All of us at DKos are all sick of the demonization of scientific thinking, exemplified by the bogus anti-climate change propaganda campaign. But it's worse than that. All this manufactured outrage is also designed to drown out the intellectual excitement of genuine scientific advances, especially when such advances might have some bearing on evolution - the ur-wedge issue of fundamentalist political agitprop.
This diary will try to explain(and, failing that, give links to some scientific and popularized literature) an amazing new scientific theory that has come to challenge the old primordial soup theory of the origins of life. Now, I would not be surprised if many find such a diary to be totally irrelevant at a political website. But the ability to publicize this kind of advance, to show how the slow-moving, but powerful, machinery of science has the ability to accept completely new ideas when completely new facts (like deep ocean hydrothermal vents) arise is critical to an open, secular, and rational democracy. If citizens can't see, and be entranced by, the science they are paying for, they have no reason to fund it. The fact that Nova, Science, National Geographic, etc. have avoided this topic is revealing.
This is going to be complicated. Its real, cutting edge science. But it is also fascinating.
Within ten years of the completely unexpected, and heavily publicized, discovery of deep ocean hydrothermal vents, complete with exotic tube-worm lifeforms, a hypothesis that these vents were the location of the origins of life was proposed, in 1988.
Over the intervening twenty-plus years, this hypothesis has been elaborated into a testable theory that includes geological, physical, chemical, and biological predictions, some of which have already been confirmed. The fact that the theory can accommodate so many known facts in so many scientific disciplines commands, at minimum, the curiosity of the non-scientific community. Its rare that such revolutionary theories can gain traction within an increasingly balkanized scientific establishment.
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1. An initial overview of the theory
Where to begin? This type of theory of the Origins of Life (OOL) began to be proposed when people reflected upon how much chemical energy was available for free from the immense output of hot, sulfide-bearing minerals from the hydrothermal vents. They thought about how chemistry alone could produce basic organic molecules like acetate and formate under these conditions.
Of course, the first vents discovered, the so called "black smokers", produced scalding hot water, 350 C, which was not conducive to micro-chemical evolution. But, upon further thought, it was hypothesized that, further from the active sea-floor spreading zone, cooler vents might exist. And, it was further hypothesized that such vents would be alkaline (much more later on why that is important). Such alkaline vents, the so-called "Lost City hydrothermal field" were found in 2000. This successful prediction really put the booster rocket under this theory, and it has been advancing by leaps and bounds since then.
There is a good popularization of this theory by Nick Lane (of University College, London) in The New Scientist. From that, here is his barest-of-bones outline of the theory.
10 steps to life on Earth
If life did evolve in alkaline hydrothermal vents,
it might have happened something like this:
1. Water percolated down into newly formed rock under
the sea floor, where it reacted with minerals such as
olivine, producing a hot alkaline fluid rich in hydrogen,
sulphides and other chemicals. This hot fluid welled up
at hydrothermal vents.
2. The early ocean was acidic and rich in dissolved iron. When
upwelling hydrothermal fluids reacted with this seawater,
they produced carbonate rocks riddled with tiny pores and
a “foam” of iron-sulphur bubbles.
3. Inside the bubbles, hydrogen reacted with carbon dioxide
to form simple organic molecules such as methane, formate
and acetate. Some of these reactions were catalysed by the
iron-sulphur minerals, which are still found at the heart of
many proteins today.
4. The electrochemical gradient between the alkaline vent
fluid and the acidic seawater leads to the spontaneous
formation of acetyl phosphate and pyrophospate, which
act just like ATP, the chemical that powers living cells.
These molecules drove the formation of amino acids and
nucleotides, the building blocks of proteins and of RNA
and DNA respectively.
5. Thermal currents within the vent pores concentrated large
molecules like nucleotides, driving the formation of RNA and
DNA – and providing an ideal setting for an RNA world and its
evolution into the world of DNA and proteins. Evolution got
under way, with sets of molecules capable of producing more
of themselves starting to dominate.
6. Fatty molecules coated the iron-sulphur froth and
spontaneously formed cell-like bubbles. Some of these
bubbles would have enclosed self-replicating sets of
molecules – the first organic cells. The earliest protocells
may have been elusive entities, though, often dissolving
and reforming as they circulated in the vents.
