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By Dave Deamer | April 16th 2009 02:02 AM | 16 comments | Print | E-mail | Track Comments
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More Stars, Planets, Life articles

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About Dave Deamer

My research focuses on a variety of topics related to membrane biophysics, including the origin of cell membranes and the use of transmembrane nanopores to analyze nucleic acids. Over the past 25... Full Bio

    Last week I described how Fred Hoyle, in 1946,  came up with the idea that carbon is synthesized in hot stars toward the end of their lifetime, and we now know that carbon and the other elements of life are strewn into interstellar space when the star explodes. In his later career, Hoyle was never able to match his earlier triumph of carbon nucleosynthesis, but he certainly tried. Together with his colleague Chandra Wickramasinghe, now at Cardiff University in Wales, he co-authored a series papers and books that proposed an alternative hypothesis for one of the remaining great questions of science, which is the topic of these columns: How did life begin on the Earth?

The scientific consensus is that life began as a chance event in which just the right mix of organic compounds was acted upon by an energy source so that growth and reproduction could occur. The earliest life would not resemble today’s highly evolved version, but more likely was a kind of scaffold that had the essential properties of life. The scaffold was left behind when more efficient living systems evolved. 


    Hoyle and Wickramasinghe did not subscribe to this view. Instead, they elaborated a version of panspermia, an older idea championed in 1903 by the great Swedish chemist Svante Arrhenius. Arrhenius proposed that life exists everywhere in the universe and was delivered to the Earth when frozen extraterrestrial bacteria or spores, drifting as interstellar dust through the galaxy, happened to land here four billion years ago and found our planet to be habitable. Hoyle took it a step further when he claimed that this was still happening, that epidemics such as the flu pandemic of 1918 were actually caused by extraterrestrial organisms in the tails of comets. 


    I met Wickramasinghe in 1986 at the Tidbinbilla radio telescope observatory near Canberra, Australia, and asked whether he and Hoyle really thought that  interstellar space was infested with bacteria. He was quite certain of it, he said, noting that the infrared spectrum of interstellar dust closely matched that of dried, frozen bacteria. I mentioned that I was working with the astronomer Lou Allamandola at NASA Ames Research Center, who had demonstrated that the infrared spectrum could be reproduced by ordinary non-living compounds called polycyclic aromatic hydrocarbons (PAHs for short). This seemed a much more plausible explanation than a galaxy full of bacteria. Wickramasinghe had a ready retort: “It is up to you to prove that they are not bacteria.”


    This was my first experience with someone who is not swayed by Occam’s Razor and the weight of evidence. Scientists are like investors, but instead of money, the capital they have to spend is time, limited to roughly 40 years of active research. Good scientists are constantly making judgment calls to decide where to invest their time. They hope their investment will be profitable, not necessarily in monetary terms (that rarely happens) but rather in revealing significant new knowledge. But a few scientists spend their lives seeking unusual explanations that others would immediately discard as implausible. Most often the ideas turn out to be not just implausible, but wrong. However, once in awhile a wild idea is beautifully, wonderfully correct, and overturns a paradigm. George Gamow had one such idea, which Hoyle jokingly referred to as the "Big Bang", and in a later column I will tell you about Peter Mitchell, another maverick whose implausible idea taught us how energy is made available in every living cell.


The game of life


Getting back to the main story, carbon and the other biogenic elements synthesized in stars can be delivered to planetary surfaces like the Earth and Mars during planet formation, mostly in the form of organic carbon compounds and carbon dioxide. These are chemically processed into a variety of other organic molecules which in turn assembled into the first living systems of self-reproducing molecules.  How could this possibly happen? After all, a living cell is incredibly complex.

I think the answer lies in the fact that  even though a list of life’s atomic and molecular components is relatively short, complexity can be produced by the exponentially large number of possible interactions among those components, subject to fairly straightforward laws of chemistry and physics. Think about the game of checkers. The parts are very simple, just black and red pieces on a checkerboard with 64 squares, and the rules that govern the way the pieces move about on the board are also easy to understand. However, the situations arising during an actual game of checkers are so complex that only in 2007, using the most powerful computer, was the game completely analyzed. (It turns out that if two players make perfect moves, the game always ends in a tie.) 


