Subtitle: Interesting ideas of Thomas Gold and Fred Hoyle

Gold asks the following questions (about hydrocarbons):

        * No microbe, plant, or animal uses helium for any biological function, so why
                    are large amounts of helium found with natural gas (and oil)? (In fact
                    most commercial helium is separated out from natural gas.)
         * If coal and oil formed from different sources (coal from land plants and oil
                    f rom marine microbes) and at different times, why are they often found
                    near each other?
         * If oil, gas, and coal are fossil fuels, where is all the excess oxygen these plants
                    put out (calculated to be 50 times! oxygen now in the atmosphere)?
         * Many solar system bodies are known to have large amounts of hydrocarbons,
                    which are (very likely) abiogenic (Titan even has methane lakes!). So
                    why couldn't the earth have been created with a lot of hydrocarbons too?
         * How is it that some heavily pumped oil fields (as oil geologists have
                    noted) appear to be refilling?
         * How come hydrocarbons found in meteorites and in deep ocean thermal vents
                    often share the signatures used to 'prove' oil, gas, and coal are biogenic?
         * How come hydrocarbons are nearly always found in deep holes drilled in
                    non-sedimentary (igneous rocks like granite) rocks?
         * Why is it that methane (with its attendant risk of explosion) seeps into the air
                    of so many deep mines?
         * Where did all the methane come from that is trapped in the huge quantities of
                    deep ocean methane hydrate and arctic permafrost?
         * How come heavy metals (not known to be taken up by plants or microbes)
                    are found in oil?
         * How is it possible for (well preserved) plant leaf fossils to be found in coal
                    when coal formation wipes away all traces of the original plant cells?
         * If coal is compressed layers of plant material, how come some coal seams
                    are (nearly) vertical?
         * How come no one in the lab has ever been able to create oil or coal from
                    biological material?

See later in this essay for a discussion of Gold's interesting ideas on the orgin of fossil (?) fuels and microbes below ground.

How did life start on Earth?
         Honest answer is nobody knows. Nobody has a clue as to how the to bridge the gap from simple amino acids (20 atoms), which can be made in the lab and are found in meteorites, to the staggering complexity of even the simplest of life forms with their DNA  memory, molecular translation machinery (ribosomes), and resultant thousands of complex proteins.

Who says life had to start on Earth?
            Maybe life developed on earth, but the seeds of life, meaning the complex chemistry of life at the molecular level, came from outside the earth, from space. This concept is Panspermia. Long an obscure and disregarded idea, in recent years it has taken on new life and is now an area of active research.

           I first learned of panspermia years ago in college, not in class but from an obscure book that I found while working in the stacks of my college library, titled Panspermia by a famous astronomer (Thomas Gold?).  I have been intrigued by panspermia ever since.

Introduction to Fred Hoyle
        I just finished reading a book on panspermia, Our Place in the Cosmos, The Unfinished Revolution, by  two astronomers the (late) Fred Hoyle & Chandra Wickramasinghe. Published in 1993 (& out of print) this book is truly over the top and full of wild speculations. When the book was published in 1993, Hoyle, the senior author, was age 78 and Wickramasinghe, his former student, was age 54. However, Hoyle had been thinking about panspermia for a long time having given a famous lecture in 1982 titled, Evolution from Space. Hoyle is quite famous and made major contributions. Hoyle with Thomas Gold and Hermann Bondi were the authors of the steady state theory of the universe, at one time the favorite theory for the creation of the universe. In fact Hoyle coined the term 'big bang' (as a way of belittling it).

        Hoyle early in his career worked on understanding fusion reactions in the sun. At the time no one could figure out how carbon (element 6) could be made in any significant quantity in helium burning stars, since when two helium (element 2) fused to form a beryllium (element 4), the beryllium decayed almost immediately (10^-16 sec) back to helium. Hoyle suggested that a way around the beryllium decay problem might exist if carbon had a particular resonance, whose frequency he could calculate, that would allow a so-called triple alpha reaction to go at a reasonable rate. However, carbon had been very well studied and the data on carbon showed no such resonance. Hoyle, nevertheless, predicted that carbon had such a resonance and encouraged researchers to look for it, telling them where it should be. Within a week the carbon resonance was found at just the frequency Hoyle had predicted! Hoyle had solved a key solar nuclear synthesis problem.

        Wickramasinghe is less well known, but appears to have solid credentials being the Director of the highly regarded Centre for Astrobiology at Cardiff University and author of 25 books and 350 papers.

Footnote on nuclear synthesis  --- In  helium burning stars carbon (element 6) easily combines with a helium (element 2) to form oxygen (element 8), but it is much more difficult (i.e. less likely) for oxygen to combine with a helium to create element 10 (neon). The result is that helium burning stars create a lot of carbon and oxygen because essentially these two elements are the stars' ash.

