Tuesday, March 20, 2007


Whoa! It's been over two months since I made my last post! And even longer since I made my last meaningful one... Anyway, this post is about evolution and what it is. I will try to keep to the facts in this post, and talk about "intelligent design" and creationism (two alternative "theories" for the origin of life) in a later one.

Boiled down to it's most basic level, evolution is a theory that postulates that new species arise, not from the ether, as it were, but by modifications to already existing organisms. Evolution is not a theory for the origin of life. It is merely a theory for how the amazing diversity we see in the natural world arose (and continues to arise). There are of course several possible explanations for how this happens, but Darwin's theory of natural selection and it's modern modifications (collectively called Neodarwinism) are the most widely accepted theories. The amount of evidence that has been collected for Darwinian evolution is staggering, with thousands, if not tens of thousands of papers published on the topic. So what does this theory say?

If the theory is simplified, it can be broken down into three bits:
  • Organisms tend to overbreed. This basically means that organisms will attempt to produce offspring at the highest level that is practical for them. This might be once every few weeks for rats, or once every few years for humans. Note that this rate isn't necessarily a reflection of the biological capacity of the organism to breed! Humans can produce (in theory) a child every nine or so months, but we don't because it is impractical for us, since the additional child would probably reduce the survival probability of both the children. In other words, organisms will tend to reproduce at the rate that represents the best trade-off between ability to for the parent(s) and offspring to survive (and thrive) and the maximum biological ability to reproduce.
  • Because populations tend to increase rapidly, the only those individuals that are healthy and have some kind of advantage over the others will survive. Even in times of plenty, this manifests itself when the time comes to mate. Typically, only the "fittest" individuals will be chosen to mate by individuals who are themselves fit. "Fitness" is of course a subjective term that changes according to species. The offspring of such a union are of course likely to be "fit" themselves, thereby increasing the probability that they will survive and so on. Over the generations, those "fitter" individuals will come to dominate the population.
  • If there is a change in the prevailing conditions, or if part of the population migrates to a new area (maybe due to lack of food or other resources, maybe due to some other change), what was previously considered "fit" for the old population might no longer apply to the new population. For example, if there was a population of large carnivores (say tigers) in a particular place where large game was abundant, they would have no problem obtaining prey of the right size. However, if some of that population (maybe due to overcrowding) moved to a new area where large game wasn't readily available, they would have to make do by killing smaller game. However, this would mean that they had to hunt more frequently, something that large carnivores don't often do. In a situation like this, obviously, individuals needing less food (i.e., smaller individuals) would be favoured. Therefore, these individuals would now have a selective advantage over the old "large" breed. In such a case, a new "small" breed of tiger would evolve. Another way this could go is that the tigers would eventually become faster or stealthier, allowing them to sustain the new requirement to hunt more often. This requirement to adapt to the conditions to survive is called "selection pressure".
A concept introduced in the last paragraph was "selection pressure". Selection pressure is the main driving force behind evolution. If there is a lot of selection pressure, evolution is rapid and vice versa (this is an oversimplification, but generally true).In general, no selection pressure equals no evolution. The one exception to this rule is when a population becomes totally isolated (i.e. there are no individuals moving back and forth). When this occurs, a slow but steady "random drift" results in the individuals eventually evolving into a new species. This process is typically far slower than evolution under high selection pressure, but it does demonstrably occur.

This is pretty much the essence of the theory of natural selection as postulated by Darwin. Our current understanding of genetics and molecular biology fits right into this theory and the resultant theory is known as Neodarwinism. But I think I've fried enough brains for the time being, and so I'll leave that for the next post.

Sunday, January 14, 2007

I'm still alive, for anyone who cares!

I know I haven't written in a while, but I've been busy with exams and other things. I have a couple of ideas for an entry, and hope to write it up in the next few days.

Monday, December 11, 2006

This is how science should be taught!

Following my first blog post on how science should be taught, here's a prime example of a school doing an excellent job of it! It proves that you don't need huge resources or fantastic facilities to get children interested in science. More details here: http://news.bbc.co.uk/1/hi/education/6161779.stm

Tuesday, December 05, 2006

Scientific Honesty

Whoa! Now that's a scary sounding title! "Scientific Honesty", honestly what does that even mean? Well, today is your lucky day, because I am going to try and answer just that. But before I get down to actually talking about scientific honesty, I think I should spend some time talking about how science works, so that I can give you an idea of why it is so important that a scientist be honest.