In living organisms, as in checkers,  immense complexity arises from the way specific rules govern a few basic pieces. Instead of two colors of checker pieces, life is based on six elements abbreviated CHONPS, as described in last week’s column. Carbon ( C ) phosphorus (P) and sulfur (S) are solids at ordinary temperature, and hydrogen (H) oxygen (O) and nitrogen (N) are gases. These elements comprise over 99 percent of the water and organic matter in a living cell. One of the chemical rules of life is that the six biogenic elements combine into four basic kinds of molecules, which in turn assemble into the structures that make a cell. This is the reason that CHONPS are the biogenic elements. No other group of six elements could be assembled into a set of simple molecules that can readily be linked together into chains called proteins and nucleic acids. 


Starting with elemental carbon, it is an interesting exercise to construct four basic kinds of biomolecules, adding one more biogenic element at each step to show how complexity increases.


Carbon by itself: Nada, unless you like graphite and diamonds.


Hydrogen and carbon are easy: they compose the hydrocarbon chains of fat, cholesterol and phospholipids, collectively referred to as lipids.


Carbon, hydrogen and oxygen: Another easy one -- carbohydrates, or “watery carbon.”


Carbon, hydrogen, oxygen and nitrogen: Amino acids of course.


Carbon, hydrogen, oxygen, nitrogen and phosphorus: A little more challenging, but there is only one biomolecule left: nucleic acids.


Oops... forgot sulfur -- a couple of amino acids contain sulfur, and one class of lipids.



And there you have it, the main players in the game of life. But where did they come from for the game to begin?

Two of my scientific colleagues – Bill Irvine and Lou Allamandola – introduced me to a fundamental yet little known fact of life: We live in an organic universe. Twenty years ago, when I first heard Bill speak at a conference on the origin of life, I naively wondered why a radio astronomer would be invited. But then as he began to show his slides, the mystery was solved.

Really cold matter in molecular clouds emits radiation in the microwave region, with each chemical bond in a compound producing a specific wavelength. If the radiation is detected with a radio telescope and then analyzed, it is possible to decipher the kinds of bonds present and determine the nature of the compound. Bill presented clear evidence that dense molecular clouds, the nurseries of stars and solar systems, had nearly a hundred kinds  of organic compounds present.  Some of these are familiar, such as  cyanide, formaldehyde, methanol, ethanol, formic acid (named after formica, Latin for ants that release formic acid as a sour spray when disturbed), and acetic acid, the sour component of vinegar. Others are truly exotic, including one with a chain of nine carbon atoms and one nitrogen atom at the end. Such a weird compound could not exist on Earth, but in the cold of outer space it is stable.

The connection between radio astronomy and the origin of life became obvious as I listened to Bill. If molecular clouds give rise to stars, planets and solar systems, maybe some of the organic matter in the clouds was delivered to the early Earth four billion years ago to help life get started. Next week I will describe an experiment in which the synthesis of organic compounds on interstellar dust particles was simulated in Lou Allamandola’s lab at NASA Ames.



Comments

adaptivecomplexity's picture
Hoyle took it a step further when he claimed that this was still happening, that epidemics such as the flu pandemic of 1918 were actually caused by extraterrestrial organisms in the tails of comets. 

Wow, he's crazier than I thought. Viruses from outer space that just happen to be able to reverse transcribe RNA and express proteins that specifically bind to proteins in human cells - but not plant cells? There's a theory in desperate need of a shave with Occam's razor.

Hank's picture
I like to quantify everything I can, including someone's work eccentricity (the chance they will do something brilliant versus devastating) and Hoyle is a tough call.   Stellar nucleosynthesis is a terrific idea but sometimes when people want to make their hypothesis explain all things they hurt its credibility of being accepted about most anything (Al Gore, for example, passed from progressive thinking climate science advocate to borderline crank by blaming everything on global warming - this does not make him wrong on all things) - I'm really getting a kick out of this.   I didn't know that chemical bonds in molecular clouds emitted radiation that corresponded to a particular wavelength, though I suppose now it makes sense given that we have an idea of the background spectrum.

