Regenesis Read online

  The enormity of such a task will become more evident in Chapter 2, where I describe modern cells and minimal versions of cells. I show a possible shortcut—that by leveraging a slightly sloppier version of current life we could avoid the precise manual synthesis and assembly of billions of chemical bonds. But for now we want to consider the implications, regardless of route. The complete synthesis of a mirror life form from the atoms up would be the next, and perhaps final, step in the overthrow of vitalism. The shortcut version would pose less of a threat to vitalism but would be just as significant in terms of its potential future applications.

  Creating a mirror world might give us a fresh lease on life, one free of disease and unwanted agricultural pest species, but subject to unintended consequences such as turning too much carbon dioxide into RDOM or encouraging the proliferation of enzymes that could attack our wonderful new mirror life—enzymes that are currently rare but in a sense are waiting for a justification for their duplication, diversification, and optimization. Unlike antibiotics, of which there are thousands of natural and totally synthetic examples to draw upon, there are only two hands, and we’ve already “used up” one of them.

  Another profound implication is that we are doubling the number of chiral chemicals in our bag of tricks. Because many chemicals have more than one chiral atom, the number of new compounds might be exponential—as high as 2N where there are N atoms with the property of mirror asymmetry. This could be especially apparent in polymers—the topic of the next section.

  Can a Synthetic Chemical Copy Itself and Evolve Without Help from Living Systems?

  Having journeyed from inorganic to organic and having considered the handedness of simple monomers, we now take a look at polymers, the next big idea in the story of the past and future of life. The key substances in most modern biological structures and catalysts are proteins, which are polymers made up of the twenty or so amino acids. The other key classes of polymers are the polynucleotides DNA and RNA, each of which is composed of four nucleotides (adenine, cytosine, guanine, and thymine in DNA, with uracil replacing thymine in RNA). Like proteins, DNA and RNA have handedness; Tom Schneider (a molecular-machine researcher at the US National Cancer Institute) maintains a web page (http://www.fred.net/tds/leftdna) dedicated to seven hundred humorous examples of wrong-handed DNA helix art in the popular press and in company brochures. (We need to create mirror DNA to make these folks seem more prescient and less foolish!) Like polypeptides, polynucleotides are capable of structural scaffolding and catalysis but have the additional feature of making replication possible (indeed obvious and compelling).

  The story of DNA (and RNA) replication is beautifully simple. The core idea is that of complementary surfaces. Just as the pairs of hands and molds in the sculpture shown in Figure 1.1 are uniquely complementary, so too are the base pairs of RNA: U (uracil) bonds with A (adenine), and C (cytosine) with G (guanine), Figure 1.4. The idea that a DNA duplex explains DNA duplication, and these two base pairs in particular, won Jim Watson and Francis Crick the Nobel Prize. By contrast, the other eight possible pairings (AA, AC, AG, CC, CU, GG, GU, and UU) are much weaker—energetically close to no pairing at all. In the case of the strong pairings, the two surfaces fit together, so to speak, whereas in the case of the weak pairings, there is a mismatch between the respective molecular shapes.

  The stability of two strands of RNA binding to each other depends essentially on their length. Given a long polymer of nucleotides, we can assemble matching monomers, or short complementary polymers, onto it by base pairing. The stability of the resulting double helices gives the second strand of RNA a chance to polymerize or ligate (join) the short bits into a new long polymer (probably catalyzed by molecules floating about). This new polymer is not identical to the original but complementary, but the complement of the complement is the original.

  Earlier I asked how we can get from atoms to replicable structures from scratch, meaning from atoms or tiny clusters of atoms without assistance from living templates. We can now see a progression of events from the beginning of this chapter as atomic nuclei randomly join to become atoms, atoms join to become molecules, and monomeric molecules randomly join up to become polymers. The chemical bonding ratios up to this point seem predetermined by physical selection rules acting on large sets of atoms. The matter that we see in the cosmos requires for its existence only a one part per billion excess of matter over antimatter in the early universe. Had there been exactly equal amounts, they would have annihilated one another. There is no consensus yet on the explanation of this asymmetry. Similarly, if there had been equal amounts of left- and right-handed molecules, life might not exist in the universe—at least not life as we know it. In any case, once we get replication, then we can expect to see, more and more frequently, small random events that can grow exponentially into interesting structures before any competing chemistry can take hold.

