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The point I want to make about methanogens is that they were the losers in the race through a bottleneck, yet nonetheless survived in niche environments. Similarly, on a larger scale, it is rare for the loser to disappear completely, or for the latecomers never to gain at least a precarious foothold. The fact that flight had already evolved among birds did not preclude its later evolution in bats, which became the most numerous mammalian species. The evolution of plants did not lead to the disappearance of algae, or indeed the evolution of vascular plants to the disappearance of mosses.
A piece of bad news wrapped in a protein coat.
Buchner proposed that fermentation was carried out by biological catalysts that he named enzymes (from the Greek en zyme, meaning in yeast). He concluded that living cells are chemical factories, in which enzymes manufacture the various products.
When a molecule of vitamin C encounters a free radical, it becomes oxidised and thereby renders the free radical innocuous. The oxidised vitamin C then gets restored to its non-oxidised state by an enzyme called vitamin C reductase. It is like a boxer who goes into the ring, takes a hit to his jaw, goes to his corner to recover, and then does it all over again.
Men are even worse: a hundred rounds of cell division are needed to make sperm, with each round linked inexorably to more mutations. Because sperm production goes on throughout life, round after round of cell division, the older the man, the worse it gets. As the geneticist James Crow put it, the greatest mutational health hazard in the population is fertile old men.
Thermodynamics is one of those words best avoided in a book with any pretence to be popular, but it is more engaging if seen for what it is: the science of 'desire'. The existence of atoms and molecules is dominated by 'attractions', 'repulsions', 'wants' and 'discharges', to the point that it becomes virtually impossible to write about chemistry without giving in to some sort of randy anthromorphism. Molecules 'want' to lose or gain electrons; attract opposite charges; repulse similar charges; or cohabit with molecules of similar character. A chemical reaction happens spontaneously if all the molecular partners desire to participate; or they can be pressed to react unwillingly through greater force. And of course some molecules really want to react but find it hard to overcome their innate shyness. A little gentle flirtation might prompt a massive release of lust, a discharge of pure energy. But perhaps I should stop there.
Pigments such as haemoglobin are coloured because they absorb light of particular colours (bands of light, as in a rainbow) and reflect back light of other colours. The pattern of light absorbed by a compound is known as its absorption spectrum. When binding oxygen, haemoglobin absorbs light in the blue-green and yellow parts of the spectrum, but reflects back red light, and this is the reason why we perceive arterial blood as a vivid red colour. The absorption spectrum changes when oxygen dissociates from haemoglobin in venous blood. Deoxyhaemoglobin absorbs light across the green part of the spectrum, and reflects back red and blue light. This gives venous blood its purple colour.
Without programmed cell death, the bonds that bind cells in complex multicellular organisms might never have evolved.
Storing genes, vulnerable informational systems, in the immediate vicinity of the mitochondrial respiratory chains, which leak destructive free radicals, is equivalent to storing a valuable library in the wooden shack of a registered pyromaniac.
Mitochondrial genes act like a female surname, which enables us to trace our ancestry down the female line in the way some families try to trace their descent down the male line from William the Conqueror, or Noah, or Mohammed.
Sex is far more widespread than seems reasonable.
Essentially all life uses redox chemistry to generate a gradient of protons across a membrane. Why on earth do we do that?
Metabolically active cells, such as those of the liver, kidneys, muscles, and brain, have hundreds or thousands of mitochondria, making up some 40 per cent of the cytoplasm. The egg cell, or oocyte, is exceptional: it passes on around 100000 mitochondria to the next generation. In contrast, blood cells and skin cells have very few, or none at all; sperm usually have fewer than 100. All in all, there are said to be 10 million billion mitochondria in an adult human, which together constitute about 10 per cent of our body weight.
multicellular life. All animals, all plants, all of them depend on
Listeria ... secretes two or three proteins that together hijack the host cell's cytoskeleton. As a result, the bacteria motor around the inside of the infected cell, pushed by an actin 'comet tail' that associates and dissociates behind them.
Occam's razor, the philosophical basis of all science: assume the simplest natural cause. That answer might turn out not to be correct, but we should not resort to more complex reasoning unless it is shown to be necessary.
Establishment. In 1966, the Dutch geologist M. G. Rutten could write, in a charmingly antiquated style that has passed forever from the scientific journals:
Ribosomes have an error rate of about one letter in 10,000, far lower than the defect rate in our own high-quality manufacturing processes. And they operate at a rate of about 10 amino acids per second, building whole proteins with chains comprising hundreds of amino acids in less than a minute.
With these new techniques, a new breed of evolutionist is emerging, able to capture the workings of evolution in real time. The picture so painted is breathtaking in its wealth of detail and its compass, ranging from the subatomic to the planetary scale. And that is why I said that, for the first time in history, we know. Much of our growing body of knowledge is provisional, to be sure, but it is vibrant and meaningful. It is a joy to be alive at this time, when we know so much, and yet can still look forward to so much more.
The igneo-aerial food. In other words, despite
The environment most realistically capable of giving rise to life, whether here or anywhere else in the universe, is alkaline hydrothermal vents. Such vents constrain cells to make use of natural proton gradients, and ultimately to generate their own.
