Chapter 3 - The Long March of Life
Imagine the entire history of the universe compressed into one year, with the Big Bang corresponding to the first second of New Year's Day and present time to the last second of December 31. This "Year of the Universe" was suggested by the late Carl Sagan (1934-1996) in his television series Cosmos. Using this scale of time, each month would result in a little more than a billion years. Important events would turn out distributed in approximately the following way (SAGAN 80):
|January 1st:||Big bang.||May 2nd:||Formation of the Milky Way.|
|September 9:||Formation of the solar system.||September 14:||Formation of the Earth.|
|September 25||Emergence of life.||November 1st:||
Emergence of sexual reproduction.
|November 12:||Emergence of plants.||December 16:||Emergence of invertebrates.|
Emergence of vertebrates.
|December 23:||Emergence of trees and reptiles.|
|December 24:||Emergence of dinosaurs.||December 26:||Emergence of mammals.|
|December 27:||Emergence of birds.||December 28:||Disappearance of dinosaurs.|
|December 29:||Emergence of primates.||December 30:||Emergence of hominids.|
|December 31, morning:||Emergence of humans.||December 31, afternoon:||Our days.|
Alexander Oparin (1894-1980), a Russian biochemist, had advanced the hypothesis that life would have developed by chance, through a progression of self replications of organic compounds, from the simplest to the most complex. His proposal was initially received with strong opposition on the part of biologists of the first half of the 20th century, who were still dominated by vitalistic
ideas.40 Since then, however, Oparin’s hypothesis grew progressively in experimental support, to the point that nowadays it is universally accepted by the scientific community. Two great scientific events occurring in 1953
contributed together to this change of opinion:
Stanley Miller, working in 1953 on his thesis at the University of Chicago with Harold Urey –a Nobel Laureate in Chemistry– managed to produce in vitro the basic components of every living matter. The young scientist submitted to heat and electric charges –simulating the Sun’s ultraviolet rays– a mixture of the gases supposed to have existed in the primitive terrestrial atmosphere –hydrogen (H2), methane (CH4), and ammonia (NH3)–, in the absence of oxygen and in the presence of water (H2O). After a few days, this mixture turned into a brown liquid, wherein floated around fifty prebiotic substances. Those substances included the alpha amino
acids41 (such as alanine and glycine),
formaldehyde,42 and cyanide43 in considerable quantities. This experiment has been replicated several times since, with variations in ingredients, widely confirming the original results. Interestingly enough, the same amino acids of Miller's Soup were found in the Murchison meteorite, fell in Australia, in similar proportions.
Such an experiment showed that the borderline between inert and living matter did not imply a qualitative leap, as many believed in those days. It conveyed a convincing empirical demonstration of what could be called the continuum of matter, which goes from its simplest embodiment, such as hydrogen, oxygen, nitrogen and carbon atoms, to its most complex one, starting with amino acids and proteins and culminating in the enormously complex networks of brain structures. It was an impressive experimental verification of the intuition of 17th and 18th century's thinkers, such as Thomas Hobbes and David Hume, who subscribed to the essential continuity of all nature.
The molecules produced by Miller’s experiment were found in similar quantities under the rotatory forms D (dextro) or L (levo).44 It is surprising, and in need of an explanation, that only L-form amino acids exist in living matter, with very few exceptions. Ribosomes,45 the assemblers of proteins, only recognize that form in amino acids. Everything seems to indicate that the L form was selected to fend off the assembly line from a combinatorial explosion. In any case, this limitation is a powerful argument in favor of the singularity of origin of all earthly living beings. For this and other reasons related to the universal character of life's chemistry, such as the uniqueness of the genetic language, scientists are convinced that all organisms living on Earth descend from a single ancestor, with basic characteristics fixed early in the history of life by natural selection.46
In primitive Earth, many and varied abiotic (i.e., inorganic) chemical reactions would have occurred. A protocell could internalize one of them, absorbing it as an additional activity of its own metabolism. For instance, if the abiotic reactive pathways A » B » C » D » E would have existed, a specific cell could begin internalizing the production of E starting from D. This would confer to it a selective advantage and –in passing– provoke a shortage of D, what in turn would put a premium on the internalization of the production of D from C. The process would be reenacted with respect to D, and so on. On the other hand, and always subject to selective pressure, some of these primitive beings would find advantageous letting other beings do the procurement of certain materials, rather than going through the trouble of producing them. On that basis they could exert predator or domesticating activities over those producers, saving time and energy. The first ecological system would have thus been established.
Mendel's discoveries in mid 19th century had made apparent that the characters of living organisms –such as the color and form of peas– were due to the action of pairs of determinants –currently called genes–, contributed one by the father and the other by the mother. Those experiments also showed that such determinants did not mix but were transmitted unaltered to descendants, in a random way and independently from each other. Such results remained unnoticed until simultaneously rediscovered by Carl Correns, Erich von Tschermak and Hugo de Vries in 1900. The science of genetics as such, however, would not emerge until the end of the first decade of the 20th century, when Thomas H. Morgan began to study the organism that would become the symbol of this science: the small drosophila, popularly known as the fruit fly. Morgan was able to demonstrate that the hereditary determinants were carried by the chromosomes, thanks to his direct observation of them within the relatively gigantic cells of the salivary glands of the small insect (Carlson, 1996).
In 1933, T.S. Painer confirmed the truth of chromosome inversions, duplications and reaccommodations, whose existence geneticists had been forced to assume in order to account for the results of their experiments. A new class of professionals, the molecular biologists, was thus born, its objective being to explain the essential phenomena of life by means of the properties of macromolecular components. Given the importance of proteins, material that both composes the cells and catalyses their biochemical synthesis, biologists of the 20’s had hastily jumped to the conclusion that they were the carriers of genes. This protein theory of the gene would persist until the 40’s. It began to falter when American microbiologist Oswald Avery showed that it was possible to transform the hereditary properties of a bacterium, the pneumococcus, by adding purified DNA to it. Gradually this substance began to replace the protein in the role of sustaining molecule for the genes (Morange, 1998).
