Chapter 4 Chapter 2 Replicating Genes

At the beginning of the world, everything was simple and simple.It's hard to tell how even a simple universe came to be.And how complex life, or beings capable of creating life, suddenly appeared, and all equipped, I think, is undoubtedly a more difficult question to answer.Darwin's theory of evolution by natural selection is satisfying because it illustrates the path from simplicity to complexity, how disorganized atoms can be grouped into increasingly complex patterns until, ultimately, man is created.People have been trying to unravel the mysteries of human existence, and so far only Darwin has provided convincing answers.I intend to state this great theory in more colloquial terms than usual, and from a time before evolution took place.

Darwin's "survival of the fittest" is actually a special case of the general law of survival of the stable.The universe is occupied by stable matter.By stable matter is meant an aggregate of atoms that is sufficiently stable or universal to be given a name.It might be a unique aggregate of atoms, like the Matterhorn, that's been around long enough to deserve a name.Stable matter may also be entities of a certain class, such as raindrops, which occur so frequently that they deserve a collective noun as a name, although the raindrops themselves are ephemeral.The matter that we see around us, and that we think we need to explain—rocks, galaxies, ocean waves—are, to varying degrees, stable atomic models.Soap bubbles tend to be spherical because that's the stable shape of a thin film when filled with gas.On spaceships, water is also stabilized into spherical droplets, but on Earth, the stable surface of still water is horizontal due to the gravitational pull of the Earth.Salt crystals are usually cubic because this is the stable form of holding the sodium and chloride ions together.In the sun, the simplest atoms, hydrogen atoms, are continuously fused into helium atoms, because under those conditions, the structure of helium is relatively stable.Other and even more complex atoms are being formed on planets all over the universe.According to current prevailing theories, these more complex atoms began to form as early as the "big bang" explosion.The various elements on our earth also come from this.

Sometimes, when atoms meet, chemical reactions occur to combine into molecules, which have varying degrees of stability.They can be very large.A crystal like a diamond can be regarded as a single molecule, known to be stable, but at the same time a very simple molecule, because its internal atomic structure repeats endlessly.In living organisms today there are other highly complex macromolecules whose complexity manifests itself at several levels.Hemoglobin in our blood is a typical protein molecule.It is made up of chains of smaller molecules called amino acids, each containing dozens of atoms in a precise arrangement.There are 574 amino acid molecules in the hemoglobin molecule.They are arranged in four chains intertwined with each other, forming a three-dimensional spherical shape, and the complexity of its structure is really dazzling.A model of a hemoglobin molecule looks like a bushy thornbush.But unlike real terrestris, it is not a messy approximation model, but a fixed structure that does not make any difference.This structure repeats more than six trillion times in the same way in the general human body, and its model is completely consistent.For protein molecules such as hemoglobin, its thornbush-like shape is stable, that is to say, its two chains composed of amino acids with the same sequence tend to form exactly the same three-dimensional coiled model like two springs.In the human body, hemoglobin tribulus form their "favorite" shape at a rate of about 400 billion per second, while others are destroyed at the same rate.

Hemoglobin is a modern molecule, and it is often used to illustrate the principle that atoms tend to form a stable pattern.What we are talking about here is that some form of rudimentary evolution of molecules may have existed long before there was life on earth, through ordinary physical or chemical processes.There is no need to consider issues such as foresight, purpose, direction, etc.If a group of atoms forms a certain stable pattern under the influence of energy, they tend to tend to maintain that pattern.The first form of natural selection is simply to select stable forms and discard unstable ones.There's nothing incomprehensible about it.That's the only way things can go.

However, we naturally cannot therefore think that these principles alone are sufficient to explain the existence of some entities with complex structures, such as human beings.Take a certain number of atoms and put them together, shake them constantly under the influence of some external energy, and one day they will happen to fall into the right pattern, and Adam will come!This is absolutely impossible.You can turn dozens of atoms into a molecule this way, but a single person has as many as 100,000,000,000,000,000,000,000 trillion atoms.To make a human being, you'd have to shake your biochemical cocktail shaker for so long that the universe's eons would seem to blink in the blink of an eye.Even then, you won't get your wish.Here we must resort to the highly generalized theory of Darwinism.The story of the slow process of molecular formation goes only so far, and the rest is left to Darwin's theory.