7. The evolution of an enzyme called pyrophosphatase,
which catalyses the production of pyrophosphate, allows
protocells to extract more energy from the gradient between
the alkaline vent fluid and the acidic ocean. This enzyme is
still found in many bacteria and archaea.
8. Some protocells start using ATP as well as acetyl phosphate
and pyrophosphate. The production of ATP using energy from
the electrochemical gradient is perfected with the evolution
of the enzyme ATP synthase, found within all life today.
9. Protocells further from the main vent axis, where the
natural electrochemical gradient is weaker, started to
generate their own gradient to drive ATP production.
10. Once protocells could generate their own electrochemical
gradient, they were no longer tied to the vents. Cells left the
vents on two separate occasions, with one exodus giving rise
to bacteria and the other to archaea.
The key fact that isn't emphasized in the previous quote is the nature of the rock formations at Lost City. The rock that forms is completely different than at a black smoker. It is almost a froth of air and rock. It is incredibly porous, honey-combed with cavities. And, two things are important for the theory:
1) The cavities are at a scale of 1 micron - the same size as a living cell.
2) The cavity walls are saturated with iron-sulfur(Fe-S) mineral catalysts.
With that in mind, here is another science news overview from 2009, focusing on the geologist and the biologist who are the foremost proponents of this theory. Here is another snippet that tries to fill in some of the details from Nick Lane's list:
Between the late 1980s and the mid 90s, Russell and his colleagues stitched all their evidence into a portrait of the 'Goldilocks' spot, where the mineral chemistry was just right for what happens in cells today. "We recognized that some types of mineralization had a lot in common with the chemical processes of life," says geologist Allan Hall of the University of Glasgow, UK, and one of Russell's principal collaborators at the time.
Their theory of how life got going starts inside the tiny mineral chimneys. This protected environment would allow chemicals to become concentrated — a key problem facing anyone trying to explain how biochemistry can begin without cells. When these chimneys formed, they would have been gels rather than rocks, with membranes that would have allowed small molecules to pass through, much as cell membranes do. And the team found they could produce such a mineral gel in the lab3. The gel's membranes contained mineral sulphides of iron and nickel that would have catalysed organic reactions — just as these metal sulphides do inside modern enzymes.
Across the membranes, gradients would have developed. Inside the vent, the water would have been hot, alkaline and rich in hydrogen, thanks to reactions between water and iron minerals in the crust, a process called serpentinization. Outside in the ocean, the water would have been cold and acidic. The vast majority of modern cells power much of their chemistry by creating similar gradients across their membranes. But they use a large variety of proteins to do it. Life's diverse ways to harness a ubiquitous energy source — the proton gradient — makes Russell think that the proteins are a secondary adaptation, and that life latched onto inorganic proton gradients before it could make its own.
What is scientifically exciting here is that the pre-biotic geochemistry of these vents has exactly the same electrochemical gradient as living cells; and that the Fe-S centers in the minerals are found in enzymes that today catalyze the same reactions (i.e., the production of methane and acetate). If you want to read what I said about this theory years ago, see this diary.
For extra credit:
If you are a chemist, this theory has been worked out in great detail. This highly-technical paper contains a 2007 version of the chemical origins of life.
2. LUCA had no cell walls; the archaea prove this
One of the key innovations of the hydrothermal vent theory (HVT) is that evolution reached an advanced state without lipid membranes (i.e., cell walls). The rocks served as the membranes; but they were porous, so that DNA/RNA etc could move between compartments. OOL people refer to the Last Universal Common Ancestor (LUCA) of life. To the HVT proponents, LUCA had no cell walls.
This part of the theory is backed up by some more science that happened post-1980, namely the realization that "prokaryotes" were really two separate families, now known as bacteria and archaea.
It was due to the new ability to read genomes that the uniqueness of archaea was discovered. At the time, the speed of genome sequencing (i.e., reading) was very slow. But, Carl Woese hit upon the idea that the 16S ribosomal RNA was a highly conserved marker of bacterial evolution that was small enough to sequence with the techniques available at the time. When he did this for many species, he discovered some startling facts.
He discovered that many extremophiles were genetically and physically different than bacteria. (Before then, it was assumed that extremophiles came after bacteria, and were adaptations.) The most salient differences were in the DNA duplication machinery and in the cell wall. The cell wall was completely different; the lipids even had a different "handedness" (technical term: chirality). Now, biologists have been fighting about whether or not the chirality of life was an accident for decades. This sort of proves it was.
