The Standing Invitation

Posts Tagged ‘Evolution

The Origin of Opacity

with 2 comments

A while back I wrote a post about vision and why it is that some things simply can not, even in principle, be described in visual terms. I focused (see how hard it is to avoid metaphors of sight?) on things smaller than atoms, but I didn’t need to go that far. Right now, you are reading these words through at least several inches of air – real-world, macroscale stuff that you are able to feel or hear when it moves, but are unable to see.

Transparency is something magical. As a child I was fascinated by glass: solid, hard, heavier than water – and yet invisible. I asked how this could be possible, and was never really satisfied with any answer I got. And it turns out this is because I was asking the wrong question. It turns out that glass’s seemingly magical transparency is not the phenomenon demanding an explanation. To gain the deep understanding I missed as a child, we must consider the origin of opacity.

Ranked in order of wavelength, the electromagnetic spectrum begins with radiowaves and continues (decreasing wavelength) with microwaves, the infrared, the ultraviolet, x-rays, and gamma rays. Note the omission: I have deliberately excluded visible light. Why?

The portion of the electromagnetic spectrum that we can actually see is vanishingly small. You could blink and miss it, though of course if you blink you do miss it. Visible light – colour – is an astoundingly narrow selection of the available wavelengths between infrared and ultraviolet. One might wonder why this particular chunk of real estate, between 390 and 750 nm, happens to be the one that we can see. And if you ask it in these terms, you are still asking the wrong question.

Recall that you “seeing” something corresponds to your brain detecting a chemical change in a substance called 11-cis-retinal in your eyeball. 11-cis-retinal only absorbs radiation with wavelengths between 390 nm and 750 nm; anything outside this range has no effect, and so is invisible. So this is why only some of the light gets “seen”. But this only pushes the question back one step further. Why do our eyes employ 11-cis-retinal, and not some other chemical with absorbance in another wavelength range?

We can narrow the possibilities using an understanding of chemistry. There are no known chemical compounds that undergo a chemical change on exposure to radiowaves. This means that no organism dependent on chemistry as we know it could ever treat radiowaves as its own personal “visible light”.  The same appears to go for microwaves, though this is contested. X-rays and gamma rays do cause chemical changes in molecules, but with wavelengths such as this it would be quite a challenge to evolve an eye that could handle them (an essay by Arthur C Clarke suggests an animal with a metal box for an eye and a microscopic pinhole to focus it, but only to illustrate the difficulties involved). So from the restrictions of photochemistry we’re limited to a window about 3500 nm wide available for seeing – and yet evolution has caused us to see only a fraction of that. Why? And why did it “choose” for us the wavelength range that it did?

Well, consider some possibilities. What if we saw in the range of about 100 to 200 nm? Chemically it’s possible. But no organism on Earth would evolve to see in that wavelength. Our atmosphere is 80% nitrogen, and nitrogen absorbs light at about 100 nm. If we saw in that range, air would not be transparent: it would be totally opaque. The ability to see in this wavelength range would be worthless, just as it would be worthless to see around 1450 nm, where water absorbs; we evolved from creatures that needed to see in water. Here is the answer to the problem of transparency, and the problem is revealed to be that the question was backwards. Air (or water, or glass) is not transparent by itself; it is transparent to us because eyes that don’t find air transparent would be of no use to us. The transparency of air is the result of the environment our genes have designed us to live in. Of course, a subterranean creature like a mole might welcome a design of eye that makes soil transparent – while simultaneously leaving worms opaque and visible. But the chemistry for that does not exist, and moles have to make do with being blind.

Practical considerations aside, it’s interesting to ask if X-ray vision might have been useful on evolutionary terms. If we saw in the X-ray region, most matter would be transparent to us, including our own bodies. This would be useful for some things, like spotting tumours or broken bones. But we would struggle to pick fruit, or detect approaching thunderclouds, or build tools out of wood. As a species, we are better off with the kind of eyes that can detect the chemical difference between an unripe fruit (green) and a ripe one (red). Evolution has selected for us a sense of vision that operates in the part of the spectrum that is richest in information relevant to our survival. Other animals make use of slightly different wavelength ranges, like bees, who prefer the shorter ultraviolet wavelengths rich in information about the availability of nectar in flowers.