  Figure 1.4 Complementary shapes of RNA base pairs. Shown at the top are the two dominant base pairs (AU and GC); just below them is an example (GU) of the other eight possible (very weak) base pairs. What seems like a subtle difference in geometry between the AU pair and the GU mispair makes for a huge difference in the context of a stack of these flat base pairs in the double helix. (The R represents the ribose sugar to which all four bases bind with very similar geometry.) The dotted lines are bonds mediated by hydrogen that are about one hundred times weaker than the covalent bonds (solid lines) in their optimal configuration.

  Had there been exactly equal amounts, they would have annihilated one another. There is no consensus yet on the explanation of this asymmetry. Similarly, if there had been equal amounts of left- and right-handed molecules, life might not exist in the universe–at least not life as we know it. In any case, once we get replication, then we can expect to see, more and more frequently, small random events that can grow exponentially into interesting structures before any competing chemistry can take hold.

  Evolution happens not only in nature but also in the laboratory, where the key processes of mutation and selection operate on inanimate molecules and structures made up of them. Even creationists can see how small changes, when made repeatedly over long stretches of time, can add up to enormous effects that confer substantial selective advantages on a given organism. What is more remarkable is how new kinds of functionality and shape can emerge out of totally random collections of RNA rather than as mere variations on something already optimized and working. This process of emergence has major implications for how quickly new genes and genomes could have arisen in the past, as well as for the design of medical and industrial materials in the near future. Totally random libraries of RNA can be subjected to powerful selection pressures that favor rare molecules capable of valuable binding or catalysis functions. We can generate an incredible number of different RNA structures in a volume equivalent to that of a small cell. If any of these RNAs has any activity for preferentially cutting and/or joining, then the whole set of RNA sequences could churn and self-modify until stable self-replicating molecules arise and persist.

  So, the answer to the question posed earlier—Can a synthetic chemical copy itself and evolve without help from living systems?—is a resounding yes. Here is an example of such evolution in the lab. A molecule of theophylline (which is used as a drug to treat asthma and other lung diseases) can form part of a fifty-five-nucleotide-long stretch of RNA that can have two different morphologies and two different functional states depending on the concentration of theophylline. It is easy to imagine that this molecule could start with either state as its “only” shape and function and could change to the bi-stable shape with as little as the mutation of a single nucleotide. Then after some other molecule adapts to the bi-stable state, another point mutation locks it into one state or the other, permanently.

  The moral of the story is that shape and function can be altered radically with just a few changes that nevertheless yield a selective advantage at each separate stage. This capacity wil
l be very handy in the future of lab-evolved designs.

  The Future Interface of Inorganic and Organic Worlds

  We have been focusing on inorganic and organic chemistry. In colloquial usage the term “organic” is attended by a certain halo effect that, upon analysis, it doesn’t deserve. When we buy organic produce, we are supporting the idea of feeding crops the essential elements nitrogen and phosphorus that are derived only from animal excrement rather than from conventional mineral fertilizers like ammonium phosphate as churned out by the chemical industry. Does this sound like a latter-day vestige of vitalism? These organic fertilizers obviously bear a public health risk in the form of fecal pathogens such as E. coli 0157:H7, Cryptosporidium, and Gi-ardia. Both methods of fertilization, if used to excess or done poorly, carry a risk of run-off into streams and ponds resulting in fish kills.