After ten years, Woese carried the day; and biologists today talk about the three classes of life: archaea, bacteria, and eukaryotes. (We will leave eukaryotes for another diary, because the endosymbiont hypothesis is another completely cool scientific advance.)
The bottom line here is that, not only does HVT explain where life originated; its proposal that LUCA had no cell walls is validated by the stark differences in the archaea/bacteria genomes.
For extra credit:
The most recent summary of HVT can be found here. They have focused in on a conserved, ancient pathway for fixing CO2 into methane or actetate, the so called Wood-Ljungdahl pathway. See this paper for details.
They also emphasize that the porous rock walls could support chemiosmosis - the mechanism used by all cells and mitochondria to turn chemical gradients into work. Truly this work ties together a great deal of facts with minimal theoretical overhead.
3. Horizontal Gene transfer, Collective Evolution, and the Darwinian Transition
Horizontal Gene Transfer(HGT) is another hot idea from 25 years ago that is now the conventional wisdom. We now know that bacteria share genetic material across species (which is why GMO crops with pesticide resistance genes are such a bad idea).
So, during OOL, in the absence of cell wall barriers, HGT was dominant. The new scientific thinking is that the "tree of evolution" does not have a single root; but, rather, it goes back to a "bush" formed by a mass of cells heavily interconnected by HGT. The conclusion of "bush, not single root" is clearly visible in the genetic comparisons that Woese used to delineate archaea from bacteria. Woese is still at work. In 2006, he followed the logic of his earlier work to propose collective evolution
We argue that the universality of the code is a generic consequence of early communal evolution mediated by HGT, and that HGT enhances optimality. Our arguments are backed up by computer simulation studies, which are necessary to probe the complex interactions between the variety of collective mechanisms that we shall present. We show that there are virtuous cycles of cooperativity: (i) the more similar the genetic codes, the greater the intensity of HGT, and the stronger the tendency for codes to become more similar; and (ii) HGT helps the codes to optimize, and optimization enforces universality and compatibility between translational machineries...
Our framework fits naturally the recently proposed picture that early evolution was dominated by HGT... The broader implication of this scenario is that innovation-sharing led to the emergence of modern cell designs from a communal state, not a unique, shared ancestor. Such a communal state existed before the point of emergence of vertical evolution, which has been termed the Darwinian transition. The defining property of the communal state was that it was capable of tolerating and using ambiguity, as reflected in the pervasive role of HGT. A Darwinian transition corresponds to a state of affairs when sufficient complexity has arisen that the state is incapable of tolerating ambiguity, and so there is a distinct change in the nature of the evolutionary dynamics (to vertical descent).
You can begin to see why TPTB want no part of the new biology. The new biology undermines "red in tooth and claw" Social Darwinism, without undermining all the knowledge we have gained about genetics and species and evolution. Scientists now actually talk of a time "before Darwinian evolution" could come into play, and they describe that time as one of cooperation and sharing. Then, they compare the current situation of our culture to such a period.
When you hear a hard scientist like Woese talking about pre-single celled life using terms like "virtuous cycles of cooperativity", "tolerating and using ambiguity", "communal state", and "innovation sharing" and applying such theories to society, you know that biology is about to get whacked the same way economics got whacked back in the 90s for proposing the network effect and lock-in.
By Darwinian evolution Woese means evolution as Darwin understood it, based on the competition for survival of non-interbreeding species. He underscores the radical observation that Darwinian evolution does not go back to the beginning of life. When Woese compared genomes of ancient lineages of living creatures, he found evidence of numerous transfers of genetic information from one lineage to another. In early times, Dyson emphasizes, horizontal gene transfer, the sharing of genes between unrelated species, was prevalent. It becomes more pronounced the further back we go in time.
"Life was then a community of cells of various kinds," Dyson points out "sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. Evolution could be rapid, as new chemical devices could be evolved simultaneously by cells of different kinds working in parallel and then reassembled in a single cell by horizontal gene transfer."
You think TPTB are going to go for such truly revolutionary thinking? Just sayin'.
Oh, BTW, Woese's computer simulations of communal evolution are based on the network effect.
