Genetics of Original Sin (7 page)

Further vertebrate evolution took place on land. Some dinosaurs acquired feathers, perhaps serving initially as a protection against a cold climate, and eventually turning into primitive wings that allowed the animals to glide and, later, to fly. First revealed by archaeopteryx, the fossil of a feathered, presumably flying dinosaur, discovered in 1864 in a Bavarian schist quarry, this story has since received confirmation from a number of
fossils found in China. Its outcome is the appearance of birds, about 150 million years ago.

Other dinosaurs became covered with hair and acquired milk-secreting glands on their chest, allowing females to feed their young. This acquisition led, some 225 million years ago, to the first mammals. These creatures remained small, enjoying a relatively modest existence in the shadow of the monstrous dinosaurs, until some 65 million years ago, when a planetary catastrophe, probably initiated by the fall of a large meteorite on the Yucatán Peninsula in Mexico, precipitated the massive extinction of dinosaurs and many other animal and plant species. Subsequent to this cataclysm, mammals underwent an extraordinary development and came to occupy all environments, even returning to the sea in some cases, as happened to the ancestors of seals and whales. Mammals gave rise, some 70 million years ago, to the primate group, out of which a line detached, some 6–7 million years ago, that was to lead to the human species.

Viewing this grand history (
fig. 3.1
), or rather its present outcome, through the eyes of the prophets who wrote the Bible or of medieval scholars, who didn't even know about microbes, one can readily understand how this whole pageantry was viewed as given once and for all, brought into being by a Creator for the sole benefit of humankind. Even the eighteenth-century Swedish naturalist Carl von Linné (1707–1778), who did know about microbes and who spent his entire career observing and describing living organisms, patiently classifying them into species, genera, families, orders, classes, phyla, and kingdoms, failed to see that the kinships he was recognizing rested, like those of human families, on a vast genealogical tree springing from a single root. Linné remained all his life an unconditional defender of “fixism” and adhered staunchly to
the biblical story. Even his later French successor Georges Cuvier (1769–1832), the founder of comparative anatomy and paleontology, adamantly refused to accept the transformist hypothesis proposed by his rival Lamarck, even though he was hardly influenced by biblical creationism. We don't have their excuses today. Evolution, as we have seen, no longer calls for demonstration.

Fig. 3.1.
The main steps in the history of life, in particular of animals.
Note that life remained exclusively unicellular during 2.5 billion years. The first animals appeared 600 million years ago, after life had already accomplished five-sixths of its history. The human species dates back a mere 200,000 years, the equivalent of the last half-hour if life had started one year earlier (and animals two months earlier).

I
n the first part of this book, I sketched a descriptive picture of the main steps of evolution. But describing is not enough for understanding. One must explain. All historians know this. That is what I try to do in this second part. It starts with three chapters devoted to three fundamental biological mechanisms that need to be known by anybody wishing to understand life and its history: metabolism, the entire set of chemical reactions that underpin the functioning of living beings since their first appearance; reproduction, which has served as a link between generations all along evolution and ensures hereditary transmission; and, finally, development, which covers the processes whereby, in multicellular beings a fertilized egg gives rise to an organism.

Natural selection, the topic of
chapter 7
, represents the central theme of the book, the conducting thread between past and future that leads to the warning at the end of this book, the beacon that illuminates the entire history of life, up to its most recent steps and, even, its future prospects.

There will be a brief mention, in the last chapter of this part, of some of the other evolutionary mechanisms that have been proposed, including “intelligent design,” which is not properly speaking a scientific mechanism, but warrants attention because of the media upheaval it generates.

T
he
New International Webster's Comprehensive Dictionary
defines “metabolism” as “the aggregate of all physical and chemical processes constantly taking place in living organisms.” The key words are “physical” and, especially, “chemical.” There is no escape. If one wishes to understand life, one has to go through some chemistry. In a book like this, we can't examine all the details that fill biochemistry textbooks with formulas of daunting complexity. Fortunately, it is possible to give an idea of how metabolism works without calling on a single formula. This is what I try to do.

Have you ever visited a chemical factory? If you've seen one, you've seen them all, for all are constructed on the same model: a collection of closed vats linked by pipes. Each vat is the site, under specified conditions of temperature, acidity, and so on, and with the eventual addition of a catalyst to facilitate the reaction, of a given step in the specified process. The pipes feed reactants into the vat and allow exit of the products. Raw materials are introduced into the system. They circulate from vat to vat, while undergoing progressive transformations, finally
to exit as finished products. The pathways thus followed vary with the nature of what is manufactured. They can be more or less complicated but rarely comprise more than a few tens of steps.

Living chemical factories follow the same model, except that they carry out a large number of different production programs simultaneously, that they include many more steps, and that, aside from a few compartments, such as mitochondria, that house a large number of reactions, there are no vats and no pipes, or their equivalent. It all takes place in a single phase, or
metabolic pool,
containing all the participating substances. This is possible because these substances may rub each other without in the least interacting. The circulation of matter through the system is entirely ensured by the catalysts of the reactions, most often
enzymes
of protein nature.