As a rule of thumb, the hermaphrodite lifestyle works well if the prospects of finding a mate are slim, for example in low-density or immobile populations (explaining why many plants are hermaphrodites), while separate sexes develop in species with higher population densities or greater mobility.
Life itself turned our planet blue and green, as tiny photosynthetic bacteria cleansed the oceans of air and sea, and filled them with oxygen. Powered by this new and potent source of energy, life erupted. Flowers bloom and beckon, intricate corals hide darting gold fish, vast monsters lurk in black depths, trees reach for the sky, animals buzz and lumber and see. And in the midst of it all, we are moved by the untold mysteries of this creation, we cosmic assemblies of molecules that feel and think and marvel and wonder at how we came to be here.
of oxygen, whether we think of it as 'good' or 'bad', is the formation of free radicals. As conventionally stated, the idea that breathing oxygen causes ageing is disarmingly simple. We produce free
This was difficult to prove as most hydrogenosomes have lost their entire genome, but it is now established with some certainty.1 In other words, whatever bacteria entered into a symbiotic relationship in the first eukaryotic cell, its descendents numbered among them both mitochondria and hydrogenosomes.
All complex life shares an astonishing catalogue of elaborate traits, from sex to cell suicide to senescence, none of which is seen in a comparable form in bacteria.
For that matter, how do we switch from simple chemical affiliations to selection for proteins? And how do we get from RNA to DNA? As it happens, there are some striking answers, backed up by surprising findings in the last few years. Gratifyingly, the new findings square beautifully with the idea of life evolving in hydrothermal vents, the setting of Chapter 1.
The shrimp's protein and ours are not exactly the same, but they're so
similar that if you turned up in court and tried to convince a judge that your
version was not a badly concealed plagiarism, you'd be very unlikely to win.
In fact, you'd be a laughing stock, for rhodopsin is not restricted to vent shrimp
and humans but is omnipresent throughout the animal kingdom.... Trying to persuade a judge that your rhodopsin is not plagiarised
would be like trying to clajm that your television set is fundamentally different
from everyone else's, just because it's bigger or has a flat screen.
Well, biology is not only about genes and environment, but also cells and the constraints of their physical structure, which we shall see have little to do with either genes or environment directly. The predictions that arise from these disparate world views are strikingly different.
Mitochondria, as we have seen, are only passed on in the egg, so all 13 mitochondrial genes come from our mothers. If these genes really do influence lifespan, and we can only inherit them from our mothers, then our own lifespan should reflect that of our mothers but not our fathers.
The story of evolution is more dramatic, more compelling, more intricate than any creation myth. Yet like any creation myth, it is a tale of transformations, of sudden and spectacular changes, eruptions of innovation that transfigured our planet, overwriting past revolutions with new layers of complexity. The tranquil beauty of our planet from space belies the real history of this place, full of strife and ingenuity and change. How ironic that our own petty squabbles reflect our planet's turbulent past, and that we alone, despoilers of the Earth, can rise above it to see the beautiful unity of the whole.
The myosin in our own skeletal muscles is more closely related to the myosin driving the flight muscles of that irritating housefly buzzing around your head than it is to the myosin in the muscles of your own sphincters
Nothing is more conservative than a bacterium.
To doubt that life evolved, even if some of the details described in this book may yet prove wrong, is to doubt the convergence of evidence, from molecules to men, from bacteria to planetary systems. It is to doubt the evidence of biology, and its concordance with physics and chemistry, geology and astronomy. It is to doubt the veracity of experiment and observation, to doubt the testing in reality. It is, in the end, to doubt reality.
Every day in the human body, some 10 billion cells die and are replaced by new cells. The cells that die do not meet a violent unpremeditated end, but are removed silently and unnoticed by apoptosis, all evidence of their demise eaten by neighbouring cells. This means that apoptosis balances cell division
At the level of their biochemistry, the barrier between bacteria and complex cells barely exists.
But whatever our beliefs, this richness of understanding should be a cause for marvel and celebration.
Pseudobiceros bedfordi, which engages in a sperm battle when mating. Each is equipped with two penises, with which they fence, attempting to smear sperm onto the other without being fertilized themselves. The ejaculate burns a hole in the skin of the recipient, which is sometimes cavernous enough to cause the loser to tear in half. The problem is that the flatworms all want to be male. The female, almost by definition, invests more of her resources in the offspring, which means that individuals pass on more of their genes if they succeed in fertilizing others, while avoiding being fertilized themselves. This equates to spraying sperm around liberally without becoming pregnant.
Rather surprisingly, to anyone who is most familiar with textbook mitochondria, many simple single-celled eukaryotes have mitochondria that operate in the absence of oxygen. Instead of using oxygen to burn up food, these 'anaerobic' mitochondria use other simple compounds like nitrate or nitrite. In most other respects, they operate in a very similar fashion to our own mitochondria, and are unquestionably related. So the spectrum stretches from aerobic mitochondria like our own, which are dependent on oxygen, through 'anaerobic' mitochondria, which prefer to use other molecules like nitrates, to the hydrogenosomes, which work rather differently but are still related.
the greatest mutational health hazard in the population is fertile old men. Thankfully, uniparental inheritance means that men don't pass on their mitochondria at all.