Gerhard Adam's picture

One of the things that strikes me is the description of "organic compounds".  Isn't this really mysterious only in the sense that we call them that?  They are "organic" because they occur in living things, but doesn't it equally make sense that whatever living things evolved from, would have come from the surrounding available molecules?   In other words, the connotation of "organic" only has signifcance because we already know how they were used. 

If there was a way to arrive at a completely unique form of life based on iron or silicon, would we call those molecules "organic"?



In addition, the article mentions that life is a "chance" event, but is it really?  There are rules that govern the interaction of fundamental particles and what kinds of structures they can form.  What kind of "chance" event would produce Uranium (which is unstable)?  It occurs because there are definite effects when circumstances bring together the right energy and components to produce a variety of elements.  Otherwise, why not simply have a universe filled with hydrogen atoms?  or free protons and electrons for that matter?

When we cause a chain reaction in Uranium nuclei we can produce an explosion or when we control it, we can produce energy.  It isn't that hard to envision a molecule that reaches some level of complexity where an additional atom causes it to become unstable and exchange particles with another molecule.  This energy might cause it to recombine (in a sort of oscillation effect) so that given the large number of component atoms, the process could become self-sustaining (like our nuclear reaction example)?  

I realize I'm grossly oversimplying the example, but isn't that effectively what cell metabolism is?  An oscillation of chemical processes that keep repeating based on their ability to have access to enough component parts and energy?  (Just like our reactor can keep producing energy as long as we have enough uranium and neutrons).

Maybe I'm way off here, but it seems that the universe is quite stable for the chemistry of life, and that the only real "chance" ingredient is the planet on which it settles. 



Thank you for your comment. I'll try to clarify what I mean by "chance event". Life is not a single entity, like a uranium atom, but in fact is a system of molecules with specific properties like catalysis and replication. We imagine that the early Earth had a variety of such molecules, most of them inactive. So when I say chance event, I mean a rare few active molecules happened to be captured in a membranous compartment and began to work together as a system.

Regarding what is meant by "organic", please see last week's column where I discuss this question.

Gerhard Adam's picture
I realize I didn't explain my point very well, but the comparison to uranium was to illustrate that the same complexity occurs for even more fundamental particles than atoms within molecules.

The very fact that a fundamentally unstable particle can be formed indicates that when the means are available, even relatively unlikely events will occur because it is in the nature of the laws of physics and chemistry for them to happen.

The point about the properties like catalysis and replication, are simply chemical reactions regardless of how unique a particular function is.  Which suggests that there is a repetition (or oscillation) given enough energy and available raw materials (or atoms), then such a process could and should occur.  In other words, many of the biochemical reactions are highly repetitious and go through specific cycles to provide the energy necessary for these processes to continue. 

As long as the atoms can be kept in close enough proximity and there are enough available, then a molecule that "needed" them would have the raw materials to gain greater complexity.  Once it was an essentially self-sustaining chemical cycle, then any confining area might have been sufficient to allow the reactions to develop more sophisticated processes.

My point regarding a chance event, is that it is highly unlikely that a singular event occurred which gave rise to life.  Therefore, my contention is that these reactions must've been common enough so that successful combinations could arise, and that failures were ultimately superceded by more successful molecules.

logicman's picture
Dave:  I am enjoying this series.  Thank you for stimulating the grey cells!

I have been mulling over the 'how does life start' problem again.  I don't have any answers, but I do have some points to raise.  Please treat these as questions, even if, for the sake of brevity, I state them as facts.

The distribution of handedness in, e.g. sugar molecules, suggests an origin in a magnetic field.  The Earth's magnetic field changes strength, and flips, so the handedness ratio, if influenced by geomagnetism,  is purely a chance happening.

Taking Gerhard's ideas about oscillations, suppose we have a 'soup of bits' in an environment such that components may form into simple chains abcd abce abdf etc.  But the bits themselves can change, so we may get variants as aBcd Abdf  etc.  Tautomers?  If the conditions are right, this cycling could lead to the accidental formation of a semi-stable chain which can link to other bits to form a second, complementary semi-stable chain.

I suggest a minimum condition under which replication can begin with a high instability / permutation rate.  It is then inevitable that a complementation will arise which has such a balance of entropy to stability that it comes to predominate in the environment.  If a single molecule can exert influence on another molecule so as to make a complementary pair, then I suggest that these two can divide and
each replicate the complementation process.  In a geometric progression, you rapidly have a soup which contains billions of 'code' snippets - RNA precursors?