In science, especially in modern science, when you want to communicate your findings to others, the most common way is to publish a paper in a scientific journal. How this process works is that you write about your experiment, what the aim was, how you did it, what materials you used, what the results were and how you chose to interpret those results. Many people will know this format by the name of IMRAD (introduction, materials/methods, results and discussion). Once you have done this, you send your shiny new paper off to a scientific journal. The journal now passes the paper on to a set of independent people called referees (usually at least three). Each referee works independently. The referees' job is to take a look at the paper and firstly, either accept it for publication or reject it outright. Their second job is to make sure you know why your paper has been rejected or if it has been accepted, what more is required for it to be (in the referees' view) publishable. This could be something as simple as just correcting the grammar or could be as serious as a bit of missing data that the referee wants to see in the paper (anything more serious than that, and it will usually get rejected). Assuming your paper has been accepted, you get an opportunity to reply to the referees' comments and suggestions and make appropriate corrections. You then return the paper to the referees and your paper gets accepted for publication. This process is called "peer review", and scientists (quite snobbishly, in fact, but also justifiably) consider that the only scientific material worth reading is either peer reviewed or based on peer reviewed articles (like science books, which refer to tons and tons of peer reviewed papers but aren't themselves usually peer reviewed).

Now, hopefully you would have noted here that no one at any stage checks to see if your paper is factually correct. What this means, that if you have a nice beautifully written paper with tons of consistent but fake data, your paper will probably get published. So, dissemination of scientific material is based on trust. Another facet of this is that scientists are obviously not able to repeat every single experiment to see if the technique is valid, there just isn't time in a single person's life to validate every single technique they use. So, a physicist, for example, simply trusts that Einstein's Theory of Relativity is correct and uses those equations as a base for his experiments. Or a biologist assumes that DNA is the genetic material and goes right ahead and bases his work on that assumption. Now, just imagine if Einstein or Avery (the guy who proved that DNA is the genetic material) had faked their results!! Unless someone had attempted to validate the experiments soon, science could have been set back quite a few years by the time someone discovered the fraud. This is especially true today because of the sheer volume of papers being published every year.

So hopefully, now you see why it is so important for scientists to be honest in reporting their findings. Outside, they could be liars, cheats, murderers, whatever, but unless they are honest about reporting their results, they aren't scientists.

There is also another type of scientific honesty, and that involves the use of other people's work. Whenever you use other people's work, whether in a scientific context or not, you must give them credit. If you don't, that is plagiarism. And I for one, wouldn't be able to automatically trust the results of someone who plagiarised. In fact, one of the most famous discoveries of our time, the discovery of the structure of DNA, was the product of scientific dishonesty. Watson and Crick received critical unpublished data from the Rosalind Franklin's lab through a colleague of hers who did it to spite her. Without this data, it is quite possible, and even likely, that Franklin would have reached the solution before Watson and Crick did! In a further bit of irony, Rosalind Franklin died before the Nobel Prize was awarded for the discovery. Since the Nobel Prize is not awarded posthumously, Watson, Crick and Wilkins (the colleague of Franklin's who gave Watson and Crick the data) got the Nobel Prize.Now this story illustrates how this second type of scientific dishonesty can powerfully affect people at a personal level. It has also made me (and I suspect many others) lose a great degree of respect for Watson and Crick, because while they have consequently made some brilliant further discoveries, this incident will mar their legacy for ever.

Fortunately, today, the penalties for scientific dishonesty are harsh, sometimes to the extent that the penalised person not only loses his or her job, but cannot find work in science anywhere in the world. And that is how it should be, since science cannot help but be based on the trust that scientists have in other scientists. If that trust is shaken, the very foundations on which science was built begin to collapse, and science as we know it will cease to exist.

Sunday, December 03, 2006

Multiple levels of understanding

Now, the title of this entry sounds philosophical, and is a bit misleading. Let me assure you that I have no intention of digressing into philosophy here (at least this time). This entry is the net result of a series of thoughts that I have had about trying to understand biological systems. In fact, after reading it, I think many people would say, "Hey! I already knew that! So what's the point?" Well, read it and judge for yourself.

As a side note, I must say, that this article is likely to contain many inaccuracies as to dates and titles of publications. Perhaps some facts are wrong as well. I invite anyone to correct me if they believe I am mistaken at any point and would positively welcome anyone who does.

I think that there are many, many ways of looking at biological systems; multiple levels, or layers if you will, of understanding.

