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Archive for March, 2012

When Vikings explored, mice accompanied them

March 29, 2012 Leave a comment
Re-enactment of a Vikings battle

Re-enactment of a Vikings battle - Courtesy: Wikipedia. Picture by Tone (http://en.wikipedia.org/wiki/User:Tone)

Here is my new piece for The Hindu. It is the first time I have written about a recently published paper. This is more like science journalism, as I talk about a new paper rather than about a particular concept. The challenges with this kind of writing are that in most cases a layperson cannot understand a scientific paper. The terminology they use, the mathematical tools adopted etc. So understanding a paper fully is, for me, near impossible in most cases. But there are other problems too.

When writing about new papers, you need to know the context. You need to know what research has already been done on this, whether this is a genuinely new finding or a repeat of an earlier study. This requires one to have a good idea of a specific area of Science, say evolution or genetics or particle physics. Googling too helps quite a bit to find out whether this research is indeed new and interesting. Another smaller problem is that people like me, non-scientists non-journos kind, do not have access to scientific journals (they are pretty expensive). I get around this problem by asking friends in scientific circles to get me copies of the papers. Except in cases where they themselves don’t have access, they unfailingly help me out.

This paper I wrote about is a relatively simple one to read. It is also open access. You can download the paper from here. Once I saw this paper, I consciously avoided reading other articles on this, lest they influence my own take on it. Only when the piece was finalised did I look at what others have to say on the paper.

The article I initially submitted had about 480 words. It was edited by the paper, in the process bringing down the word count to about 340. Though it is a small piece, it took me close to 3 hours to come up with. Have a look at the article and let me know what you think.

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Categories: Writing

My Picks – 26th March 2012

March 26, 2012 Leave a comment

Here are some things that I read this week.

So far, humans are still ahead of programs in solving crosswords. This will keep my dad happy.

Time to start donating a different kind of blood. Umbilical cord blood contains stem cells that could be useful to others.

Is it not comforting to blame our faults on something else? That is why I like science. Babies delivered by a C-section have a higher chance of being obese. There is a small hitch though. My mother gave birth to me without the surgery. But I need not worry. I am sure I can find some gene to blame for my weight :-).

Are brain dead people really brain dead?

How to get the job you want?

Want to see around corners? Here is how?

Brilliant stuff from Carl Zimmer. He talks about how “Virologists, in other words, are still waiting for their Penicillin Moment.” At the end of the read, you feel like an expert.

Another piece by Carl Zimmer. This time, a profile of a neuroscientist, who is trying to map the connections in 1 cubic milli metre of our brains. Read why even that is not easy as it sounds, and why it is so important.

Here is the new “unprinter”.

A doctor talks about the problems with screening tests, and why she would not undergo one.

Categories: Links

My picks – 18th March 2012

March 18, 2012 Leave a comment

Here are some links that you might be interested in. I have not been doing this weekly as I had planned, thanks to my insane work load.

Categories: Links

Understanding RCTs

March 16, 2012 Leave a comment

Here is my next article for the New Indian Express. It talks about the need for Randomised Controlled Trials. A very simple basic piece. I feel that an understanding of how hypotheses are evaluated is key to debunking myths like alternative medicine,  ghosts, after-life etc. Of course the word limit is so narrow that the article ends before it starts, but then I have to work with what I have. BTW, I hate the title they gave so much that I don’t even want to mention it here :-(.

Categories: Writing Tags: ,

Why group selection is not true

March 14, 2012 Leave a comment

I occasionally buy the magazine Science Reporter, run by CSIR, a government funded research body. The quality of the articles is not usually great, but in the March 2012 issue, there is an article on evolution of sex which exposes a fundamental problem in thinking about Natural Selection. So let us have a look at what that is so that we understand Natural Selection better.

I have earlier mentioned that evolution by natural selection is best understood when looked at from the perspective of the gene. Talking about the genes as if they are conscious entities striving to maximise the number of copies of itself in the population is a good way to understand Natural Selection. Of course, genes are no more goal seeking entities than a table or a chair, but a gene that happens to contribute towards the individual’s well being, will leave more copies of itself (by leaving more children), and so by default such genes tend to survive well.

If the purpose of a gene is to make maximum copies of itself, then sex seems to be a disadvantage because from the gene’s perspective sexual reproduction means that it has only a 50% chance of having a copy of itself in the children. For example, a gene in your mother will only have a 50% chance of being in you. So is the case with every gene in your father. But in case of asexual reproduction, every gene in the parent will definitely be in the child (except for the occasional random mutation), since the child is just a clone of the parent. So genes in asexually reproducing organisms will leave twice the number of copies when compared to sexually reproducing organisms. This is referred to as the dual cost of sex. To compensate for this, sex must some how bestow benefits to a sexually reproducing gene that is at least twice that of an asexually reproducing organisms.

