Archive for the ‘Biology’ Category

An old article I wrote about language

September 7, 2013 Leave a comment

This blog has been in a coma for sometime, and I dont have any hope of writing anything new, in the near future. As I was listening to this podcast episode where Noam Chomsky was being interviewed about his work in linguistics, I was reminded about an article I had written a couple of years back for Science Reporter, a government run science magazine. It does not have a website where you can read the article online, but I have a scanned copy with me.

It is my longest article ever (and therefore the one with the maximum goof ups too, I guess), but given the drought on this blog, I thought I could inflict this upon you, just so you dont start raising your hopes of seeing the death of this blog. Not so soon, people, not so soon!

Here you go.

Categories: Biology, Writing Tags: ,

Reading a paper on evolutionary psychology

April 24, 2013 3 comments

Having not much to do at work yesterday, and not having an internet connection, I started reading this paper on evolutionary psychology, that I had stored sometime back on my phone. It is an interesting and informative paper, which I intend to read again (I normally need 2-3 readings of a paper to really understand it), but there was one point in the paper where it stuck me that the authors were probably attacking a straw man. But first, we will see what is evolutionary psychology.

We are all products of evolution and have no problem in believing that our hands, eyes, ears were all sculpted by Natural Selection. So, when someone asks why we evolved eyes, we dont hesitate to say that we have eyes because it helps us find predators, so we can run away from them, find food to eat, find mates to mate and so on. But we hesitate to think that our behaviour too could be a result of evolution. Or at least, we dont attribute evolutionary purposes to our behaviour as readily as we assign such purpose to parts of our physical body. Evolutionary psychology addresses this gap. It studies our behaviour, psychology, by looking at what pressures in our ancient past would have driven us to the way we behave today. The problem today with evolutionary psychology, it appears, is that many scientists are putting forward theories that are not really testable, or at least not have been tested. Read this post from Jerry Coyne to get an idea of the issue.

Now coming back to that paper I referred to in the first sentence. It is a good paper that covers the issues in evolutionary psychology and explains them clearly, but the following question posed stood out for me.

Don’t people just solve problems using rationality? Wouldn’t one domain-general rationality mechanism be more parsimonious than postulating many domain-specific mechanisms?

In human readable English, the question means this. Dont people always use their brains and rationally think about the consequences when faced with a particular question in hand and then behave in a manner best for them? Or are there circuits in our brain that are specific to the situations we are in, which means we react immediately without any logical thought process? The authors point this out and give the following example to explain why domain general rationality does not seem to be how our brains behave.

Domain-general theories of rationality imply a deliberate calculation of ends and a sample space of means to achieve those ends. Performing the computations needed to sift through that sample space requires more time than is available for solving many adaptive problems, which must be solved in real time. Consider a man coming home from work early and discovering his wife in bed with another man. This circumstance typically leads to immediate jealousy, rage, violence, and sometimes murder (Buss, 2000; Daly & Wilson, 1988). Are men pausing to rationally deliberate over whether this act jeopardizes their paternity in future offspring and ultimate reproductive fitness, and then becoming enraged as a consequenceof this rational deliberation? The predictability and rapidity of men’s jealousy in response to cues of threats to paternity points to a specialized psychological circuit rather than a response caused by deliberative domain-general rational thought. Dedicated psychological adaptations, because they are activated in response to cues to their corresponding adaptive problems, operate more efficiently and effectively for many adaptive problems. A domain-general mechanism “must evaluate all alternatives it can define. Permutations being what they are, alternatives increase exponentially as the problem complexity increases” (Cosmides & Tooby, 1994, p. 94). Consequently, combinatorial explosion paralyzes a truly domain-general mechanism (Frankenhuis & Ploeger, 2007).

I have written an article earlier on the gene’s eye view for the New Indian Express on how it is because there is a genetic advantage in loving children that we ended up being so nice to our progeny and ended it with the following paragraph.

This does not mean that every time parents tend for children, they do calculations in their heads, or that they do it for selfish reasons without genuine love. It only means that evolution has come up with emotions like love and empathy as a mechanism for the genes to achieve their goals.

So I never thought that we were always doing a rational analysis of the situation before we react to something. Our brains definitely seem to be wired for some quick reactions (imagine your son who is about to fall down and hurt himself seriously. Would you calculate how much of your genes he has got before trying to save him?) We obviously have some context specific wirings in our head. So it is hard to see why anyone would believe in such patently wrong ideas. I, obviously, do not know the history of this field and there might have been people who have argued that way, but today it seems to be impossible that there could be people who support this theory.

