Showing posts with label genetics. Show all posts
Showing posts with label genetics. Show all posts

2015-03-01

Our notions of "race" and Wittgenstein on "family likenesses"

[Our] craving for generality is the resultant of a number of tendencies connected with particular philosophical confusions. There is- [....] The tendency to look for something in common to all entities which we commonly subsume under a general term.-We are inclined to think that there must be something in common to all games, say, and that this common property is the justification for applying the general term "game" to the various games; whereas games form a family the members of which have family likenesses. [....]

Ludwig Wittgenstein, The Blue Book, pp 17, 18.

There's an excellent piece from Dr Adam Rutherford in in today's Observer: "Why racism is not backed by science"

in it Adam writes:

We now know that the way we talk about race has no scientific validity. There is no genetic basis that corresponds with any particular group of people, no essentialist DNA for black people or white people or anyone. This is not a hippy ideal, it’s a fact. There are genetic characteristics that associate with certain populations, but none of these is exclusive, nor correspond uniquely with any one group that might fit a racial epithet.

Claims like this seem surprising and counter-intuitive to a lot of people, but the science tells us unequivocally that they are true.

As far as I am aware, the philosopher Ludwig Wittgenstein never wrote directly about the biology of "race", but he did have a lot to say about our use of language and the kind of thinking that underlies our use of language. As ever, I make no claims to do justice to his legacy here, but one of his themes has always struck me as being particularly relevant to our confused notions of "race".

Wittgenstein argued that particular instances of things to which general terms - such as "game" - apply, do not necessarily possess any one feature in common but form a group in much the same way as members of an extended family do when considered with respect to their physical appearances - a shared chin shape here, a shared idiosyncrasy there.

[So here we're going to be using a biological metaphor to illustrate a sports metaphor in order to illustrate a general point about our use of language concerning an apparently biological phenomenon, but please bear with me :-)]

If Wittgenstein is right, then it might be possible (in principle at least) to quantify the extent to which "family likeness" is shared between different particular cases. If we were to label the various features of particular cases of a general term with letters of the alphabet we might come up with something like the following (this is my example not Ludwig's):

  1. ABCKL
  2. ABCDF
  3. ABCGE
  4. ABHDE
  5. ABCDE
  6. AICDE
  7. JBCDE
  8. ABMNE
  9. AOPDE

These nine entities form a group, from which (given no further information) we should almost certainly exclude an entity such as "VWXYZ", and yet these entities have no one feature in common. Entity number one shares three features with three other entities, two features with four other entities, and one feature with one other entity. Entity number three shares four features with one other entity, three features with six other entities, and two features with one other entity. By counting the number of other entities with whom a feature is shared, and adding these numbers together for each entity it would be possible to calculate a "coefficient of shared features" for each entity. In the example provided, the coefficients would be as follows:

  1. 18
  2. 23
  3. 24
  4. 24
  5. 29
  6. 23
  7. 22
  8. 19
  9. 18

It now becomes clear (as could probably have been guessed by simply looking at the example presented) that entity number five shares its features more widely than any other member of the group. If the entities in question were games, then number five might be cricket (which has most features we normally associate with games) and number one might be frisbee (which has players and equipment, but no formal rules, no competition, and no winning or losing*). Whether playing frisbee should be called a "true" game is the kind of issue over which we could imagine disputes. An activity such as cricket (some other examples would serve equally well) is not only secure from such controversy, it actually belongs to the very heart of the concept of game playing**. In the same way, entity number five enjoys a distinct centrality within the family of entities to which it belongs. (Conveniently, in the above presentation, entity number five is also centrally positioned). It is number five which we should choose if asked to pick one example from the above group to serve as a paradigm.

Analysing general terms in this way sheds light on why we have concepts of "racial groups" and think we can describe paradigm examples of members of those "groups" - a "typical negro", a "typical caucasian", or whatever - even though there are no genes which are unique to people we would tend to classify as "black" or "white" or "asian". Even the outward indicators of race: curly or straight hair, dark or light skin, eyes with or without epicanthic folds etc (let alone the complex genetics that underlie such traits) are spread across many different population groups that are often seen as distinct "races".

