Regenesis

CHAPTER 1

-3,800 MYR, LATE HADEAN

At the Inorganic/Organic Interface

What follows is the greatest story ever.

It’s the story of a once invisible being, nameless for eons, now called “the genome.” Its being—its existence across time, its depth and complexity as a natural artifact, and the vast abundance and variety of its manifestations—is the story. It is ancient and modern, older than our oldest ancestor and yet fresher than a newborn baby. It has covered our planet with its descendants, now over a billion times a billion times a billion copies (10²⁷).

The tale of the genome involves more sex than the most pornographic novel imaginable. The narrative is replete with incredible action scenes, countless life-and-death struggles, wild improbabilities that turn out to be true, and overwhelming successes in the face of staggering odds. It is a story about families and universal truths. In the retelling, it becomes, in part, your own personal story. The tale reveals a vibrant past and may lead us to a better future. As the ultimate self-help manual, it offers better health and longer life, along with “descendants as numerous as the stars in the sky and as the sand on the seashore” (as in the Judeo-Christian-Islamic tradition), or “as numerous as the sands on the Ganges” (in Buddhism).

As befits the greatest story ever, this is a multiplex tale, enacted and told in a spiral of understanding. Through its abundance, fidelity, and diversity, the genome adapted to the physical world, solving a small number of basic problems repeatedly, passing on the answers, and occasionally even rediscovering solutions once lost. We see these problems solved in the first instance biologically, by the process of evolution. Nature turned inorganic materials into organic substances. Natural organisms read and interpreted genomes. And natural organisms have created huge amounts of genetic diversity. That network of natural interactions comprises our first tale.

It begins long ago, in the Hadean era.

Can Organic Arise from Inorganic? Selection Among Atoms and Molecules

The Hadean geologic era lived up to the image of an underworld inhabited by the ancient Greek god Hades—lifeless and full of hot lava—3.8 billion years ago. If a living cell were unfortunate enough to travel back through time to the Hadean landscape, it would be cooked: all water vaporized and its precious complexity of living stuff dry-roasted and then mineralized, turned from delicate, filmy proteins into charcoal (graphite), water vapor, and other waste products.

Before this, all the way back to the big bang, the universe was made up almost entirely of hydrogen nuclei, the simplest of all elements, consisting of just one proton. These protons would collide and fuse together to form helium nuclei (2 protons). Inside stars these helium nuclei would in turn fuse to form carbon (6 protons). Carbon nuclei would then enter a cycle (the carbon-nitrogen cycle), taking in hydrogen, and by adding nitrogen (7) and oxygen (8) intermediates, would catalyze the formation of yet more helium. The new helium would, as before, make more carbon. The net outcome of all this is that in hot stars carbon catalyzes the formation of copies of itself. (By “catalyze,” I mean causing or accelerating a reaction without the catalyst itself undergoing a permanent change.)

These thermonuclear transformations, which occur at Hades-plus temperatures within stars, are accompanied by the release of enormous amounts of energy in the form of radioactive particles such as gamma ray photons, positrons, and neutrinos. (And also of course by the heat and light that drive life on this planet.)

The processes that make up the carbon-nitrogen cycle can be thought of as a form of natural selection for favorable reactions and stable elemental forms (atoms and their isotopes). This seems analogous to the mutation and selection of living species, and still later the mutation and selection of synthetic organisms. Today those five (hydrogen, helium, carbon, nitrogen, and oxygen) of the eighty stable elements are the most abundant in the universe. These processes selectively skipped over weakly represented lithium (3), beryllium (4), and boron (5).

A list of such atomic elements (substances that chemically cannot be broken down further) is a prerequisite for understanding the next level of selection complexity—the combination of those basic atoms into the compounds (molecules) of nature. Antoine Lavoisier wrote the first comprehensive list of the elements in the first modern chemistry text, Traité élémentaire de chimie, in 1789. He listed thirty-one in all, together with light and “caloric” (heat), making up a total of thirty-three “simple substances belonging to all the kingdoms of nature, which may be considered the elements of bodies.” As Lavoisier presented them:

Each element in the table above is followed by the abbreviation that is commonly used in most branches of science, and even within the general culture—for example, H₂O (water), NaCl (salt), and CO₂ (carbon dioxide). Jöns Jakob Berzelius, who developed an interest in chemistry in medical school, introduced these symbols in 1813. By 1818 he had measured the masses of forty-five of the eighty stable elements. As we will see in Chapter 3, as few as six elements may be sufficient to create the major molecules of life: S, C, H, P, O, N (sulfur, carbon, hydrogen, phosphorus, oxygen, and nitrogen—pronounced “spawn”—shaded gray in the table above). These constitute the most abundant elements in living systems; also needed are metal ions such as magnesium (Mg) that are involved in key reactions of these compounds.