Assuming some one does believe in domain general rationality (assuming the straw man is not just a straw man but a real person), the author’s point of there existing too many permutations for us (men) to evaluate and to react, when we see our spouse in bed with another man, though correct, is a round about way of countering the argument. An easier way to argue against domain general rationality is that if that were true, then this man who sees his bed in wife with another man though initially gets jealous and angry (because, if his wife becomes pregnant now, he cannot be sure if he is the father) must immediately calm down if he sees that this other man was wearing a condom (which means he couldnt have impregnated his wife). I am sure those supporters of the rationality theory will also agree that this scenario will never happen? So, what are they supporting then?

How my children are growing

November 29, 2012 2 comments

It has been more than 3 months since I wrote my last post. While I have never been a daily poster, this is way too much delay between posts even for me. The blame (you readers, might like to use the word “credit”) goes to my two children and insane work schedules at my workplace. Though I have not been writing much, I have not stopped thinking about it. And every time I see my children I am reminded of the wonders of the universe.

“We are a way for the cosmos to know itself” – Carl Sagan

The last time it happened was when Aman was jumping standing on my tummy with me holding his hands for balance. It is almost impossible to believe that a year and a half ago, he did not even exist. A year ago, he was not more than the size of a peanut, he was not even a “he” then. But today, there they are, with all their body parts in perfect shape (more or less), the entire body working together well, growing up at an astounding pace, and slowly gaining intelligence. And that is what fills me with wonder. Let me explain.

I have talked multiple times about evolution, and how we all ended up here. Evolution by Natural Selection is fundamentally simple. Genes change randomly. And bodies change accordingly. The better suited bodies survive better, and naturally, the genes that made the better suited bodies survive too. That is the crux of evolution by natural selection. But that hides an awesomely complex phenomenon. When genes change, how do bodies change accordingly? Or, how do genes make bodies?

Darwin’s theory considers this to be a black box. It assumes that when genes change, bodies change too, which is true. But it does not talk about how that happens. It does not need to. But this area is called developmental biology. I have not read much on this, except for a single book “Endless Forms Most Beautiful” by Sean Carroll. But the feat achieved by the genes is impressive. From a single cell containing the DNA, it goes on to this 2 feet form jumping on my tummy.

Take for example the five fingers of one’s hand. Each of our fingers are different and cannot be substituted with one another. So, the body must know, that at one extreme there must be the thumb and at the other extreme there must be the little finger. And the rest of the fingers needs to be in order too. The extremes should not be mixed up either. Similarly, your hand must sprout from your shoulder and not from your hips. Every positioning has to be accurate with extremely narrow margins of error. Timing too has to be perfect. The cleft lip problem we see in children, is because of a timing issue in development. There must be a 4 dimensional map somehow, so that the body can be accurately built. How does it happen?

The entire development happens with the help of what are called switches, or from my programmer’s perspective, if-then clauses. Coming back to the example of the five fingers, there is a chemical, whose concentration varies along the entire breadth of the base of the hand (when the fingers are yet to be built). Where there is high concentration of that chemical, the genes start building a thumb, at slightly lower concentration, it builds a pointing finger, even less concentration, the middle finger, and so on till the little finger. This means, the genes that build the thumb, do their job, only if a certain amount of concentration of that chemical is achieved. If very high concentration, then thumb. If very low concentration, then little finger. It is this kind of logic that builds the entire body.

Let not this simple example of the hand, make you think, body building is a simple thing. For example, though concentration of a chemical explains the orientation of the fingers, what guarantees that this chemical does not appear near the knee or the elbow, or on the face? We will need to go one step back and then we will see, that this chemical is built by other genes, which are activated only at the base of the hands. That too is another switch.

If at the base of the hand, then release the chemical. ==> If chemical found, then build finger.

You can go one step back and ask how the body decides when a hand is built. And this questioning can continue backwards still you reach the egg. To be sure, these switches are almost never based on a single chemical. Typically they will depend on multiple circumstances. If-this-and-that-but-not-that-and-that,-then-do-this is the kind of logic we will get to see usually. These are influenced by external factors too, since what the mother eats and what she does, could lead to a change in chemical composition of the womb that could in turn affect development. That is why mothers are asked to have nutritious food and to avoid things like cigarettes, when pregnant.