For a high rate of proto-evolution, perhaps we should look at what chemicals might occur in an environment where volcanic activity in or near sea water creates the 'bootstrap' molecules: e.g. uracil and phosphates.  These seem to me to be the most fundamental.  Phosphorylation: what might its proto-chemistry be?

Hydrothermal activity might adjust the balance of various essential elements and compounds: heating/cooling adjust solubilities and reaction speeds, chemicals from molten rock in direct contact with water might catalyse reactions and / or precipitate out excesses of compounds.  Spray, turbulence, compression waves in hollows, all may be factors.  (Compression waves fracture rocks and increase the erosion rate.)  In a sufficiently large hydrothermal pool, there will be temperature and chemical gradients such that a zone might be found in which the gradients intersect so as to form an optimum zone for the creation of just the right kinds of molecules.

These are just some ideas thrown into the mix, to promote further discussion.

Gerhard and Patrick -- I'm delighted that my columns have stimulated some gray matter, as Patrick put it. A complete response will require another column or two, and in fact future columns will discuss the origin of chirality and replication. Gerhard's concern will also be addressed next month in an essay I wrote for MIT Technology Review. In it, I argue strongly that life could not begin as a single event, in agreement with Gerhard, but that vast numbers of protocells were involved which to varying degrees displayed the properties of living systems. Evolution began when selection began to work on these variations. In any event, I take Gerhard's point and will be more careful with my language in the future.

Now to Patrick's comments: Much depends on what kind of energy was available to drive chemical reactions toward the synthesis of ever more complex molecules, and particularly the antecedents of what we now call nucleic acids and proteins. You are on the right track putting phosphate up front, but in fact very few of my colleagues have taken the time to do the necessary experiments. We can only speculate about how phosphate first came into the picture as a primary activating agent, and in a future column about the bioenergetics of first life, I will describe the main ideas that have been put forward.

Gerhard Adam's picture
I recently read an article based on the work of Stanley Miller that carried a strong suggestion that organic molecules may have evolved in frozen water and cold conditions, since that would have provided a lower energy state (with less heat) so that chemical reactions weren't too energetic, and a confining environment in which proximity would have generated more opportunities.

This certainly sounds like it would be reasonable since some of the fundamental criteria that needs to be applied is to have enough time for reactions to occur and essentially sort themselves out in terms of what works.  In addition, the system can't be in too high an energy state because this could cause workable reactions to collapse because of the volatility of the environment.

Anyway ... just thought it sounded interesting.

Hank's picture
An unmapped reservoir of briny liquid chemically similar to sea water, but buried under an inland Antarctic glacier, appears to support unusual microbial life in a place where cold, darkness and lack of oxygen would previously have led scientists to believe nothing could survive

- Blood Falls - Microbes Have Thrived In Antarctic Cold And Darkness While Lacking Air For A Million Years

Gerhard -- You are probably referring to a 1994 paper by Bada and Miller, who pointed out that important biomolecules become increasingly unstable as temperature rises. Their solution was an icy environment in which such molecules would at least hang around long enough to undergo interesting reactions. We (my research group) have explored this possibility and published a couple of papers which showed that ice matrices did in fact promote certain polymerization reactions leading to RNA. But there are also a few drawbacks. First, the presence of large icy regions on a hot early Earth is controversial. The global temperature when life began was pretty hot -- 60 to 70 degrees C, so it is not easy to imagine where ice could exist. Even if ice were present, and polymers could be synthesized, there would need to be transient melting to allow the primitive organisms to have continuing access to energy sources. And that brings up perhaps the most difficult hurdle which is a problem for all scenarios of life's beginnings: What energy was available to activate monomers so that they could undergo polymerization? An icy site would seem to me to have the least access to a continuous source of energy. This is why I think that geothermal environments such as volcanic hot springs represent plausible sites for the origin of life.

Gerhard Adam's picture
Might such a scenario (of transient melting) occur at altitude on volcanic peaks?  One could easily imagine periods of dormancy where there would be snow at higher elevations and the necessary freezing to confine molecules to allow for the slow formation and confinement talked about by Miller, and yet volcanic activity could have also produced enough seasonal heat (or at least during periods of activity) to create a boost in new energy and also allow for dispersal of these molecules.

