The story of evolution-7: Genes, chromosomes, and DNA

In order to understand how inheritance works and the mathematics involved, it may be helpful to have a quick summary of some basic facts about genetics (a little simplified), using the human genome for concreteness.

All the genetic information in our bodies is found in the DNA, whose famous double helix structure was discovered in 1953. Thanks to the Human Genome Project, we now have a complete map of the DNA of humans, called the human genome, and know that it consists of a sequence of 3.1647 billion sites arranged in a row, each site containing one of four complex molecules (called bases) labeled A, C, T and G. It is this long arrangement of the four bases that define each of us genetically. Almost 99.9% of the arrangement of these bases is identical in all humans, and about 98% is identical between chimpanzees and us.
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The story of evolution-6: The probabilities of natural selection

There are three mathematical ideas that one needs to come to terms with in order to get the full flavor of how natural selection works.

  1. One is the rate at which favorable mutations occur in organisms. These do occur by chance and the question is whether the frequency of such occurrences is sufficient to explain evolution.
  2. The second is the rate at which favorable mutations become more numerous in the population. It is not enough to produce a single favorable organism. The population of varieties with advantageous properties has to eventually grow to sufficiently high numbers that it dominates the population and can form the basis for yet further mutations.
  3. The third is whether the rate at which repeated small and favorable mutations build on each other is sufficient to produce major changes in complex systems (the eye, ear, and other organs for example) and even entirely new species.

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The story of evolution-5: How probability intuition can lead us astray

One of life’s ironies is that the difficulty in understanding the mathematics of Darwin’s theory of natural selection may actually be caused by natural selection itself.

As we saw earlier, natural selection does not try for maximum benefit but instead works on a ‘just good enough for now’ principle. Steven Pinker in his book How the Mind Works (1997) is a cognitive scientist who believes that natural selection has been the driver for most aspects of our bodies and our behavior, and that the brain, being just another organ, has evolved to do what it does to effectively meet the challenges it faced at various times in our somewhat distant past. Pinker points out that humans, when compared with other animals, have unusually large brains compared to body size but that this rapid expansion in brain size occurred more than 100,000 years (or about 5,000 generations) ago (Pinker, p. 198) and then leveled off after that. This means that the structure of our present brains has been largely determined by a time when humans were hunter-gatherers and foragers. [Read more…]

The story of evolution-4: Darwin gets an idea from Malthus

In Darwin’s travels to distant lands from 1831 to 1836 on the Beagle, the different climates and environmental conditions he encountered made him aware of the weakness of the existing theory of ‘special creation’, where god was assumed to have created creatures best suited for their environment. Darwin saw for himself that very similar climates could produce hugely different kinds of species, and that the nature of these species seemed to be more influenced by the species in nearby areas than by anything else. This seemed to him to suggest that new species arose from the modifications of the old.

The discovery that the Earth was much older than had been previously thought, and the evidence for which was in the geology book by Charles Lyell that he had read on the boat, told him that it may be possible for these changes to occur gradually by very small steps provided that there was enough time for the changes to accumulate.
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The story of evolution-3: Natural selection and the age of the Earth

It is clear that many people find it hard to accept Darwin’s theory of evolution by natural selection. One reason is of course because it completely undermines the need to believe in a creator, making god superfluous when it comes to explaining the nature and diversity of life, and thus people may have a negative emotional reaction that prevents them from seeing the power of the theory. As I have discussed earlier, people are quite able to develop quite sophisticated reasons to believe what they want and reject what they dislike.
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The story of evolution-2: The lack of evidence for perfect design

In the first post in this series, I showed with the example of a soap spray nozzle how natural design could come up with systems whose intricacy and complexity is such that it was superior to the efforts of intelligent human designers. But what about the argument that a god-like designer would be able to come up with an even better nozzle design? It is true that if we allow for the existence of such a designer, we could get the best possible design for a nozzle. The catch is that assuming that god is a perfect designer opens up a whole set of new problems, not the least of which is why if god is so powerful he would need any kind of nozzle at all and not simply create any kind of spray he/she needed.
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The story of evolution-1: The power of natural selection

We are rapidly approaching 2009, a year that marks a major scientific milestone that is going to be commemorated worldwide. It is both the 150th anniversary of the publication of the landmark book On the Origin of Species that outlined the theory of evolution by natural selection, and the 200th anniversary of the birth of its author Charles Darwin.

Darwin’s theory represents arguably one of the most, if not the most, profound scientific advances of all time, ranking well up with those scientific revolutions associated with the names of Copernicus, Newton, and Einstein. And yet it is widely misunderstood, or more appropriately, under-understood because most discussions of it remain on too high a level of generality, enabling critics to make statements about the theory that are not valid but yet seem plausible.

