Lonely Planets

by David Grinspoon

  ronment, excretes waste material of lower chemical energy, and surfs

  the energy difference between food and shit to go on living. Life is a

  breakfast cereal, a board game, a very long sentence, a bitch and then

  you die. I’ll let you in on a dirty little secret: We don’t really know what

  life is. We may as well try and catch the wind as pin life down with a

  tidy definition.

  Even if we found a decent definition that worked for all life on Earth,

  we wouldn’t know if it applied anywhere else. We have no outside per-

  spective. The fact that we have only one form of life to study was not

  obvious when biology was a new science. After all, trillions of diverse

  creatures are on Earth to compare and contrast. Now we know that

  they—and we—are all branches of one sprawling evolutionary shrub

  with a single root. Our limited and parochial knowledge of the nature

  of life makes any confident statement about life elsewhere an affront to

  the scientific method. Nevertheless, we can’t help it, because we so des-

  perately want to know about life in the universe. We will study Earth

  life with the finest-toothed combs we can find, drawing great and uni-

  versal significance from what may be random or unique events.

  Of course, we can always use our definition itself to limit what it is

  we are looking for, declaring that any extraterrestrial phenomenon that

  does not conform is, by definition, not alive. A better approach is to

  accept the ambiguity. Though we cannot precisely define life, we can

  describe many of its properties and make reasonable guesses about

  which ones are universal. It may be that life, like true love, is impossible

  to define, but you know it when you see it. And perhaps finding

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  extraterrestrial life will be more like falling in love than confirming a

  specific hypothesis. When it happens, we’ll know.

  H O W I T S T A R T E D

  Now that I’ve established that we don’t know what life is, I’ll continue

  to describe where we think it came from. After the rains, the first

  oceans were laced with amino acids and other goodies. A seething brew

  of organic goo began to whoop it up. Carbon chemicals combined in

  new ways, evolving without memory or intention, but with plenty of

  time. It was a self-organizing organic orgy, each molecule getting it on

  with all comers, unafraid of the consequences of complete promiscuity.

  For some it proved fatal, but a lucky few wound up in long-term

  arrangements of greater stability. Once some of these learned to start

  copying themselves, there was no turning back.

  The first self-replicating molecules didn’t have to be very good at it.

  Any random assemblage that could make even imperfect copies of itself

  found its chemical type increasing in number. Structures with self-

  replication proclivities became more abundant, interacting and combin-

  ing to form new molecules, with novel properties and behavior. Some

  of these new models were even better at self-replicating. You see how

  this could quickly get out of hand. In the right kind of environment,

  with a ready supply of organics and without catastrophic interruption,

  what was there to stop it? Maybe this ocean just had to come alive.

  We believe that it did. The story goes as follows: Chemical evolu-

  tion led inexorably to self-replicating molecules, which in turn evolved

  into the first primitive cells. Through Darwinian selection, these cells

  evolved into modern organisms.

  This statement seems so reasonable and consistent with what we

  know about the natural world that we scientists accept it as true. The

  problem is, it’s difficult to prove. No one has succeeded in creating life

  from nonlife in the laboratory. It would be hard to repeat the experi-

  ment the way nature did it originally, because that probably took mil-

  lions of years. Even the most patient scientists or the most aimless grad

  students don’t have that kind of time on their hands. In our labs we try

  various tricks to speed things up: concentrating the most promising

  chemicals and adjusting temperature, acidity, or other conditions to

  encourage evolutionary activity. We’ve come up with many promising

  and suggestive results, chemical brews that point down the path toward

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  self-replication. But nothing we’ve created has crawled out of a flask

  and introduced itself, or even met the obvious minimal requirements

  for a living organism.*

  Though we don’t want to admit it, our belief that chemical evolution

  can lead to life is still an article of faith. Let’s call it informed faith, to

  give justice to the great strides that we’ve made in finding the potential

  pathways of life’s origins. The creationism-versus-evolution debate has

  unfortunately pushed science into a defensive corner from which we

  exude overconfidence, pretending to have certainty in places where

  we really have only reasonable inference. Instead of saying, in effect,

  “We have proof whereas you only have faith,” we could, more hon-

  estly, say, “At least our faith is testable in principle, and wherever tested

  has been borne out by observation.”