The science of developmental biology is not as well known among the general public as other areas in biology, but it is interesting because it tells us how our astonishingly complex bodies that don’t miss a beat for 70-80 years, are built. I don’t have any illusions that I have explained much in that area in this post, but I hope to have evoked in you a sense of curiosity as to how indeed are bodies built from a single cell. In my next post, I will look at a different reason, this time at a cosmic level, why our very existence should be a source of wonder.

What my son taught me about my genes

July 2, 2012 1 comment

My two children: Akash (left) and Aman(right)

They are my two sons: Aman and Akash. When Prabha was discharged from the hospital after the delivery, she and I were given the blood reports of our two sons. Their blood reports told me something about my own DNA. In this post, I am going to explain what I learnt and how. Knowing that needs an understanding of what dominant and recessive genes are. So here are the basics.

All our DNA resides in strands called chromosomes. You can think of them as long strips holding our genes. Different genes reside on different chromosomes, and we need 23 of them to build a complete body. But all our cells (except for sperms and eggs) contain not 23 chromosomes, but 23 pairs of chromosomes. We get one set from the mother and one set from the father. Every cell provides two plans of building a body. But then, as we all know from personal experience, only one body is built. How is the choice made?

Consider for example the colour of your eyeballs, and assume that this depends on only one gene (this is hypothetical and need not be true, as some traits depend on multiple genes). Now if your mother gave you a gene for a brown eye colour and the father gave you a gene for a black one, which colour will be yours? That depends on the type of genes.If the gene for a brown colour is a dominant gene, then that will get precedence over the other gene and you will end up with a brown eye . In such a case the gene for the black eye is called recessive, because, the only way for you to have a black eye is if both parents give the black eye gene to you, so that the black is not dominated by the brown gene.

Similarly, our blood groups too are determined by the two genes we get from our parents. The commonly used blood group system is called the ABO system*. In this there are 4 blood groups: A, B, AB, O. Any person will belong to one of these types. This is determined based on what genes your parents gave you. To explain that, see the picture below which gives the different types of blood groups that a child can have for the different combinations of genes that the parents can give.

Blood group type that a child’s blood will belong to, for different combinations of genes received from parents.

The yellow boxes are the easy ones. Both mother and father have given the same gene, and so the child also has the same blood group. But if one parent gives an A/B and another parent gives an O, what happens is that the A or B overrides O (the green cells). This means the gene for A blood type is dominant to O. Similarly B is also dominant to O. If one parent gives A and another gives B gene, then the child’s type is AB (the blue cells). This is another way in which genes can interact. One need not always be dominant over another. They can be co-dominant. And this is what happens in AB. Both the A gene and the B gene are expressed. Here is a picture from Wikipedia explaining the same thing.

Blood group inheritance

Now that we have learnt the fundamentals, let us get on with the meat of my post. My wife’s blood group is O, which means, as you can see from the table above, she has two O genes. So, she is capable of giving only O gene to her children. My blood group is A, but that does not help me determine whether I am an A, because both of my chromosomes have A gene (let us call it AA possibility), or if it is because I have an A and an O, and I am an A because of the dominance (let us call this AO). This, I dont know.

I mean, I did not know. But my sons’ blood reports have solved this for me. One of my sons, Aman, has a blood group of O, and the other son Akash has a blood group of A. Both of of them would have received one gene each from Prabha and me. Prabha has definitely given an O to them, as I explained in the last paragraph. What I could have given them is not clear. Since Akash has an A, and Prabha cannot give that, it came from me. But this still does not tell me whether I am an AA or an AO. But Aman has got a blood group of O, which means I too, in addition to Prabha, must have given an O (refer to the table above. Only if both DNA strands have an O gene, will the blood group be O). Which means, I too must have had an O. That I have an A gene, is obvious becaues my blood group is A. But Aman has confirnmed that I have an O too. I have genes for both A and O in my genome. Elementary.

A final point before we close. Note that, if I had two A genes, I can never deduce that from the blood group of my children. Because even if both my sons were of A group, it is possible that I still have an O, but gave only A to both my sons. So the only way to confirm an AA would be to study my genome. Another option could be for me and Prabha to have as many children as we can have in our lifetime, and do a statistical analysis based on a 50% probability of my giving an A or an O to my children. But even that would still be subject to a very small chance of error (Just in case you are wondering, No, we are not planning to do that).