In order to create a better awareness of what the theory involves, today I will begin an occasional series of posts that looks at the details of the theory, including the mathematics that underlies it and which was developed later by people like J. B. S. Haldane, Sewall Wright, and R. A. Fisher.
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Highway merging and the theory of evolution

Some time ago, I wrote about the best way for traffic to merge on a highway, say when a lane is closed up ahead. There are those drivers who begin to merge as soon as the signs warning of impending closure appear, thus making their lanes clear. Others take advantage of this lane opening up to drive fast right up to the merge point and then try to squeeze into the other lane.

I said that although people who followed the latter strategy were looked upon disapprovingly as queue jumpers, it seemed to me like the most efficient thing to do to optimize traffic flow was to follow the lead of the seemingly anti-social people and stay in the closed lane until the last moment since that had the effect of minimizing the length of the restricted road. To merge earlier meant that one had effectively made the restricted portion longer.
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Asking the wrong questions about science history

In his influential book The Structure of Scientific Revolutions, Thomas Kuhn points out that the kinds of questions we often ask about the history of science and that we think are simple and have been adequately answered (such as “who discovered oxygen and when?” “Who discovered X-rays and when?”) turn out on close examination to be extremely difficult, if not impossible, to answer.

It is not that there are no answers given in authoritative sources. It is that when we actually do examine the historical record, the situation turns out to be very murky, giving rise to the strong suspicion that such questions are the wrong ones to ask about the scientific enterprise. The simple answers that are given to such questions represent a rewriting of history to give readers a simple narrative but at the expense of giving a distorted sense of how science is done, as if scientific discoveries were clear and decisive events. I remember being very impressed by Kuhn’s examples to support his thesis when I first read his book and subsequent readings of science history have convinced me that he is right.

For example, the latest issue of the newsletter of the American Physical Society’s called the APS NEWS (vol. 16, no. 5, May 2007, p. 2) has an account of the discovery of the neutron. (The article is here but the current issue is password protected and non-APS members will have to wait a month before it is archived and people are given open access.) The title says “May 1932: Chadwick reports the discovery of the neutron” and recounts the familiar (to physicists anyway) story of how James Chadwick 75 years ago this month made the famous discovery for which he received the Nobel prize in 1935.

As the article proceeds to describe the history of the process, it becomes clear that its own story contradicts the impression given in the title.

As early as the 1920s, people had suspected that there was something in the atom’s nucleus other than protons. Some thought these additional particles were made up of an electrically neutral combination of the already known proton and electron but no one could confirm this. But experiments went on trying to isolate and identify the particle, and around 1930 two scientists Bothe and Becker found radiation coming from a target of Beryllium that had been bombarded with alpha particles. They thought that this radiation consisted of high-energy photons. Other experiments done by Frederic and Irene Joliot-Curie also found similar radiation that they too attributed to high-energy photons.

Chadwick thought that this explanation didn’t quite fit and did his own experiments and concluded that the radiation was caused by a new neutral particle that was slightly heavier than a proton. He called it the neutron. He published a paper in February 1932 where he suggested this possibility and then in May 1932 submitted another paper in which he was more definite. It is this paper that gives him the claim to be the discoverer.

But like all major scientific discoveries, acceptance of the new idea is not immediate within the community and it took until around 1934 for a consensus to emerge that this neutron was indeed a new fundamental particle.

So who “discovered” the neutron and when? Was it the people who concluded much earlier than 1932 that there was something else in the nucleus other than protons? They were right after all. Was it Bothe or Becker, or the Juliot-Curies who first succeeded in isolating this particle by knocking neutrons out of materials? They had, after all, “seen” isolated neutrons even if they had not identified it as such. Or do we give the honor to Chadwick for first providing a plausible claim that it was a neutron?

As to when the neutron was discovered, it is also hard to say. Was it when its existence was first suspect in the early 1920s? Or when it was first isolated experimentally around 1930? If we say that since the title of discoverer was awarded to Chadwick, the date of discovery has to be assigned to something he specifically did, when exactly did he realize that he had discovered the neutron? In his first preliminary paper in February 1932? Or in his more definite paper in May? Clearly he must have known what he knew before he submitted (or wrote) the papers.

All we know for sure is that sometime between 1930 and 1934, the neutron was “discovered” and that certain scientists played key roles in that process. For historical conciseness, we give the honor to Chadwick and fix the date as May 1932 and the judgment is not an unreasonable one, as long we insist on demanding that such events have a definite date and author. But it is good to be reminded that all such assignments of time and place and people for scientific discoveries mask a much more complex process, where “discoveries” involve extended periods of time involving large numbers of people during which understanding is increased incrementally. There is often no clear before-after split.