  Another inorganic/organic dualism can be seen at the interface between life and machines. I/O means not only the intimate dance of inorganic/organic, but also input/output. Today scientists are recapitulating what we might call the first inorganic/organic transition that occurred eons ago. We take simple molecules and form them into linear polymers that are the building blocks of both natural and synthetic structures. We increasingly want to see input/output between inorganic electronics and organic DNA. On the input side of I/O, megapixel CCD (charge-coupled device) and CMOS (complementary metal oxide semiconductor) electronic cameras can be used to record spatially patterned light, such as bioluminescence or fluorescence, to inorganic (i.e., silicon-based) computers. This would allow us to read genomes speedily, whether for diagnostic testing or environmental monitoring. Coupling these inorganic/organic, input/output features together permits us to design, synthesize, and assess the quality of large collections of DNA and anything that they encode.

  Back in the early stone age of DNA engineering (circa 1967–1990) we made DNA in solution and had to purify very short intermediate products. The low yields for each step, multiplied by the short lengths per step, made DNA synthesis a challenging, tedious enterprise. Nowadays we can literally “print” arrays of DNA by machine. This is a really big deal. To see why, let’s explore analogies with other types of printing.

  Today we use spatially patterned light and optics or ink-jet printers to print photographs on paper, which are two-dimensional artifacts. But it is possible for those same ink-jet printers to “print” (i.e., to construct, layer by layer) three-dimensional objects. Ink-jet systems can hold many colors and activate many jets in parallel. If the ink consists of colored minerals or glue, then we can deposit (or “print”) one layer on top of a second layer (typically 0.1 mm per layer), and then repeat this process successively to create three-dimensional rapid prototypes of artifacts in plastic or plaster.

  We can use similar approaches of spatially patterned light or ink jets to build up long chains of DNA called oligonucleotides, or “oligos” (from the Greek oligos, for small), up to 300 nucleotides in length. Typically each layer is one nucleotide (= 0.4 nm) thick, with the four ink-jet “colors” (A, C, G, and T) used per layer. By this method we can make millions of different patches of DNA on a 3- by 1-inch glass slide or portion of a larger silicon wafer.

  In 1980 commercial DNA synthesis services were available, at the going rate of $6,000 for a small amount of product, only about ten nucleotides long. They were used either to find valuable genes in cellular RNA or to synthesize them. By 2010 we could make a million 60-nucleotide oligos for $500. Just as the global appetite for reading DNA seems insatiable—growing a million-fold in six years and still increasing—the appetite for DNA synthesis, or “writing,” will probably grow similarly and go in many unexpected directions. Since DNA in cells is very long-lived (billions of years), we might want to preserve the whole Internet in the form of DNA molecules. This would be the ultimate backup, made possible by converting the Internet’s 0s and 1s to the DNA molecule’s As, Cs, Gs, and Ts, and synthesizing the molecules accordingly. The Internet Archive contains 3 petabytes (1015) of data, and is expanding at the rate of 1 petabyte per year. This granddaddy of all backup copies would cost $25 billion, an amount that is not out of the question, but bringing that cost down by three to six factors of ten would be desirable. Because of its very small size, launching copies into space and icy moon polar craters could be very inexpensive.

  Today, oligonucleotide chips are becoming the lifeblood of synthetic biology. However, spatially patterned light and ink-jet printers can be used to make objects as complex as patterned cells. Various options exist: (1) the cells themselves can be shot directly from ink jets, (2) scaffolding proteins can be deposited in such a manner that the cells self-assemble onto those proteins, or (3) the cells can be assembled onto photo-reactive scaffolding and then selectively stabilized or released by light. These and other methods hold the potential of making synthetic and even personalized tissues and organs suitable for testing pharmaceuticals—and ultimately for printing copies of whole organisms.

  As we go forward we will be seeing more hybrid inorganic/organic systems. Our children already inherit our mechanically augmented biology, in the form of cars, smart-phones, hearing aids, pacemakers, and so on, and these devices have become increasingly integrated into our daily lives; indeed, many people would find it hard to live without them. Since the 1980s we have added recombinant DNA-based parts to our bodies in the form of insulin, erythropoietin, monoclonal antibodies, and other medically useful substances. The addition of complex synthetic biological systems to this mix will ultimately blur the distinction between life and nonlife.

