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Thursday, May 08, 2014

More primordial soup nonsense

I just discovered a new paper on the origin of life (Keller et al. 2014). The authors think they are looking at the first primitive biochemical pathways, which they identify as glycolysis and the pentose phosphate pathways.

Here's what they did. They took a bunch of pure sugar phosphates1 and dissolved them in water containing salts and metal ions that were likely present in the primordial oceans. They heated the solution up to 70° C and looked at the degradation products. Low and behold, the sugar phosphates degraded and sometime the products were other intermediates in the glycolytic and pentose phosphate pathway, including pyruvate and glucose.

They conclude that ...
It is therefore apparent that heat exposure is sufficient to convert intermediate metabolites of glycolysis and the pentose phosphate pathway into pyruvate and glucose that constitute thermodynamically stable products also in the modern, enzyme‐catalysed metabolism, and to induce isomerization between pentose phosphate metabolites.
Next they looked at the rate of degradation using a concentration of 7.5 μM. They found that there was no significant spontaneous degradation at 40° but at 50° or higher there was a lot of spontaneous degradation to pyruvate.

This is significant, according to the authors, because ...
It is assumed that the pathways that mediate sugar phosphate interconversion, glycolysis, the pentose phosphate pathway, as well as the related Entner-Doudoroff pathway and Calvin cycle are evolutionarily ancient, as they are conserved and fulfil their central metabolic functionality virtually ubiquitously. Known as central, or primary, metabolism, their reaction sequences provide ribose 5-phosphate for the backbone of RNA and DNA, building blocks for the synthesis of co-enzymes, amino acids and lipids and supply the cell with energy in form of ATP and redox equivalent.
If it's true that the first metabolic pathways were glycolysis and other catabolic (degradation) reactions then there had to be an abundant supply of glucose in the primodial soup (ocean). If that was true, then the authors think they've identified primitive catalysts (e.g. iron) that catalyzed nonenzymatic pathways resembling the modern biochemical pathways. These might have been precursors to the biological pathways that evolved when life originated.

The authors conclude the paper with ...
In summary, we report that plausible Archean ocean chemical compositions serve as catalysts for a series of sugar phosphate interconversions among pentose phosphate pathway and glycolytic metabolites. The reactions connect important metabolic intermediates including ribose 5-phosphate and erythrose 4-phosphate and eventually feed into the metabolite pools of pyruvate and glucose, the stable products of modern glycolysis and gluconeogenesis. These results indicate that the basic architecture of the modern metabolic network could have originated from chemical and physical constraints that existed in the prebiotic earth’s ocean. These findings suggest that simple inorganic molecules, abundantly present in the Archean ocean, may have served as catalysts in early forms of metabolism and facilitated sugar phosphate interconver sion sequences that resemble glycolysis and the pentose phosphate pathway. These results therefore support the hypothesis that the topology of extant metabolic network could have originated from the structure of a primitive, metabolism-like, prebiotic chemical interconversion network.
I think this is nonsense. The most common pathway present in all species is gluconeogenesis—the pathway that makes glucose (and glucose 6-phosphate) from carbon dioxide (CO2). I think that was likely to be the most primitive pathway, a hypothesis that's consistent with the Metabolism First scenario for the origin of life [Changing Ideas About The Origin Of Life] [Was the Origin of Life a Lucky Accident?] [Why Are Cells Powered by Proton Gradients?] [Metabolism First and the Origin of Life].

In order to see what the soupists are up against, let's calculate the amount of glucose 6-phosphate that has to be present in the primordial ocean.

The volume of the oceans = 1.3 × 109 km3 or 1.3 × 1021 litres (National Geophysical Data Center (USA)). (The ancient ocean was probably larger.) The molecular mass of glucose 6-phosphate is 260.136 (Wikipedia). (We'll assume that it's all stereochemically pure D-glucose 6-phosphate.)

If the concentration was 7.5 μM then this represents 2366 billion metric tonnes of glucose or 2366 gigatonnes (Gt). This amount of glucose 6-phospahte degrades to other molecules within 24 hours, according to Keller et al. (2014) so that's the amount that has to be resupplied every day in order to maintain a constant concentration of 7.5 μM. This has to continue for millions of years while life evolved.