        As they see it, this new genetic material is the driving force behind evolution on earth and may very well be responsible for some diseases on earth. When the oort cloud (where comets live) is disturbed by a passing molecular cloud, the rain of new genetic material is especially heavy and evolution gets a real goose. Here are some of their arguments:

        * Their only piece of hard data is this --- An infrared spectrum taken of dried (ecoli) bacteria matches very well (the match is impressive) the transmission spectrum of infrared radiation though some 'dust' clouds in the galaxy. The size of the dust particles in the clouds is about the same as bacteria (about 1 um). On this basis they argue that much of the so-called 'dust' in the galaxy is actually dried out bacteria!

            * Some earth bacteria are able to withstand very low pressure, extremely cold temperature, and very  high levels of radiation. Since these conditions don't exist on earth, how, they ask, did bacteria come to possess the genetic machinery to handle these stresses?  They note these are just the properties that bacteria traveling in space would need, and spaceborne bacteria would be under evolutionary pressure to develop these characteristics.

            * They agree that classical Darwinian adaptation based on the accumulation of small random changes can explain how genes can be disabled (or disabled and later revived), but they question whether this process can build up new (useful) genes because the number of possibilities is staggering high. In other words cutting back is easy, but building up is hard. They note this problem fades away (from an earth evolution point of view) if genes come (ready made) to earth in the form of bacteria and viruses.

        This strikes me as a powerful argument. Statistically I see no way a gene can be built up incrementally from scratch, the complexity is too great. It could be that new genes are made by copying old genes and then reworking them step by step. I know that gene duplication happens. I note also that evolutionary biologist seem to be backing away from the purely incremental approach to evolution, as evidence has been found of gene swaps and lateral genetic transfers. Darwin's position was 'Natura non facit saltum' (nature makes no leaps).

        (After writing the paragraph above) I found out that the well known biologist, Lynn Margulis, who advocated the (initially heretical) view that organelles in eukaryotic cells evolved from incorporated bacteria, also has very negative views of NeoDarwinism. She thinks a driving force in evolution of higher animals has been the incorporation of complete genes from bacteria and viruses into their genome.

            * Episodic spurts of evolutionary change in the fossil record (like the rapid development of most multicellular life forms about 570 million years ago), they argue, can be best explained as due to occasional huge increases in comet bacteria and viruses hitting earth that occur when the oort is disturbed. They estimate the oort clould is disturbed a little about every million years by a passing star and disturbed in a big way every 50-100 million years by a passing molecular cloud.

            * They note the historical record shows that in the days before air travel some disease epidemics started at widely spaced locations on earth (like UK and India) at almost exactly the same time. This can be explained, they say, if the cause of the epidemic is disease causing bacteria and viruses raining down from space all over the earth (see below).

            * And, of course, (while they barely mention it) the big enchilada has got to be that no one has a clue as to how life arose on earth. Panspermia, while not solving the problem, at least neatly punts it!

Panspermia on History Channel
        In Oct 07 the history cable channel did a show on panspermia featuring Chandra Wickramasinghe. A strong argument on the show was made that very strange features of the 1918 influenza epidemic can be explained if it fell from the sky (from comet dust). The disease 'started' (passing some threshold) on the same day in the US and in Bombay. This was before air travel. The virus also spread extremely rapidly across Alaska including throughout the rural Eskimo communities. Alaska is as big as Europe and in 1918 only 50,000 people lived there. How did the virus spread so quickly through the widely spread Eskimo villages if it wasn't falling from the sky?

        Another strange feature of the 1918 virus was that it was more likely to kill young healthy adults. Almost no disease acts like this. Chanda speculates maybe its because young healthy adults were more likely to be outdoor and so were more exposed (from sky). (Not a very strong argument)

        All influenze viruses are known to be mutated bird viruses. Obviously any virus drifting down from the sky will come into contact and be easily ingested by birds flying in the air.

        A US rocket mission has just returned with samples of comet dust, but Chandra argues that the way the dust was collected would not detect anything organic or keep anything alive (because the mission planner didn't consider that comets might contain such material). No details were give on the analysis of the comet dust in the show.

Human genome project data
        Very interesting new data from the human genome project is beginning to provide some support to Hoyle and Wickramasinghe' s theory. Hoyle (et al) in their book proposed that the driving force in evolution is the incorporation (in an unspecified manner) of 'outside' genes. Consider this Wikipedia excerpt (from Lynn Margulis entry):

        (Examination of the Human Genome Project output shows that) "significant portions of the human genome are either bacterial or viral in origin—some clearly ancient insertions, while others are more recent in origin. This strongly supports the idea of symbiotic—and more likely parasitic—relationships being a driving force for genetic change in humans, and likely all organisms."