In fact, it’s arresting to imagine an alien world, lit by sun that emits different wavelengths of light to our own – populated by aliens based on very different chemistry to our own, with strange eyes for detecting wavelengths we cannot ever hope to see. If ever they came to visit us, their children might well look at us in fascination, wondering why it is that we humans are as transparent to them as glass…


Daniel C Dennett: Consciousness Explained

Richard Dawkins: Unweaving the Rainbow

Arthur C Clarke: Report on Planet Three and Other Speculations


Written by The S I

May 6, 2012 at 1:10 am

The Good Book

leave a comment »

At the end of the film The Time Machine (the scene does not appear in H G Wells’ original novella), the Time Traveller leaves the present day to spend the rest of his life in the distant future, helping to rebuild the society he has helped to liberate. Before he goes, he takes with him three books from the library, and we are not told what they are. It is an open question directed at the film’s audience: what three books would you take with you?

I’d be tempted to say The Origin of Species. I’d like to get that one absolutely sorted out on day one.

Evolution is a fact. It really, really is. I can just about imagine someone who can look at the overwhelming evidence in its favour and come to some other conclusion; I wouldn’t mind meeting this person, we might talk about it over coffee and an apple danish, it’d be fun. But the existence of people who think that to acknowledge the truth of evolution is a political stance rather than an empirical one truly astonishes me.

And yet people like this do exist. There are countries when a candidate can lose an election for acknowledging that evolution is real, or that climate change is real. Fine, if the objections raised are grounded in facts – but they are not. They have become matters of personal identity, religious orthodoxy and party-political loyalty. To call attention to facts is seen as a personal attack on one’s values. And other people’s values are to be respected, however baseless they are.

What do I ask for, then, in a well-run society? That the veracity of evolution be constitutionally protected?

No. That kind of mindset would only make things worse in the long run.

And this is why, over and above The Origin of Species, I would choose another book. I would find space in my time machine for Mill’s On Liberty. Although Darwin’s book is invaluable for showing us, better than anything else, our true position in the universe, I would argue that On Liberty transcends even this in importance, because it tells us about how to react to theories like Darwin’s.

This book, written in the 1850s, is a brutal attack on anyone who wants to see an idea ­– any idea at all – as being above criticism. It says, beautifully, that the only way of arriving at the truth, or of preventing us forgetting the truths we’ve already uncovered, is by exposing it to constant criticism. Yes, feel free to have your opinions, but be prepared to fight for them. By calling on everyone to attack opinions they do not like – and to defend against attack the ones they hold dear – it casts suspicion on anyone who holds an opinion for any reason other than because they have evidence for it.

The power to criticise ideas – all ideas, held for whatever reason – and to see which ones stand and which ones fall based solely on what the arguments for and against are them are, is a necessary condition for a decent, well-constructed, compassionate society. It might even be a sufficient one.


On Liberty can be found here. Don’t be put off by this man’s egregiously long sentences; his stuff is gold.

Written by The S I

October 25, 2011 at 11:59 pm

Domesticated Animals

with 2 comments

Here at the S I we like nothing more than a nice glass of milk after a long day of studying. But drinking milk is, in evolutionary terms, a very strange thing to do.

Fact of the day: most of the peoples on Earth are unable to digest milk. Surprising, isn’t it? Note the ‘s’ in ‘peoples’; that is where the clue is.

All mammals* are able to produce milk, but humans are alone on Earth in drinking it as adults. The problem is the carbohydrate lactose, a disaccharide sugar formed by a reaction between glucose and galactose in the mammary gland. Lactose is unique to milk, being found nowhere else in the body. As such, it requires special chemical equipment to break it down and digest it.

Lactose is broken down in the small intestine by an enzyme called lactase, which, in most mammals, is produced only when the mammal is very young; production tails off shortly after birth. After lactase production shuts down, it is impossible to digest lactose in the small intestine; one becomes ‘lactose intolerant’. In this event, lactose digestion occurs downstream, as it were, in the large intestine, where decomposition by intestinal bacteria fills the gut with unwanted gas and water. Naturally, people with lactose intolerance tend to avoid milk.

