Monday, September 20, 2010

Book 27 – Genome: The Autobiography of a Species in 23 Chapters

By Matt Ridley

Ok, so this book was published way back in 1999. I especially like how on the final page the author makes a point of how this book will be out of date before it even gets published… and here I am reading it more than a decade later. That’s ok cuz I know next to nothing about genetics, and what little I know I’d forgotten in Biology 11. So really now I’m just a dozen years out of date as opposed to +20!

Genome is categorized as “popular science” but this doesn’t quite do it justice. Not only does Ridley explain scientific phenomena clearly and concisely for the average layperson, he also writes beautifully and eloquently. Even when describing homogentisate dioxygenase, a “boring gene, doing a boring chemical job in boring parts of the body, causing a boring disease when broken” it’s all quite fascinating. Right off the bat, he lays out what he wants to accomplish in Genome :

A coherent glimpse of the whole: a whistle-stop tour of some of the more interesting sites in the genome and what they tell us about ourselves. For we, this lucky generation, will be the first to read the book that is the genome. Being able to read the genome will tell us more about our origins, our evolution, our nature and our minds than all the efforts of science to date. It will revolutionize anthropology, psychology, medicine, palaeontology and virtually every other science.

This is not a book about the Human Genome Project –about mapping and sequencing techniques-but a book about what that project has found. Some time in the year 2000, we shall probably have a rough first draft of the complete human genome. In just a few short years we will have moved from knowing almost nothing about our genes to knowing everything.

He was right. The HGP completed this goal in April 2003. As the HGP website states: Though the HGP is finished, analyses of the data will continue for many years. And since I have a better understanding of genetics, I can see how the HGP will be busy for a while yet!

The bibliography is also impressively well laid out, including websites the author visited in order to get up to date information as he was writing his book. Not only does Ridley want to share the knowledge with his readers but encourages them to do research on their own, if they feel inspired to further their understanding. I can attest that as a non-sciencey layman, I have learned a good many neat things about genetics and how they play a part in the human condition. Here are just a few things that particularly struck me:

a) Ridley repeatedly states “genes are not there to cause diseases”. Read up on it if you want to find out more!

b) Genes don’t just work together but they can also conflict with each other, like a kind of battlefield between parental genes and childhood genes, or between male genes and female genes. This was “a little-known story outside a small group of evolutionary biologists. Yet it has profoundly shaken the philosophical foundations of biology.”

A quick google search of “genes in conflict” resulted in a recent scientific discovery that was published earlier this year in March:

Traits that help one sex can harm the other, resulting in conflicting evolutionary pressures on males and females…This battle of the sexes is thought to extend to the genetic level, with individual genes favoring one sex over the other. Some of the strongest evidence for these sexually antagonistic genes comes from studies showing that fruit fly lines with high reproductive success in one sex typically have low reproductive success in the other. Thus, if males in a particular line have many offspring, the females do not and vice versa.

The genes underlying this sexual tug-of-war, however, have been difficult to find. Now, Paolo Innocenti and Edward Morrow reveal this conflict's genetic basis by linking the expression of sexually antagonistic genes in the fruit fly Drosophila melanogaster to the reproductive success of one sex at the expense of the other.

Pretty neat stuff! This goes to show that Ridley was onto something, since the theory of sexual antagonism as an important evolutionary force was open to debate in the 1980s, but it was only in the first decade of the 21st century that the subject has gained substantial attention.

c) I have wondered why people have different blood types and I’ve read articles about studies where men and women actually prefer the body odour of members of the opposite sex who are most different from them genetically. Since blood groups tend to be linked to cultural groups, this has not only provided insight into the history of human migrations, but since the 1990s they “promise understanding of how and why our genes are all so different. They hold the key to human polymorphism.” Ridley further states “Variation is an inherent and integral part of the human – or indeed any – genome”!

d) The fact that what we know as “personality” is to a considerable degree based on mere brain chemistry, in how our system manages serotonin levels. Romantics and spiritualists may cry “our behavior isn’t based on mere biological determinism!” and may never bother to delve any deeper than that since it’s easier to be in denial. But Ridley explains this does not mean, as it is usually assumed to mean, that our behaviour is socially immutable. Quite the reverse: our brain chemistry is determined by the social signals to which we are exposed. “Biology determines behaviour yet is determined by society.” He further clarifies by saying:

There are a score of different ways in which this one chemical, serotonin, can be related to innate differences in personality. These are overlaid on the score of different ways that the mind’s serotonin system responds to outside influences such as social signals. Some people are more sensitive to some outside signals than others. This is the reality of genes and environments: a maze of complicated interactions between them, not a one-directional determinism. Social behaviour is not some external series of events that takes our minds and bodies by surprise. It is an intimate part of our make-up, and our genes are programmed not only to produce social behaviour, but to respond to it as well.

e) “ … so close are the similarities between genes that geneticists can now do, almost routinely, an experiment so incredible that it boggles the mind. They can knock out a gene in a fly by deliberately mutating it, replace it by genetic engineering with the equivalent gene from a human being and grow a normal fly. The technique is known as genetic rescue. …Indeed, they work so well that it is often impossible to tell which flies have been rescued with human genes and which with fly genes.