        Whether or not this is strong argument depends on whether there is a way to 'walk' your way to a new gene. In other words can existing genes slowly (one amino acid at a time) be modified to work better and better. I have never seen this (gene walking) discussed by biologists. Seems to me one consideration is how far away the starting point is. A yeast has 6,000 genes, so presumably it makes about 6,000 proteins. How different are these proteins? There is also (it seems to me) the very major problem that often a single (or a few) DNA changes would result in no usable improvement. In classical Darwinian evolution if there is no improvement for selection to act on, then the process stalls, no further change in this direction is possible. (And, of course, new proteins would need to evolve in support of new biochemical pathways, which typically uses a bunch of proteins all carefully coordinated.) So without researching the biological arguments, Hoyle and Wickramasinghe's evolution arguments make a lot of sense to me.

        Of course, superficially this sounds like a creationist argument, which as Dawkins explains, is underlain by the failure to understand that (virtually) all biological complexity results from the accumulation of a huge numbers of tiny statistically likely steps. I doubt that Hoyle & Wickramasinghe were this naive or ignorant about evolution, but I believe they made their argument when the DNA of genes was only partially known, certainly prior to the DNA of any organism being mapped . I presume they made their argument based on their understanding (or guess) that the number of small changes required to go from one gene to another is probably very large, maybe huge, and that the likelihood of the intermediate steps being useful is small. With DNA of genes now fully mapped it would be very interesting to see how close genes are, whether they fall into families, whether they can be seen as being the recombination of other gene fragments. A large pool of substantially isolated genes (in gene space) would give strong support to Hoyle & Wickramasinghe argument.  (A good search phrase would be 'gene evolution'.)

Aside on proteins, amino acids, and codons --- Most genes in all known living creatures code for proteins. Proteins are long strings of amino acids. Only 20 amino acids are used by (all) biological life. A short protein string is 100 amino acids, a long one 2,000 amino acids. Proteins make life possible by acting as catalysts that greatly speed otherwise slow chemical reactions. Wikipedia notes 4,000 different reactions are known to be catalyzed by protein enzymes, and the speed up can be enormous, as high as 10^17, which is 78 million years reduced to 18 msec! For proteins to function as catalysts the amino acid string must fold up in a very specific way forming pockets (think lock and key) that bring reacting molecules into the proper contact and alignment. Since each amino acid in the string can be any of the 20 allowed amino acids, the number of possible proteins is staggeringly large (100^20 to 2,000^20).

        It takes three base pairs (in sequence) in DNA, called a codon, to specify each amino acid of a protein. Proteins are built by cell machines (called ribosomes) that travel down the DNA helix (via messenger RNA) reading the codons and pulling in and linking the specified amino acids. The codon reading is aligned with the DNA by a start codon (there are also stop codons). Since each rung of DNA can be any of four bases, there are (4^3 = 64) possible codons. It turns out that all 64 codons are mapped (as scientists say) into the 20 amino acids (+stop signal). Each codon specifies one and only one amino acid, although obviously, since there are 64 codons and only 20 amino acids, more than one codon can specify the same amino acid. Only two amino acids are specified by a single codon.

        The mapping of codons to amino acids is the same in most of life, and for 48 codons the mapping is universal, meaning the mapping is exactly the same in every known creature. However, the differences in the codon to amino acid mapping are considered so fundamental that it may be evidence for multiple evolutionary origins of life.

 'Silent' mutations
        An article in Scientific American (June 2009) discussed single point DNA mutations where the new codon created by the single base pair change maps to the same amino acid. These were/are called 'silent mutations' and were just assumed to harmless because the resulting protein created by the gene should be unchanged. But a more detailed look at the DNA translation process shows it's not so simple, there is a way for a single point DNA mutation like this to cause problems.

Introns
        Bacterial gene coding is continuous along DNA, but animals and plants (eukaryotic cells) have DNA genes that are kind of a mess. They are almost all broken into pieces with coding triplets (codons) separated by many long stretches of non-coding, often repetitive(?) base pairs called introns. In the translation process from DNA to RNA there is molecular machinery that 'reads' the base pairs and has to figure out where introns start and stop, so they can be snipped out. The RNA that is used to make proteins needs to be continuous. The problem is that start/stop codons don't signal the codon/intron boundaries, the intron snipping machinery needs to figure out on its own where to snip. Wikipedia says this: "Nearly all eukaryotic nuclear introns begin with the nucleotide sequence GT, and end with AG (the GT-AG rule)", so the introns themselves are (vaguely?) marked.