The extraordinary discovery of the DNA structure occurred in the same memorable year as the Miller experiments. The British biophysicists Francis Crick and Maurice Wilkins, in conjunction with the American biochemist James Dewey Watson, managed to build a three-dimensional model of the molecule with the help of a photograph of X rays diffraction obtained in 1951 by Wilkins. This work, which earned the three of them the Nobel Prize in Physiology and Medicine in 1962, would lead to the deciphering of the genetic language. This team of researchers determined that the external part of the molecule is composed of phosphoric acid and a sugar (desoxyribose), as a linear repetitive structure of large extension. That part of the molecule is a kind of exoskeleton, serving to support the internal part which contains the genetic information. That content is an assemblage of four nitrogenous bases (adenine, thymine, guanine and cytosine), chained together in a succession of complementary pairs, kind of rungs in a spiral staircase. This structure was perfectly agreeable with the self-replicating properties of genes: the function of so big a molecule with regular –but not monotonous– constitution could not be other than codifying information. The hypothesis of a genetic code sprang forth, namely that there exists a correspondence between the lineal succession of DNA components (nucleotides) and the assembling of amino acids in proteins. Such a hypothesis, proposed by physicist George Gamow, was immediately accepted by Francis Crick, who succeeded in confirming it experimentally, discovering the genetic code, eight years later.
It is a remarkable historic fact that the 50’s of the past century witnessed the birth and development, practically simultaneous, both of computer science and molecular biology, two scientific revolutions which have hallmarked the second half of the 20th century. Both fields, in close alliance, still in creative turmoil at the beginning of the new century, are contributing to one of the most daring and fruitful research programs of all times: the sequencing and interpretation of the human genome.47 The parallelism of the two sciences is hardly surprising, given that computers and genomes both have a clear digital character. The computer, an industrial approximation to Turing's abstract "universal machine" which has radically changed our culture, is digital by design. As to genomes, neither the determination of the complete sequence of the first ones –those of bacteria and yeasts– nor the subsequent of the human genome itself, have revealed any trace of a non digital organization which could be in charge of coordinating the genes' actions. The genome is no-more-no-less than a set of genes, and these are nothing but digital combinations of nucleotides, the letters of the genetic alphabet. The fact that some of them act in collaboration, regulating each other, does not detract from their digitality: computer instructions do as much, as a matter of routine.
The DNA molecule is a truly elaborated construction of evolution. In all likelihood, its emergence was considerably posterior to the origin of life, whose subsistence and replication must have been supported at the beginning by a different structure, much less stable and efficient. The DNA enclosed in the nucleus resembles more to our backup disks kept away in a safe or a bank vault, than to the ever-changing information on the hard drives of our computers. Indeed, its essential function seems to have been from the very beginning the preservation of the identity of the species, as an authenticity criterion for the production and maintenance of bodily cells, tissues and organs of all the different types. RNA, on its part, which nowadays plays the subdued role of a messenger between DNA and proteins, must have been at the beginnings a one-man-show: owner, worker and constituent material of the incipient small business which primitive life must have to have been. So much so that Walter Gilbert has proposed the thesis that an RNA world did exist prior to the DNA one we live in today. This thesis has accrued high credibility thanks to the extremely important discovery made by T. Cech48 and S. Altman49 in the mid 80’s, namely that RNA is catalytic, i.e., capable of performing the function normally associated with enzymes. In fact, still today, the peptide bonds assembling proteins in the
ribosome50 are created without any participation of enzymatic proteins: the links among the amino acids are created by ribosomal RNA. It is logical to assume, therefore, that the “polymerase” of the RNA world must have been something similar to the RNA currently found in the structure of ribosomes. Thus, when proteins had not yet been invented, RNA must surely have catalyzed itself and, since DNA would have not appeared either, it would have constituted the whole of living matter at that distant time.
The first replicators, precursors of all living beings, must have been then small RNA strands. They would not have had a body, in the sense in which multicellular organisms do; in other words, genes had no need to express themselves, and no messengers were necessary to build proteins since there were no instructions to be read: RNA sequences replicated themselves directly, today messages being at that time the real thing. They had neither a protective nuclear membrane, nor even a cellular one, both defenses being considerably posterior inventions of life. The RNA chain was a factotum: replicable body, replicating tool, and pattern to be replicated. Its survival, both as individual and as species –since there where no such distinction then–, would have been extremely precarious. In fact, in all likelihood, the life phenomenon would have been erased entirely from the Earth –and produced all over again– not once, but many times. The one instance that would have finally stuck would have lacked anything homologous to the copying-error correcting machinery giving today stability to our sophisticated genetic-material repositories. Under such conditions, replication was random and crude, and genetic drift51 much wider and frequent than today's. However, that very situation should have produced many opportunities for some individual to arise with more stability and some degree of replication fidelity. When it did appear, it must have been immediately selected. It would have become the unique precursor of stable life and reliable replication; in one word, it would have been the singular individual referred to in scientific jargon as cenancestor.52
Let us place ourselves at the very beginning. We know that carbon and water did not originate at the Big Bang but much later, within the influence zone of supernovas, an widely extended region in the universe. The combinatorial properties of carbon are especially favorable to configure biologic material, whereas the quantum properties of water make it expand with the cold and float as solid in the sea. Without such conditions planets like ours would have never become what they are today. In addition, we know, through experiments such as Stanley Miller’s, that monomers were relatively easy to form in the early Earth. The four nucleotides of RNA undoubtedly synthesized themselves at the beginning in an abiotic way. On the other hand, the transition most difficult to explain in the origins of life is that from monomers to polymers, i.e., from nucleotides to RNA. The process can be represented as follows, where A and B are monomers and AB is obviously a dimer:
As we see from this formula, polymerization implies dehydration; it is a reversible chemical reaction. Because of Le Châtelier’s53 principle of mass action, in an aqueous environment dehydration goes against the grain. To be produced, it is necessary either to eliminate water or to incorporate energy. The easier of the two processes is to evaporate water, a common phenomenon occurring, for instance, in tide poodles. A shallow sea, before the Earth’s crust broke into plates, would have offered an ideal environment for dehydration and the subsequent transformation of monomer assemblages into polymers. Clays, abundant in our planet and favoring anhydride reactions, would have offered an ideal refuge where polymers, once constituted, could have been able to hide from water until reaching stability (Cairns-Smith, 1982). The first peptides must have formed abiotically, as we have seen, and the first polymers must have been of a minimum size, as lipids.54 This would have made possible the emergence of liposomes, lipid bilayers spontaneously sprouted from the mixture of water and oil. The existence of lipids would have allowed the entrance to a new stage in the foundation of life, as macromolecules adhering to a liposome would have become more stable –not too easy to disintegrate into its components. A stage of viable polymers would have been inaugurated, replacing that of frail and ephemeral polymers.