Let us give Wittgenstein the final word:

There is a tendency [....] to think that the man who has learnt to understand a general term, say the term "leaf", has thereby come to possess a kind of general picture of a leaf, as opposed to pictures of particular leaves. [....]

Instead of "craving for generality" I could have said "the contemptuous attitude towards the particular case".





* This may have changed of course, but it was true in my day :-)

** Even though I have no idea whatsoever what is going on when I watch a game of cricket.

2011-09-09

What is a Gene?

Alongside their usual “UNICORNS CAUSE CANCER” style headlines, the tabloid press are also quite fond of “BOFFINS DISCOVER THE GENE FOR BELIEVING IN UNICORNS” style headlines. I think it kind of goes without saying that most of those who write such headlines have only the vaguest idea of what a gene is. To be fair, the more we discover, the vaguer the scientific notion of what a gene is has become, but the basics are very well established.

So what is a gene?

There are all sorts of useful analogies, similes, and metaphors we can use here. I think my favourite is the story of the pilgrim who asked for an audience with the Dalai Lama.

He was told he must first spend five years in contemplation. After the five years, he was ushered into the Dalai Lama's presence, who said, 'Well, my son, what do you wish to know?' So the pilgrim said, 'I wish to know the meaning of life, father.'

And the Dalai Lama smiled and said, 'Well my son, life is like a beanstalk, isn't it?'

“In Held 'twas In I” by Procol Harum

But I’m going to try here to describe what a gene (the real secret of life) really is instead of what it is a bit like.

Now we’ve all heard of the “chromosome”. Say this word to most people (and indeed Google images) and it probably conjures up an image like this:


Now there’s a good reason why the word “chromosome” conjures up an image like this. Basically, it’s when chromosomes look like this that we can see them under normal microscopes. But chromosomes only look like this (all bunched up and double) when they are getting ready to divide. Most of the time, and in most organisms, chromosomes look nothing like this.

Most people (even journalists) who’ve heard of chromosomes have also heard of “DNA” and are aware that it comes in the form of a double helix:


This is basically what you are looking at (ignoring all sorts of caveats that we can sweep under the lab bench for now) when you look at a length of chromosome (or at one of the strands of the chromosome in the doubled up chromosome in the chromosome picture).

So there you have it, chromosomes are (caveats aside) basically long strands of DNA.

But we haven’t mentioned “genes” yet I hear you cry.

Well a gene is a short(ish) bit of chromosome (or DNA strand if you prefer). Now (returning to analogies) “genes” are often compared here to beads on a string. But, since there isn’t really any “string” (just molecules and links between them) popper beads maybe provide a better analogy …. except that there aren’t really any beads either.

Let’s look at the DNA molecule in more detail:

DNA is made from Nucleotides – which is what the “N” stands for in “DNA”. There are just four different nucleotides involved Adenine, Cytosine, Guanine, and Thymine - which are often denoted by their initial letters: A, C, G and T.

If we un-twist the DNA and look at a short bit of it, it looks a bit like this:


But that’s already a bit complicated, so let’s simplify things still further:


(For any pedants reading, each box here represents a nucleotide together with a phosphate deoxyribose; but let's keep things simple.)

Now the more astute among you will have noticed that these two strands are complementary – the sequence of Gs, Cs,As and Ts in the strand at the bottom can be inferred from the sequence of Gs, Cs,As and Ts in the strand at the top (and vice versa).

As this implies, we only really need one strand and, indeed, we are only really interested in one stand today: the” sense” strand. The complementary strand is “anti-sense” and we can ignore it until we come to DNA duplication – which we’re not going to come to in this post.

Going back to analogies again for a second, it’s a bit like every time Guardian journalist Ben Goldacre (@BenGoldacre / http://www.badscience.net) writes a sensible sentence in his blog, Daily Mail journalist Melanie Phillips (@MelanieLatest / http://melaniephillips.com) writes a completely irrational and nonsensical sentence in her blog, and the two kind of cancel each other out.