        Evidence is now piling up that some of the so-called 'silent DNA mutations' confuse the intron detecting machinery, so even though the new codon codes for the same amino acid as the old codon the mutation can confuse the translation machinery and the resulting protein is bad.

       You can make your own 3d model of MV-1 bacteria ferrite magnetic crystal by downloading the color coded .pdf  below that you cut out and fold up. I did it in about 90 minutes. A 3d model is much better than words or pictures to see how 6 + 6 + 8 crystal faces fit together.  The resultant shape looks to me reasonable for a magnet. Notice it's shaped like a bar magnet, longer than it is wide, with symmetrical, parallel ends making it stackable. The poles of the magnet would be at the ends. Poles of a bar magnet need to far apart if the magnetic field is to extend into space. Many of the crystal faces just serve to trim back the edges a little.

        http://www.gps.caltech.edu/~jkirschvink/martiianMagnetosomesCutout6.pdf

Microbes living below the surface
        In recent years microbes have been found living deep below ground in mines and drilled holes, in the deep ocean near thermal vents in rift zone and at so-called cold smokers, and in many other extreme environments.  Much of this life is archaea, ancient bacteria that make up the 3rd domain of life. This is consistent with a theory first developed in 1982 by the late Thomas Gold, astrophysicist and all around gadfly. Even though Gold was a member of the National Academy of Sciences it was 1992 before he could get his ideas on microbes published. In his 1999 book Deep Hot Biosphere Gold lays out a scenario for how (huge numbers of) microbes could (potentially) be living a few km (deeper is too hot) below the earth's surface.

Thomas Gold, an introduction
       Thomas Gold, Emeritus professor of Physics at Cornell, is best known as one of the inventors (with Fred Hoyle and Hermann Bondi) of the Steady State Theory of the universe, which for more than a decade was the principal alternative to the Big Bang Theory. For 20 years Gold ran the Cornell Center for Radiophysics and Space Research, where he oversaw the construction and operation of the world's largest radio telescope, in Arecibo, Puerto Rico. He designed the stereo camera used by the Apollo astronauts. He controversially predicted the astronauts would find the moon's surface covered with a fine grain powder, and in 1969 when astronauts stepped on the moon that's just what they found.

        Gold, though an astronomer by training, had widespread interests. As a graduate student (in astrophysics!) he disagreed with physiologists who argued the brain, not the ear, allowed humans to be so good at discriminating musical notes. Gold argued there had to be resonating structures within the ear, and he designed an "elegant experiment" to prove his theory. As the Cornell press release put it at his death in 2004, "his research (on the ear) was largely ignored until nearly 30 years later" when a new generation of physiologists discovered tiny resonating hairs in the ear.

        When pulsars were discovered, Gold quickly published that they were most likely rotating neutrons stars. Another crackpot idea from Gold? Here is Gold describing what happened in just a few months following his 1967 publication:

        "My idea that rotating neutron stars were responsible for pulsars was totally ridiculed at an international conference. I was not allowed to speak from the podium for five minutes in a two-day conference because it was regarded as such a monstrous idea. That was in the spring, and I think by November or December of that year, observations of the pulsar in the Crab Nebula had confirmed every damn thing that I'd said - confirmed that the frequencies of a young pulsar would be higher, confirmed that good places to look would be supernova remnants, and a number of other things." (from Wired interview, July 2000, when Gold was age 80)

              http://www.wired.com/wired/archive/8.07/gold_pr.html

        And for 30 years Gold has argued that (nearly) all hydrocarbons found by drilling are not fossil fuels, i.e. oil, gas, and coal are not the remains of life that has been reworked by geology (cooked by heat and pressure).

        What? Everyone knows oil and gas are fossil fuels. Is Gold just a nutjob? Consider this: The 1947 Nobel Prize winner for Chemistry was Sir Robert Robinson. He won the prize for study of the structure of chemicals made by plants. After making detailed studies of natural petroleum, he published a paper in the famous journal Nature, saying (note the wording):

        "Actually it cannot be too strongly emphasized that petroleum does not present the composition picture expected from modified biogenic products. All the arguments from the constituents of ancient oils fit equally well, or better, with the conception of a primordial hydrocarbon mixture to which bio-products have been added." (Sir Robert Robinson, 1963)

Here's a link to a (short) 1997 paper by Gold on this subject -- http://j_kidd.tripod.com/b/103.html

Alfred Wegener --- a cautionary tale
        In the early 20th century a German named Alfred Lothar Wegener, noticing (as many have) that the Atlantic bulge of South America seems to fit into the indentation of Africa, spent years gathering up evidence for movement of continents and published a book in 1915 arguing that continents move, which he revised and expanded until his death 15 years later. Some of his arguments were strong, others vague and tantalizing. Wegener was a meteorologist, not a geologist, and the geologists, sure that continents could never move though the rock of the sea floor, denounced him and his work in the strongest possible terms.

