Late Night Musings on the Origin of Life

The conventional view of the origin of life is that some combination of simple-enough chemicals was able to catalyze the synthesis of the same chemicals, and that was enough to begin a process of evolution that became more efficient as it became more intricate.  One problem with this idea is that no such self-reproducing combination of chemicals is known, or has ever been synthesized or engineered.  The simplest known self-replicating systems are enormously complex compared to anything that might plausibly have arisen by chance.  Improbable as is the conventional view, the alternatives are far stranger.

The paradox in a nutshell

Consider what we might deduce from these three facts.

  1. The oldest fossils are almost as old as the earth.  So life must have appeared on earth as soon as the earth was cool enough to have liquid water.
  2. Biochemists have devoted a great deal of ingenuity to the task of creating a molecule or network of molecules that can self-reproduce, when immersed in a bath with appropriate chemical feed-stock.  They haven’t made it to first base.
  3. All life on earth is related, all descended from the same proto-cell.

When we think of the transition from non-living matter to living systems, we imagine some network of molecules that formed a self-catalyzing loop.  Typical bio-molecules have thousands of carbon atoms arranged in a precise shape and structure that could never have come about by chance.  The earliest proto-living system did not have to be efficient, because there was no competition, but it had to be simple, because once you start combining more than a dozen or so carbon atoms together, the number of ways they can be linked is so large that any one combination would not be expected to appear even once in all the vast oceans over many millions of years.  So what we need is a system of molecules, for example A, B and C are all simple enough to have arisen by chance, and A makes it more likely that common molecules in the neighborhood will come together to form B, and B likewise catalyzes C, and C increases the probability of formation of A.

We think it must have happened somewhere, sometime.  In the early days of biochemistry, it was common to assume that this first step with self-replicating organic molecules must be easy.  In 1953, Stanley Miller and Harold Urey passed sparks through a tank of water, ammonia and methane, simulating the earth’s early atmosphere in the presence of lightning, and he found that some common organic molecules were created, including some amino acids.  Bingo!  Harlow Shapley wrote in Of Stars and Men (1957),

No longer is the origin of life a deep mystery.  Supernatural “intervention” in the biochemical development which we call life is not required.  Natural operations, most of them already known, will suffice.  We have bridged, at least provisionally, the gap between life and the lifeless.  The microbiologist probing down from cells toward the inanimate and the chemist moving up from atoms toward the animate are practically in contact.  Much detailed work, however, remains to be done.

Much detail, indeed.  We realize now that there is a mystery.  The gap between non-living and living systems seems wider now that we’ve spent 60 years trying to bridge it.  For comparison, the number of people playing with cellular automata is much smaller, but the self-replication problem has been solved handily in that context.  Cellular automata are “toy worlds” that obey simple, made-up rules, for propagating from one generation to the next.  The most famous is John Conway’s Game of Life, and here is a self-replicating pattern that works with those rules.

So Fact #1 would lead us to expect that maybe the first steps in the formation of life were easy and probable, while Fact #2 implies the opposite.

Fact #3 suggests maybe life appeared only once, adding more weight in favor of “difficult and improbable”.  Or maybe life evolved in many places at many times, but one of these simply out-competed the others, and so descendents of just this one life remain on earth today.  This is potentially the biggest loophole in my thesis, so I want to dwell on it for a few paragraphs.

 

All life on earth has a common ancestor.  Does this mean that life arose only once?

We know that all life on earth has a common ancestor because there are many things that all living cells have in common with each other, and some of them are quite arbitrary.  One example is the genetic code, which seems to be composed of three-letter “words” for specifying amino acids (= protein building blocks) which appears to be as arbitrary as any association between letters and meaning in a human language.  Another example is the fact that all biological amino acids are left-handed, and all nucleic acids are right-handed.  In other words, these molecules are different from their mirror images, and we know that a mirror image of all of life’s chemistry would behave identically to life as we know it (provided that all the molecules were mirror-imaged).  Inorganic chemical processes always create left- and right-handed molecules in equal numbers, but biochemical processes always create exclusively one handedness only.