  It is certainly not immediately obvious that the beauty and complex-

  ity of life on Earth all came about through billions of years of random

  variation and selection. Our prescientific forebears can be forgiven for

  their intuitive inference that such a wonderful design requires a super-

  human designer. Science has given us reason to doubt this need, but sci-

  ence has also revealed the design to be far more intricate, complex, and

  finely tuned than anyone imagined hundreds of years ago. Modern

  thinkers, too, are reasonable to doubt that natural selection could come

  up with all this. If you have never, ever, doubted it, then you’ve never

  really thought about it, only accepted the ideology and authority of

  your teachers. Within each living cell, from paramecia to paramedics, is

  a chemical factory far more complex and elegant in design than the

  most sophisticated chemical plant ever built by humans.

  H O W I T W O R K S

  Without a chemistry book and a chemist, how does nature know how

  to construct these intricate factories? What keeps them running?

  Proteins. What makes the proteins? DNA.

  Life on Earth is largely a game played between two types of macro-

  molecules (giant molecules), proteins and nucleic acids (DNA and RNA

  are nucleic acids). Each is a long, thin, tangled chain of thousands of

  *If we succeed in creating life from scratch in the lab, we may still not know how it actually happened historically. But our belief that it did happen will gain several notches in credibility.

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  nearly identical subunits. Because they are made up of an enormous

  number of these smaller units, they are analogous to sentences made up

  of many letters. In the run-on sentences of protein, the letters are amino

  acids. Proteins are the basic structural materials of living organisms.

  They are what you are made of—except for some parts such as fa
t,

  bones, and teeth, but even these are constructed under the close super-

  vision of proteins.

  Even more important, proteins control the chemical machinery of

  life. Every chemical reaction in every cell of your body—all your life’s

  work—is mediated by proteins acting as catalysts. The colloquial use of

  this term is closely analogous to its meaning in chemistry. Someone

  who is known as a catalyst makes connections, brings people together.

  A chemical catalyst grabs this molecule over here and that one over

  there and says, “Why don’t you two get together? Let’s make some-

  thing happen.”

  Proteins are organic catalysts with an incredible ability to recognize

  other molecules, pull them together, and moderate their interactions.

  They regulate all the chemical reactions that, collectively, we call life.

  How do they do this? It all has to do with the unique 3-D shape of each

  protein.

  A typical protein is made of thousands of amino acids. An amino

  acid looks like this:*

  They are all exactly the same, except for the side group, here labeled

  R, which is different in each one. This amino acid, the simplest, called

  glycine, has a single hydrogen atom for its side group:

  *H, N, and C are atoms of hydrogen, nitrogen, and carbon, respectively. Notice that each carbon atom insists on forming exactly four bonds with other atoms. Thus the C that is

  “double-bonded” to an oxygen.

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  Here’s one, called tryptophan, that’s among the most complex:

  When thousands of amino acids are strung together in a particular

  order, you’ve got a protein. It is the specific sequence of amino acids

  that gives each protein its unique abilities. Here’s how: When you string

  a large number of amino acids together to make a protein, the different

  side groups (the R’s), all dangling off the main string, interact with one

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  another. Some of them are strongly attracted. Other pairs find each

  other repulsive and can’t get enough distance between them. These

  forces of attraction and repulsion cause the protein chain to fold up

  into a complex twisted shape.

  Imagine a long rope with a large number of cats tied to it at regular

  intervals. Some of the cats would try to get as far from each other as pos-

  sible, whereas others would seek each other out to fight, groom, or play.

  Now, picture this happening in a fluid tank where they all have kitty

  Aqua-Lungs, or in the weightlessness of an orbital cat house where all

  the cats can move about in three dimensions. The final shape of the rope

  would be quite twisted because of the complexities of feline social life.

  Proteins become twisted and folded because of the social interactions

  among all the side groups of their amino acids. Each protein folds in its

  own way, and the final shape is precisely determined by the specific

  amino acid sequence. It is the 3-D, folded shapes of these molecules that

  give them their amazing ability to “recognize” and bind to other mole-

  cules. Each protein has evolved so that its amino acid sequence causes it

  to fold up into just the right shape to precisely fit specific molecules and

  encourage them to react in ways needed to keep our cells running.

  How do the amino acids know what order they should assemble

  themselves in to make a protein fold in just the right way to work its

  magic? That’s where the other group of macromolecules, nucleic acids,

  come in. DNA is a nucleic acid.* It stores and passes down the infor-

  mation on how to string together amino acids in the right way to make

  the proteins needed by living cells.