These elements chemically combined with one another to form molecules, such as water, as the newly formed earth cooled. How did life arise from nonlife? To understand this, we need to explore the universe of simple, nonliving chemicals. As far as we know, the physical and chemical properties of the elements are set largely by particles in the nucleus (as well as by those in the surrounding electron cloud), and not by the specific arrangement of those particles. For example, it matters only that there are six protons in carbon; the exact structural relationships among the protons are irrelevant. Those six protons, irrespective of how they are arranged in the nucleus, attract and retain an equivalent number of electrons in the surrounding electron cloud.

In molecules, by contrast, the physical arrangement of the component atoms is crucial. For example, a molecule of water, H₂O, is not just ten protons and ten electrons packed together randomly in a jumble. The order of the atoms and their shape matters. Water is not H-H-O but rather H-O-H, meaning that each hydrogen atom can only bind to the oxygen atom, and not to two atoms. Molecules are like intimate social networks. Some atoms, such as hydrogen, tend to make single bonds with only one other atom. Oxygen makes two bonds, nitrogen three, while an atom of carbon can bond with four other atoms. So, water has each hydrogen bonding with one atom, oxygen, and its oxygen bonding with two atoms.

Let’s now replace each hydrogen in water with a carbon (keeping each carbon happy with its own three hydrogens): this will give us dimethyl ether, CH₃-O-CH₃. So let’s check the bonds. The oxygen still has two single bonds—one to each carbon—and each carbon has four single bonds, three to hydrogens and one to the central oxygen.

Now we can illustrate the importance of spatial arrangement. If we keep all nine component atoms but rearrange them slightly, say to CH₃CH₂OH, we get a radically different set of physical and chemical properties in a molecule called ethanol.

What a difference that simple rearrangement makes! Dimethyl ether boils at -24 degrees C while ethanol boils at +78 degrees C. Many people like to drink ethanol (typically 8 to 15 percent in water), but you would not want to drink dimethyl ether. These rearranged molecules are called isomers of each other (Greek for “the same parts”). Ethanol is an isomer of dimethyl ether: each molecule has two carbons, six hydrogens, and one oxygen, but differently arranged.

Berzelius came up with the concepts and terms for catalysis, polymer, and isomer, among others. He also provided experimental evidence for the law of definite proportions (first stated by the French chemist Joseph Proust), which holds that the proportions of the elements in a compound are always the same, no matter how the compound is made. Even though we have been introducing these ideas by appealing to the simple bonding of discrete atoms, Berzelius discovered them by doing two thousand analyses over the course of a decade, purifying and weighing chemicals and their reaction products. He noticed that the ratios were reproducible and generally came in values that were expressible in whole integers. Berzelius was also the first to recognize the difference between organic compounds that were derived only from living matter, and all other chemicals, which he lumped together as “inorganic.” This distinction contributed greatly to our understanding of life and set the stage for inquiries into vitalism, the theory that life and its processes are not reducible to the laws of physics and chemistry. Berzelius believed that something kept living matter distinct from nonliving matter. But work done in four areas—the synthesis of urea, the investigation of mirror molecules, the investigation of polymers (especially of the DNA/RNA polymers), and the self-reproduction of molecules—argues to the contrary.

Berzelius’s protégé Friedrich Wöhler also came to chemistry through the study of medicine. In 1828 Wöhler (accidentally) became the first person to synthesize an organic compound, urea, from an inorganic substance, ammonium cyanate. The reaction in question is NH₃HNCO → NH₂CONH₂. This is a rearrangement of atoms similar to that of the isomers mentioned above. But at the time it was more mysterious, in part because the description of chemicals as precise arrangements of atoms was just becoming evident from experiments. Second, urea was thought to come only from the urine of certain vertebrates as well as, less obviously at the time, other species. Ammonium and cyanate were considered to be inorganic components of minerals.