4. Other implications: the ancient origins of Viruses
Another implication of the strong HGT of the pre-Darwinian era is that viruses have always been with us. (The only paper I have is way too technical, so I don't recommend it.) The origin of viruses is another area of contentious speculation in science. Remember folks, contrary to the "teach the controversy" fundies, contention in science is a good thing. New theories always arise when new facts resolve old, inconclusive debates. In this case, the old ideas are:
Traditionally, these ideas have revolved around three themes: i) origin of viruses from primordial genetic elements, ii) degeneration of unicellular organisms to the virus state, and iii) "escaped genes" hypotheses deriving viruses from genes of cellular organisms that have switched to the selfish mode of reproduction.
With the new ideas from HVT, the first theme has taken the lead; while the other themes have taken major hits. Below are some excerpts of a general nature.
at the early stages of evolution, including the LUCA stage, the entire genetic system was, in a sense, "virus-like". Initially, all RNA segments in the population would be completely selfish, and there would be no distinction between parasitic, "viral" elements and those that would give rise to genomes of cellular life forms. However, this distinction would emerge as soon as the first "selfish cooperatives" – relatively stable ensembles of co-inherited genetic elements – evolve. Inevitably, the selfish cooperatives would harbor parasitic genetic elements that would divert the resources of the ensemble for their own replication...
The distinction between the progenitors of viruses and the ancestors of cellular life forms may be described as one between primary infectious agents, that routinely moved between compartments, and increasingly complex and "sedentary" ensembles of selfish cooperators that would spill from one compartment into another on much rarer occasions.
Like other models of the early stages of evolution of biological complexity, this scenario faces the problem of takeover by selfish elements. If the primordial parasites become too aggressive, they would kill off their hosts within a compartment and could survive only by infecting a new compartment. Devastating "epidemics" sweeping through entire networks and eventually eliminating all their content are imaginable, and indeed, this might have been the fate of many, if not most, primordial "organisms"...
under this scenario, virus-like entities are older than typical, modern-type cells: agents resembling modern viruses, some of them even with capsids, existed before the emergence of membrane-bounded cells with large dsDNA genomes. Moreover, these agents would, effectively, have a virus-like life style because the primordial life forms are perceived as non-cellular but compartmentalized and would support ancient virus-like agents moving between compartments much like modern cells support viruses...
To conclude the discussion of viral origin from the primordial genetic pool, we would like to emphasize, once again, the tight coupling between the earliest stages of viral and cellular evolution.
So, there is another major problem that is seeing some movement towards resolution thanks to HVT. And, doesn't this massively viral HGT world resemble our Internet-wired society? Just askin'.
5. Summary
The largely untold (in the corporate media) story of HVT and HGT is a poster child for how good science is done. New facts come to light. They give rise to new theories and/or new tests of old theories. The old theories are found to have limitations, and are modified.
In the case of HVT and HGT, one very major theory (Darwinian evolution) needs to be limited to a point in time after the "Darwinian transition" of the HGT world. This is how science changes established theories - not by throwing them out completely, but by limiting their scope. OTOH, the formerly well-publicized speculative hypothesis (primordial soup) has taken a major hit.
But, it all happened within the normal bounds of the scientific method; and this major change happened within a period of 30 years. This shows how strong the scientific method is. It allows many different fields of science to interact and collectively improve their theories - because scientific theories are based on facts, on reproducible experiments or observations. As I write this, scientists are busy constructing systems that reproduce a vent (anaerobic, with mineral catalyst froth, and two types of water: hydrothermal fluid and CO2-saturated primordial ocean). We are beginning to test this testable hypothesis.
These theories prove that science works. Unfortunately, this essay demonstrates how many of those facts you have to know and to correctly weight in order to merely follow this argument, much less make a contribution to the scientific method. It demonstrates how uninformed the public is and how dangerous lack of education is.
Now compare that level of knowledge and methodical interaction to our politics. There is no rigor to our law creation or our political campaigning (nor, increasingly, to our rightwing activist judicial process). The only methods in demand in our politics are psychologically manipulative advertising, vote rigging, voter disenfranchisment, push polling, and scandal mongering. No wonder we are screwed as a society.
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But, I hope that some of you enjoyed this diary. I even dare to hope that such a simplistic explanation can convey to you the exciting things that are happening in the scientific community. At minimum, I hope you can even use it to bash fundamentalists about OOL and Darwinism, and to bash Social Darwinists about cooperation.
Peace.