And it is this advantage that scientists are facing a tough time to understand. It is not for lack of attempts though. I don’t intend to lay out what scientists think on this. If you want to understand that you can refer to this absolutely fantastic book, by Matt Ridley, called The Red Queen. I cannot recommend it enough. It cost me somewhere between Rs. 250 and Rs.300. For such a price, the book is a treasure.

Now coming to the common understanding of natural selection. At one time, there was this idea of “Group Selection” that was popular among evolutionary biologists. The idea is that a gene that gives an advantage to the group of individuals to which it belongs, will tend to survive more. For example, consider a gene that makes the individual ready to sacrifice one’s life to save the clan he/she belongs to. It is definitely an advantage to the clan, because such dedicated soldiers will do much better in protecting the clan than those who are worried about their own lives. Thus, it was supposed, a gene that works for the betterment of the group will leave more copies (after all the clan is protected).

This argument, that something that is good for the group will spread, in spite of the disadvantage to the individuals, was widely touted and believed. The problem with such an argument is simple. Imagine a group that has individuals ready to put down their lives for the group’s sake. And suppose, that in this group a child is born who is more bothered about his own life than about the clan’s. Such individuals will stay away from any clan fights and thus have very little chances of dying without reproducing. So the genes of such individuals begin to spread. Thus the group will slowly start to have more and more individuals, who are selfish. Thus the gene for sacrifice will stop spreading.

One might say that, this is the case even within a single individual. After all, an individual too is a collection of genes, and since the gene’s eye view is the best perspective on natural selection, the genes too can be selfish and need not be bothered about the individual. But the difference between the group and the individual is the idea of a reproductive bottleneck. For a gene in an individual, the only way for it to make copies is to make more copies of the individual, since that is the only way they can leave offspring. Thus, all the genes within an individual will cooperate for the benefit of the individual. But in case of a group, all the individuals within the group do not reproduce in one go, or through one such common pathway. Each one can reproduce on its own. This lack of a reproductive bottleneck leaves Group Selection without a mechanism to work. That is the reason why it is not considered to be true.

There are exceptions to this which beautifully illustrate the point being made. Imagine a group of bees. As is common knowledge, bees usually have one queen that does all the reproducing. The rest of the worker bees are sterile in that they cannot reproduce. Thus if the genes in the sterile workers have to leave copies, the only way to do that would be to help the queen to reproduce (since the workers share genes with the queen, who is after all their mother). In this case, the queen acts as the reproductive bottleneck and thus in bees, you find individuals who are ready to put down their lives for the group.

Thus the existence of a trait cannot be explained by listing out the advantages it gives to the population. The only way to explain a trait is to explain the benefit to the individual and thereby to the gene. Now I come to the article that I referred to in the beginning. The author talks about how the sex is an advantage because it protects us from parasites and thus prevents the species from going extinct. If I have done my job well, so far, you will spot the problem right away. The genes are not worried about the species going extinct. It is only bothered about itself, and about the individual (to the extent that the individual benefits the gene, which in most cases is quite a bit). And that is what is wrong with the article.

So I wrote a letter to the editor pointing this out. I am reproducing it here.

Dear Editor,

This is regarding the article titled “Evolution of Sex” in the March 2012 issue of Science Reporter. In this the article talks about how sex evolved and why it is advantageous, but there is a fundamental problem in the author’s approach to this question of sex.

It has long been recognised by most evolutionary biologists, except for a few on the fringe, that group selection does not work and there is no evidence for it happening. But the idea was popular at one time. And that has left a hangover. This hangover is visible in this article too. The last paragraph of the article says:

“Why did sex evolve? From the evolutionary point of view sex is definitely an inefficient way to reproduce, but it acts as a safeguard against extinction”

That traits are selected to prevent species from going extinct is a group selectionist argument. This assumes that natural selection works to help species or groups survive. This is not true. Natural selection works only for the benefit of the gene. All the genes in an individual have to reproduce via the individual, who acts as a genetic bottleneck, and thus in most cases what is good for the individual is also good for the gene. There are exceptions for that too. But no gene is selected for the survival of the groups (except in cases like eusocial insects, where there is a genetic bottleneck like the queen). Thus the idea that something is good because it prevents extinction of the species, is flawed.