Wöhler’s synthesis of urea was arguably the first great challenge to vitalism. Since then, scientists have tried to make ever more complex organic living systems from inorganic or otherwise simple nonliving atoms and molecules. With hindsight, urea was a very simple case (consisting of just eight atoms of carbon, hydrogen, oxygen, and nitrogen) and was thus poised for success in this first of five grand challenges to vitalism—all of which reflect milestones in practical synthetic biology as well.

The second challenge to vitalism concerns the phenomenon of the handedness of molecules—one of the distinguishing features of living systems. The challenge is to determine whether natural single-handedness can arise spontaneously or be reversed, and if so, what the consequences would be.

The chemistry of life is based on polymers made by linking monomer molecules together in long linear sequences, just as written texts are made of linear sequences of letters. These two terms share the common root “mer,” from the ancient Greek meros for “part.” A monomer, accordingly, is a single molecule (one part), whereas a polymer (many parts) is a molecular structure composed of many similar molecular units bonded together. Amino acids are monomers whereas combinations of them are polypeptides (a.k.a. proteins), which are polymers. The large molecules known as RNA and DNA are also polymers—polynucleotides—consisting of many simple molecular subunits known as nucleotides. Those three types of polymers can bind and catalyze the formation of other polymers as well as the metabolism of the basic components of living things. A single typo in a biopolymer sequence could make the polymer nonfunctional and nonliving. So the third challenge to vitalism is to find out whether those long, precise sequences could arise spontaneously and possess the functions of life such as catalysis. Can new kinds of life exist that have no ties to ancient life—a truly artificial or synthetic life form?

The fourth challenge is determining whether a fully synthetic chemical network could make a copy of itself and evolve (i.e., change with time) and in so doing, prolong its own survival. And the fifth challenge is whether consciousness (or a mind) can arise synthetically. This will be addressed in the Epilogue.

Is Biological Handedness Special? What Are the Consequences of Reversing It?

This section will consider the second challenge to vitalism: biomolecular handedness. There are six compelling reasons to care about handedness.

First, when we inspect meteorites and other matter that has fallen to the earth from space, we look for an excess of molecules of the same handedness (one “enantiomer,” meaning one of a pair of molecules that are mirror images of each other). In space there are more molecules of one specific handedness than of the other. Does this mean that life arose far away and landed here, or rather that one hand is more likely to spontaneously arise or survive? The answer to this question has profound implications for our place in the universe.

Second, the two different hands have different pharmacological effects. The drug thalidomide was used in Europe between 1957 and 1961 to treat morning sickness in pregnant women. Thalidomide was made chemically and not biologically and hence both hands were made in relatively equal amounts. It turns out that one hand cures the morning sickness while the other causes severe limb malformations in the developing fetus (a result described by the BBC as “one of the biggest medical tragedies of modern times”).

Third, chemicals whose molecules exist in only one spatial arrangement tend to be more economically valuable than those that are mixtures of molecules having a given arrangement together with those of their mirror images. The “unnatural” versions are more expensive (1,400-fold more for the amino acid isoleucine).

Fourth, the oceans contain a large mass of carbon trapped in the form of recalcitrant dissolved organic matter (the ominous sounding RDOM), much of which consists of mirror-image forms of easily recycled (nonre-calcitrant) matter. The handedness of these trapped carbon molecules causes them to persist in the oceans for millennia.

Fifth, the ability to reverse the handedness of useful polymers, such as cellulose, wool, and silk, could retard decay. Biodegradable plastics may come to be seen as a mixed blessing. The usual route of biodegradation is through release of carbon dioxide, which is currently an unwelcome output. Also, the energy normally expended in recycling or replacing degraded polymer products might be saved in some cases.

Sixth, at the extreme, a mirror cell or a mirror organism (composed of chemicals of reversed handedness) might be resistant to all or nearly all parasites and predators, a tremendously valuable result.