As every parent possibly does, I too have some wild ambitions (I would not want to dignify those thoughts with the word “plan”) on how and what I want my children to learn. But to my complete surprise, within a week of their birth, they taught me something about myself. There sure lie interesting times ahead.


* – While writing this post, I learnt that this ABO system is just one of more than 30 systems in which blood groups can be classified.

Chimpanzee shows ability for foresight and deceiption

May 18, 2012 Leave a comment

When you walk into the Vandalur zoo, one of the first animals you meet is the Chimpanzee. Thanks to their striking similarity to humans, many visitors stand trasnsfixed wondering whether these animals too think like us. While some may deny that, and others might think it is obvious, science is yet to have its last word on this debate. A new study suggest that those who think it is obvious that the Chimpanzees too think like us, might not be very much off the mark.

The chimpanzee Santino, from Sweden, shot into limelight when a study was published in 2009, that suggested that it had the ability to plan for future events. The study showed that the chimp was collecting objects, like stones, and keeping them in store, so that he can hurl them at visitors.

But it was hard to establish, if the chimpanzee was indeed planning for the future. What if he was just collecting stones for some other purpose, but when he saw the visitors, realized that he could use the same stones at the visitors too.

A new study published in PLoS one, an open access journal, on May 11th 2012 titled Spontaneous Innovation for Future Deception in a Male Chimpanzee,  went one step further in giving chimpanzees the benefit of doubt on whether they have foresight or not. In the 2009 study, it was observed that the pile of objects was visible to all, and every time he was about to send one from his collection flying at a visitor, he would precede it with an aggressive display.

Zookeepers spotted this hint and started warning visitors to back off, as soon as the chimpanzee put on its aggressive display. This time around, the chimpanzee acted smarter. He learnt to avoid giving such a cue to the zookeeper, by not displaying his aggression before throwing. In one instance, he took two objects, held it in a hand, and walked slowly towards the visitors. On the way, he also casually picked up an apple lying down, and put it in its mouth. When he came close enough, he threw the stones suddenly at the visitors without any warning.

Santino walking towards the visitors, on the way pick up an apple, possibly to give the impression to the visitors that he is not really planning to throw those stones he has in his left hand (Picture taken from the paper. See reference at the end)

Moreover, he also started storing his ammunition in places the visitors cannot see, like behind a rock or behind a log. Such concealment did not stop with naturally available hiding places. Santino also covered up the visible piles with hay brought in from a different place.

“By combining his old strategy of gathering projectiles in advance with his new strategy of concealment and behavioural inhibition, he could extend his ability to throw stones at visitors from close range” says the study.

But the authors are cautious enough not to attribute a theory of mind, the ability of an individual to think of what another individual could be thinking, to Santino yet. “What the behaviour does appear to show is that the chimpanzee is able to predict the behavioural responses of others not present at the time of the prediction”, the authors write.

Reference: Osvath M, Karvonen E (2012) Spontaneous Innovation for Future Deception in a Male Chimpanzee. PLoS ONE 7(5): e36782. doi:10.1371/journal.pone.0036782. A PDF of the paper can be downloaded from this link.

How to register for cord blood donation

May 6, 2012 Leave a comment

Sometime back I mentioned about cord blood banking and that Prabha and I are going to store the cord blood at the time of delivery with Jeevan Stem Cell Bank (JSCB). We completed the registration procedure today. I thought I can talk about it here so that those interested will know what it is all about.

The last time we went there, they gave us a set of forms to be filled in. They were mostly questionnaires asking us about our medical history, details of the pregnancy and other such details. There were also a couple of forms to be signed which essentially said that if for some reason, like complications during delivery, JSCB is not able to collect the cord blood they cannot be held responsible for it etc. The entire form filling took us just fifteen minutes. In addition to the form, we also had to give a copy of the latest scan report. That was all what was needed to complete the registration.

Once we gave them the form, the person there showed us the cord blood collection kit. The kit contained a pouch in which cord blood will be stored, a couple of small test tube like containers for samples of the mother’s blood. The kit also contained a pouch of gel to maintain the temperature of the cord blood till it reaches the bank. This gel has to be kept in the freezer a day before the delivery. Since we might not know when the delivery is going to be, I feel we can just keep it in the freezer, when we get closer to the date and let it stay there till the day comes. Apart from these there is a pair of gloves for the nurse to use and a couple of syringes to collect blood samples. We need to keep this kit with us and take it to the hospital when we go there for delivery.