Up to now I have presented a summary of the standard theory about the first steps of life. In the following, in broad strokes, I will review some alternative theories, for the sake of completeness.
The clay world. According to Alexander Graham Cairns-Smith, the first organisms would not have used organic molecules as key components. He favor clays (the biblical “dust of Earth”?) over carbon derivatives. Subsequent processes would have transformed these low-tech beings into high-tech ones, with a different structure. Interestingly, he believes that primitive organisms would not have needed nucleotides or lipids but rather evolved to produce them. Beginnings usually include mechanisms later discarded. Think for instance, in the construction of a granite wedge arch: it must be supported with props during building, but once the structure is finished these scaffoldings can disappear without leaving a trace. This proposal agrees with the most general strategy of design: each subsequent stage is made easier and constrained by previous designs, precisely what we have called the accumulation of design (Cairns-Smith, 1982; Gutierrez, 1990).55
The thioester world.56 For Christian de Duve,57 in between the prebiotic stage and the world of RNA, biology must have been based on thioesters. Since they are substances born from the condensation of carboxylic acids with thiols, they offer an easy leap toward polymerization (Duve, 1990).
The peptide-nucleic acid world. Finally, it is appropriate to mention a recent “research advance” which accounts for the artificial creation of a precursor molecule for RNA, branded PNA (peptide nucleic acid). It is capable of supporting the bases in the same way as RNA does, with more stability, being also capable of assembling into a double helix. Unlike RNA, all its components can be generated directly in an abiotic system (Knight & Landweber, 2000). It just might have existed naturally at the dawn of life.
Proteins and the corresponding translation process from RNA to them, still operative today, must have been designed58 during the period of the RNA world. RNA would have existed then as a two-strand super molecule, one strand catalytic and the other a non catalytic complement, working as replication facilitator. The transit to DNA would have been justified by evolution as a way to ensure genome stability.59 RNA, more and more overcharged by its new function of enriching life with proteins, could be eventually discharged from its original one –to assure the continuity of the species–, passed on to DNA. This new macromolecule would still not be surrounded by a nucleus, as it is today in the case of multicellular beings, since such a device of genome protection will be invented much
later.60 It would be, though –most probably– already protected –along with RNA– by a cellular membrane.
The emergence of DNA required as previous inventions two novelties of great importance:
Another enzyme capable of removing the oxygen in position 2' from the pentose.62 This would have been required to make DNA sterile, in the sense of lacking catalytic ability. That ability of RNA depends precisely on the pentose having two oxygen atoms at that 2' position.
Any five-carbon sugar is called “pentose.” In this case, we are dealing with ribose, a monosaccharide sugar, which when losing the oxygen in question turns into desoxyribose (deoxidized ribose), as shown in the figure. The operation transforms RNA (ribonucleic acid) into DNA (deoxyribonucleic acid). The RNA object of the attack would have stopped being active –it would no longer be catalytic– but, at the same time, it would have acquired great stability, an excellent property for genome preservation.63 The RNA world and the new DNA world must have coexisted for a very long time, riboorganisms having disappeared only gradually.
It is possible that the transition between RNA and DNA worlds has occurred through the creation of a heteroduplex, i.e., a double band where the positive strand would have been RNA and the negative DNA. This arrangement would have offered the best resource to defend the genome from ribonucleases, the enzymes today in charge of destroying RNA messages floating in the environment, their mission of creating proteins already accomplished and not needed any longer. 64
Manfred Eigen65 has posed in relation with the DNA world a serious difficulty, based upon the fact that the original polymerases would have had to function with error rates so high that neither genome preservation nor its evolution should have been possible. By simple law of probabilities, a big genome –whose transcription errors would accumulate– would have had scarce chance of reproducing itself. This author concludes that RNA primitive genomes must have been small in size and prone to federate among themselves, rather than to enlarge through progressive assemblage. Polymerases would have had to undergo a long selection process to acquire better error rates and, only then, allowed for the existence of bigger genomes. However, the polymerases could have been selected only if the genome reproduced itself effectively, which is precisely the question. This thesis is confirmed by the fact that RNA viruses tend to be small and come often divided in several independent sections. As a solution to this paradox, Eigen proposes the idea of a hyper cycle: molecules of a group would reciprocally favor their replication, in a similar way to how politicians form alliances to support each other; for instance, A can act as primer for B, B for C, … N-1 for N. The result would be equivalent to a sort of large viable federated genome. Once better quality controls were obtained, the federation could finally compress itself into a unified genome.
Watson, one of the discoverers of DNA structure, has proposed, on his part, as a way out of this difficulty, the hypothetical existence of an early transitional ribosome, modification of an RNA polymerase preceding the ribosome existing today. The message would have been incorporated in the ribosome instead of being readable from an RNA messenger. Later on, the message would have gained independence from the reading machinery and the current multi-use ribosome would have begun to exist. Just as the hypothetical federated genome, the transitional ribosome could have been a solution for overcoming the paradox. Life, on the other hand, could very well have outsmarted us and solved the problem in a recondite alternative simpler way.
There is a consensus among contemporary scientists in postulating the common origin of all current living beings from a single ancestor, a well-consolidated replicator beyond prebiotic evolution and the instability of the purely statistical copying of RNA
strands.66 Such a primogenial ancestor, called cenancestor, would have existed about the middle age of Earth, some two billion years ago.67
In the 80’s, American microbiologist Carl Woese provoked a revolution in biology with his proposal to classify all living beings in three grand domains resulting from the speciation of such postulated cenancestor: archaea, bacteria, and eukarya.68 He supported his theory by a careful study of microorganisms, which led him to prove that animals, plants and fungi are more related among them than existing bacteria among each others (Woese, 1990). Notwithstanding the clarity with which the vision of the separate genomes of the three domains has been outlined, it is also accepted as a fact that there may have been gene migration between the domains, through means complementary to genetic transmission, commonly known as genetic crosstalk. 69
The accompanying tree represents the dominating view of recent years about the origin of the three domains. In it, you can notice the endosymbiotic absorption70 of the protobacterium that gave origin to mitochondria71 in animals and plants–an extreme case of genetic crosstalk–, just as that of the cyanobacterium, which gave origin to chloroplasts in plants. In the picture, microsporidia and giardia are also distinguished, two archezoans considered having diverged from the eukaryotic lineage before the acquisition of mitochondria.
Cenancestor would already have had the common characteristics of all current living beings, such as DNA genome, polymerases for DNA and RNA replication, divided ribosomes, universal genetic code, most of the metabolic features, and many of the properties of the cellular-cycle and growth regulation. The details of the large diversification in three domains (which of the three diverged first from the original stem, which later and under what circumstances) are still a mystery and perhaps always will be. Nevertheless, it is extraordinary that molecular-biology techniques, some of which will be described in the following section, have allowed us to learn so much and with so much detail about such tremendously distant events.
A friend of mine, with whom I was talking recently about those exciting topics, asked me why he should believe such phantasmagoria. The question was only natural.
We are dealing here with events from a far distant past, read-out from microscopic structures, our genes and those of other organisms. The answer is that we should believe in them because we trust scientific method. I offered him (and will offer my readers here) some comments on the tools used by researchers, as well as some results thereof, as an example of the way scientist manage such complex issues. Scientists follow, in their work, consciously or by instinct or training, a wise maxim attributed to Francis Bacon: look at the simpler to comprehend the more complex, as practitioners of all disciplines have done since the dawn of science. We already mentioned how Mendel performed his experiments with
peas,72 and how Morgan clarified important issues working with drosophila, the tiny banana fly. We will deal in this section with still some other examples of simple organisms employed by biologists to make general sense of the machinery of life.
Viruses are not living beings in the proper sense of the word: they are not self-sufficient. Rather than living beings they are spongers, they exploit living beings using their cellular machinery to replicate themselves. They are, so to say, parasite replicators. They have accompanied living beings since their origins, as is testified by the fact that some of them are made of RNA, not of DNA.
A bacteriophage (phage for short) is a type of virus that infects bacteria, for instance the Escherichia coli, inhabitants of our digestive system. It is composed of a very small quantity of genetic material enclosed in a protein capsule, and a syringe (normally called tail) to inject itself into the bacterium. In general terms, once the phage infects the bacterium, all synthesis of DNA, RNA or proteins of the latter stop, the phage's genome taking over to synthesize its own genetic material and proteins using the host's machinery. The different parts of the phage (genome, capsule and tail) get assembled into a large number of replicas; thereafter, the phagic lisoenzymes break the bacterial wall and deliver from one hundred to two thousand new phages per lysed cell to the environment. A. Lwoff,73 François Jacob,74 and Jean Monod75 discovered a phage, which they named lambda, in the water of a drain gutter of Paris, in 1940. This phage is a DNA virus, quite big when compared with other viruses. The phage genome, of a linear type, circularizes itself after injecting into the bacterium. It has two particular places –called COS– where the DNA is cohesive, being formed by opposite non complemented double strands;76 as soon as these places get in contact, circularization of the genome is produced.
One of its interesting features is that the phage can exist in the cell in either of two different states: reproducing itself massively, with the resulting breaking-up of the bacterium (we say that the phage is in a lytic phase)77 or embedding into the bacterial chromosome (we say that it a lysogenic –“breaking producing”– phase). The phage dormant in the host's genome can wake up later from its lethargy (after having eventually reproduced itself with the host cell) to enter the virulent lytic phase. The probability of taking either of the two courses are 1% for becoming incorporated into the bacterium genome, and the remaining 99 for destroying the bacterium. If the decision is to incorporate itself, a ligase of the host takes charge of carrying out the splicing into the bacterial genome. The phage itself catalyzes the recombining reaction.
The phage genome enters the bacterium with all the genetic material to fend for itself: control and replication genes, genes in charge of building head and tail, and genes for breaking the bacterium membrane. The most interesting among them are the regulatory ones: operators, promoters, and repressors, all interacting with each other, with other kinds of genes and with the appropriate proteins, in the best style of corresponding routines in a computer program. The main result of those interactions will be the production of either one of the two phagic phases. The gist of the matter is the competition between a repressor, called CI, and a protein, called CRO. The latter promotes the lytic phase and thus the destruction of the bacterium; it almost always wins. The repressor, on its part, promotes the lethargy or embedding phase; it rarely wins. The battle is decided78 based upon the nutrition state of the host: if it is good, rupturing the bacterium is favored; if deficient, the embedding phase takes over, preserving and reproducing the bacterium (and and the phage), waiting for better times.
There exists in the E. coli bacterium a DNA sequence known as “fertility factor” or “F factor.” It is a plasmid, i.e., a small genome distinct from the chromosome, capable of reproducing independently by means of the rolling circle technique79 and of injecting itself in another cell, usually of the same species. It occasionally embeds itself into the chromosome, in a similar way as the lambda phage does. At some other times, when injecting itself in another cell, it takes with it the chromosome to which it is blended, producing the formation of a merodiploid, a bacterium with more than one chromosome. Plasmids probably constitute an adaptation for unpredictable environments, allowing the bacterium to acquire genes which may be useful in emergency situations. They constitute, in the case of unicellular beings, a way to acquire variety, function much more effectively accomplished in the case of complex organisms through sexual reproduction. Plasmids, although they are not true organisms in the proper sense, serve us as models to study functions that occur in complex ones, on the basis of their genetic autonomy and operating flexibility. Their special powers have been exploited by molecular biology and engineering, using them as vectors to add extra genes to a species.80
The drosophila fly is a truly respectable model organism, whose well-defined brain is already endowed with some 20,000 neurons. The most interesting aspect of the fruit fly, however, lies on other aspects of its structure. We already dealt with the size of its chromosomes in the salivary glands, which allowed their study early on in the history of genetics. The subject we will be dealing with here is the discovery of a body plan in animals. A repetitive structure in the drosophila larva, called imaginal disk, is capable of giving rise to organs other than the ones normally produced, if artificially transferred somewhere else in the body. Thus, for example, one can obtain a leg where an antenna was expected or, instead of an eye, get a genital organ. When moving a piece of material (the imaginal disk) to some other relative place within the larva, sometimes the material imposes itself to the place for the determination of the result; in other cases, the opposite occurs: the place imposes itself over the material. It has been possible to establish maps of these transdeterminations that show which transformations are possible and which are not.
Experiments of this kind have led to the discovery of the homeotic genes. They constitute the developmental guides, representing the basic physical framework of the organism structure. This can be experimentally demonstrated by means of producing artificial alterations in hereditary DNA. In many cases, these transformations have very similar results to those of imaginal transdeterminations. The drosophila has two homeotic clusters: thoracic and abdominal. The order of the genes in the DNA strand follows the anteroposterior sequence of the larva's body. A gene exists for each segment, starting from the first thoracic segment. If any of the genes is missing, the next structure will be a repetition of the previous one. The second thoracic segment is the default value, producing wings and legs. The corresponding gene is considered the ancestral, from which the others must have emerged through duplication81. Each homeotic gene has a HOX box, namely 160 pairs of bases codifying a protein domain of 60 amino acids; it is a control domain destined to stick to the DNA as a means of controlling development through a cascade of gene expression.82
All insects have homeotic sequences similar to those of the drosophila. Things go far beyond that: a system of gene expression patterns, which comprises the genes of the HOX box and other similar genes, encodes the relative position of the body parts in all animals. In all likelihood, this system is very conservative, probably already existing in the common ancestor of all organisms of the kingdom. J. M. W. Slack and his collaborators have proposed to call it “zootype,” and take it as criterion for deciding whether a living being is an animal. The zootype is simply a positional information system and does not necessarily encode specific structures (Slack, 1993).
Caenorhabditis elegans is a nematode, small but visible to the eye, whose simple development makes it a model organism. It throws light especially upon apoptosis, the self-death program of the cells.83 Its genome contains 19,099 genes, consisting of 38 megabases assembled into five chromosomes. The germinal cell, after 528 binary divisions, gives rise to a hermaphrodite worm inside an egg. Once this egg brakes up, and after several more cellular divisions which make it go through shedding and larvae stages, it acquires maturity and begins to lay its own eggs. Specialized genes govern apoptosis for the “sculpting” of a 1064-cell adult, in a similar way as the hand is sculpted in human beings starting from the primordium, a primitive fetal organ containing more cells than the hand.
C. elegans' celles are determined by their lineage rather than by their physical relative location. One of these lineages is the germinal line. The nervous system comes from another of the precursor cells and is formed by 302 sensory, motor or inter neurons, connected by a total of five thousand synapses. A node in the neck with the shape of a ring functions as a proto brain. Sensory neurons have cilia that act as sense organs. There are eleven pairs of olfactory sensors capable of discriminating hundreds of smells, for instance, the ODR-10 (for “odor”) identifies the diacetil molecule. C. elegans is the first known organism susceptible to habituation: in the presence of a tactile stimulus it withdraws, but with each repetition it withdraws less and less, provided the stimulus is not traumatic. Furthermore and remarkably, habituation can be conditioned by an aversive stimulus of light or sound (vibration).
There are two different vines of C. elegans: the solitary and the gregarious, predicates that qualify their attitude exclusively during feeding, since both vines produce solitary individuals at all other times. The difference between the two vines is marked by two alleles84 from the same gene.
Another tiny organism, the mollusk Aplysia California, is neurologically more complex than C. elegans; it has twenty thousand neurons. Its importance as a model lies on the fact that it is possible to physiologically dissect it and isolate each of its proteins.