Enzymes display on their surface binding sites that specifically fish out of the metabolic pool the substances, or substrates, that participate in the reaction catalyzed by the enzyme. The substances thus caught find themselves within the field of action of another site, called catalytic site, that ensures their transformation. Once the reaction is terminated, its products fall off the enzyme and join the metabolic pool.

Foodstuffs brought into the cells from the outside circulate from enzyme to enzyme in such systems, progressively transforming into the final products. These include: cellular constituents, made to replace damaged molecules and to sat-isfy the needs of growth, reserve substances that are held in storage by the cells, and, to be discharged outside, even-tual secretory products and waste substances. The pathways followed by this chemical circulation are called metabolic pathways.

Cellular factories, like chemical factories, require energy to support their activities. Many different mechanisms have evolved to generate this energy in relation with locally available sources. There are
heterotrophic
organisms and
autotrophic
organisms. The former derive their energy from the degradation, with oxygen (aerobic) or without it (anaerobic), of organic foodstuffs provided by other (
heteros,
in Greek) living beings. They use the same foodstuffs as building blocks for their biosyntheses. Such is the case for all animals, including humans, and for fungi and many microbes.

Autotrophs are divided into
photosynthetic,
which derive energy from sunlight, and
chemosynthetic,
which exploit mineral chemical reactions. Green plants and algae belong to the first group. Methanogens (
chapter 3
) are a particularly simple example of the latter. Autotrophs differ from heterotrophs by their ability to do without any foodstuff of living origin for their biosyntheses. Hence their name, which underlines the fact that they are self-sufficient (
autos
means self in Greek); they have no need for any other living organism. They use water, carbon dioxide, sometimes atmospheric nitrogen, and a few mineral elements that they extract from the soil. Their foodstuffs, when needed, are the mineral fertilizers, with, among others, nitrates as source of nitrogen, that gardeners or farmers provide when the soil is too poor.

Remarkably, this extraordinary diversity of mechanisms clusters around a bioenergetic core common to all living organisms and centered on a key compound designated by the acronym ATP (for adenosine triphosphate). This substance
also serves, with the help of appropriate transformers, as source of energy for the other forms of work—motor, electric, osmotic, informatic, and so on—carried out by living beings.

ATP is the
universal energy mediator.
It is sometimes replaced in that capacity by closely related chemical substances known as GTP (guanosine triphosphate), CTP (cytidine triphosphate), and UTP (uridine triphosphate). The four “NTPs” (nucleoside triphosphates) are also the basic precursors in the synthesis of ATP. One recognizes the four canonic bases—A, G, C, and U—already mentioned in the first chapter. This fact creates a bridge, of impressive significance for the origin of life, between energy and information.

Metabolic pathways are delineated by the agents that catalyze them. These comprise mainly the protein enzymes, already mentioned. A few natural catalysts are of RNA nature and are called
ribozymes
. To this catalytic armamentarium must be added a number of small molecules, called
coenzymes,
that, as their name indicates, play an essential auxiliary role in many enzymatic reactions. Coenzymes often contain a vitamin as active constituent. Several of them include in their structure a derivative of one of the NTPs mentioned above.

In turn, enzymes and ribozymes are synthesized, together with other cellular proteins and RNAs, according to blueprints stored in DNA molecules, subject themselves to replication, all of it being catalyzed, like everything that goes on in cells, by specific enzymes and ribozymes.

Most of the substances that participate in metabolism are involved in a dual capacity, as products of one or more reactions and as substrates (reactants) of one or more others. Those substances, called
metabolic intermediates,
or
intermediary metabolites,
link together the reactions concerned. As an example, imagine two reactions: one whereby substance A is converted into substance B, and another that converts B to C. Those two reactions are linked together by the intermediate B, product of the first reaction and substrate of the second: A→B→C. This is the start of a linear pathway that could be prolonged by reactions in which C leads to D, D to E, and so on. Things can be more complicated.

Thus, if a second reaction starting from B exists, leading to C', B becomes the origin of a bifurcation of which one branch leads to C and the other to C'. Things can be even more complicated, with, for example, substances other than A converging on B, or with reactions involving two different substrates issued from two different pathways, as is the case for most metabolic reactions, or again with intermediates participating in more than two reactions, and so forth. Such assemblages can lead to a vast, multidimensional network made of linear pathways, bifurcations, crossroads, stars, roundabouts, cycles, and even more complex configurations.

Cell metabolism constitutes such a network. Represented by the metabolic map, it is a single network in which everything holds together, with a few rare entrances for outside substances feeding into the network, and a number of exits leading newly synthesized cell constituents to their locations
in the cells, reserve substances toward their deposit sites, and waste products and secretory materials to the outside (
fig. 4.1
). Think of the road map of a country, with its limited entry and exit points at the borders. The complexity of the metabolic network, however, exceeds by far that of our densest roadway networks. Some of its crossroads, such as those occupied by coenzymes that participate in up to several tens of reactions, may form the starting and endpoints of as many distinct roads. L'Étoile in Paris, Piccadilly Circus in London, or Times Square in New York pale by comparison.