The Standing Invitation

Posts Tagged ‘Biology

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

On the Relative Merits of AMPium

leave a comment »

“The problem with randomised controlled trials is that they don’t show how therapeutically useful homeopathy is.”

Statements like this elevate my blood pressure. They are often signify an oncoming attack against this wicked thing called Science. One encounters the word ‘homeophobia’: the denial by scientists that unknowable truths exist, motivated by the scientists’ fear that this would shatter their precious little calculations. (They are not so quick to offer a name for the phobia’s counterpart: the fear of being told you are not in fact a beautiful and unique snowflake endowed with mystical powers and the blood of Númenor flowing through your veins; in essence, the fear that there is such a thing as a wrong answer, and you might just have given it.)

Complaining about science in this way tends to be more about identity politics than a real issue of scientific methodology. Nevertheless, let’s take the above claim at its word, and make for it the best case that we can.

The assertion, minus the controversial H-word, is this:

“There exists, or might exist, such a treatment that has two properties: 1) it has some therapeutic value; and 2) it does so in a way that randomised controlled trials do not detect.”

This is the statement that proponents of randomised controlled trials (RCT) must disprove; and since the RCT is held as the gold standard, the burden of proof lies with its supporters.

Imagine a chemical called archibaldmatthewphillipsium or AMPium for short. This is a natural plant extract that has no medicinal value whatsoever – unless your name is Archibald Matthew Phillips. For this one lucky man, regular doses of archibaldmatthewphillipsium reduce the odds of cancer by 95%.

This is an extreme case. But it is well known that different people do react to some drugs differently, and personalised medicine is an important field. A patient with a certain illness will often be given a series of treatments in order to find out which one is best for him.

It so happens that AMPium is exactly the right treatment for Mr Phillips to take, and any systematic drug test that missed its value would let Mr Philips down. In this case, yes, a randomised controlled trial would not be the answer.

But this is unlikely. Nobody is that special. What is far more plausible is that what is 95% effective for Archibald Michael Phillips is, say, 90% effective for his immediate family; 80% for his extended family; 50% for people from a similar genetic or socioeconomic background, and so on, tailing away to a large proportion of the population for whom the drug is essentially valueless. Now we are back in the realms of ordinary statistics.

What should a doctor do when presented with a new patient? Of course the best thing to do would be to test him with every conceivable chemical compound, mystical trinket and shamanistic rite to find out exactly what the best treatment is best for him personally, and I would dearly love to see this happen. But this is impossible: it would take too long, and his symptoms might grow much worse before the tests were completed. This is a fact; not to acknowledge it is extremely irresponsible.

What we ask instead is: which group do we think he belongs in? The group for which treatment x is perfect? The group for which x is just an okay sort of treatment? Or the group for which it’s effectively useless?

Given our imperfect knowledge of the patient, we would base our decision on the sizes of the groups, and start him on the treatment that is most effective for the greatest number of people. And it is precisely that information that a randomised controlled trial provides.



Jeanette Winterson OBE took the opposite view here. I advise you not to click. She doesn’t need the hit count.

Written by The S I

October 15, 2011 at 11:59 pm

The Power of Names

leave a comment »

Sometimes, it is enough simply to give it a name. That is all it takes to change the way people think about something.

Of course, it helps if the name is a good one ­– or at least a big one. Here is a name that I particularly like:


This is one hell of a name: 1185 letters long. Not particularly memorable, but marvellously descriptive in its own way. It is the name of a naturally-occurring molecule; following the iron rules of its etymology allows you to derive its exact chemical structure.

The name describes a very long molecule made out of a series of modules called amino acids, all strung together end-to-end like beads on a rosary. There are 22 amino acids found in nature, and they can be combined in any order to make up a protein. The protein is therefore defined by the sequence of amino acids that make it up – its primary structure. Forces between amino acids pull this immensely long thread into a tight three-dimensional tangle, generating a secondary and tertiary structures ­– the protein’s folds and creases, in which different kinds of chemistry can take place.

The name provides the primary structure, with the sequence of amino acids narrated in code: seryl is the code for the amino acid serine, tyrosyl stands for tyrosine, isoleucyl for isoleucine and so on.

Now, it would be a major synthetic challenge, but there is nothing in principle preventing us from making this molecule from scratch. Given the name, a peptide chemist (with a lot of time on her hands) could build it out of the original amino acids. The amino acids could themselves be made with crude oil drilled from the ocean floor as a starting material. Our gigantic molecule could be created afresh, in a laboratory, with no natural process involved ­– and yet the result would not just be like the molecule found in nature; it would be that molecule. The artificial form would be indistinguishable from the natural one.

Now, what is this molecule?

It is the protein coat of the Tobacco Mosaic Virus.

The protein coat is protects a strand of RNA that contains instructions, written in code for making the coat; these two things, coat and code, are all the virus is. Both have structures that are known down to the last atom. Both are reasonable targets for synthesis ­– things that could be made, from scratch, out of nothing at all.

And yet the Tobacco Mosaic Virus is a parasite, capable of self-replication in living cells. It causes disease in plants.

A lot of people would call the Tobacco Mosaic Virus a living thing. And yet it is only a molecule. Where does one end and the other begin? What is the sharp line between living matter and chemicals in jars?

Being able to give a living thing a purely chemical name highlights that there is no such line.

Written by The S I

September 21, 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

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