I enjoy thinking about LUCA, the Last Universal Common Ancestor, a single cell existing perhaps 3 billion years ago from which you and I and every mushroom and mosquito and all life on earth has descended.  Strange as it seems, there is no alternative hypothesis that isn’t far stranger.

If we think life evolved from molecule to primitive cell within 300 million years, that suggests that there has been ample time and opportunity for life to have arisen in other times and places, before and since.  Why wouldn’t descendants of these other origins of life appear somewhere on earth today?

We are used to thinking in terms of varieties that vie for a niche, and one does a better job than the other, and so the former drives the latter to extinction and takes over.  It has been argued that once Life I got a head start, it might be so efficient that newly-formed Life II and Life XIX would not have a chance of invading its territory.

I am not convinced this is true.  Life forms that are very similar may vie for the same niche:  they are attacked by the same predators, get the same diseases, and rely on the same resources.  But why would Life II be vulnerable to Life I if the two were very different?  There is a mathematical theorem from evolutionary theory (Gause’s Law), purporting to prove that two varieties cannot coexist stably in the same niche.  Whichever reproduces faster will drive the other to exinction.  While this is true in theory, it seems that in richly productive ecosystems, the niches are sliced awfully thin, so that in tropical rainforests and coral reefs (the two most prolific ecosystems in the world), many species with very similar characteristics manage to co-exist and thrive together for long periods without getting in each other’s way.

How much more true would we expect this to be if two forms of life had an entirely different chemical basis!  Life II might be based on carbon chemistry, but using neither proteins (amino acids) for signaling and as workhorse molecules, nor DNA (nucleic acids) for information storage.  Life I would not eat Life II, because Life I lacks the enzymes necessary to digest Life II.  Even if it could be digested, it is unlikely that the chemical constituents of Life II would be useful to Life I.  We (Life I) can eat sugars and proteins, but we can’t digest diesel oil or polyethylene, even though these feedstocks contain chemical energy in abundance that could, in theory, be useful to us.

In what sense would Life I and Life II be competing at all?  Only in the sense of both needing water and an energy source – say mineral compounds at undersea vents, or sunlight.  Certainly it is probable that Life I or Life II might be much the more efficient at converting energy into biomass, and at rate of reproduction; still It is not at all clear that Life I and Life II would not be able to stably co-exist, or that one form would necessarily drive the other to extinction.

 

Life before LUCA

The (ultimate) energy source for most life today is sunlight.  Furthermore, the earliest fossils that we have are the blue-green algae (cyanobacteria), the alchemists that alone are able to capture the energy of the sun and store it as chemical energy.  This is the chemistry of chlorophyl and photosynthesis, and, as far as we know, it evolved only once.  The cyanobacteria had a monopoly on the process for more than 2 billion years, until they colonized early eukaryotes (complex nucleated cells) and were tamed by them as chloroplasts, which remain to this day the “green” in green plants, and the energy factories for everything from moss to Giant Sequoias.

And yet the biochemistry of photosynthesis is far too complex and sophisticated for us to imagine that cyanobacteria evolved first from non-living matter.  There must have been some intermediate life form with lower complexity, and we are not surprised that it left no fossil imprints.

There are many competing theories, many scenarios for the way in which life might have arisen from non-living matter.  My favorite, explored with a masterful knowledge of chemistry and a creative imagination comes from Nick Lane.  My point is that all these are descriptive, and lack detail.  There is nothing like a proof or demonstration that life could have arisen in the brief time in which we know life did appear, and, of course, there has been no success engineering a chemical system capable of reproduction in the laboratory, let alone a system simple enough that it might plausibly have arisen by chance.

 

If anything is worthy of cosmic wonder, surely it is this

Where all this is headed – the epiphany that started me writing this essay – is the improbability of the first life forms, the bridge that carried nonliving matter into the realm of the living.