        We now know Wegener was right and virtually the entire geological community was wrong, continents do move. Alfred Wegener is now recognized as the principal founding father of plate tectonics, one of the great scientific revolutions of the 20th century. The experts were right on the details (continents don't move through sea floor rock), but wrong on the big picture. It turns out that convection cells in the mantle cause sections of the crust (now known as plates) to move about the earth (carrying the continents with them) as new sea floor rock is created along thousands of miles of rifts under the ocean and as plates sink into the mantle at plate boundaries in a process known as subduction.

        Interestingly in 2008 I came across a a natural gas association web site. It admits, "There are many different theories as to the origins of fossil fuels", and lists three ways methane and natural gas are formed: thermogenic (cooked organic matter), biogenic (waste product of archaea), and abiogenic (from deep in the earth). And curiously the site describes abiogenic methane as being "similar to" thermogenic methane. (see below)

        "A third way in which methane (and natural gas) may be formed is through abiogenic processes. Extremely deep under the earth's crust, there exist hydrogen-rich gases and carbon molecules. As these gases gradually rise towards the surface of the earth, they may interact with minerals that also exist underground, in the absence of oxygen. This interaction may result in a reaction, forming elements and compounds that are found in the atmosphere (including nitrogen, oxygen, carbon dioxide, argon, and water). If these gases are under very high pressure as they move towards the surface of the earth, they are likely to form methane deposits, similar to thermogenic methane." (www.naturalgas.org from National Gas Supply Association)

        Gold says it's almost certain that the bodies that accreted to form earth contained a lot of hydrocarbons. In support of this he argues is that we see hydrocarbons on many other bodies of the solar system, and these are clearly not (or are very unlikely to be) the product of life. A recent space probe (Cassini) sent to Saturn's moon Titan found methane clouds in the atmosphere and what are thought to be methane lakes on the surface! There's a type of meteorite that has a lot of carbon it in, called the carbonaceous chondrite, which makes up about 5% of meteorites. Some volcanos, which bring things up from miles below, belch substantial amounts (20% or so) of methane (CH4), which is the lightest hydrocarbon. There are well documented stories of Anak (the son of) Krakatoa, when erupting below the surface of the sea, spewed gas that for a long time burned with flame on the sea's surface.

        I would add that while beginning geology text books often have a little sketch showing how oil forms from dead plants and animals, the certainty this picture presents is vastly overstated. Princeton emeritus professor of geology, Kenneth Deffeyes, in his books on oil, explains that (amazingly) there is no really good, accepted model of how oil forms. Deffeyes himself authored a geology text book with the classic oil forming sketch, but he admits the theory "has a weakness". That weakness is nowhere on earth at the present time is enough biological material being laid down and sequestered to form oil in the future! Deffeyes, however, had an opportunity to study the source rock (rock that holds the oil) from the world's largest oil field in Saudi Arabia (Ghawar), and he reports that its source rock is "fecal pellet limestone", implying strongly that the oil in this field is cooked shit.

confirmation?
Lost City --- new type of undersea vent (update 7/09)
        Recently a new totally different type of undersea thermal vent has been found. They were predicted theoretically to exist a few km from the upwelling where black smokers are found and the first was found where predicted in 2000. They are alkaline as opposed to black smokers which are acidic and occupied by different microbes (archaea instead of sulfur oxidizing bacteria in black smokers). The famous one in the Atlantic is called "Lost City". (This info from a 2009 book I am reading:  Life Ascending: The Ten Great Inventions of Evolution, by Nick Lane (biochemist at University College London).

        What's remarkable, and exciting to those investigating the orgin of life, is that the geochemistry of the vent causes small bubble of free hydrogen gas to continuously form. Free hydrogen is very rare on earth, and CO2 and free hydrogen together can react (very slowly) say thermodynamics to produce organic material (methane?). Here is a non-life way to generate (some) organic material.

        -- The microbial communities found in Lost City are dominated by a single group of methane-metabolizing archaea (related to the methanosarcinales).

New story (1/31/08):

Deep-ocean vents are a source of oil and gas
        Hydrocarbons bubble up from the mid-Atlantic's Lost City. Undersea thermal vents can yield unexpected bounty: natural gas and the building blocks of oil products. In a new analysis of Lost City, a hydrothermal field in the mid-Atlantic, researchers have found that these organic molecules are being created through inorganic processes, rather than the more typical decomposition of once-living material. (Wood Hole researchers as reported in Nature News 1/31/08)

Doesn't oil have a biological signature?
        Yes. While small in proportion, there are huge quantities in oil of molecules that definitely are biological in origin, for example some are known to come from cell membranes. In the standard theory of oil this is taken as evidence that oil is cooked (marine) biological material.