Since biomolecular handedness is so important, what is it? The basic idea is conveyed by the fact that our right and left hands are mirror images of each other and are not related by simple rotations. If we take a sculpture of a right hand and press it into a soft mold, we will discover that we cannot fit our left hand into the mold (Figure 1.1). However, if we fill that mold with plaster, the resulting new copies are considered complementary and are of the same handedness as the originals.

Figure 1.1 A sculpture on the left and corresponding negative mold—illustrating handedness and complementary shapes.

This same phenomenon exists on the molecular level. For example, there are two ways to arrange the four atoms that can bond to a carbon atom, and each will be a mirror image of the other. Furthermore, each will have predictably similar properties.

This left-right feature is also known as chirality, from the Greek for “hand.” Even scientists who don’t think about mirror worlds initially show great confusion as to whether the properties of mirror versions of molecules, cells, and bodies can be accurately predicted based on the properties of their nonmirror versions. Consider this. If you build a replica of an old-fashioned clock by only looking at its reflection, the copy will predictably tell time, but the numerals will be mirror images of the originals and the hands will rotate counterclockwise. These outcomes are precisely as anticipated.

Here’s a simple demonstration that relates the hands and clock examples to molecules. Start with a central cantaloupe ball, and use toothpicks to successively place around it, in a clockwise order, a raisin, a piece of coconut, and a piece of nectarine all flat on the table. Then make another such structure using the same pieces of fruit but placing them counterclockwise. You can flip one over so that the two structures match, but if you add a bit of honeydew above and attached to the central cantaloupe, then no matter how you orient the structures you can still tell which was clockwise originally and which wasn’t. If you place them in front of a mirror you can see that they are each other’s mirror image. Now let’s replace fruit with atoms: H, CO, R, N. This is the general structure of an amino acid. The NH₂ is the amine and COOH is the acid. R refers to a “radical” (a group of atoms that behave as a unit) that varies with amino acid type.

Figure 1.2 Another example of handedness uses a ball and stick model of a carbon atom with its four bonds (to H, CO, R, N groups).

Amino acids have a known handedness. You can impress your friends by your ability to identify the natural form. In nature, for reasons still unknown, almost all biomolecules vastly prefer one of the two hands (amino acids and proteins being designated as left-handed). Life itself, in a way, is fundamentally single-handed. Here is a procedure for telling whether a human hand, or a molecule, is right- or left-handed. Looking at your left hand palm up as in Figure 1.2, go from thumb to index finger to pinkie, the direction is clockwise, which indicates left-handedness. Performing the same observation on the right hand gives a counterclockwise direction, indicating right-handedness.

Now let’s do the same for molecules. When looking down the bond from the hydrogen (H) to the central carbon, if the other groups going clockwise are CO, R, N, as on the left of Figure 1.2, then the configuration is normally seen in natural proteins (sometime called levo or L, for left-handed). On the right is the mirror version (dexter, Latin for “right,” or D). The R (radical) group distinguishes the twenty (or so) types of amino acids, each with its own personality (and its own single-letter code). Some are electrically negative while others are positive. Some are greasy and fear water (or hydrophobic), while others love water (hydrophilic). Glycine is the only amino acid that is its own mirror image, since its two hydrogen atoms are normally indistinguishable. Just to keep us on our toes, natural nucleic acids (RNA and DNA) were long ago designated D and their mirror forms L.

By now you may be wondering about the cash value of this talk about handedness. Just as there can be mirror molecules, there can also be mirror life. Mirror life would be the result of changing the handedness of an entire organism and all of its components, so that you have a mirror image of everything from the macro level all the way down to the atomic level. While mirror life may look identical to current life, it would be radically different in terms of its resistance to natural viruses and other pathogens. Mirror life forms would be immune to viruses and other pathogens, the reason being that the molecular interactions of life are exquisitely sensitive to the mirror arrangement of their component atoms and molecules. Normal viruses would not recognize a mirror organism as a genuine life form whose cells it could invade and infect. Such multivirus resistance would be an incredible boon to humanity. But it would come at a steep price because mirror life would be unable to digest foods by means of normal enzymes, which would mean that we would need to develop, cultivate, and mass-produce a whole range of mirror foodstuffs. (Although biohackers could in principle synthesize mirror viruses and other pathogens, mirror humans would still be resistant to natural pathogens—and even to genetically engineered nonmirror superpathogens.)