Anyway, this leaves us with:


These are a bit like popper beads I suppose, but they are nucleotides not genes. There may be, not billions and billions and squillions (said in a Lancashire accent), but certainly hundreds or thousands of these in one gene.

So what use is that?

Well these for nucleotides form a kind of code – a code comprising only four “letters”, but a very powerful code for all that.

But if a chromosome is just a long series of nucleotides and a gene is a simply a part of that series, how do we know where one gene ends and the next one begins?

Well I suppose (and here I’m going to resort to a serious(ish) analogy) it’s a bit like the old style telegrams where you were restricted to twenty-six capital letters and that was it. You had to write stuff like ….

LEAVE THE CAR STOP JACK WILL PICK YOU UP FROM THE STATION STOP BILL WILL BE THERE TOO STOP LATE ON FRIDAY NIGHT WELL MAKE OUR WAY UP TO KATES STOP BUM A LIFT IN THE MORNING TO CHARLIES STOP AUNT DORIS WILL ALSO STOP STOP

…. in order to avoid misreading (try it without the STOPs).

It’s like that with the genetic code. There’s no punctuation, it’s all in the sequence of “letters”, but, as has been noted, we don’t even have twenty-six, we only have four. These make up three letter “words” called “DNA triplets” and each triplet codes for one amino acid.

Just as a DNA strand is a string of nucleotides, a protein is a sequence of amino acids and each gene coded for the string of amino acids that make up a particular protein. Like this:


So the sequence of nucleotides CTA codes for the amino acid “aspartic acid”, AAA codes for the amino acid “phenylalanine” and ATG codes for “stop making protein”.

Since this “protein” only has two amino acids in it, I’m not sure you can really call it a “protein”. It would more usually be called a “dipeptide”. But you’ve almost certainly eaten some of this (give or take a methyl group); it is the artificial sweetener called “aspartame” or “Nutrasweet”. I doubt that there are actually any real genes out in the wild for making aspartame, but I suppose there could be, and it’s a nice simple example of what a very short gene could do.

Conclusion

So now you understand what a gene is. It’s a sequence of nucleotides that codes for a protein (or at least part of a protein – some proteins are made from more than one amino acid chain).

I suppose, armed only with the understanding presented above, you could (naively) begin to imagine that if you have lots of genes for (say) muscle protein (or genes that produce extra good quality muscle protein) you might be more likely to make it as athlete, but how does it all get so complicated and how can you have a gene for believing in unicorns?

Well part of the answer (the full answers really are complicated) is that proteins, as well as being structural like muscle proteins, can be regulatory, like enzymes – which control all sorts of things that go on in our bodies.

Once you consider that the products of some genes can control what other genes do (in all sorts of complicated direct and indirect ways that we don’t need to go into here) you begin to realize that genetics is very sophisticated and subtle and complex.

Your computer is not really built from transistors any more (and still less from valves) but the principle is the same. A transistor is a switch that turns another switch on and off. Once you start putting a few transistors together, you rapidly start to get quite complex behaviour. Put shedloads together and you get something that can do stuff like decide to stall my Ford Galaxy just before I want to set off from a junction (while producing a fault-code which my garage insists doesn’t exist).

Anyway I digress. My point is that even simple feedback mechanisms (and the feedback mechanisms in genetics are far from simple) can produce really really complex behaviour.

Some species of bird are genetically programmed to build very sophisticated nests to lie in. My cats are genetically programmed to catch birds (fortunately for the birds they’re both rather crap at it) but are not genetically programmed (and not bright enough) to even move a twig out of the way before lying down on an otherwise perfectly comfortable and sunny patch of grass in the garden.

These complex behaviours require lots of genes (and maybe lots of so called “junk” DNA) working in harmony. On the other hand, the colours of my cats (one is black and the other is tortoiseshell) arise from the actions of just one or two genes (though even here – especially in the case of the tortoiseshell – things are a bit more complicated than you might imagine).

So while you probably can’t really have a gene for believing in unicorns, you probably can (for example) have a genetic makeup that makes you more susceptible to superstition and irrational views.

At heart, however, a gene is simply a code for making a protein.