That's a lot of sugar. To put it into perspective, the total production of cellulose by all the plants on Earth is 180 Gt per year (Stricklen, 2008). (Cellulose is mostly a bunch of glucose molecules attached to each other.) Something would have to produce ten times this amount per day in order to resupply the glucose in the primordial ocean.

I'm not saying that the soupists are wrong. I'm just saying that they don't think through the implications of what they are proposing.

But I'm also saying that papers like Keller et al. (2014) are not good science for another reason. It's okay to advocate for one side of a controversial issue. That's what science is all about. It's not okay to completely ignore your opponents and present opinions as if they represented the overwhelming consensus in the field.

Here's a list of a few papers that are in my "origin of Life" file.
Lane, N., Allen, J. F. & Martin, W. (2010). How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays 32, 271-280.

Lane, N. & Martin, W. F. (2012). The origin of membrane bioenergetics. Cell 151, 1406-1416.

Martin, W., Baross, J., Kelley, D. & Russell, M. J. (2008). Hydrothermal vents and the origin of life. Nature Reviews Microbiology 6, 805-814.

Martin, W. & Müller, M. (1998). The hydrogen hypothesis for the first eukaryote. Nature 392, 37-41.

Martin, W. & Russell, M. J. (2003). On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, 59-85.

Martin, W. & Russell, M. J. (2007). On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical Transactions of the Royal Society B: Biological Sciences 362, 1887-1926.

Martin, W. F. (2012). Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation. FEBS letters 586, 485-493.

Nitschke, W. & Russell, M. J. (2009). Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W, Co, S and Se, forced life to emerge. Journal of molecular evolution 69, 481-496.

Russell, M., Hall, A. & Martin, W. (2010). Serpentinization as a source of energy at the origin of life. Geobiology 8, 355-371.

Russell, M. J. & Martin, W. (2004). The rocky roots of the acetyl-CoA pathway. Trends in biochemical sciences 29, 358-363.

Schwartzman, D. & Lineweaver, C. (2004). The hyperthermophilic origin of life revisited. Biochemical Society Transactions 32, 168-171.

Sousa, F. L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A., Allen, J. F., Lane, N. & Martin, W. F. (2013). Early bioenergetic evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 368, 20130088.
Nick Lane, Bill Martin, and Michael Russell are well-known contributors to the field. None of them would agree that the glycolytic pathway came before the gluconeogenic pathway. You have to make glucose before you can degrade it. None of them would agree that life arose in a primordial soup of amino acids, sugars, and nucleotides.

The Keller et al. paper has 61 references. There's only one single reference to a paper by Lane, Martin, or Russel. It's the Sousa et al. (2013) paper. Here's how they refer to it ...
In modern cells, most metabolic reactions are catalysed by protein-based enzymes. Modern enzymes possess, however, highly specialized and complex structures, and it is unlikely that they evolved before a metabolic system was in place. The major question about the early forms of metabolism is thus the nature about their precursors, the first metabolic catalysts (Lazcano & Miller, 1999; Shapiro, 2000; Anet, 2004; Sousa et al, 2013). RNA could be an option; however, central metabolism lacks examples of RNA-catalysed reactions [and synthetic ribozymes that catalyse aldolase reactions require a bivalent metal for its activity (Fusz et al, 2005)]. Here, we demonstrate that simple inorganic molecules, frequently found in sediments dated to the Archean period, can catalyse reactions analogous to what is observed in modern pathways.
There's no mention of the fact that prominent authors disagree strongly with the premises of their argument. That's not good science. The paper should never have been published as it is. Blame the journal and the reviewers for failing to do their jobs but, most of all, blame the authors for misleading readers by ignoring contrary opinions. They should be ashamed of themselves.

1. glucose 6‐phosphate (G6P), fructose 6‐phosphate (F6P), fructose 1,6‐bisphosphate (F16BP), dihydroxyacetone phosphate (DHAP), glyceraldehyde 3‐phosphate (G3P), 3‐phosphoglycerate (3PG), phosphoenolpyruvate (PEP), 6‐phosphogluconate (6PG), ribulose 5‐phosphate (Ru5P), ribose 5‐phosphate (R5P), xylulose 5‐phosphate (X5P) and sedoheptulose 7‐phosphate (S7P)

Keller, M.A., Turchyn, A.V. and Ralser, M. (2014) Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean. Molecular Systems Biology 10:725 [doi: 10.1002/msb.20145228] [text: open access]

Sticklen, M.B. (2008) Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol. Nature Reviews Genetics 9:433-443. [doi: 10.1038/nrg2336]


Wavefunction said...

