Undeniable (36 page)

When I was in engineering school at Cornell University, I moseyed over to the Space Sciences building now and then. John Olsen (Jolse) was and is a good friend, a fellow serious bicyclist and very much into astrophysics and he always nudged me to attend symposia and small graduate-level talks, etc., up there in Space Sciences. As John often pointed out, it's just wild, the things they talked about: black holes, the center of the universe (or lack thereof), energy production, and the synthesis of new elements in stars. These meetings included Carl Sagan, Kip Thorne, and Hans Bethe. What a time to be hanging out in that not especially good-looking cinder block building. On one of my wanderings, I ended up in a lab, which I'm pretty sure was on the third floor, and there before me was a fabulous tangle of glassware and tubing connecting large metal bottles of various gasses to a very large central spherical flask. It was a version of the Miller-Urey experiment, eagerly sparking away.

Hold on; let me back up for a moment. The idea of these setups, which were first proposed, designed, and run in the 1950s by chemists Stanley Miller and Harold Urey, was to simulate the conditions on Earth in primordial times, three or four billion years ago, when life appeared for the first time. The experiments were intended to see if they could make something come alive using nothing but nonliving chemicals.

Do you know what emerged? Not life, but something fascinating all the same. The chemicals gave rise to significant chemical compounds: a handful of amino acids, essential components in the chemistry of life. Amino acids are molecules that hook together to form the proteins that run almost every aspect of biology. They are the building blocks of living things. The details are fascinating, but as a general description, acids are chemicals that can yield or “donate” a proton to another atom or molecule. An acid can be weird and deadly, or it can be mild or gentle like salad dressing.

When it comes to amino acids, they all have a single carbon atom in the middle and a carbon-oxygen-oxygen chain on one side. The remarkable property of carbon is that it carries four places for other chemicals to attach, four “bonding sites” as they're called. In amino acids, one of the sites is a chain of atoms: carbon-oxygen-oxygen. On its own, we call it carboxylic acid. When it's connected to another molecule we refer to it as a carboxyl group. In amino acids, one of the central carbon's sites is for the carboxyl group, and the other three sites carry various other configurations of carbon, sulfur, nitrogen, and especially hydrogen.

I mention all this detail, because it's astonishing to realize that that's it. There are only twenty or so naturally occurring amino acids. (There's some debate about exactly how many are used by living things, but at most it may be a few more than twenty.) They all come from combinations of just a few different types of atoms. Amino acids form the so-called peptide molecules that link together to create the polypeptides that form proteins. Proteins, in turn, do much of the work in cells. They build structure; they run metabolism; they regulate responses, the whole shebang. And these amino acids were produced in the several versions of the Miller-Urey experiment. Actually, they produced the natural amino acids, along with a few additional but nonnatural, chemically logical configurations of other amino acids. It's astonishing. Just five chemical elements, and look at all the living things they create!

To create these compounds, Miller and Urey had to infer the composition of the primordial Earth's atmosphere and the primordial Earth's ocean. With the advantage of a few decades of additional knowledge, biologists today generally believe that they played it more conservatively than perhaps they needed to. They loaded the big glass flask with some natural gas or methane, some water vapor, and some ammonia. If you're scoring along with us, those are CH
4
, H
2
O, and NH
3
in chemical notation. They gave it a spark, which they reasonably figured would have happened during primordial thunderstorms. One key missing element: They didn't have a source of sulfur.

It's a safe bet that there were a lot of volcanoes erupting all over the place on the young Earth, spewing out the rotten-egg smelling hydrogen sulfide (H
2
S). It's a deadly poison to animals like us now, but in those long-ago times it may have led to an important amino acid called cysteine. Hydrogen sulfide might also have been useful to early life as a primary energy source. Even today there are whole ecosystems in deep-ocean hot water vents that run on hydrogen sulfide. One organism's trash is another organism's treasure, as I like to say.

It is interesting for me to note that creationists generally dismiss Miller-Urey style experiments, saying that the idea of life arising from chemicals that are not imbued with some divine power is preposterous. One reason creationists dismiss these results is that they say the quantities of amino acids produced are so small as to be insignificant. That is just plain wrong. Any quantity of the basic molecules of life is infinitely more than zero—infinitely more. The origin of life just requires some raw material that could allow the spark of life to emerge. Evolution is a powerful amplifier. Once a self-replicating system is established, it has a chance to scour the environment for resources and systematically make more copies of itself. Even 0.79 percent of a 10-liter volume—the concentration of amino acids in the Miller-Urey experiment—might very well amount to enough to start life on its way in the uncontested environment of the primordial Earth.

From there, this idea that creationists call molecules-to-man is quite reasonable, because a lot can happen in 3.5 billion years. The process is often called abiogenesis (life from not life), and it is still the leading theory of how biology got started on Earth. Abiogenesis may be what led to you and me. An aside: At one time abiogenesis was used to describe another pseudoscientific presumed phenomenon called “spontaneous generation.” Barnacles, for example, seem to grow out of nowhere or nothing. It was just that the people making those observations didn't use magnifying lenses. Barnacle polyps are tiny, yet they grow into shelled creatures that are quite tough. They were in the seawater all along. That adult barnacles seem to generate themselves spontaneously is just a product of not looking closely enough.

It's important to keep in mind the enormous amount of space and time that life had to work with. Experiments like the one crafted by Miller and Urey used a system the size of a laboratory flask; the surface of Earth is about a trillion times greater. The experiment ran for two weeks, whereas life on Earth had something close to a billion years. Furthermore, I suspect that these experiments were missing a key ingredient, a key type of electromagnetic, or electrical, or chemical energy, and if we figured it out, we could create molecules that made replicas, even crude replicas, of themselves. There is just so much we don't know about what conditions were like on the primordial Earth. And by the way, what's to keep real abiogenesis from happening here on Earth right now? Something to think about, yes?