(This is the original “chicken and egg” problem, and it carries us to the brink of Creationism.   To offer “God did it” as an explanation seems to me to offer no advantage compared to the simpler statement, “we don’t know” or “it is an enduring mystery”.  On the other hand, I think that evolutionary scientists have been less than honest in acknowledging the vulnerabilities and mysteries in the evolutionary process, in part because they have felt the need to take a hard line against attacks from fundamentalists.)

James Russell Lowell, the 19th Century transcendental poet, wrote

We pass unconscious o’er a slender bridge,
The momentary work of unseen hands
Which crumbles down behind us.  Looking back,
We see the other shore, the gulf between,
And, marveling how we won to wear we stand,
Content ourselves to call the builder Chance.

So I look as an (independent, heretical) scientist on the evidence, and I ask: what could explain the highly-improbable appearance of living forms on earth, so soon after the early earth cooled sufficiently to make life possible?

One answer is an extra-terrestrial origin for life.  Perhaps the earth was deliberately seeded by some advanced civilization (after all, the Universe was already 9 billion years old, ⅔ its present age, when sun and earth were born)…this leads to the Fermi Paradox and other mysteries.  Or else there are bacterial spores sufficiently resilient that they can ride a rock ejected from a planet by violent volcanism, then survive dormant for millions of years in interstellar space, and survive (yet again) the heat bath of re-entry into a planetary atmosphere.  The spores then detected water and hospitable temperatures, and they awakened from a long, long sleep.

Unlikely?  As I see it, the alternatives are Little Green Men or mysticism.  Panspermia is the hypothesis of a single origin for all life in the universe, a recognized and legitimate hypothesis (if not dignified by the Science establishment) with roots that go back to Anaxagoras, and a following that includes no less a luminary than Francis Crick.  Panspermia does not solve the riddle of the origin of life, but only pushes the question back to a previous planet in a previous epoch, but the available space and time for life to appear is vastly increased.

…or maybe the biochemists have overlooked something that’s not so difficult, and the origin of that first cell is not as improbable as it seems….or maybe there is a propensity for life that is woven into the behavior of matter, and shielded from our view by what Quantum Mechanics calls irreducible randomness, electrons and protons are biasing their trajectories in tiny ways that aim toward life, perhaps toward awareness.  The boundary between science and speculation is where I love to hang out.

 

pf button Late Night Musings on the Origin of Life

5 thoughts on “Late Night Musings on the Origin of Life

  1. An elegant ride you take us on Josh! Reading this piece, I felt like I do when I stare up at the sky on a very clear night. Awed by what is staring back down at me. This will be a chapter in your much anticipated book I hope.

  2. To bridge the gulf between the complex organic molecules and living things is not a trivial journey – we really have no idea – except to imagine several already complex systems came together. It must have been a molecular complex that adjusts the environment to produce more of itself – a machine, a contraption – but must in every stage of its evolution have done the same. That way complexity can grow by addition of rare states to rare states. So it might well be that life arose here (if you assume life arose elsewhere you’re just kicking the can down the road, how did it arise there?) once,and only once, and by the most unlikely and unrepeatable of accidents life arose once on Earth (we don’t know otherwise). The occurrence of life might be an extremely rare event, – one that might not occur in but one of hundreds of galaxies = there’s no way to know – unless we go out to meet them – or visa versa. . Of course it may well be that we are the only reachable life in the universe (not much of a conversation with the nebula in Andromeda – when a round trip message (to and from) takes at least five million years). In that case, maybe we will evolve to a thousand, thousand species as we colonize Our Galaxy, become our own aliens (separation by interstellar distances can do that;_ Tell the truth I’m all for life extension, but I’m not sure I’d like to live that long (but I’m willing to give it a shot).

  3. Interesting. I think the most likely explanation is that proto-life evolves fairly easily, but once life is abundant the process of proto-evolution is short circuited.