If life is one, we may find many lessons concerning our own genome by examining the genome of not only organisms from our own kingdom but also from different kingdoms, such as plants. That has been a dominant reason to undertake the sequencing of a model plant at the same time that the larger task of the sequencing of the human genome. The chosen plant was Arabidopsis thaliana. Its genome, formed by only 366,000 kilobases, was found to contain around twenty-four thousand genes. Some sequences are being compared –used as probes to search for correspondences– with genomes of better-known species. This allows the discovery of their functions. Such method has already identified homologous genes, some of them related with human illnesses. Thus, for instance, defective ear-cilia genes, causative of certain types of deafness, have been identified which –naturally– have other functions in plants, still unknown. It seems to be a rule of life that, as in music, equal themes usually produce contrsting effects in different contexts.
Plants are characterized, in comparison to animal species, by an abundance of DNA. Part of the explanation of this fact is their frequent polyploidy85. Another reason is the existence of organelles, particularly the abounding chloroplasts, which –just like mitochondria existing also in animals– possess their own DNA.86 In addition, plants have a larger quantity of non codifying DNA, such as pseudogenes, introns, transposons87 and other similar beasts. Finally, numerous “gene families” occur in plants as result of ancestral repetitions, much vaster than those found in other organisms. All these phenomena, also present in the human organism, are more easily observable and manipulated in plants, particularly in this interesting model organism, obviously an ancient relation of ours.
We all have had the voluptuous experience, in a bright summer day, of reclining against the strong stem of a tree and, looking up, admiring the extraordinary richness of its recursively bifurcated branches. There cannot be a better representation of the course and result of the evolution of living beings. Starting from its root in the prebiotic world, the tree of life has spread itself out, creating at each step a binary division originator of a new degree of variety. We may conceive each one of those divisions as the result of a very specific invention, simple in itself but full of consequences for the future. Just as in the history of human culture, each small invention, once settled and adapted to different uses and situations, serves as foundation for further inventions, equally simple and full of future possibilities. Let us recall that all this has been happening gradually, by the force of the natural-selection algorithm, thanks to an accumulation of design in no need of a conscious designer88 or some preexisting plan. Life itself rehearses possibilities based on the fact that, throughout generations, accidental differences produced in different replicas of the same genome create opportunities for a richer variety. It is the environment of populations that, blindly but intelligently, punishes the unfavorable mutations and rewards with lavish descent such changes that constitute successful innovations. Let us examine some of the most transcendental of these turning points occurred since life consolidated itself at the level of unicellular faithfully-reproducible beings.
The nucleus was originally invented through invagination of the external cellular membrane. Observe in the figure the double membrane at the moment of closing the nucleus; the double wall that connects the internal and external membranes will disappear later on. This invention creates protists, the group of organisms comparatively simple but already complexer than bacteria since it already possess the elemental features of plants, animals, or fungi. The invention transforms them into eukarya, according to the classification stated
before.89 They are still composed of only one cell, just as bacteria; unlike them, their DNA is sheltered by an internal membrane in a reserved space inside the cell. Such a garrison is extremely advantageous, protecting the genetic endowment and being instrumental in the extraordinary proliferation of the populations which happen to enjoy it. In fact, their fast multiplication produced a large variety of life in innumerable forms and styles, adapted to many different kinds of environments. However, and in spite of their similarities with more evolved eukaryotes which will appear later, protists continue to lack tissues, for their being still unicellular.
Protoplants, protists predecessors of plants, can produce their own food by means of photosynthesis, thanks to their internal symbionts,90 chloroplasts. Protofungi, on their part, extract the food from their surrounding environment but, unlike plants, are incapable of absorbing the solar energy, due to their lack of chloroplasts. Protozoans, the protists similar to animals, have no chloroplasts either, even if they possess the ability to look around for food, impelled by flagella. They feed themselves above all by predation of other unicellular beings, especially their ancestors lacking nuclei, bacteria. There are more than 20,000 known protozoan species,91 some of which form colonies, falling short of becoming multicellular organisms. Many of their species are aquatic, part of the ocean plankton. Others constitute parasites of plants and animals (human being included), with which they tend to establish symbiotic relations, beneficial to both life forms. All protists –protoplants, protofungi or protozoans– contain already in their cytosol large quantities of mitochondria.92
Protists invented93 differentiated expression. A representative example much studied occurs among unicellular yeasts (a kind of protofungi). Its unique cell can appear in three different varieties, within the same species. It is a differentiation in time; it could not possibly differentiate in space since there is only one cell per individual. Two of these varieties (the a and the alpha types) are haploid, like the sexual cells in our species; the third variety is diploid, a conjunction of the other two genomes (a/alpha type). Meiosis, which transforms this diploid cell into two haploid spores, is caused in its case by stress stimuli. In favorable circumstances, in compensation, the two diploid variants tend to couple up, so as to form once again the diploid variant. Thus, although all genes are present in the three variants –which makes them one and the same species–, their expression is discriminated as result of environmental influence. The mechanism for such reversible transformation depends on a gene which, when expressed, suppresses meiosis. This gene does not express itself in the haploid variants, being blocked by a protein; in the diploid one, this protein suppressor is, on its turn, blocked by still another protein. This mechanism of blockage and counter blockage is a regulation technique often found in genetic expression of higher organisms.94 It constitutes the marrow of one of the most transcendental invention of evolution: differentiated general gene expression.
Sponges (phylum Poriphera) constitute the simplest and first of multicellular animals. Though they already possess tissues, no organs are recognizable. Most sponges are marine animals but they can also be found in fresh water. They live glued to a substrate and feed themselves by the passing of water through their body's pores, during which they extract food particles with their flagella. Although they do not yet have a nervous system they do react to stimuli. Their elemental skeleton is composed of fibers and minerals. Some forty-eight thousand species exist. The invention that gave origin to this first metazoan includes the export95 of an extracellular matrix capable of supporting cells in a relative steadfast position. Such support is a necessary condition for the transition of a simple colony of unicellular creatures to a multicellular organism. However, it is not a sufficient one; a physiological coupling among the different cells is also necessary, essentially constituted by an intercellular exchange of chemical signals.96 This active coupling constitutes the effective criterion to decide about multicellularity of an organism. Such a remarkable invention, the tight socialization of same-species cells, must have occurred around six hundred million years ago. Conjoined with a revolutionized use of the previous invention (differentiated gene expression), it will radically determine the whole later course of evolution by opening the door to the existence of higher organisms, humankind included.