The highest (and by highest, I mean most high-level, and not necessarily the best) level is the study and understanding of behaviour. I call this the highest level, because it is the sum total of what that organism is. By the way, this is called ethology. Now, the study of behaviour was probably the first thing that our ancestors (by ancestors, I mean humanoids from way, way back, possibly even before the evolution of modern man) systematically studied biology. Why? Because this gave them an understanding of how to get lunch and how not to become lunch. So, our ancestors probably observed, over the course of a few weeks, months, or years, how certain animals would take flight if you made a noise, while certain others weren't bothered. Still others would charge you with horns parallel to the ground and maul you to death if you weren't careful. They must have observed how deer and other herbivores congregated at water holes in the summers and how they hibernated in the winters. They would also have seen how wolves, tigers and other predators were dangerous to themselves and their children and devised strategies to keep them away. Maybe this involved pushing a boulder in front of the cave where you slept at night, an extremely effective strategy against large predators; but if the predator had been really good at digging, it wouldn't have worked. So, primitive man really was quite an ethologist, the need to survive meant that he had to be. Primitive man was also a taxonomist (one who classifies animals), but the real spark that set off the study of taxonomy was Carl Linnaeus, the man who invented the binomial nomenclature that we use, with some modifications, even today.

Later on, humans must have started studying anatomy. This might initially just have taken the form of, "The hooves of all deer are difficult to eat, but the haunches, now they taste good!" Eventually, this would have got more generalised to, "Hey, all animals have intestines, and all intestines taste like crap!". And finally, much, much later, humans started figuring out what each organ actually does. This took longer than you might think, even the ancient Greeks thought that the heart was the organ that did the thinking, and that the brain was just so much grey goo (and that was only a couple of millenia ago!). This understanding of the anatomy of an organism then, is the second highest level of understanding we can have. And what an important step it was! Because the next level was understanding how these organs work.

Understanding how organs do what they do is called physiology. While most people look upon physiology as a relatively mature science, I disagree. Physiology as a systematic science has an age measured in mere centuries, while the earliest humanoid fossils date back a 6 or 7 million years! Even the earliest fossils of modern humans are two hundred and fifty thousand years old. A lot has been understood about physiology in the last few centuries, but we still aren't remotely close to understanding everything about it. We have however, understood enough about it, that we have been able to go one step further, to the next level of understanding, cellular biology.

The study of cellular biology was pioneered by Robert Hooke, the inventor of the compound microscope, who published a work, "Micrografia" in 1665. Micrografia contained many, many drawings and descriptions of life when viewed through a compound microscope. It was Hooke who first coined the term "cell". Another person of note was Antony van Leeuwenhoek, a contemprary of Hooke's, who made unparalleled (at that time) compound microscopes that allowed him to observe microorganisms, which he called "animalcules". He too wrote a book with fantastic illustrations of his observations with a microscope. A nice history of Robert Hooke, along with some illustrations from Micrografia, can be found at http://www.ucmp.berkeley.edu/history/hooke.html and of Leeuwenhoek at http://www.ucmp.berkeley.edu/history/leeuwenhoek.html . Cellular biology has really kicked off since then, with bucketloads of information now available on cells, their structure and how they interact with each other. It is also important to note that later, more detailed studies, continuing even to the present, have given us a profound insight into that very unit of life, the smallest thing that can be said to be living, the cell. The next level of understanding, in my opinion, though many may disagree with the exact placing of it in the heirarchy, is the study of inheritance (genetics) and evolution.

Now, the study of genetics, or inheritance was fueled by two seminal works, Gregor Mendel's 1865 publication, "Experiments on plant hybridization" and Charles Darwin's 1859 publication "On the origin of species by means of natural selection". Now both these, as you can see, were published less than 200 years ago, and we are still working on our understanding of these two questions, i.e. how organisms transmit their genetic data to their children and how organisms evolve. Far more recently, Griffith and Avery in 1928 and 1944 respectively, proved that DNA is the genetic material. In parallel with the study of genetics, another discipline was emerging, the study of the chemistry of life, or biochemistry.

All living beings have a huge number of molecules in them. Many of these molecules are huge, so huge in fact, that very few molecules outside the living world ever attain that size. For example, proteins have molecular weights in the hundreds of thousands or even millions of units, while a hydrogen molecule (not a hydrogen atom!) has a molecular weight of 2! Such molecules are called macromolecules. Even the smaller molecules found in organisms, with a few exceptions, tend to be rather large compared to molecules found outside the living world. The size of macromolecules has had rather an unfortunate side-effect i.e. until recently, we couldn't understand a lot about their chemistry. We could see them react with various things and postulate how they reacted, but why the molecule was shaped like it was and what were the chemical factors contributing to its shape, for example, were questions that we couldn't answer. Luckily, with the advent of computers, this has changed, and we are slowly unravelling the mysteries of macromolecule structure. For those that are not professional biologists or chemists, a useful analogy would be to try and imagine the function of each atom in a chair or a table and trying to figure out how each atom contributes to the overall properties of the chair! Which leads me to the next level of understanding, the chemical/physical one.