But I can drink milk. If you are reading this, there is a good chance that you can too. What makes this possible? The answer is surprising.

The ability to drink milk is an evolutionary phenomenon, and it occurred extremely recently. Only ten thousand years ago, before the agricultural revolution, people with a tolerance to lactose were the minority. This made sense in the terms of evolutionary economy: since your mother will stop producing milk, why continue to produce a costly enzyme to digest it?

Nevertheless, there was variation. Some people continued to produce lactase a little longer than the others. This variation was meaningless noise until the domestication of the cow, when suddenly it became a real advantage. For the first time, people other than children were able to access the energetic and nutritional powerhouse that is cow’s milk.

In times of scarcity this additional food source was a matter of life or death. Children who were able to drink cow’s milk later in life were more likely to survive than those who stopped producing lactase early. That’s one hell of a selection pressure. Effectively, in those parts of the world where cows were domesticated, the lactose-tolerant outbred the intolerant. In short, we evolved.

‘Domestication’ is the process by which a wild animal becomes accustomed to an agricultural environment. We think of cows as being domesticated by humans, but what the story of milk tells us is that it works both ways. On a world map, the presence of milk-producing cows is tracked by a detectable change in human genetic makeup.

We domesticated the cows to produce milk more or less consciously. But without realising it, we simultaneously domesticated ourselves to consume it.


Harold McGee, McGee on Food and Cooking

Richard Dawkins, The Ancestor’s Tale

* Well, half of them.

Written by The S I

September 19, 2011 at 11:59 pm

Alu and You

leave a comment »

Selfish gene theory is a gene-centred view of natural selection. Your genome is made up of thousands of individual genes, each one of which has only one goal: replication. And since the resources available for replication are finite, the genes compete.

One way in which a gene might ensure it gets reproduced is to gang up with some other genes to make a body. This body will act as a temporary, disposable vehicle, to be thrown away once it has had children, but worth designing carefully. The genes try to make the body survive at least to childrearing age, by equipping it with sharp teeth or keen eyes. Genes have to learn to work together: a gene for light bones might do well to pair up with a gene for wings; genes for gills and flippers go hand in hand. All of the wonderful good design of life comes from genes cooperating to compete ­– building bodies that enhance their chances of replication.

But even within a body, the competition between genes is still going on.

Imagine your genome as a sequence of letters, T, C, A and G – 2.9 billion letters arranged in a line, maybe on a tape of paper. Every generation, this piece of paper gets transcribed and copied. Sometimes, mistakes are made.

About 65 million years ago, early in the evolution of primates, an error in gene replication created a monster called Alu.

Alu is a transposon: a short piece of DNA ­– about 300 letters long ­– that is able to reproduce itself within the genome. It appeared when a gene necessary for protein synthesis was mistranscribed. It only had to appear once. Since then, Alu has been quietly copying itself in the genomes of primates – humans included.

Its success has varied over history. Right now it is believed to create one extra copy of itself in the genome every 200 generations or so; in times it has been more successful. In those periods, almost every child had one more Alu unit than its parent.

Like other genes, it is copied from one generation to the next; the effects are cumulative. Over the immensely long course of its existence, Alu has done well. Imagine huge segments of your DNA existing as the same sequence of letters repeating over and over again – not just hundreds of times, but millions of times.

65 million years after it first appeared as a mutation in a single primate, Alu now occupies 10% of your genome. 10% of your DNA is made up of these 300 letters, meaningless junk repeated over and over again, simply because in the great competition of evolution, Alu found a way to cheat.

But even Alu can mutate, adapt, evolve, and now there are subtle variations of Alu, superfamilies that compete with each other, trying to out-copy one another…

And the game goes on.



Richard Dawkins: The Selfish Gene and The Ancestor’s Tale

The numbers vary from one paper to another; I took the above from “Alu Repeats and Human Genetic Diversity”, Batzer and Deininger; see also Molecular Biology of the Cell, second edition.

Written by The S I

August 21, 2011 at 11:59 pm

An Unsolved Problem

with 2 comments

You are walking in the countryside, William Paley-style, and you encounter a penny, lying on the ground, with heads facing up, tails facing down. It is reasonable to assume it just happened to fall that way ­– it could just as easily have fallen tails-up ­– and you would think nothing of it. But if you found thousands of thousands of coins, all with heads up, that would require an explanation.