        Gold has his underground (as deep as 10km) microbes 'feeding' by oxidizing hydrocarbons that rise up in the earth. This makes sense to me. Oil is food, it provides energy if oxidized. Microbes are going to eat it to the extent they are not limited by some other resource. Are there known microbes that eat oil? Absolutely, 'bugs' are now deliberately spread on oil spills to eat it up. Hence Gold has a good explanation of why biological material is found in oil. A lot of microbes have lived in it, died in it, and shit into it.

Oxidizing hydrocarbons
{        Both the hydrogen and carbon in hydrocarbons provide energy when oxidized (combined with oxygen, or technically when it loses electrons.). Gold says it's a matter of simple chemistry that hydrogen (in a hydrocarbon) is more easily oxidized than carbon. (I'm not sure I understand this. Does this mean oxidizing hydrogen yield more energy than oxidizing carbon, or is there an energy input threshold to initiate the reaction and that threshold is higher for carbon??). Gold say a free oxygen atom encountering a hydrogen molecule is more likely to grab off the hydrogen than the carbon.

        Probably there's an energy threshold. Here is Wikipedia on the how energy is obtained from the energy transport molecule ATP --- "The bond itself is not high in energy (like all chemical bonds it requires energy to break), but energy is produced when the bond is broken and water is allowed to react with the two products. Thus, energy is produced from the new bonds formed between ADP and water, and between phosphate and water." }

        Gold argues that as hydrocarbons rise up in the earth they slowly lose hydrogen (reconfiguring in the process). Gold had a graduate student do an experiment that showed under temperature and pressure equivalent to 10km down that a hydrocarbon with three carbon substantially reconfigured in a matter of hours to a range of hydrocarbons with one to five carbon (hydrogen to carbon total ratio of the mixture remaining constant). This explains Gold says why methane with the highest hydrogen to carbon ratio is found deep, then oil, then coal (with least hydrogen) near the surface.

Gold on coal
        Gold points out that coal sometime contains fine fossils of leaves or twigs that themselves are made of coal. He asks how is it possible for a finely detailed fossil, sometime even showing cell structure, to exist in a supposed matrix of plant remains in which all traces of its original structure have been erased?

        Fossilized trees made of quartz (silicon dioxide) exist. When sawed open, they look exactly like the a sawed tree trunk except its rock. (Yup, I've seen them.) It's well accepted that they formed when a liquid percolated though the cell structure and preserved it by slowly replaced all the hydrocarbons of the wood with quartz/silicon (SiO2). Gold says it's likely the same explanation applies to leaf fossils found in coal. A slowly flowing liquid hydrocarbon gradually replaced the biological structure of the leaf with less hydrogenated 'coaly' (his word) material.

        Gold raises a bunch of other problems with the biogenic (standard) theory of the origin of coal.
        ---  Certain metals like mercury, gallium, and germanium are found concentrated in coal at levels much above those in sedimentary rocks. These are not normally though of as metals that would be concentrated by plants.
        ---  There are some large coal seams that are vertical. Gold says the biogenic theory does not have an explanation that is even remotely plausible to explain this.
        --- The ratio of minerals to carbon in any present day accumulation of plant debris is much higher than mineral levels found in coal. Coal is almost all carbon with mineral levels as low as 4%. If coal is decayed plants, where did all the minerals go?
        --- The standard theory posits that oil is the biological debris of marine organism and coal comes from terrestrial vegetation. Since the sources of oil and coal are thought to be totally different, if you map where they are each found and compare maps you should see no correlation. But this is not the case. There are regions where the oil and coal maps are fairly similar, for example, South America. Gold's book has a map of oil and coal locations in South America. Explain that!

Lynn Margulis --- another cautionary tale
        The Endosymbiotic Theory was first proposed by biologist Lynn Margulis at Boston University in the 1960's and officially in her 1981 book "Symbiosis in Cell Evolution".  Although now accepted as a well supported theory, both she and the theory were ridiculed by mainstream biologists for a number of years.

        She proposed that 2-3 billion years ago when the earth's atmosphere began to be 'poisoned' by waste oxygen from photosynthetic bacteria (cyanobacteria) that photosynthetic anaerobic bacteria began to take up residence inside aerobic cells. The aerobic cell would protect the anaerobic bacteria from oxygen, and in turn the photosynthetic anaerobic bacteria (now as an organelle) would feed the cell in which it lived. Both cells benefit.