Sadly, soupists owe their origins to the dominance of Stanley Miller who ruled the origins-of-life world by fiat for many years.

Mikkel Rumraket Rasmussen said...

I'm not sure I took soupist implications from their paper. What I gathered was that they're suggesting the chemical composition of the archean ocean could have contributed to early metabolism, not that the authors think or even suggest that the entire primordial ocean was basically a dilution of glucose.

Isn't all they're really saying basically encapsulated in the concluding remarks "These findings suggest that simple inorganic molecules, abundantly present in the Archean ocean, may have served as catalysts in early forms of metabolism and facilitated sugar phosphate interconver sion sequences that resemble glycolysis and the pentose phosphate pathway." ?

It doesn't read to me like they're suggesting this was something taking place everywhere throughout a planetary ocean. Only that the catalysts themselves were ubiquitous. Since they're also heating the solution to 70 degrees C, doesn't this imply some kind of hydrothermal activity(?), which I would gather would be localized and provide compartments/enclosure of some sort.

Unless I'm mistaken, they don't even explicitly say they think the pentose-phosphate pathway was the first metabolic cycle, only that it is conserved and therefore ancient, possibly even every early. My main criticism with that is that it's all a bit vague.

Neil Taylor said...

Why do the entire oceans have to be invoked in a primordial soup, and not temporarily isolated tidal, or flood pools etc.

I've no dog in this fight and do not have any knowledge to comment on the chemistry, but feel Prof Moran's put down is pretty unreasonable.

Temporarily isolated areas can surely have concentrations well beyond those of the average ocean.

Do "soupists" insist the entire ocean was like this, or is this an unnecessary distortion?

Unknown said...

My understanding of Miller and the like is that abiotic processes can produce chemicals necessary for life. In that, they succeeded. That doesn't mean that their observations are what actually happened.

Let's face it. The process by which life originated will never be known with certainty. Even if we can produce life in a lab, we can't say that this was the process that created life on Earth.

And if we are ever successfully at creating life, Quest and his low IQ friends will simply argue that it is proof that an intelligent designer is necessary.

Anonymous said...

Wouldn't be easier and more cost effective to spend tax payers money on preserving life rather than on this nonsense...? Who approves this...? Must be Satan himself....
Why not put a living cell in the "primordial soup" break it open and see if it is going to reassemble...? Or put it by the hydro-vents Rum has been experimenting by and see if the cell membrane is going to reassemble... miracles apparently do happen.. even in the so-called science...

Joe Felsenstein said...

Quest, it would be easier if you, who ask lots of questions, were willing to answer even one question, the one I asked you on another thread: what evidence you would accept for common descent. Showing up on all threads to ask multiple questions, but never being willing to answer questions or to say what would constitute evidence, shows that you are nothing but a troll, certainly not someone who can engage in a serious scientific discussion. Oh, Brave Sir Robin!

Joe Felsenstein said...

Quest: Still no answer from you, eh? Oh Brave Sir Robin!

Unknown said...

OK Quest, finally a discussion about the origin of life. So, please, dazzle us with your brilliance. Please provide us with a detailed description on how life originated on Earth. But, as all good scientific theories must be, also explain how your theory is falsifiable, predictive and testable.

Or, maybe you can change the subject and answer Joe's question.

Anonymous said...

A simple question:
How do you build a wall..? Don't you need bricks, cement, sand, water and hardening compounds at the same time...? Lets say you only have bricks and water...? You can put the brick on the top of each other.... but how is that going to be a wall..? And water now can only create problems... So, how do you build a perfect wall with the materials needed...?

Joe Felsenstein said...

Quest: you came to a discussion of neutral change and raised questions about common descent. So I thought it would be interesting to ask you for clarification and get you to have a serious discussion. To see whether you understood how biologists make inferences of common descent. That is done without manipulating genes in the lab, of course. Your responses show you do not know what you are talking about. No clue.

You could have dealt honestly, way back then, with this question. And as for money, why it would not have cost you a cent! But it would have ended up with you saying "I guess I didn't understand that" and "I guess I was wrong".

Instead Brave Sir Robin ran away, showed up other places, asked more wild questions, and then ran away again. So much for Brave Sir Robin.

Uncivilized Elk said...

Brick walls are perfect...?

Larry Moran said...

Please feel free to propse a hypothesis based on thousand year old tidal pools full of amino acids and sugars. Be sure it explains where the organic compounds came from.

The paper is about the composition of the Archaen OCEAN (see the title). I didn't make that up.

Larry Moran said...

Do you believe that glycolysis is a more ancient pathway than gluconeogenesis?

Mikkel Rumraket Rasmussen said...


Opus7 said...

Hello, here is one of the authors. This blog puts a lot of claims into our mouth that we did not make. We would highly recommend the interested reader of this blog to read the paper by themselves.

AllanMiller said...

1) The mountains round here are covered in walls that are just 'one block on top of the other'. They've been standing for centuries.

2) Molecules aren't bricks. Nor are atoms.

Larry Moran said...

Hi Marcus,

Thanks for showing up. Could you do me a big favor and list a few of the "claims" that I got wrong?

Meanwhile, why didn't you mention anything about origin of life theories that make your experiments meaningless? Don"t you think that scientists have an obligation to discuss alternative explanations that conflict with their own premises and assumptions?

Larry Moran said...

Good. Do you think there was ever a time during the origin of life when there were significant levels of sugar phosphates produced spontaneously by metal catalysts in the oceans? If the authors of the paper really believed that the gluconeogenesis reactions were primitive then they should have started with a solution of PEP and looked for glucose or fructose, right?

Why do you think they didn't try such an experiment, or at least didn't report it?

Many scientists in this field think that there was a primordial soup full of complex organic molecules created by lightening bolts and/or delivered by meteorites. Those authors tend to reference the original experiments that showed that the reactions were possible under certain conditions. They also tend to claim that life got started when primitive protocells got energy by breaking down these complex molecules from the soup.

It seems to me that the authors of this paper assume that the primordial soup scenario is true. They certainly didn't make any effort to describe any other possibility.

William Martin said...

I don't usually blog but this is all pretty interesting. In the discussion of the paper there is a passage that reads:

"Importantly, as we worked with average concentrations of molecules found on the early planet, the availability for these catalysts was not restricted to niches or extreme conditions—a metabolism that bases on these molecules could thus had occurred throughout the oceanic environment."

That sounds to me as if Larry's criticism about oceanic concentrations has some substance. It is not clear to me which claims he is putting into anyone's mouth. "Molecules" in that passage can not really refer to the catalysts, because they are metal ions (charged atoms) not molecules. Or maybe the metal ions are being designated as molecules? That can't be, the term "molecule" has a specific definition. Maybe the term molecules and atoms are being used here interchangeably? If so, maybe other technical terms are being used with similar freedom? The term "throughout" would generally be taken to mean side to side and top to bottom, a volume in other words.

AllanMiller said...

The ocean as a dilute soup of carbon molecules is not a plausible origin, but local concentration is. It's hard to see how any theory of a chemical OoL can avoid some appeal to local effects. If one circumscribes the environment in which these reactions are thought to take place, and ignores the early placement of glycolysis, there seems little to take exception to. It's a 'metabolism-first' paper, just the 'wrong' metabolism!

To me, non-enzymatic catalysis - amino acid synthesis, citric acid cycle etc - indicates an easy route in for biological catalysis, not necessarily a precursor of it. Early metabolism will have channelled down thermodynamically favourable routes. But I think the role of phosphate could be key. A proton or sodium gradient coupled to phosphate activation has the potential to explore the chemical landscape much more thoroughly than simple solution chemistry, which rapidly runs out of thermodynamic steam.

Larry Moran said...

t's a 'metabolism-first' paper, just the 'wrong' metabolism!

By Jove, I think you've got it! The only minor problem with the paper is that instead of looking at nonenzymatic synthesis of simple amino acids and three-carbon sugars in a local environment they looked at degradation of complex sugar phosphates in the ocean.

Trivial. I can see why the editors of the journal didn't think this was worth bothering with.

Tom Mueller said...


Thank you Allan.