My account of the origin of life can only be purely theoretical.In fact no one was there.There are many doctrines with opposing views in this regard, but they also have certain common characteristics.My general statement probably won't be too far from the truth. Before the appearance of life, we don't know what abundant chemical raw materials were on the earth.But there is likely to be water, carbon dioxide, methane and ammonia: all simple compounds.As far as we know, they exist on at least some other planets in our solar system.Some chemists have tried to imitate the chemical conditions that the earth had in ancient times.They put these simple substances in a flask and provided a source of energy such as ultraviolet light or an electric spark -- a simulation of the phenomenon of lightning in primitive times.After a few weeks, there was usually something interesting to be found inside the bottle: a thin brown solution containing a large number of molecules that were more complex than those originally put in the bottle.In particular, amino acids are found in it -- the building blocks used to make proteins, one of two major classes of biomolecules.Before this kind of experiment was carried out, it was originally believed that natural amino acids were the basis for determining whether life existed.If amino acids are found on Mars, then the existence of life on Mars seems certain.But today, the presence of amino acids may just mean the presence of some simple gases in the atmosphere, with some volcanoes, sunshine and thunderous weather.In recent years, laboratory simulations of the chemical conditions of a pre-life Earth have resulted in organic substances known as purines and pyrimidines.They are the building blocks that make up the genetic molecule deoxyribonucleic acid, or DNA.

Presumably the formation of the "primordial soup" must have been the result of a process similar to this.Biologists and chemists believe the "primordial soup" was what the oceans were about three to four billion years ago.Organic matter accumulates in places, perhaps on scum that dries up on the shore, or in tiny droplets of water suspended.After being further influenced by energy such as the sun's ultraviolet rays, they combine into larger molecules.Today, large organic molecules don't last so long that we don't even notice they're there, and they're quickly eaten or destroyed by bacteria or other organisms.But bacteria, and us humans, were latecomers.So in those days, large organic molecules could float freely in thick soup without incident.

At a certain point, a remarkable molecule was formed by accident.We call it a replicator.It's not necessarily the largest or most complex of those molecules.But it has a special property - the ability to make copies of itself.It seems that this chance is very small.Indeed.The chances of this happening by chance are slim to none.In one's lifetime, such once-in-a-millennium situations can practically be considered impossible.That's why your soccer lottery ticket will never hit the jackpot.But when we humans estimate what is likely or impossible to happen, we are not used to considering it in such a long period of hundreds of millions of years.If you bought a lottery ticket every week for 100 million years, you might hit the jackpot a few times.

In fact, a molecule that can make copies of itself is not as rare as we originally thought, it only needs to happen once.We can think of replicators as models or templates.We can think of it as a macromolecule composed of a complex chain, which itself is composed of various types of building block molecules.Such little building blocks abound in the soup surrounding replicators.Now let's assume that each building block has an affinity for attracting its kind.As soon as this building block from the soup comes into contact with another part of the replicator for which it has an affinity, it tends to stick there.The building blocks attached together in this way will automatically follow the sequence of the replicator gene itself.At this time, it is not difficult for us to imagine that these components are connected one by one to form a stable chain, which is exactly the same as the formation process of the original replicator.This process of gradually stacking up layer by layer can continue.This is how crystals are formed.On the other hand, it is also possible for the two strands to split in two, thus creating two replicators, each of which can go on to make copies of itself.