This is the culminating triumph of the digital hypothesis with which this book began. Genes are just chunks of software that can run on any system: they use the same code and do the same jobs. Even after 530 million years of separation, our computer can recognize a fly’s software and vice versa. Indeed, the computer analogy is quite a good one.”

f) I have often wondered by different species of animals can have such different life spans. A trio of evolutionists separately put together the most satisfying account of the aging process: “Each species, it seems, comes equipped with a program of planned obsolescence chosen to suit its expected life-span and the age at which it is likely to have finished breeding. Natural selection carefully weeds out all genes that might allow damage to the body before or during reproduction… But natural selection cannot weed out genes that damage the body in post-reproductive old age, because there is no reproduction of the successful in old age… A mouse is unlikely to make it past three years of age, so genes that damage four-year-old mouse bodies are under virtually no selection to die out. Fulmars are very likely to be around to breed at twenty, so genes that damage twenty-year-old fulmar bodies are still being ruthlessly weeded out.” Well, how about that!

g) There is a little protein called P53 which is also known as ‘Guardian of the Genome’, or even the ‘Guardian Angel Gene’ because it regulates the cell cycle and plays a role in apoptosis, genetic stability (apoptosis is the suicide of cells and is Greek for the fall of autumn leaves – pretty ,no?). In fact, apoptosis is the most important of the body’s weapons against cancer, the last line of defence. But what’s interesting is that for a while, many people including specialists, did not fully understand how therapeutic cancer treatment worked against cancer. It’s only been quite recently that chemotherapy works not in killing cancer cells, but because it induces apoptosis by alerting P53 and its colleagues.

h) Instinct versus learning. “The two have little in common, or so the behaviourist school of psychology would have had us all believe during much of the twentieth century. But why are some things learnt and others instinctive? Why is language an instinct, while dialect and vocabulary are learnt? “ Ridley’s book explains very eloquently!

i) How baffling and unique these protein-y genes known as prions are. Prions cause neurodegenerative disease, such as BSE (aka mad cow disease) in cattle and CJD in people. They are not only not like viruses, they replicate in a protein-like manner that nobody quite knows how exactly, thus undermining one of the messages Ridley has been evangelizing throughout his book, that the core of biology is digital.

Here, in the prion gene, we have respectable digital changes, substituting one word for another, yet causing changes that cannot be wholly predicted without other knowledge. The prion system is analogue, not digital. It is a change not of sequence but of shape and it depends on does, location and whether the wind is in the west. That is not to say that it lacks determination. If anything, CJD is even more precise than Huntington’s disease in the age at which it strikes.

More than a decade later after the publication of Genome, not much more is known about prion disease. Yet Ridley holds nothing but humble respect for mysteries that cannot yet be explained by science, he is still able eloquently explain how:

Prions have humbled us with our ignorance. We did not suspect that there was a form of self-replication that did not use DNA—did not indeed use digital information at all. We did not imagine that a disease of such profound mystery could emerge from such unlikely quarters and prove so deadly. We still do not quite see how changes in the folding of a peptide chain can cause such havoc, or how tiny changes in the composition of the chain can have such complicated implications. As two prion experts have written, ‘Personal and family tragedies, ethnological catastrophes and economic disasters can all be traced back to the mischievous misfolding of one small molecule.’

Another reason that compelled me to read this book is my self-education on the science of evolution. Many of the theories Charles Darwin had were proven by genetic discoveries in the 20th century, but it wasn’t until the 1970s that for the first time, evolution became genetic. In the 1976 book, The Selfish Gene, Richard Dawkins wrote what many evolutionary biologists at the time were just starting to grasp: that evolution by natural selection was not much about competition between species, not much about competition between groups, not even most about competition between individuals, but was about competition between genes using individuals and occasionally societies as their temporary vehicles.

When scientists started reading the code for life, they found that each gene is far more complicated than it needs to be: it is broken up into many different chunks with “long stretches of random nonsense and repetitive burst of wholly irrelevant sense, some of which contain real genes of a completely different (and sinister) kind.” In fact, 97 per cent of the human genome does not consist of true genes at all, but rather “a menagerie of strange entities called pseudogenes, retropseudogenes, satellites, minisatellites, micrsatellites, transposons and retrotransposons, all collectively known as ‘junk DNA’, or sometimes, probably more accurately, as ‘selfish DNA’. Some of these are genes of a special kind, but most are just chunks of DNA that are never transcribed into the language of protein.”

Nobody predicted that when we read the code for life we would find it so riddled with barely controlled examples of selfish exploitation. Yet we should have predicted it, because every other level of life is parasitized. There are worms in animals’ guts, bacteria in their blood, viruses in their cells. Why not retrotransposons in their genes?

So what does it all mean then? I suppose nothing and everything, depending on how you want to look at it. Once more, Ridley brings it all home:

The truth is nobody is in charge. It is the hardest thing for human beings to get used to, but the world is full of intricate, cleverly designed and interconnected systems that do not have control centres.

No comments: