Notes on Matt Ridley's Genome

Chap. 1:

I find the opening paragraph to this book so uplifting:

In the beginning was the word. The word proselytised the sea with its message, copying itself unceasingly and forever. The word discovered how to rearrange chemicals so as to capture little eddies in the stream of entropy and make them live. The word transformed the land surface of the planet from a dusty hell to a verdant paradise. The word eventually blossomed and became sufficiently ingenious to build a porridgy contraption called a human brain that could discover and be aware of the word itself. (p.11)

It is said that humans have a need for mythmaking. Here is beautiful, poetic version of a very old myth--a version that we can relate to.

A few pages later, Ridley suggests that the 120-letter gene called 5S RNA that repeats over and over on Chromosome 1 is "as close as we can get to an echo of the original word."

What is Life?

• "...consists of two very different skills: the ability to replicate and the ability to create order."
• Organisms "...build packets of order and complexity called bodies ... from the random chaos of the world."
• "Anything that can use the resources of the world to get copies of itself made is alive..."
• Information and entropy are opposite faces of the same coin--as entropy increases, information decreases.

One theory of the beginning of life is that there was an"RNA world" long before DNA came along. RNA can copy itself without assistance (w/o proteins). RNA was the replicator and the thing that was replicated.

DNA was invented by trial and error, because RNA degrades in 2 hours.

We've been told that Luca, the Last Universal Common Ancestor, may have been a "bacterium in a warm pond," but now it's thought more likely that we are descended from "the whole community of genetic organisms" because there was a lot of gene swapping before there were permanent bodies. On page 20 Ridley says

You can look on such a conclusion as a fuzzy piece of comforting, holistic philosophy-we are all descended from society, not from an individual species-or you can see it as the ultimate proof of the theory of the selfish gene: in those days, even more than today, the war was carried on between the genes, using organisms as temporary chariots and forming only transient alliances; today it is more of a team game. Take your pick.

You may recall that in one of our book club meetings Julie talked about how her professor said that life is moving in the direction of increased cooperation.

One scientist argues that the first modern organisms may have been protozoa-like, and that bacteria that live in hot volcanic vents at the bottom of the seas came later. "... Bacteria are much more 'highly evolved' than we are" because we retain very old RNA in our cells, doing unnecessary things, whereas the bacteria dropped these pieces of RNA.

Chap 2:

Wow--the human Chromosome 2 is a fusion of two ape chromosomes!

"Evolution has no pinnacle and there is no such thing as evolutionary progress." (p. 24)

"Human beings are an ecological success ... Yet the remarkable truth is that we come from a long line of failures." (p. 25)

Our timeline--I find if helpful to write this down, because I never can remember these dates:

• 10 million years ago: Two apes:

One the ancestor of humans & chimps
Other the ancestor of gorillas.

• Around 5 mya: The ancestors of humans & chimps split apart
• Or, "less than 300,000 human generations since the common ancestor of both species lived in central Africa."

It's clear that humans underwent a genetic bottleneck, because compared to other species we have less variability in our genome.

Why did our brains grow so big?

"Big brains, meat eating, slow development, the 'neotinised' retention into adulthood of childhood characters (bare skin, small jaws and a domed cranium)-all these went together." (p. 33)

Sexual selection may have driven the development of bigger brains. The fact that there was less sexual dimorphism in humans that in other apes means that humans probably had developed monogamous relationships. In monogamous relationships, men become choosy too (not just women)--both sexes preferred the neotenous look of the large-domed head, which drove evolution of bigger brains.

The division of labor over food is unique to humans. Sharing plant food meant men could take the risk of hunting. Women got high protein food without having to leave their offspring. Division of labor led to ability to share.

A clump of trends: meat for big brains--->food sharing allowed a meaty diet--->need big brains for foodsharing, to keep track of cheaters--->sexual division of labor promoted monogamy--->monogamy led to neotenous sexual selection (desire for youthfulness in mates)

Chap 5:

Mendelian genetics: "Your peas are either wrinkled or they are smooth"

"The world is not like that ... Mendelian genetics is no more relevant to understanding heredity in the real world than Euclidean geometry is to understanding the shape of an oak tree."

Pleiotropy: multiple effects of multiple genes--Unlike in last chapter on Huntington's disease, where the certainty of getting the disease was determined by the number of repeats

Increase in asthma and related "atopies?"

• dust mites--from central-heated indoor winter stuffiness, carpets, bedding
• Mycobacteria stimulates one part of immune system, the two parts are in kind of a balance--since kids don't get the mycob. from dirt, but do get vaccinated, leads to hyperactive Th2 system (which flushes parasites from the wall of the gut w/ massive release of histamine. (NOTE: current info on good effects of mycobacteria)
• IgE fought roundworms, tapeworms, hookworms & flukes during Stone Age (note: someone brought this up in a previous meeting, the guy who infected himself in order to cure his asthma.)
• common colds on increase

Ch. 6:

"Being in the same family has no discernible effect on IQ at all." (p 83) This is what Pinker said in The Blank Slate. Separated identical twins are similar in intelligence; adopted siblings are not.

"The influence upon our intelligence of events that happened in the womb is three times as great as anything our parents did to us after birth." (wow) p. 84

Francis Galton: two sticks floating downstream; hit obstacles and so forth, but pretty much travel at nearly the same rate overall. Thus with intelligence.

There are differences between individuals, but there is not difference among racial categories.

Perhaps fewer developmental stresses in the womb or in childhood (facial symmetry among high IQ-people)

"The genes may create an appetite, not an aptitude."--Yes, this makes so much sense!

Chap. 7:

Back to what we learned about with Pinker. "The tabula was never rasa"

Determinism. (I personally am too much of a reductionist; I tend to see everything as being caused in some way by the physics that led to the chemistry that led to the biology. I think this is largely right, but I am often reminded (such as by this chapter) that this is another form of determinism.)

Chomsky: "argued that human language, the most blatantly cultural of all our behaviours, owes as much to instinct as it does to culture."

(William James had also thought this way)

Universal human grammar: 4-year-olds just seem to know rules about grammar which we are never taught.

Pinker: "human language instinct"

• All languages are of comparable grammatical complexity (even though speakers deny this!! Spanish speakers have said Portuguese is badly spoken Spanish; a Portuguese speaker told me that his language was more advanced than Spanish). Slang dialects have a grammar.
• Children make mistakes like "goed" at certain stages in their development, after using "went" properly. "They learn to speak by themselves at a much younger age with the least of help from us"--unlike reading & writing, which are taught.
• Examples of pidgins, with no grammar--just people of different languages struggling to get points across. Second generation spontaneously develops a grammar (at which point the language becomes a creole rather than a pidgin.)

Why it is so hard to learn second languages: "the instinct works on speech that it hears, not rules that it memorises."

The idea that language determines thought has been a hoax.

Broca's aphasia: difficulty with the grammar encoded in word order

Damage to Wernicke's area: people can produce a rich but senseless stream of words.

K family: Speak English (their native language) the way the rest of us speak a second language--problems working out plurals, past tense, passive voice, various word-order rules, suffixes, etc. of English--"stuff that we each so unconsciously know"

Evolutionary Psychology: Pinker, Tooby, Cosmides (and William James):

The human brain has modules, like a Swiss army knife. "The machines are meaningless except when described in terms of their particular function: what is this blade for?"

Chap. 8:

In this chapter we are reminded that evolution

• is not about the survival of the species
• is not even really about the survival of the individual
• but is about the survival of the genes themselves, and many of those genes are retroviruses and other parasites embedded in the DNA of any particular species

And this can be very depressing to a human being, who likes to think that they are "here for a reason." But reading this chapter just confirms for me that Existentialism is the life-philosophy that makes the most sense: There is no meaning, so you have to go out and make your own meaning. (At least that's my limited understanding of existentialism.)

One thing that is uplifting is that Matt Ridley is actually an optimist! He thinks the world is becoming a better and better place. Here's an interview with him about his latest book, The Rational Optimist: How Prosperity Evolves.

Reading about selfish genes in this chapter and the previous one ("Chromosomes X and Y, or Conflict") does make me wish that more people knew this information. I think it would make us a lot more honest. Mostly the news is filled with people outraged by this and saying the government should do something about that, and there seems to be little introspection into "it would benefit me personally if the government would do such-and-such." (And there's not too much introspection into, "well, I am using fossil fuels every day, and that is the ultimate reason that BP drilled an offshore oil well ...")

But is honesty even the proper goal? It makes sense in terms of evolutionary psychology that we don't know our own true motives--deception, including self-deception, is a big part of our cogntive makeup. I think that before the 20th century, we were probably more honest about our own selfishness--if you happened to live in the castle you probably didn't spend give much thought to the impoverished lives of the peasants--but now we are taught that we should care about all the creatures on the planet, especially the other humans, so we are more dishonest with ourselves about our true motives. Maybe it's not dishonesty but hypocrisy that is the most annoying trait.

Chap. 9:

A key idea that I wish everyone in the public understood:

"The very combination that is most beneficial in your generation guarantees you some susceptible children." (p. 140)

Pressures of parasites cause human genetic variation?

In nature, "there might be no equilibrium outcome: that eternal chaotic motion could flow from a deterministic system. ... Chaos theory." Another thing I wish the public understood was that there is no long-term balance in nature--in fact there is a book on this topic in the Rust Shop called The Balance of Nature that I started reading last week.

Chap. 10:

Fascinating suggestion that the Ice Age in Europe selected for "better able to withstand cold in these parts: people with high metabolic rates" but "just as in foxes and rats, shy and suspicious types are paler than bold types"--we also saw this in Covenant of the Wild--research about puppies by Raymond Coppinger I think. So blue-eyed, fair people might be more anxious.

Chap. 13:

One of my all-time favorite topics: The connection between the spread 0f genes and the spread of languages.

Luigi Luca Cavalli-Sforza: Genes, Peoples, and Languages covers this and is something we might want to read.

Cultivators can afford more polygamy that h-g's, and "do not allow their women to marry the foragers, but the male cultivators do take forager wives." And we can see this is Finland, where the people are genetically similar to the rest of Europe, but they have a "distinct Y chromosome, which looks much more like the Y chromosome of northern Asian people." The Finns speak a Uralic language. Obviously the Uralic people invaded the Indo-Europeans at some time in the past.

Jews were able to almost eliminate cystic fibrosis from U.S. Jews by discouraging marriage between carriers of the gene.

Lactose intolerance: Most westerners have a gene mutation that allows us to digest milk as adults. This happened because certain populations started dairying and drinking milk. Possible reasons for the difference:

• milk drinking was a convenient and sustainable food supply for pastoralists
• northern Europeans needed extra vitamin D, so drank raw milk
• dairying began in dry places such as Arabia (camels)

Someone asked if there was any similar reason that there is so much gluten intolerance in our population.

Take-home message there is that cultural change can lead to evolutionary change.

Chap. 17:

Cancer is an unfortunate side effect of evolution. The zeal of the gene to reproduce itself, and the occasional mutations that arise when DNA is copied, lead not only to evolutionary change but also to cancer. And cancer seems kind of inevitable, if one lives long enough.

Mutiny is a perpetual problem. Cells are continually forgetting their patriotic duty, which is to serve the germ cells, and setting out to reproduce themselves. After all, each cell is descended from a long line of reproducing cells; it goes against the grain to cease dividing for a whole generation. And so, in every tissue every day, there is a cell that breaks ranks and starts to divide again, as if unable to resist the age-old call of the genes to reproduce themselves. If the cell cannot be stopped, we call the result cancer.

TP53, "a gene that detects abnormal behaviour in a cell and issues an instruction to different genes to dismantle the cell from the inside: to commit suicide," is broken in 55% of human cancers. There is a cascade of mutations that has to happen to let cancer develop.

The longer we live, the more mistakes we accumulate in our genes, and the greater the chance that an oncogene may be jammed on and three tumour-suppressor genes jammed off in the same cell. The chances of this occurring are almost unimaginably small, but then the number of cells we make in our lifetimes is almost unimaginably large. As Robert Weinberg has put it: 'One fatal malignancy per one hundred million billion cell divisions does not seem so bad after all.'

Radiation and chemotherapy work by damaging the cells enough to activate TP53 to "help the body help itself" by instructing cells to undergo apoptosis (cell suicide).

One reason to sequence the genome was because it was necessary for cancer research.

Five-month-old fetus: nearly seven million germ cells

This is culled down to 400 that will be ovulated during the lifetime! Apoptosis is what gets rid of the rest.

But, Ridley asks, how could apoptosis have evolved? Only by group selection--a body whose cells kill themselves off if they are imperfect or selfish, survives better than a body whose cells are less unselfish in this way.

Also in this chapter: Interesting comments about the social insects; Ridley says they are similar to the individual cells in our body. I wrote about this in my blog on Anthill in April,but now I realize I probably got this idea from Ridley when I read Genome several years ago!