Taking a very different approach, Craig Venter—the scientist who first sequenced a complete human genome—asserts that he has already created artificial life. He and his team separated or captured a bacterium and determined its gene sequence. They then created their own synthetic or novel DNA and inserted that into the bacterium, converting it to a new artificial strain. It reproduced like crazy, creating billions of a new human-made or artificial species of bacteria. Unlike Miller and Urey, Venter is not aiming to create life purely from raw chemicals, at least not so far. Still, the result—it's wild.

Venter's immediate plans are fairly pragmatic: to create artificial bacteria that can produce renewable fuels and new medicines. Just creating a chunk of synthetic DNA took an enormous amount of trouble. But of course, the longest journey starts with but a single step. The same researchers produced an artificial virus seven years earlier. They implanted a genome of their own design into a living cell (a bacterium), and sure enough the cell was directed to produce copies of the implanted gene sequence. It was an artificial virus. It could not live on its own, but it could induce a living cell to make copies of the artificial virus, if I may, just like a natural virus. By the way, Venter Institute is very carefully watched for sound ethics and microbial safety practices.

Research has come a long way since the Miller-Urey experiments. Investigators have studied the growth of complex carbon-based molecules in ice. They've studied the chemistry of clays that have strong alkaline properties, which might induce chemical reactions that would give a nascent molecule enough of a jolt to start replicating. They've looked at possible early life based on the molecule called ribonucleic acid (RNA), the simpler cousin of DNA.

Very recently, research led by MIT physicist Jeremy England suggests that life may happen automatically, a result of physics, specifically thermodynamics. Professor England argues that molecules assemble themselves in the most energy-efficient way they can find. Molecules may be driven to seek thermodynamic equilibrium, and that may lead to life. The idea is as compelling as it is wild.

Researchers have even looked hard at the possibility of life starting on another planet, Mars being the logical one, and finding its way here through interplanetary space. And besides, would we even know a nonliving thing from an extraordinarily slow-growing living thing, even if it were to literally bite us in the leg, albeit on the microscopic level? Yes, it probably would have a membrane, but unfortunately a lot of small nonliving things are also round or rod-shaped, just like bacteria.

For the first 3 billion years of life on Earth, as we know, the progression from self-replicating molecules to the Cambrian Period, when fossils got big enough to see, is still a bit unclear. What if we found life like Earth's own primitive life, microscopic and soft? Would we recognize it?

I remember very well my older brother coming home from school and posing the question: Are viruses alive? Are they living things? You can leave them in a jar for years, and they'll pop right back out and start doing what they used to do. In the presence of other organisms, they reproduce like mad. They mutate. They interact with other cells. But when they are by themselves, they exist in a kind of stasis. My brother and I had a protracted discussion and came to the conclusion that the answer is clearly: Maybe …

Looking at them from where we are on the Timeline of Life, it's clear that viruses do reproduce. They induce cells to do the reproducing for them. A cell, any cell, cannot live without its environment, something like drifting in a chemical broth or being stationed close to a blood capillary. So from this standpoint, a virus is a living thing that, instead of having chemical nutrients around, it just has to have another living thing around. It is obliged to live in and among cells—other living things. So, we call it an “obligate parasite.”

But what does it take for us to consider an organized bunch of chemicals to be a living thing? Astrobiology research helps guide us here. Generally, we want it to have a membrane. We expect it to reproduce, and we want it to maintain a steady chemical balance or steady state within itself. In biology, we say a living thing by definition can maintain equilibrium, the official word being
homeostasis
(“stays the same”).

When it comes to bacteria, no question. There they are with membranes and walls, they keep their metabolisms going in different surrounding conditions, and they certainly reproduce. When it comes to viruses, it depends how you look at it. Viruses do not maintain homeostasis. From the virus's point of view, why bother? If your molecules can all hold their arrangement in what might be considered hostile environments, why bother doing anything else? Why complicate things, when your systems work fine as they are? To my way of thinking, we just wouldn't have viruses, or the whole domain Vira, if we did not have the domain Bacteria. So they belong on any depiction of categories of living things on Earth.

In fact, viruses could be the key to this whole conversation, because they may show how life emerged in the first place. Could viral molecular structures have existed before self-replicating bacterium-like molecules came to be? Or, are viruses a side product, an unintended consequence of the natural processes that brought about self-replicating molecular arrangements in the first place? Viruses are simpler than bacteria, which would seem to make them good candidates for arriving earlier.

There are other aspects that make them not look like a very good model for the first living thing, however. For one thing, unlike bacteria (and you and me), viruses do not seem to have a common ancestor. In the strange world of viruses, there is nothing akin to the way that all other living things use DNA to reproduce. Each virus attacks or latches onto specific, sometimes surprisingly specific, living cells. When a virus attacks, it does not exchange genes, or transfer genes with or from the cell it's attacking. A virus's genes go into a cell, never the other way around. So, in these important traditional senses, a virus is not alive. Viruses seem to have come into existence after self-replicating, stasis-maintaining organisms (the things we consider definitively “living”) came to be. But let's face it: Viruses are a very significant part of our world. Without viruses, every living thing would be different.

Viruses are somehow part of the spectrum of life, and they are somehow related to the question of how it all began. We are still sorting out the thick and tangled branches of the Tree of Life; only within the past decade have biologists identified the giant viruses that help build the case that they qualify as a fourth domain of life. The harder we push on the search for the origin of life, the more surprises we find. These discoveries keep me wondering: “Mother Nature, what else haven't you told me?”

 

36