        Margulis predicted that if this theory for the origin of chloroplasts (and other organelles) was right, then organelles would be found to have DNA and the type of DNA would be similar to the DNA in bacteria. In the 1980's it was indeed found that chloroplasts and mitochondria organelles both have DNA and it is similar to the DNA of bacteria.

        The mainstream biological thinking now, after 30 years of additional evidence, is that the Endosymbiotic Theory provides the most plausible explanation for the development of organelles within the eukaryotic cell. Richard Dawkins in 1995 speaking of Margulis said, "(Her theory) is one of the great achievements of twentieth-century evolutionary biology, and I greatly admire her for it."

        http://www.biology.iupui.edu/biocourses/N100/2k2endosymb.html

Origins of Eukaryotic Cells: Mitochondria and Chloroplast (Indiana Univ & Purdue Univ Biology 2002 class notes)

How do early microbes on earth get energy to live?
        Note the food source for early life on earth is a non-trivial problem. Today the (root) energy source for (virtually) all surface life is the energy of solar photons captured in plants by photosynthesis. The only known exceptions are life in a few caves and near some vents and seeps on the sea floor. Gold analogizes that getting energy from the sun is like trying to catch machine gun bullets (because solar energy comes in discrete, high energy packets called photons). The photosynthesis process in plants works, but to 'catch these bullets' requires a very complex biochemical process. Early life very likely needed some (easier to process) chemical source of energy. That food source for early microbes may very well have been methane or some other light hydrocarbon. We now know the energy source for the microbes that support the food chain in sealed dark caves and and deep sea vents is indeed chemical energy.

Microbes need reduced (unoxidized) carbon
        For carbon in the earth to be source of (chemical) energy to the microbes it must be in a reduced (unoxidized) state. Free oxygen is very active and if has access to a hydrocarbon it will oxidize the hydrogen to water (H2O) and the carbon to carbon dioxide (CO2). Gold points out that no net energy gain is available in a process that starts with CO2 and ends with CO2. However, there are some methane generating archaea (methanogens) that take in CO2 and hydrogen, using the hydrogen for energy and to reduce the carbon. Gold says that estimates are that 20% of the carbon near the surface of the earth is unoxidized. Much of the near surface oxidized carbon is in limestone (calcium carbonate, CaCO3) and dolomite (CaCO3 + MgCO3) under the sea with the carbon in these rocks deriving from the atmospheric/ocean pool of CO2. Calcium carbonate precipitates naturally out of sea water and also biologically precipitates in the form of calcium carbonate shells that get buried.

Wouldn't the hot, molten earth have oxidized all the accreting hydrocarbons?
        Gold says yes they would have all been oxidized if the the earth was really a molten ball. For Gold's theory to work some of the material accreting to form the earth could not have been heated too much, some of the primal hydrocarbons must have remained unoxidized. Gold says that the molten earth theory has been losing favor, but he gives little documentation on this point. Other researchers have reported that synthesis of gaseous and liquid hydrocarbons in the earth's mantle at high temperature and pressure may be possible.

Temperature of the earth vs time
        The heat of the earth has come from two sources: gravitational energy released when materials the formed the earth came together and energy released by decay of radioactive elements within the earth. The former can be thought of as kinetic energy gained from gravity that gets transformed to heat when the accreting bodies collide. This energy, of course, was mostly released early in the life of the earth. The second major source of energy, energy from the reduction of mass in radioactive atoms, has occurred slowly and fairly evenly over the life of the earth.

        What would be interesting would be so see plots of the calculated earth's temperature (at various depths) vs time. I have never seen such a plot. I wonder if the earth is cooling or heating. There's a well known physics story that in the late 19th century the thermodynamics expert Lord Kelvin calculated that the earth would cool from a hot ball to its present temperature in about 100 million years. This was before radioactivity had been discovered, so Kelvin on the basis of this calculation argued the earth could not be more than 100 million years old. Since 100 million years is only a little over 2% of the 4.6 billion year lifetime of the earth, this means, if Kelvin's calculation was anywhere near right, radioactive heating must be responsible for nearly all of the earth's current heat.

Where do underground microbe get oxygen?
        For microbes to get energy from hydrocarbon 'food' they need a source of oxygen so they can oxidize the carbon. Gold assumes there is no free molecular oxygen below ground, so the oxygen must come from chemical reactions. Rocks contain lots of oxygen since they are built of minerals that are mostly oxides, but the microbe needs to obtain oxygen without expending too much energy. The oxygen atoms in rock oxides are so tightly bound that they are unavailable to the microbes, because it takes more energy to break these oxygen bonds than can be obtained by using the freed oxygen to oxidize hydrocarbons.