The prospect of mirror humans raises unusual and startling possibilities. Supposing that there will be a transition to a mirror version of human beings at some point in the distant future, the changeover would be gradual, with a substantial interregnum period when two types of human beings would exist: natural humans composed of natural-handed molecules, and mirror humans made up of mirror versions of them. In this situation, it’s almost as if two separate species of humans existed simultaneously. Or we might see an equilibrium between the two types if mirror pathogens arose.

These mirror humans should have an unusual smell. Members of the two versions could marry, but producing children would require what today would be considered extraordinary efforts. However, by the time we can make mirror humans, making designer (or random) children of either mirror type will not seem as challenging as it does today. We might even be able to make mirror identical twins or bodies that are mixtures of both types of cells.

Finally, creating a race of mirror humans is not without risks. Although new mirror molecules interact with mirror versions of existing molecules in predictable ways, how they interact with biomolecules in general is unpredictable. However, they are no more unpredictable than any newly synthesized drug, chemical, or material; nevertheless, careful screening of mirror molecules by computational methods or by actual experiment will be necessary to ensure safety.

Louis Pasteur had the first inklings into what natural chemical chirality is all about. He acquired this understanding by performing what the magazine Chemical and Engineering News once referred to as the “most beautiful chemistry experiment in history.”

Pasteur’s seventy-two years on earth are remembered mainly for his contributions to microbiology—especially for inventing pasteurization, discovering the “Pasteur effect” (the anaerobic growth of organisms), developing the first vaccines for rabies and anthrax, and contributing to the understanding of fermentation, as well as for his clever experiments in support of the germ theory of disease. Nevertheless, his earliest and equally great achievements came from his work as a crystallographer. In 1848, the seventy-three-year-old French physicist Jean Baptiste Biot sponsored the twenty-five-year-old Louis Pasteur in his first experiments at the elite college École Normale Supérieure in Paris.

This is a story about tartar, a chemical extracted from grapes. The modern chemical term “racemic” (meaning a mixture of the two hands) comes from the Latin racemus for “cluster of grapes.” In 1838 Biot found that tartaric acid, unlike its isomer, racemic acid, was optically active, meaning that it rotated the plane of a beam of polarized light. Both isomers are found in wine, the latter in sediments or by heating tartaric acid. These two acids were one of the first examples of an isomer pair and they turned out to be unusual in that almost all of their physical and chemical properties were identical except for their solubility and their ability to rotate polarized light.

Pasteur first showed that an equal mixture of the two forms of a salt of tartaric acid will spontaneously separate into small crystals. He heroically separated these microscopic crystals with tweezers and then dissolved them and showed that the solutions rotated polarized light in opposite directions. This key optical property is independent of orientations of the molecules, since in solution the molecules can take on all possible orientations. Furthermore, he made the profound observation that tartaric acid originating from natural systems (yeast from his wine making) came in only one of the two-handed states, the left-handed version. Since then we have learned that this propensity for single-handedness is a characteristic of most molecules that are constituents of living systems.

Omne vivum ex vivo: “all life from life,” the irreducibility of living matter to anything nonliving, became one of Pasteur’s most strongly held convictions. Indeed, Pasteur’s key role in debunking the theory of “spontaneous generation of life” in 1859 could be construed as equally aimed at propping up the idea that the living forms of chemicals cannot be synthesized. That idea was consistently opposed by French chemist Marcelin Berthelot, who believed in the power of synthetic chemistry and experimentally synthesized organic substances that did not occur in nature. The dispute between Pasteur and Berthelot was not settled until 1971, when H. P. Kagan synthesized the aromatic chemical helicene, a helical-shaped molecule, following Le Bel’s 1874 proposed asymmetric synthesis using circularly polarized light.

Figure 1.3 The mirror forms of tartaric acid at the atomic level on the left and the corresponding crystals of the salts: for each pair the natural one is on the left. The handedness at the atomic (nanometer) scale building blocks is amplified up to the human (millimeter) scale, a key requirement at the time of Pasteur, since the ability to manipulate molecules was still quite primitive. Just as the arrangement of the atoms of the two molecules can only be superimposed by use of mirrors, not by mere rotations, the same is true of the arrangement of the faces of the two crystals.