Just a thought....

logicman's picture
Gerhard:  I was thinking about the 'hot world' v 'cold world' scenario earlier today. 

It seems the planet was fairly hot back when life started.  Suppose ice began to form at a pole, probably the Antarctic.  Add in some solar cycles to give long-term cold effects, some volcanic activity to give geothermal effects, and maybe you have a zone in which 'cold' molecules can interact with 'hot' molecules, something like your suggestion.  Melting ice might fall into a pool, or ice might be impacted with magma.  Either way, there should be both a temperature gradient and a chemical gradient - just right for the complexity Dave mentioned in part 1 of this series.  And then there is runoff for dispersal, but whatever gets dispersed had better be equipped to survive in the oceans.

It seems to me that until an ATP precursor mechanism evolved,  proto-life must have depended on thermal energy.  That's not a problem in a hot world.  Perhaps a cooling world with less cloud favoured the evolution of photosynthesis?  I am also visualising a 'mutual catalysis' process in which pairs of molecules each act as a substrate for the other.  That's as far as I can go with this for now.  I'm looking forward to the next episode.

Gerhard Adam's picture
Actually I'm not really envisioning any form of life, but rather that complex organic molecules get a chance to form by not being exposed to excessively high energies that might be prone to break the bonds.  That's why I'm suggesting that higher elevations invariably are cooler than the surface temperature, so it doesn't seem that forming snow/ice should necessarily be a problem even for a quite hot earth.

By keeping the atoms/molecules confined and subject to slow reactions, then there is a greater likelihood that complex compounds could form, which would be much more likely to survive a burst of energy or higher temperatures.  I'm certainly not envisioning anything resembling the more common micro-organisms we see today since the atmosphere would have been substantially different as well, but rather the organic molecule formation that is key to proteins, RNA, and ultimately DNA.

As the environment changed, each stable compound would have been slightly better equipped to deal with the changes and increased complexity could have formed as a result of variations in temperature (energy) and the availability of water (frozen or liquid). 

It would appear that the molecular combinations that result in the required proteins are miniscule compared to the number that are potentially possible.  This would suggest that there were probably large numbers of organic molecules formed, of which only a small subset were useful to form the structures we see today. 

logicman's picture
As the environment changed, each stable compound would have been
slightly better equipped to deal with the changes and increased
complexity could have formed as a result of variations in temperature
(energy) and the availability of water (frozen or liquid).


That's what I meant by 'proto-life', Gerhard.
Perhaps I should have said 'pre-life'.

I wonder about the state of the young Earth when the pre-life chemicals started to replicate.  Was it pre-tectonic?  If there were no mountains, then the highest peaks would have been volcanic, which is what you were suggesting, I think. 

I would expect ''chemical evolution' to progress quite far before some of the first cells could withstand the osmotic shock of being flushed out to sea.  Would you agree?

Gerhard Adam's picture
I was reading a book that brought up an interesting point when one considers proteins and amino acids.  If we assume that all proteins are of length 100 (which they aren't, and some are much longer), then each position in that length would be filled by one of 20 amino acids.  This gives rise to about 10 ^ 130 possible proteins which is far greater than the available particles (in the universe) to create them.

Therefore "chemical evolution" has a resulted in a surprisingly small set of workable proteins from the vast set that is technically possible.  What this suggested to me, was that there are literally billions of combinations that may have occurred but never worked out (for whatever reason).  As a result, we have a small subset that proved successful and came to be the basis for life as we know it.

This also suggests that there are potentially billions of alternatives that may have played out under slightly different circumstances, which also suggests that the formation of organic molecules ultimately giving rise to cells isn't nearly the chance event we tend to think of it as.  What would also be interesting, is to determine if we have ever discovered the existence of such proteins, since they would have no role to play in living systems, their discovery would suggest that these chemical occurrences are much more common than we think.

This would tend to follow the same basic rules of natural selection since the more successful molecules would tend to utilize the available elements more readily than those that were slower to react.  This would cause those "successful" molecules to dominate the chemical landscape leaving few resources available for other "experimental" directions. 

thanks dave for all the info. this is some really interesting stuff

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