ITMT – I urge everybody to check out the links that Larry cited.
especially this one

Regarding "local effects”

Russell postulates that alkaline vents, akin to the modern Lost City vent system in the mid-Atlantic (Figure 3), were the ideal incubators for life, providing a steady supply of hydrogen gas, carbon dioxide, mineral catalysts, and a labyrinth of interconnected micropores (natural compartments similar to cells, with filmlike membranes; Lane et al. 2010). Alkaline vents are, in essence, electrochemical reactors that operate in a state far from equilibrium.

AllanMiller said...

Another opinion on this:

Mikkel Rumraket Rasmussen said...

I can't answer your first batch of questions, I'm not a biochemist. Given your comments I would agree it seems odd to start analyzing how products of reactions they have no idea how would have been produced, are broken down given certain metal catalysts. I'm with you on that. I also totally agree with your general criticisms of the many reportings of "amin acids in space/meteors/comets"-type findings as being generally uninteresting because they either never say how this fits into a plausible scenario for the origin of life, or simply make vague general statements about them being "delivered to earth/primordial oceans". Yeah, to break down and become even more diluted in no time.

When it comes to the soupist implications of the paper, at least in the portions you have quoted in your blog post, I can only repeat that they don't explicitly come out and say they think the entire ocean was full of glucose. They don't make any effort to say how it was produced, where, or how much. That of course puts their experiment into the "how do we then know whether this is at all significant?"-category.

However, given the comments by Bill Martin further below, I think you may be right about the soupist implications of their paper. Either they're misusing terms (molecules), or they really do believe in some kind of soup. Looks like one of the authors turned up, maybe he can clarify. I'd like to know myself.

Chibiabos Winnegan said...

Looks like they mean inorganic molecules. I'm more concerned with how much credence you're putting into Moran's back of the envelope calculation. Moran's an expert in his own field. What the hell does he know about anything else?

Larry Moran said...

@Chibiabos Winnegan,

I know a little bit about biochemistry. Is that sufficient?

Gary Gaulin said...

I have to mention that (reciprocal) causation based models need a forward (consumer) and reverse (producer) cycles always coexisting, in symbiosis, such as in cellular microbe mats that Lynn Margulis is famous for studying. The sugar would get used up as fast as its made, to be converted back into what it needs to make more all over again. Clues to the origin of one are then found in the other.

If the chemistry results are repeatable then the new paper on the origin of life (Keller et al. 2014) may be much more novel than it may first appear. What then becomes important is how well the their chemistry compliments coexisting “Reverse” cycles such as:

Xiang V. Zhang and, Scot T. Martin, “Driving Parts of Krebs Cycle in Reverse through Mineral Photochemistry”, Journal of the American Chemical Society 2006 128 (50), 16032-16033

Anonymous said...


Lets go to the lab and settle the dispute forever.... Let's delete genes for the bacterial flagellum, put it under selective pressure and see if it is going to evolve something resembling a common ancestor of a flagellum, such as jet engine or a hydrothermal vent... What do you think...? That would be a valuable piece of science if it turned out to be true... finally some proof for your beliefs....

Joe Felsenstein said...

So Quest, have you answered the question: what evidence should be used to infer common descent of humans and chimps? We've been waiting for your answers. Oh, I see, you've run away to the becterial flagellum instead of calmly discussing chimp/human common ancestry and what methods ought to be used to make inferences about it. Brave Sir Robin!

Unknown said...

The idea that the reduction of carbon dioxide by geochemically generated redox potentials, rather than atmospheric reactions or the infall of extraterrestrial materials, was the source organic matter for the earliest organisms was extensively developed by Günther Wäcthershäuser in the late 80s. Although some of his ideas (namely the "surface metabolism" hypothesis) have lost credence, he pointed out the importance of understanding chemoautotrophic processes in a a field which was them dominated by so-called "heterotrophic hypothesis".
This new perspective brought attention to the study of plausible anabolic processes driven by the reducing constituents of the early oceans, such as hydrogen, divalent iron, and sulfides. However, it is hard to conceive a living entity or ecosystem without the simultaneous existence of both anabolic and catabolic reactions. It seems to me pointless to speculate whether glucolysis or gluconeogenesis came first unless a surrogate pathway can be proposed to do the opposite job.
Metabolic sequences are actually series of near-to-equilibrium reactions whose direction is determined by the depletion of their products. Organisms can, and often do, use these steps in the opposite sense. Even the most exergonic of these sequences, the tricarboxylic acid cycle, has been shown to be used by many organisms in the "reversed" sense.
Although many papers implying that the "primordial soup" conception of the origin of life remains valid are still being published, and even the analysis of a box of leftover vials forgotten by Stanley Miller himself was given by journals the same reverence the faithful devote to holy relics, I would not agree that Keller et al. (2014) belongs in that category. Rather, it seems to me a well guided and interesting effort to understand the emergence of the interconversions of sugar phosphate esters, and it may prove useful in elucidating the subsequent takeover of these pathways by enzymes.