        Luckily, there are some common rock minerals where the oxygen atom is much more loosely bound. These are minerals with highly oxidized iron compounds (Fe2O3) and oxidized sulfur compounds called sulfates (SO2 and H2SO4). A microbe can generate net energy by breaking apart these iron and sulfur compounds and using the freed oxygen to oxidize the carbon (generating carbon dioxide CO2) and hydrogen (generating water H2O). This process also makes available to the microbe carbon atoms that it needs to form structure. To build its biochemical machinery the microbe also needs some metal atoms (for proteins) and some light atoms, like chorine and sodium.

Iron as a waste product
        If a microbe uses iron oxide to obtain oxygen, one end result is iron in a less oxidized state, which happens to be magnetic. Small crystals of magnetite are the most common form of iron in this state. And suggestively small magnetic crystals of magnetite were found in a famous Marian meteorite, known as meteorite ALH84001. This 4.5 billion year old meteorite, which was found in the Antarctic, is thought to have been blown out of deep crater on Mars and was featured in a NASA press conference (introduced by President Bill Clinton) as possible evidence of ancient life on Mars.

Carbon isotopic ratios
        Carbon has two stable isotopes: C12 (99% of carbon) and a slightly heavier version C13 (1% of carbon), the 99:1 ratio due to the fusion processes in stars. C14 (used for carbon 14 dating) is not stable. It has a lifetime of 5.7k years and exists in trace amounts on earth only because it is continually made in the upper atmosphere. It turns out that some biological and geological processes favor C12 over C13, so plotting the ratio of C13/C12 vs time and/or location is often useful in understanding these processes.

        All isotopes share the same chemistry because they have the same electron structure, but a heavy isotope will have a slightly lower thermal velocity than a lighter isotope. The reason for this is that thermal energy in an atom (or molecule) is stored in its kinetic energy (1/2 mv^2), so for mass (say) 2% higher, velocity is 1% lower.  One process where molecular velocity is important is in diffusion. Faster (lighter) molecules are able to get through tight spaces more easily (quickly).

Plants take in C12 more easily than C13
        The structure of all photosynthetic plants and algae require CO2 to diffuse through semi-permeable membranes. CO2 with C12 atoms (with their high thermal velocities) diffuse in more easily and so are taken up more efficiently than CO2 with C13 atoms. For this reason all plant material is deficient in C13, meaning the C13/C12 ratio in plant material is lower than C13/C12 ratio in the atmosphere. And the same C13 deficiency applies to animals too, because animals get all their carbon from eating plant material.

        To give a feeling for the numbers: The molecular weight of (common) CO2 is 44 because the atomic weight of carbon is 12 and oxygen is 16 (12 +16 +16 = 44). CO2 with a C13 atom in it has a molecular weight of 45 making it about 2% heavier (45/44 = 1.023) than common CO2, hence about 1% slower moving. Measurements of some CO2 fixing reactions in plants showed about a 2% difference in the speed of the reaction between C12 and C13 containing molecules.

J Harlen Bretz --- still another cautionary tale
           In the 1920's J. Harlen Bretz, a professor of geology, after years of field work in the scablands of eastern Washington proposed the dramatic scab lands were created almost overnight by a huge flood of water. After his presentation at a famous geological meeting, his explanation was dismissed out of hand and called ludicrous. Geologists in those times were all trained to be uniformitarians (geological features of the landscape are created very gradually by processes still happening on earth), and almost by instinct rejected catastrophic explanations that to them smacked of the biblical flood. (For the same reason the theory that a meteorite killed the dinosaurs had an uphill battle to be accepted.)  Bretz (& J.T. Pardee) worked for the next 30 years collecting data to support the theory.

        Evidence has piled up and it's now well accepted that Bretz & Pardee were right and virtually the entire geological community was wrong, the scablands were scoured out by a huge torrent of water. The water came from a huge glacial lake, now called glacial Lake Missoula, that drained almost overnight when an ice dam collapsed. (It's now thought the lake may have formed and drained several times.) In 1979 at age 96 Bretz received the Penrose Medal, one of geology's top prizes, saying after this award "All my enemies are dead, so I have no one to gloat over."

         http://www.gps.caltech.edu/~jkirschvink/
         http://palaeo-electronica.org/2001_2/editor/mars.htm

         In the first site look for a link to the slides of the Carl Sagan (memorial) Lecture given at the American Geophysical Union Meeting, Dec 2001 by Joseph Kirschvink (CarlSaganLecture.ppt). These slides are in Power Point ( .ppt) format, so you need a Power Point viewer on your PC. A good, free one is OpenOffice.org Impress. Try clicking each slide, some have hidden comments.

        A good and very readable introduction to the arguments for life in a 4+ billion year old Martian meteorite (ALH84001) is this book:

         The Rock from Mars: A Detective Story on Two Planets
         by Cathy Sawyer, Random House, 2006