A more complicated possibility is that each building block has no affinity for its own kind, but has a mutual affinity for some other kind of building block.If this is the case, the role of the replicator as a template does not produce a perfect copy, but some kind of "anti-image" which in turn produces an identical copy of the original positive image. It is irrelevant whether the original replication process is from positive to negative or from positive to positive; but it is necessary to point out that the first replicator gene in modern times, that is, the DNA molecule, uses a positive to negative replication process.Remarkably, suddenly, a new kind of "stability" arises.Previously, the soup probably didn't have a very large number of complex molecules of a particular type, because each depended on building blocks that happened to produce particularly stable structures.Once the first replicator was born, it must have rapidly spread its copies throughout the ocean until the smaller building block molecules became scarcer and other larger molecules had less and less opportunity to form.

Thus we reach the stage of a large population with all identical replicas.Now, we must point out that any copying process has an important property: it cannot be perfect.It's bound to go wrong.I hope there are no typographical errors in this book, but if you look closely you may find a mistake or two.These mistakes may not seriously distort the meaning of the sentences in the book, because they are only "first generation" mistakes.But we can imagine that before the printing press, all kinds of books, such as the Gospels, were copied by hand.No matter how careful people who copy books are by profession, they will inevitably make some mistakes, not to mention that some copyists will deliberately "improve" the original text on a whim.If all the scribes were based on the same original, the original meaning would not be distorted too much.However, if the manuscripts are based on manuscripts, which are also copied from other manuscripts, then the false seeds begin to circulate, accumulate, and become more serious in nature.We tend to think that mistakes in copying are a bad thing, and it is hard for us to imagine what mistakes could be made in a document that people copied that could be considered superior to the original.When the compilers of the Jewish scriptures mistranslated the Hebrew word for "young woman" into the Greek word for "virgin," I think we can at least say that their mistranslation had unintended consequences.Because the prophecies in the Holy Book became "Behold! A virgin shall conceive and bear a son...".In any case, as we shall see, errors made by biological replicators in their replication can indeed produce improvements.For the process of life evolution, some mistakes are necessary.How precisely the original replicators made copies is unknown.Today, the DNA molecules of their descendants are astonishingly accurate compared to the most sophisticated photocopiers possessed by humans.Mistakes, however, ultimately make evolution possible.The original replicator probably made far more errors.In any case, there is no doubt that they have made mistakes, and these mistakes are cumulative. As replication errors arise and spread, the primordial soup is filled with populations of several varieties of replicators, not all identical replicas, but all "descendants" of the same ancestor.Could some of them have more members than others?Almost certainly he said: yes.Some breeds are inherently more stable than others.Certain molecules, once formed, settle for the status quo and are less prone to splitting than others.In the soup, molecules of this type would be relatively plentiful, not just as a direct logical consequence of "longevity", but because they have ample time to make copies of themselves.As a result, longevity replicators tend to thrive.All else being equal, there would be an "evolutionary trend" in populations of molecules towards longer lifespans. But other conditions may not be equal.For a breed of replicator to have another, even more important property, for its spread in a population.This is the speed of reproduction or "fertility".If type A replicators make copies at an average rate of once a week, type B replicators make copies every hour.Obviously, it won't take long for the type A molecules to dwarf.No matter how long the "life" of type A molecules is, it doesn't help.Therefore, there may well be an "evolutionary trend" towards greater "fertility" among the molecules in the soup.A third property that replicator molecules will definitely select for is accuracy of replication.Assume that type X molecules live as long as type Y molecules and replicate just as fast, but that type X molecules make an error on average once in every ten replications while type Y only makes one mistake in every hundred Wrong, there must be more Y-shaped molecules.The team of X-shaped elements in the population will lose not only the "offspring" they have raised by mistake, but also all their current or future offspring. This last point might seem paradoxical to you if you know anything about evolution.We say that replication errors are an essential prerequisite for evolution to occur, but we also say that natural selection favors a high-precision replication process.How can these two statements be reconciled?In general, we think, evolution seems to be a "good thing" in some vague sense, especially since humans are the product of evolution, and nothing actually "want" to evolve.Evolution