Earlier in the article too, one can see this sentence.

“If all organisms continue to reproduce asexually, the genetic variations of its species as a whole will slowly grind to a halt and it becomes likely that a parasite that can kill one member of the species can wreak havoc on the entire population, which will not be able to get rid of the harmful effects of mutation”.

Here too, the author talks about parasites being the bane of the species. That parasites are considered an important cause for the evolution of sex is true, but that is not because it will “wreak havoc on the entire population” but because without sex, it puts the individual at a disadvantage when facing parasites. The difference, though seemingly subtle, is key to a correct understanding of evolution by natural selection.

Madhav.

The author of the science reporter article is a “Retired reader and Head, Department of Zoology, Madurai College, Madurai. He has a teaching experience of 35 years”. What surprises me is how somebody who has so much experience misses this very important point.

PS: For a recent kerfuffle on this topic, you can refer to this post by Jerry Coyne. The name of this post is inspired from the name of his website (he does not like people calling it a blog).

Kanzi, the bonobo

March 13, 2012 Leave a comment

Who does not like apes? They are so adorable. Watching them do things like we do gives us a lot of pleasure. One of the greatest morale boosters for me, is to sit down and mull over the fact that we and all the animals are literally related, right from an ant, to a plant to a fish. So it is only natural to wonder which other organisms are as intelligent as us. Self-awareness appears to us to be a fundamental aspect of being intelligent. After all, if we don’t even know we exist, how can we call ourselves intelligent. To know if an organism is aware or not, we can do a mirror test. Apes have, of course, passed the test. Some dolphins have, too. I read somewhere that pigs too are self-aware.

Considering all that, it is only natural to wonder if any of these animals are capable of our levels of intelligence. Though not the only means through which intelligence can be expressed, language does indeed feel to play a very important role. When I was walking out of my workplace yesterday, the thought that we are all apes came to my mind, and for a minute, I saw all the people around me through that perspective. It was fun, but the fact that they keep talking to each other quite a lot (or over phone), is what seems to set them apart from other apes. Of course, we have built buildings, computers etc, but at a fundamental level, it is tough to imagine how all this technology could have come about without language.

I am currently reading this book Apes, Language and the Human Mind (courtesy Connemara) by Sue Savage-Rumbaugh and two other authors. The author is a well known name in ape language research, and has done language research on bonobos, especially Kanzi, who is popular in his own right. In the first part of the book, the author talks about her experiences while training Kanzi. Kanzi is capable of recognising lexigrams and can communicate his intent to the trainers. That includes not just the food he wants, but where he wants to go, what game he wants to play and so on. You can see him using the lexigrams in the video below.

But lexigrams are only symbols for words. That alone does not mean apes have language. To understand language is to understand the grammatical structure behind sentence formation. At least the rudimentary ones. In this respect too, Kanzi seems to be doing well. Here are some examples from the book that Kanzi understood.

  • Let’s go to the trailer and make a water balloon
  • Would you give Panbanisha an onion?

Kanzi responsed to this with doing exactly what was intended. Can you imagine the excitement they would have had while carrying out these tests? But one might, quite rightly, suspect that Kanzi probably did not understand the sentence as a whole, but it heard “trailer”, “water” and “balloon” and made a connection without bothering about the sentence. Similarly, it could have heard just “Panbanisha” (another bonobo) and “onion” and did what was expected. Just to be sure that Kanzi did understand sentences as they are and not because of the context, they tried instructions with objects which are not natural. Like..

  • Tickle Liz with the umbrella.
  • Stab the ball with the sparklers.

Here too, Kanzi succeeded. Moreover, they also successfully tried ambiguous sentences like

  • Pour the coke in the lemonade.
  • Pour the lemonade in the coke.

Kanzi even understood somewhat complicated sentences like “Put on the monster mask and scare Linda”. But the problem with such experiments have always been that unconscious verbal or physical cues might have given the necessary suggestion to Kanzi as to what was expected. But that too was scrupulously avoided, by keeping Kanzi in a glass room (through which trainers from the outside can see Kanzi, but Kanzi cannot see the trainers) and giving instructions from outside.

There does not seem to be a complete consensus on whether apes do really understand language. The fact that the apes are not physically capable of making the different kinds of sounds that we make while talking, impairs its ability to speak (though they can hear what we say). As the author says “just because apes lack the requisite anatomical equipment to speak, it does not necessarily follow that they also lack the intelligence to use language”. She does seem to make a strong case for it.

Here you can see Kanzi following the given instructions.