Since it is a nurse from JSCB which will do the actual work of collecting the cord blood (and not someone from the hospital that Prabha is going to get into), just before starting for the hospital we need to give a call to the JSBC nurse whose mobile number we were given. We can call her any time 24 x 7, and she will be there at the hospital as quickly as possible. Even if we forget to take the kit to the hospital, we can just inform them and they will arrange for another one.

It is all pretty simple. And all steps are taken by Jeevan to make it as easy for us as possible. I just need to inform our doctor the next time we go to meet her, to let her know that we we have registered with Jeevan to save the cord blood. That is all, there is to it.

If you want more details you can reach them on 9790897918. They will be glad to help you.


Umbilical cord blood stem cells

April 13, 2012 1 comment

The different kinds of cells that Hematopoietic stem cells (the ones found in cord blood) can differentiate into. Source: FujiMan Production(Japan) via Wikipedia (

As my wife and I are on the cusp of parenthood, a little bit of Googling pointed us to cord blood banking. The umbilical cord, that is usually discarded at the time of delivery, contains stem cells that can specialise into different kinds of blood cells. It was this that led me to write an article on stem cells sometime back. The idea is that these stem cells could be preserved at a “bank”, so that in case the child (or even the parents) have a blood related disorder in future, these cells could be used. The cells will be a direct match for the children, but for the parents it will match with a 50% probability.

When I enquired further, I learnt that banking cord blood for a child costs somewhere in the range of 60,000 to 70,000 rupees. Though I am generally optimistic on what science will achieve in future with stem cells, Prabha and I felt this was something that we could not afford now. But we were also worried if we are putting pecuniary concerns ahead of the child’s welfare, even before it was born.

All is not lost though. It is not that you always need your own cells. There is a very small chance (somewhere in the range of 1 in of tens of thousands) that cord blood cells of another unrelated person matches yours. What I mentioned in my last paragraph, was about private banking, where you store cord cells for your own possible use in future. There is also the concept of public banking, where you just donate your cord blood to a bank. They will store this free of cost. Anybody who needs such stem cells, can search the public banks to find a match. And when they do find it, they can pay for it and get it.

What is more, if I donate my cord blood today to a public bank, and if I need it tomorrow, I can get my own cells back on payment, assuming it has not been given out to others in the meanwhile. It is not as if everybody will need their stem cells. So rather than wasting it, why not give it to a public bank, where it might end up being useful for others.

Considering all this Prabha and I went to Jeevan Blood Bank and Research Centre which has a public stem cell bank. It looks like this is the only public bank in India. There we met a person Kishore, who explained to us the details of the cord blood bank. When we talked to him, we learnt about the dismal donation levels of cord blood cells. He told us that every month, about 15 people donate cord blood, and that the bank now has about 400-500 samples. Considering the staggering odds of finding a match, this number looked insignificant. It is true that there is still lot of progress yet to be made on using these Stem Cells, but there are some disorders, like leukemia, where this is already being used for treatment. Kishore told us that today, if one has to get a unit of stem cells from abroad after finding a match it would cost about 14-15 lakhs, whereas if a match is found with Jeevan, the cost would be around Rs.50,000. Jeevan also donates the stem cells free of cost for people who cannot afford the payment.

He then showed us around the centre. We were shown the machine the extracts the stem cells from the blood, the huge cylinders, as wide as 2 people and reaching up to my shoulder’s height, which stores the cells at ridiculously low temperatures (I don’t remember the numbers now). It was all fascinating for us.

The key obviously is to build up a huge repository. This can be achieved only by increased awareness. Science has today achieved, what it could not have imagined 30-40 years ago (no doubt there have been some disappointments too). So I feel 30-40 years from now, we would be capable of using these stem cells really well, and it would be a shame if the only reason we are not able to cure somebody of , say, blood cancer is because we do not have a compatible sample. True, it could turn out that 40 years down the lane, not much progress has been made (I think that is very unlikely), but even then what do you lose? You would have anyway discarded the cord blood. Why not save it?

Private banking, is still dicey, as you are expected to invest so much on something that you are not sure will be useful to you. But I don’t see a reason why anybody would say to no to Public Banking. The procedure is safe and non-invasive. After the umbilical cord is removed from the mother, the blood from it is collected, and stored separately. There can absolutely be no harm to anybody involved. So if you know somebody about to have a child, spread the message, ask them to consider this. It is in some sense a social insurance policy we are taking out for our next generation.