What I mean by a chemical/physical level of understanding is trying to figure out how properties and laws from chemistry (especially physical chemistry) and physics affect all the higher levels of organisation. We have discovered over a long time, many properties of the world around us from gravity to the general structure of an atom. We have also shown that these properties apply to every single entity (living or non-living) in the universe. What we rarely consider, is how these affect life in general. This is because, as I said, life is composed of such complex interactions between these properties, that separating them often becomes downright difficult. We are now, with super powerful computers, slowly beginning to understand what exactly is going on.

Finally, the last level of understanding (so far at least), is that of sub-atomic physics. Now, I will not dwell too much on this level, partly because we are now leaving my comfort zone and partly because this is where it gets really really complicated. Suffice to say it can sometimes be useful to look at certain biological systems in a sub-atomic sense. Indeed, sometimes it is the only way of truly understanding some systems.

Now, why have I waffled on and on about these so-called "levels of understanding"? It's because I think that very few people are ever encouraged to think about or even made aware of these multiple levels at school, college or even university. It is (at least for me) impossible to think about all these levels at once, it gives me a headache! But what I do try to do, is try to think about them sequentially, over a period of days, or even weeks. For example, if I am studying biochemistry, I try and see how whatever I am studying would affect the behaviour, classification, anatomy, physiology, cell biology of the organism. I also try and see how it evolved and how they are passed on to subsequent generations. Finally, I try and take a look at the levels below the one I'm currently studying to see how I can better understand what exactly is going on. It is by no means necessary for each person to look at each and every one of these levels when they're studying biology, but looking at multiple levels, instead of just the one that interests you, deepens both your understanding of the level that you are studying, as well your love and enthusiasm for the subject. It did for me. And that, my friends, is how biology should be taught, not as a science in isolation, but as one facet of a many-sided structure.
Why we don't have more scientists

Why is interest in science, especially in the pure sciences steadily declining in the schools of today? Why aren't we seeing more Stephen Hawkings or Charles Darwins in an age where the information required to develop minds in such a way is ridiculously easy to access? Why is there more and more funding for developing new technologies, but less and less to try and understand how those technologies actually work? If you disagree with that last sentence and think that a new technology cannot be developed without an understanding of how it works, think again. The very first technology developed by human beings was controllable fire. Do you think the stone-age men knew why wood burns? Or why fire releases heat? Or why water puts out a fire? It took us a good many millennia to answer those questions, and in all that time, we continued to use fire freely and indiscriminately, not really worrying that we didn't know why it happened. Don't get me wrong, I think that discovering and inventing new techniques and technology is crucially important to us as humans, but understanding how these technologies work is in my book, every bit as important.

In my opinion, the whole point of teaching science in schools is to encourage kids to take an interest in the world around them. It's quite amazing how often people lose sight of that basic goal. For example, when talking about something as fundamental as gravity, I have yet to see a science teacher express a feeling of wonder or amazement about this phenomenon that affects every single facet of our lives. Yes, teachers talk about how, without gravity, we'd all just float up into space. But do the students (or even the teachers) realise that without gravity, the very planet we would float away from, wouldn't even exist! My earliest memories of being taught "biology" as part of primary school consisted of being asked to classify things as "living" and "non-living". That in itself wouldn't be so bad, if we hadn't had a third category added the next year that said that things can be classified into "living", "non-living" and "dead"!

I can't think of any real value to teaching this in a school, except maybe as a classroom exercise that had at most, one hour devoted to it. We on the other hand, had this as part of our regular syllabus and were actually expected to write exam answers where we had to classify things into these three categories. What would make this exercise far more valuable, is if the teacher had first explained why some things are living and others aren't... What makes a thing alive in the first place? What is life? Why don't we understand the most basic question of what makes us alive? What defines a living organism? All these questions (those that we have answers for, at least) were only discussed in later years, when people already knew those things anyway. What's the point? The point of teaching science, is to make the students ask questions, not learn formulae by rote. An inquisitive nature is what got man from the stone age, right up to where we are now, thrashing in the throes of the computer age. A good science lesson, I think, should raise far more questions than it answers, and this, more than anything else is what I think is missing from science lessons in schools.

I am of course limited in my experience, since I have only ever experienced the Indian primary education system, but I have a sneaking suspicion that this would be true to a greater or lesser degree in any country in the world. I am soon going to get to test this theory first hand with the British system, so look for more rants on this topic! I must say, with all this, it's amazing that any children take up science in the first place. I think those who become scientists today, do it inspite of the system, not because of it.