The detailed stories are almost always more fascinating than the truncated histories we are taught.

The nature of consciousness

In the model of Cartesian dualism, we think of the mind as a non-material entity that interacts somehow with the material brain/body in some way. Descartes thought that the locus of interaction existed within the pineal gland in the brain but that specific idea has long since been discarded.

But that still leaves the more fundamental idea, referred to now as Cartesian dualism, that states that I do have a mind that represents the essential ‘me’ that uses my material body to receive experiences via my senses, stores them in my memory, and orders actions that get executed by my body. This idea that there is an inner me is very powerful because it seems to correspond so intuitively with our everyday experience and the awareness that we have of our own bodies and the way we interact with our environment. Even the way we use language is intricately bound up with the idea that there exists some essence of ourselves, as can be seen by the way the words ‘we’ and ‘our’ was used in this and the previous sentences. The power of this intuitive idea of something or someone inside us controlling things has resulted in phrases like ‘the ghost in the machine’ or a ‘homunculus’ (from the Latin for ‘little man’) to describe the phenomenon.

For religious people, the mind is further mixed up with ideas of the soul and thus gains additional properties. The soul is considered to be non-material and can exist independently of the body, allowing for the possibility of an afterlife even after the body has ceased to exist. This soul model causes some problems that resist easy answers. For example, life begins with the creation of a single fertilized egg. This single fertilized cell (called a zygote) then starts to multiply to 2, 4, 8, 16 , 32,. . . cells and so on. All these cells are material things. At what stage along this progression did a non-material entity like the soul appear and attach itself to the collection of cells?

I think it is safe to say that almost all cognitive scientists reject the idea of a non-material mind, some kind of homunculus inside the brain somewhere that ‘runs’ us. This immediately rules out the religious idea of a non-material soul, at least in any traditional sense in which the word is used.

But even though the existence of a non-material mind or soul has been ruled out, the Cartesian dualistic model is still a seductive idea that can tempt even those who reject any religious ideas and accept a framework in which the material body (and brain) is all there is. The reason it is so seductive is that even if we discard the mind/body distinction as being based on a nonmaterial/material splitting, the idea of a central processing agent still seems intuitively obvious.

Consider a situation where I am responding to something in my environment. We know that we experience the external world through our five senses (sight, sound, smell, touch, taste) and that these senses are triggered by material objects coming into contact with the appropriate sense organs (eyes, ears, nose, skin, tongue) and excite the nerve endings located in those organs. These excitations are then transmitted along the nervous system to that part of our brains called the sensory cortex after which they. . .what?

At this point, things get a bit murky. Clearly these signals enter and proceed through our brain and excite the neural networks so that our brain becomes ‘aware’ of the phenomena we experienced, but the problematic issue is what exactly constitutes ‘awareness.’

Suppose for the moment we stop trying to understand the incoming process and switch to the outgoing process. It seems like we have the ability to make conscious and unconscious decisions (pick up a cup or shake our head) and then the brain’s neural networks send these signals to the part of the brain known as the motor cortex which transmits them to the appropriate part of the nervous system that sends the signal to the body part that executes the action by contracting muscles.

It seems reasonable to assume that in-between the end of the incoming pathway and the start of the outgoing pathway that I have described that there is some central part of the brain, a sort of command unit, that acts as a kind of clearing house where the incoming signals get registered and processed, stored in memory for later recall, older memories and responses get activated, theories are created, plans are made, and finally decisions for action are initiated.

As a metaphor for this command unit, we can imagine a highly sophisticated kind of home theater inside our brain where the screen displays what we see, speakers provide the sound, and is also capable of providing smell and touch and taste sensations, and banks of powerful computers by which memories can be stored and retrieved and action orders transmitted. ‘Conscious events’ are those that are projected onto this screen along with the accessory phenomena.

Daniel Dennett in his book Consciousness Explained (1991) calls this model the Cartesian Theater and warns against falling prey to its seductive plausibility. Accepting it, he points out, means that we are implicitly accepting the idea of a homunculus, or ghost in the machine, who is the occupant of this theater in the brain and who is the inner person, the ‘real me’ and what that inner person experiences is sometimes referred to as the ‘mind’s eye.’ One problem is that this approach leads to an infinite regress as we try to understand how the Cartesian Theater itself works.

But if this simple and attractive model of consciousness is not true, then what is? This is where things get a little (actually a whole lot) complicated. It is clear that it is easier to describe what cognitive scientists think consciousness is not than what they think it is.

More to come. . .