The differentiated expression of genes, invented by protists, accedes –given multicellularity– to a new field of application of incalculable projections. Merely successive differentiation (transition of a form of gene expression to an alternative one at a different time) will be joined by the much more powerful simultaneous different expression of the same gen set in spatially separate groups of cells. Basically, in multicellular organisms, not all genes will be expressed in all parts of the body. Some of them will remain silent, particular ones in different regions. Hence, different collections of proteins will be produced in each region, giving rise to diverse kinds of tissues and varied organs and systems of such, all over the body.97 This new kind of gene expression, much more complex than the preceding one, will be instrumental in the immense variety of features and conducts which began to characterize species of all kingdoms of life starting from the biodiversity explosion of the Cambrian era.
According to these erroneous conceptions, living cells would have some factor (referred to by the French philosopher Henri Bergson with the poetic name élan vital –French for 'vital impulse'–), not reducible to physicochemical elements.
Note 41: Constituents of proteins, the essential blocks of life; so called for their having an amino function in the atom at the alpha position within the molecule.
Note 42: CH2O, the simplest aldehyde.
Note 43: HCN, hydrogen cyanide, also known as prussic acid, extremely poisonous.
Note 44: A substance is said to be levo-rotatory if it possesses the property of making the polarization plane of light revolve counterclockwise. It is dextro-rotatory if it rotates clockwise.
Note 45: See Appendix J: RIBOSOMES.
Note 46: See this chapter, THE CENANCESTOR AND THE THREE DOMAINS OF LIFE.
Note 47: See Chapter 5, THE SEQUENCING OF THE HUMAN GENOME.
Note 48: North American biochemist, a winner of the Noble Prize in Chemistry in 1989, along with S. Altman, for his discovery that RNA is capable of catalyzing chemical reactions, as proteins do too. In 1982, Cech discovered that a particular messenger RNA was capable of catalyzing itself in order to eliminate its non encoding part (intron) without the intervention of protein enzymes. He hence called this substance “ribozyme.”
Note 49: Canadian chemist who shared the Nobel Prize with Cech for having confirmed the discovery by means of independent experiments. Altman had discovered in 1983 an enzyme composed of both proteins and RNA, noticing furthermore that the protein component could not perform the reaction acting by itself. Isolated, the other component proved it could perform the reaction by itself. The agreement between Altman’s and Cech’s works was able to convince the scientific community about the validity of a theory which would revolutionize molecular biology and the explanation of the origins of life.
Note 50: See Appendix J: RIBOSOMES.
Note 51: See Appendix c: MUTATIONS AND GENETIC DRIFT.
Note 52: Unicellular construct postulated by molecular biologists as a theoretical necessity to make sense of the tree of life. See this chapter, THE CENANCESTOR AND THE THREE DOMAINS OF LIFE.
Note 53: Principle formulated in 1888 by Henri Louis Le Châtelier, French chemist who contributed to the study of thermodynamics. According to this principle, any change in the pressure or temperature of a component in a system at equilibrium has little effect, since it is compensated by an automatic adjustment of the other contributors to the configuration.
Note 54: Glycerol and fatty acid compounds, a diverse group of essential substances for the construction and operation of living beings. They differ from other types of compounds in that they do not dissolve in water but rather in alcohol, ether, and other organic solvents.
Note 55: See Chapter 1, THE ACCUMULATION OF DESIGN.
Note 56: A thioester bond is obtained by eliminating one water molecule while joining a thiol function (SH) with an acid function (CO2H) (Maugras, 1996).
Note 57: Belgian cytologist and biochemist. He received the Nobel Prize in Physiology, together with Albert Claude and George E. Palade for describing the structure and function of cell organelles.
Note 58: Although in our effort to be clear, we sometimes resort to metaphors or analogies, we must warn you that in this case we are not using one of them. Evolution designs are genuine designs, even if there is no personal designer responsible for them. We are aware that this way of presenting things amounts to a proposal for vocabulary reform, but it fulfills the conditions that credit such resource, namely: it preserves old usages while facilitating a new one which dissolves uncomfortable enigmas.
Note 59: By genome we understand the set of genes which give identity to the species. The genome of heavily evolved beings contains today more than that, since the ups and downs of evolution have added to it large quantities of non coding DNA –unfit to be read as instructions.
Note 60: This hypothesis is supported only by the parsimony principle: if DNA had been designed after the appearance of the nucleus, it would have needed to be created at least twice, since there are organisms with DNA and no nucleus; or else, the nucleus would have had to disappear in some types of organisms. The hypothesis with fewer steps is preferred, although it might be refuted later on the basis of new evidence.
Note 61: Reverse transcriptase, as the one that RNA takes today from a virus intruded in the cell. The RNA copies that virus into the nuclear DNA, where from it proceed to reproduce the virus, eventually destroying the cell.
Note 62: Ribonucleotide reductase, capable of reducing (removing oxygen from) ribonucleotides. Notwithstanding its impressive name, it is a very simple enzyme, consisting of only one monomer.
Note 63: The substitution of uracil for thymine would occur by a later design.
Note 64: Be aware of the fact that at this point we have entered the DNA world and RNA is accommodating itself to its new major role of messenger for the genomic DNA.
Note 65: German biophysicist, 1967 Nobel laureate in Chemistry, together with Ronald G. W. Norrish and George Porter.