happens by accident, whether you like it or not, although replicator genes (and genes today) go to great lengths to prevent this from happening.Jacques Monod made this point brilliantly in his speech in memory of Herbert Spencer.He said, humorously, "Another incomprehensible aspect of evolution is that everyone thinks he understands it!" Let's go back to the primordial soup, in which there are now stable varieties of molecules.Stable means that those molecules either exist for a long time, or they can replicate rapidly, or they can replicate precisely and without error.Evolutionary trends toward these three stabilities occur in the sense that if you take samples from the soup at two different times, the latter sample must contain a greater proportion of long-lived or fertile Or reproduce varieties with high accuracy.When a biologist talks about the evolution of organisms, what he means by evolution is essentially this, and the mechanism of evolution is the same - natural selection. Should we, then, call the original replicator molecule "living"?That is irrelevant.I can tell you, "Darwin was the greatest man in the world," and you might say, "No, Newton was the greatest."I hope we will stop arguing. It should be noted that no matter what the outcome of our debate is, the substantive conclusion will not be affected.Whether we call Newton or Darwin a great person or not, the life stories and achievements of the two of them exist objectively and will not change in any way.Likewise, the situation with replicating gene molecules is likely to be as I have stated, whether we want to call it "living" or not.Most of us don't understand that words are just tools for our use, that the word "living" in the dictionary doesn't necessarily mean something specific in the world.Whether we call the original replicators animate or inanimate, they were the ancestors of life; they were our creators. The second important piece of the argument is competition.Darwin himself emphasized its importance, although he was talking about animals and plants, not molecules.The primordial soup is not enough to sustain an infinite amount of replicator molecules.One reason for this is the limited size of the Earth, but other limiting factors are also very important.In our imagination, the replicator that acts as a template or model is floating in the primordial soup, surrounded by a large number of small building blocks necessary for replicating copies.However, when there are more and more replicators, the consumption of components will also exceed the supply and become a precious resource.Replicators of different breeds or strains must have fought each other for control of them.We have studied what factors promote the reproduction of those replicators that are favored.We can now see that the less favorable breeds actually became rarer as a result of competition, and at last some of them became extinct.There have been life-and-death struggles among the various breeds of replicators.They don't know they're in a struggle for survival, and they don't get annoyed by it.Replicants engage in this struggle without any emotion, let alone arouse ill-will on either side.But in a sense, they are indeed in a life-and-death struggle, because any replication error that leads to a higher level of stability, or weakens the opponent's stability in a new way, is automatically perpetuated and grow exponentially.The process of improvement is cumulative.Ways to bolster one's own stability or destabilize one's opponents become more subtle and productive.Some replicators even "discovered" ways to chemically split molecules of opposing species and use the split building blocks to make copies of themselves.These primitive carnivores ingest food while eliminating competing competitors.Other replicators may have figured out how to defend themselves chemically, or by wrapping themselves in a protein coat.This may be the growth process of the first living cells.Replicators arose not just to survive, but to make containers for themselves, vehicles on which to live.The replicators that survived were the ones that built themselves survival machines in which to live.The most primitive survival machines may be just a protective suit.Later, new competitors emerged one after another with better and more efficient survival machines, so the struggle for survival gradually intensified.Survival machines are getting bigger and bigger, and their structures are getting more and more complex.This is a cumulative and gradual process. Over time, the skills and tactics that the replicators use to ensure their existence in the world have gradually improved, but is there no end to this improvement?The time for improvement is endless.What grotesque self-preservation machine would a thousand years of change produce?After four billion years, what fate will the ancient replicators have?They haven't disappeared because they are veterans of the art of survival. But today, don't think they will still swim in the ocean.Long ago, they had given up this free-spirited way of life.Today, they live together in clusters, living safely in the bodies of huge, shambling "robots", isolated from the outside world, communicating with the outside world through tortuous indirect channels, and manipulating the outside world by remote control.They exist in the bodies of you and me; they created us, our bodies and minds; and their preservation is the ultimate reason for our existence.These replicators have a long history.Today we call them genes, and we are their survival machines.