  CHAPTER 2

  -3,500 MYR, ARCHEAN

  Reading the Most Ancient Texts

  and the Future of Living Software

  The greatest story ever—the story of the genome—continues through the Archean geologic era, which started roughly 3,500 million years ago. The name “Archean” stems from the Greek arche, which means “the beginning.” (The same ancient Greek term also refers to the keel of a boat, the part from which everything else rises.)

  Back in the Archean, the earth scarcely resembled the planet that exists today. For one thing, there was no free oxygen in the atmosphere, which consisted largely of gases such as methane, ammonia, hydrogen sulfide, and the like, a lethal mixture for humans. For another, the earth at that time was hot, with average temperatures exceeding 130 degrees F. This was heat from the planet’s molten core, produced during the earth’s accretion, frictional heating arising from denser materials sinking to the planet’s center, and heat from radioactive decay.

  During the Archean one of the most important and dramatic events in the history of the planet occurred: the rise of life on earth. Early life took the form of single-cell organisms (and colonies) lacking a distinct, membrane-bound nucleus, the primary examples of which are bacteria, archaebacteria, and photosynthetic forms (like cyanobacteria). That life originated during the Archean means that metabolism, reproduction, and DNA all arose during this period.

  The appearance of DNA some 3,900 million years ago makes it the most ancient of all ancient texts. Ancient texts of other types are still revered today, including the 5,000-year-old Yi Ching (2852–2738 BCE), the Bhagavad Gita (Hindu, oral Sanskrit 3137-1924 BCE, written Sanskrit 400 BCE), the Qur’an (Islam, 630 CE, written in Arabic 650-656 CE), Tipitaka (Buddhism, 580-543 BCE, written in Pali in 30 BCE), and the Bible. These texts are widely translated (in up to 2,200 dialects), widely printed (3 billion copies), read, interpreted, downloaded (1.4 megabytes), and even memorized. The Torah has 304,805 Hebrew characters and in the centuries since the original, ascribed to Moses (1444-1280 BCE or Josiah’s 620 BCE revision), the number of “mutations” worldwide is only nine (among the Ashkenazi, Sephardi, and Yemenite lineages), all of which are considered to be a result of minor spelling differences that do not impact meaning.

  The original ancient text is written in the genomic DNA of every being alive today. That text is as old as life itself, and over 1030 copies of it are distributed
around the earth, from 5 kilometers deep within the earth’s crust to the edge of our atmosphere, and in every drop of the ocean. A version of this text is found in each nucleated cell of our bodies, and it consists of 700 megabytes of information (6 billion DNA base pairs). It contains not only a rich historical archive but also practical recipes for making human beings. For such a significant text, its translation into modern languages began only recently, in the 1970s.

  Other naturalistic, geological, and astronomical resources can also be considered ancient texts. We surmise that the ancient texts written by humans, as well as the texts of natural data, are all transmitting profound truths that are not intrinsically contradictory. We try to align and weave these various threads to help us understand the past and the future.

  Because the engineering of that most ancient text, the genome, takes place at the cellular and subcellular levels, it’s important to understand the cell and its workings in some detail. In fact, it would be nice to know exactly what it’s like to be a cell. But is it possible, even in principle, to know such a thing?

  In 1974 the American philosopher Thomas Nagel published a mind-stretching essay that became an instant classic, “What Is It Like to Be a Bat?” The piece was an attempt to understand the subjective character of a conscious experience that is fundamentally different from our own. Nagel found that his ability to do this was rather limited. He tried to imagine having webbed arms, hanging upside down by his feet in an attic, navigating through the air and catching insects by echolocation, and so on. “In so far as I can imagine this (which is not very far),” he said, “it tells me only what it would be like for me to behave as a bat behaves. But that is not the question. I want to know what it is like for a bat to be a bat.”