  The famous double helix is made of two strands of DNA, each built

  up from a long string of subunits called nucleotides. Just as amino

  acids are the individual repeating “letters” in a protein molecule, the

  nucleotides are the letters in DNA. There are only four nucleotides in

  DNA: adenine, thymine, guanine,† and cytosine. These four structures

  function as the four letters in the genetic code, and we abbreviate them

  with the letters A, T, G, and C. The information content of the genetic

  code is entirely contained in the ordering of the A, T, G, and C

  nucleotides along strands of DNA.

  *So-called because Friedrich Miescher, the German chemist who first isolated them in 1869 (while experimenting with pus!), didn’t know what they were but suspected they came from the nuclei of cells.

  †So-called because it was first isolated in bird shit or guano. I wonder how many more dis-gusting bodily fluids I can work into the footnotes of this chapter. . . .

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  Now for the vital connection between nucleic acids and proteins.

  Contained in the sequence of nucleotides composing a strand of DNA

  are coded instructions for stringing together a list of amino acids in the

  right sequence for making specific proteins. That’s all it is. Nothing

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  more and nothing less. The entire genetic code—the information on

  how to make all of you out of a single fertilized cell—is a set of instruc-

  tions for making a large batch of proteins that will fold into the shapes

  needed to get the job done.

  Each “word” in the genetic code is three letters long. That is, every

  three nucleotides in a strand of DNA codes for one amino acid in a pro-

  tein. For example, the sequence GGT stands for the amino acid gly-

  cine, and CAA stands for glutamine. So a sequence of DNA reading

  CAACAAGGT contains the instructions “Add two glutamines and

  then a glycine.” A DNA code for making an average protein contains

  thousands of these little words. Inside each cell is chemical machinery

  that can read the DNA chain, putting together amino acids in the spec-

  ified order. The resulting proteins then promptly fold into their 3-D

  shapes and make the “desired” chemistry happen in your cells. If “love

  is just a four-letter word,” life is just a long series of three-letter words.

  T H E T W I S T

  That’s quite a stunt for dumb old nature to pull off—encoding the 3-D

  shapes of our all-purpose molecules (proteins) within the linear

  sequence of a different molecule (DNA). Why didn’t we think of that?

  But, wait, it gets better. DNA molecules can perform another amazing,

  essential trick: they can make identical copies of themselves. That gives

  us heredity, without which we would still be nothing more than a

  skanky brew of chemicals sloshing around in the ponds of a dead rock.

  In DNA’s double helix, each coded strand lives in a twisted pair with

  another. This allows each molecule to contain a template for its own

  reconstruction. The two strands of the double helix are identical except

  for the letters of the code, which form a complementary message.

  Bonds form between the nucleotides on each strand, joining the two

  together like the rungs of a twisted ladder. Each nucleotide reaches

  across and bonds to one on the sister strand. Because of their shapes,

 
; they are choosy about whom they will bond with. G and C bond only

  with each other. Likewise, A and T are a faithful, exclusive pair. So,

  the sequence of the nucleotides on one strand is exactly specified by the

  sequence on the other. Each contains a complete description of the

  other’s structure.

  When they’re in the mood to replicate, the DNA molecules, with

  some protein midwives to help them unzip, sequentially break the

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  bonds forming the rungs of the ladder, leaving two naked strands dan-

  gling free. The nucleotides strung along the two resulting individual

  DNA strings, suddenly finding themselves single again, are quick to

  bond to any attractive nucleotides floating by. In this way, each of the

  two separated strands immediately builds itself a new partner. But G

  will only bond to C, and A will only bond to T. The result? When each

  nucleotide along these chains hooks up with its desired counterpart, the

  two new double chains are in every way identical to the parent double

  helix. Each of these will then build the same proteins as its parent did.

  Really, each one is its parent. The parent molecule never died, but sim-

  ply replicated. In this sense there is only one molecule of DNA on

  Earth. The ones dividing right now in your toes and in the grass

  beneath them are all pieces of the original founder. And so it divides,

  never forgetting, forever and ever, amen.

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  To recap: What keeps the complex chemical factories in the cells of

  all Earth life running? Proteins. What makes the proteins? DNA. How

  does DNA copy itself? Proteins. A very clever design, indeed, yet it

  seems to have arrived here through evolution by natural selection.

  When I learned the details of this surprisingly complex machinery for

  the first time (and here I’ve only scratched the surface), I felt that intel-

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  lectual honesty required me to rethink my opinion of evolution.

  Doesn’t it strain credulity to think that the intricate, streamlined, fan-

  tastically clever, and totally uniform building code found in all life, even

  its simplest known forms, could ever come into existence through such

  an aimless process? I’ve heard this many times, and I’ve thought it