Note 66: Replication at that time produced a population similar to the old one only in a certain proportion. Species would have had only blurred identities, error-repairing routines not existing yet. It is worth noting that the transcription of DNA onto RNA –necessary for the creation of proteins– lacks a quality control even today.
Note 67: According to this theory, the most ancient fossils found today (the stromatolites), approximately three thousand eight hundred million years old, would have still belonged to the RNA world.
Note 68: Bacteria and archaea were classified up to that time as “prokaryotes”, a term that has been abandoned for not corresponding to any genuine natural group.
Note 69: In general, phylogeny has always been complemented with the (import and export) commerce of genes. Two species distant from each other often appear with similar, even almost identical, genes. The only reasonable explanation is that they must have traded genes. The mechanism of those transfers has been proven in multiple cases. Let us quote here three of them: an agrobacterium “colonizes” a plant by introducing in it a vector that invades its genome and makes it produce its own genes. Similar mechanisms are used by the lambda phage and the F factor, topics which we will deal with later on.
Note 70: See Chapter 4, ENERGY GENERATION IN THE CELL.
Note 71: See Appendix L: MITOCHONDRIA.
Note 72: See Appendix A: MENDELIAN INHERITANCE.
Note 73: French microbiologist, a winner of the Nobel Prize in Physiology and Medicine in 1965, along with Jacques Monod and François Jacob. The three researchers from the Pasteur Institute in Paris were awarded the prize in recognition to their discoveries concerning genetic control of enzymes and virus synthesis.
Note 74: French biologist and Nobel laureate, he studied the way in which DNA and RNA transfer genetic information and researched the genetic control of embryo growth.
Note 75: French biochemist and Nobel laureate who discovered the operon system that controls genetic action in bacteria.
Note 76: French biologist and Nobel laureate, he studied the way in which DNA and RNA transfer genetic information and researched the genetic control of embryo growth.
Note 77: From 'lysis,' destruction of a cell.
Note 78: The use of metaphorical language should not mislead the reader. We are allowed to use it to discourse about scientific subjects, provided we know what we are doing. The following question from a student in Professor Pedro Leon’s graduate seminar, where I became acquainted with these matters, was perfectly normal.
–How does the system know the state of the bacterium in order to decide?
The answer alluded to a universal signal used by these processes, the presence of cAMP (cyclic adenosine monophosphate), which offered the scientific solution to the problem. The instructor did not correct the way in which the student formulated the question since, at his level of learning, he could not possibly be still thinking in terms of a homunculus –a dwarf magically endowed with consciousness to know and to decide– at the bottom of biological processes. His scientific principles firmly entrenched, he was just indulging in a handy turn of speech in order to concisely formulate a relevant question.
Note 79: See Appendix I: THE AMAZING REPRODUCTIVE METHOD OF THE LAMBDA PHAGE.
Note 80: See Chapter 5, GENETIC ENGINEERING.
Note 81: See Chapter 5, ARCHAEOBIOLOGY.
Note 82: Gene expression, as we have seen, is the translation of genes into proteins. When these fulfill the function of sticking to a gene in order to activate it, as a way to enable it to produce another protein, and this on its turn sticks to another gene with similar objective, and the cycle repeats several times, we speak of a gene-expression cascade. It is one of the characteristic formats of genetic regulation. It is extremely powerful, as will be appreciated by those readers experienced in computer programming, where similar control cascades are used in the design of particularly complex algorithms.
Note 83: See Chapter 6, ON HOW DEATH SCULPTS LIFE.
Note 84: See Appendix F: ALLELES.
Note 85: A type of event in which the number of chromosome copies for a species is greater than two, considered the normal number. This anomaly is due to the fact that a complete set of chromosomes does not separate in meiosis, producing a gamete with double number of chromosomes. Polyploidy is the only known process through which a new species can be born in just one generation. Viable and fertile polyploids are known only in hermaphrodite organisms, such as most plants with flowers and some invertebrate animals.
Note 86: Chloroplasts are exclusive of plant and algae cells. They are responsible for photosynthesis and the green color of these organisms. Just like mitochondria, illo tempore they constituted independent beings.
Note 87: Transposons are unstable elements, fragments of DNA susceptible of moving over the genome. They are composed of two short sequences, repeated and inverted, which frame the necessary genes for their motility and codify for a transposase, an enzyme in charge of operating the transfer of the sequence, together with some other proteins. Transposons constitute half of the human genome, having been incorporated in it in ancient times as retrovirus (whose RNA acts “backwards,” producing the DNA that incorporates them to the genome of the host). Transposons were originally so harmful that they became subject to an intense selection during meiosis, with a multitude of mechanisms contributing to neutralize them. In general, they are now inert, having lost through mutation the sequence that codifies the transposase. However, they may operate again (jump) if the transposase is produced in the environment for any other reason.
Note 88: See Chapter 1, THE THEOLOGICAL ARGUMENT OF DESIGN.
Note 89: See this chapter, THE CENANCESTOR AND THE THREE DOMAINS OF LIFE.
Note 90: See Chapter 5, THE CELL'S POWER PLANTS.
Note 91: Familiar examples of protozoans are paramecia and amoebae.
Note 92: See Appendix L: MITOCHONDRIA.
Note 93: The reader should already be aware that my choosing of the word 'invented' here, referring to novel designs of life, is intentional. It underlines the characteristics of both creativity and automaticity of natural selection, the mother of all algorithms introduced and grounded in A CONTEMPORARY TRINITY.
Note 94: And, again, in highly complex computer programs.
Note 95: Another example of export, less important but more easily recognizable, is that which produces hair in higher animals.
Note 96: See Appendix K: INTERCELLULAR SIGNALS.
Note 97: Successive or temporal differentiated expression will continue to exist, though, and will acquire extraordinary importance. For instance, it will rule the different stages through which the organism passes during development, creating the all-important distinctions among intrauterine, childhood, and adult live stages.