There are some things that have a property called chirality, or handedness. If a thing is chiral, it has a mirror image version of itself that is not identical with itself. Gloves are chiral: a right glove and a left glove weigh the same amount, are made of the same material, have the same number and arrangement of fingers and thumbs. Importantly, they take the same amount of effort to make. But a left glove is not a right glove; they are non-superimposable mirror-images.

Chirality is a hugely important part of chemistry, because many molecules are chiral: they have mirror-image versions of themselves. The two mirror images of a molecule will have the same properties, the same weights and compositions. They take the same amount of energy to make, and when they are made they are made in equal amounts. Just as a coin tossed in the air is equally likely to land on either face, a molecule that is deciding which handedness to become in a chemical reaction will have no preference ­– resulting in equal amounts being formed.

So far, so good.

But we find that, in their interactions with living things, chiral molecules behave in rather odd ways. We have already agreed that a left-handed molecule has the same properties as its right-handed twin. But why does one molecule taste, to us, of lemons, and its mirror image of oranges? If one is molecule the active ingredient in cough syrup, why is its mirror image a drug a hundred times stronger than morphine?

The answer is that we are chemically chiral. And, just as a left and right shoe will fit differently onto a left foot, left-handed and right-handed flavour molecules will fit differently onto our left-handed taste receptors, producing different flavours, or will fit differently into our left-handed drug metabolism pathways, resulting in different medical effects.

But yes. I did just say left-handed. I did not say right-handed or an equal mixture of the two. Because, even though left-handed and right-handed things are equally probable, equally easy to make, living things are made from only left-handed molecules.

Every sugar molecule in your body – in all bodies everywhere ­– every amino acid and every protein and every DNA spiral has a possible mirror image form of itself, but these are nowhere to be found. In a world of symmetry, living things, surprisingly, are built of only one kind of chiral building block.

This is called biological homochirality, and how it came to be the case is one of the biggest unsolved problems in modern science.

Written by The S I

July 26, 2011 at 8:30 pm

The End of Evolution

leave a comment »

The problem, I am told, is that we are no longer evolving.

In the good old days of the African savannah, imperfections in body and mind were weeded out by harsh winters and community-spirited sabre-toothed tigers. The weak and the stupid were killed off. Only the smart and healthy survived, only they reproduced.

Now that is no longer the case. We are now able to keep alive people who would normally not have gone on to pass on their bad genes. We are being outbred by idiots. We see violence and stupidity all around us: blame modern medicine.

These thoughts are as old as H G Wells, who thought it necessary to sterilise inferior races for the good of mankind. Although rarely taken to such extremes, the notion that society will collapse because we have stopped evolving is still something you hear from time to time. And this is surprising, because it is totally wrong in every important respect.

Fortunately we do not need to discuss the barbarity of seriously trying to reintroduce natural selection in the modern world to see that the above concerns are misplaced in the extreme. The thesis is simply not factually accurate. In fact, that the exact opposite is true should be, well, blindingly obvious.

In the last two thousand years, people’s average height has increased dramatically. So has longevity. But a thousand years is nothing on an evolutionary timescale. We are genetically indistinguishable from people two thousand years ago. Evolution has had nothing whatsoever to do with us being taller or living longer. But if not evolution, then what?

The answer is obvious: nutrition, medicine, hygiene, housing. These are not evolutionary changes, but cultural ones. They are exactly the product of a societies that pass on knowledge from one mind to another, improving it as it goes, with the goal of keeping alive people who would otherwise die.

The idea that technological advancement, coupled with human compassion, leads to some kind of genetically-determined societal decline should be too silly to comment on; and yet it is something I have often heard repeated, in mournful tones, by concerned, intelligent people who have nothing but the wellbeing of humanity on their minds. History has shown us what can happen when this misunderstanding comes to dictate policy.

The unravelling subtleties of genetic evolution and cultural development continue to shape our ideas of where we stand in the world, as well they should. It is important to ensure that people understand these things in all their nuances, because when this understanding is only partial, great harm can result.

Written by The S I

July 10, 2011 at 10:24 pm

Posted in Science

Tagged with ,