    Primitive evolution might have been pre-chemical. For example, a smudge on a rock in the ocean might tend to concentrate certain materials. Pieces break off the smudge and accrete on other rocks. This simple system would have the necessary elements of replication and random variation. Some class of smudges might tend to accumulate precursors of chemical evolution. I.E. An evolution of the tendency to increase concentrations of various sets of chemicals might create favourable circumstances for the step into chemical evolution?

  4. 1) The oldest fossils are almost as old as the earth. So life must have appeared on earth as soon as the earth was cool enough to have liquid water.

    Wrong.
    The geochemical evidence is that there was liquid water on earth as early as 4.4 – 4.3 billion years ago;

    Simon A. Wilde, John W. Valley, William H. Peck & Colin M. Graham. “Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago” Nature, 2001; v. 409, pp. 175-178.

    Mojzsis, Stephen J., T. Mark Harrison, Robert T. Pidgeon “Oxygen-isotope evidence from ancient zircons for liquid water at the Earth’s surface 4,300 Myr ago” Nature 2001; 409, 178-181

    There is the earliest geochemical evidence for life on earth about 3.7 – 3.8 billion years ago;

    Rosing, Minik T. and Robert Frei, “U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis” Earth and Planetary Science Letters, 2004: 217 237-244

    Fedo, Christopher M., Martin J Whitehouse and Balz S Kamber
    2006 “Geological constraints on detecting the earliest life on Earth: a perspective from the Early Archaean (older than 3.7?Gyr) of southwest Greenland” Phil. Trans. R. Soc. B 361, 851-867

    There are the oldest known fossils of cells ~3.5 billion years ago;

    Schopf, J. William
    1999 “Cradle of Life: The Discovery of Earth’s Earliest Fossils” , Princeton University Press

    The time between the oldest liquid water and the earliest detected life is between 1/2 and 1 billion years. Not soon even by geological time scales.

    2) Biochemists have devoted a great deal of ingenuity to the task of creating a molecule or network of molecules that can self-reproduce, when immersed in a bath with appropriate chemical feed-stock. They haven’t made it to first base.

    Wrong. See;
    Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR,
    1997 “Emergence of symbiosis in peptide self-replication through a hypercyclic network.” Nature, 390: 591-4

    Lincoln TA, Joyce GF (February 2009). “Self-sustained replication of an RNA enzyme” Science 323 (5918): 1229–1232 DOI: 10.1126/science.1167856

    Reader, J. S. and G. F. Joyce
    2002 “A ribozyme composed of only two different nucleotides.” Nature vol 420, pp 841-844.

    Turk, Rebecca M., Natayliya V. Chumachenko, Michael Yarus
    2010 “Multiple translational products from a five-nucleotide ribozyme” PNAS vol. 107 no. 10 4585-4589

    Lincoln, Tracey A., Gerald F. Joyce
    2009 “Self-Sustained Replication of an RNA Enzyme” Science, Jan 8, Vol. 323 no. 5918 pp 1229-1232; DOI: 10.1126/science.1167856

    3) All life on earth is related, all descended from the same proto-cell.

    Probably wrong. See;

    Woese, Carl
    1998 “The universal ancestor” PNAS Vol. 95, Issue 12, 6854-6859, June 9

    2002 “On the evolution of Cells” PNAS Vol. 99 13:8742-8747, June 25

    For a fairly recent review of origin of life research see:
    Deamer, David W.
    2011 “First Life: Discovering the Connections between Stars, Cells, and How Life Began” University of California Press

    • Gary –
      Thank you! You’ve given me a lot of references on topics that I find fascinating, and I’m eager to see what I can learn – and maybe you’re right that the result will be to alter the big picture that I’ve painted.
      -Josh

Leave a Reply

Your email address will not be published. Required fields are marked *

* Copy This Password *

* Type Or Paste Password Here *

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>