-will. In fact, Physics does not give scope for any mechanism that could give us free-will. What I mention here is determinism, which is defined as

Noun: The doctrine that all events, including human action, are ultimately determined by causes external to the will

By the way, what I am saying here is not destiny or fate. The key difference between the concepts of destiny and determinism is that destiny says that something or somebody knows what is already in store for us. It says that something has already been decided for you, and that you cannot really do anything about it. What determinism says is that what happens next is an effect of what happens now, and what happened a moment back, but nobody knows what will happen next since that is not practically predictable. But you are definitely not making choices.

It is not hyperbole, when I said that this might give you sleepless nights. If you don’t make the decisions you think are making, then what is the purpose of doing anything at all. If you don’t do anything, then it is not because you chose not to do anything, but because there is nothing you could have done. Thinking on these lines, there is really no need to do anything since you anyway don’t have the choice. I am yet to come to terms with the idea. It all seems too pointless. But I still find it easy to forget this uncomfortable question and continue with my life. That does not prevent this thought from  surfacing from time to time (Am I free in choosing what to think of). What do you think about this? Do you think we have any more free-will  than a washing machine?