Gary Gaulin said...

ITMT – I urge everybody to check out the links that Larry cited.
especially this one

Tom, do you (or anyone) know whether proton gradients are powering the motion of what appear to me to be very energetic coacervates? Please excuse blurry picture, I don't have a microscope that can record what they look like close up.

Red Cabbage & Egg Yolk Coacervates & Bubble

The video is from an experiment I tried on a whim. I'm still not 100% sure though how their propulsion system works. I suspect the color changes indicate proton gradient pH and light might help power the system but I cannot confirm.

Tom Mueller said...

Hi Allan,

“…fools rush in where angels fear to tread!”

I am guessing that my lines of speculation are beyond naïve and I beg the indulgence of cognoscenti Biochemists. I am going to ask for help here.

The very fact that the vials were incubated between 50 and 70°C is intriguing.

It is possible that the Pre-biotic oceans had temperatures of 70°C, but unlikely.

Such rebuttal is rendered moot when the localizing effects of hydrothermal vents are invoked.

Thank you, Allan, for that review by Pier Luigi Luisi who raises a very interesting point, that to my reading, appears to address Larry’s query of the precedence of gluconeogenesis vs. glycolysis.

Thus, it cannot be excluded that a primordial ‘reversed’ glycolysis (that is, a primordial ‘gluconeogenesis’) could have contributed to carbon fixation or facilitated the formation of the complex sugar phosphates required for the assembly of RNA and other biological molecules.

But that is the whole point isn’t it? What we today consider to be catabolic reactions were in fact anabolic reactions under pre-biotic conditions. In the “metabolism-first” scenario, I ask my students to think of a primitive Citric Acid Cycle running backwards. In other words, the Citric Acid Cycle becomes anabolic under appropriate reducing conditions.

OK – now I am going out on a real limb here, distinctions between gluconeogenesis vs. glycolysis would be rendered even more moot if we consider the phenomenon of a “chemical clock” (which is actually how I imagined the earliest primitive prebiotic metabolism)

I am no expert on thermodynamics, but let’s say that reversible reactions are not going to generate useful biological building blocks unless there is some constant input of energy. But then, that is the whole point of invoking thermal vents, if I understand this debate correctly. A constant source of energy is supplied and able to maintain prebiotic proton gradients.

I hope you do not mind me paraphrasing myself from an earlier post:

Stranded” high energy electrons in a reducing atmosphere were thought to generate chemical networks that were recursive (generated its own constituents) and self-catalyzing.

The network must be feedback-driven and able to “self-prune” any side reactions (that’s the tricky part), resulting in a limited suite of pathways capable that concentrate reagents just like the metabolism/metabolite story. Just the same, these earlier anabolic side-reactions could have generated the building blocks for our familiar monomers and eventually polymers that ultimately gave rise to proto-cells.

That all said – I am also partial to the notion that much of this could have occurred on ice just as Miller suggested.

At least that is what I have started telling my own students after gracious correction of my previous naiveté; gratis the patient intercessions of those better versed in the esoterica of abiogenesis on this forum.

Tom Mueller said...

Some quick google-whacking indicates Larry is in good company. Jack Szostak echoes some of the very points that Larry made:

Here is the relevant bit:
‘In the absence of coupling to an energy input, even reversible reactions are not going to spontaneously generate useful biological building blocks. I would conclude that metabolism had to evolve, within cells, one reaction and one catalyst at a time,’ Szostak adds.

Ralser agrees that this presents a difficulty. However, he maintains it doesn't rule out that the reverse reaction could occur without enzymes too. 'If you prove non-enzymatic glycolysis can happen it is plausible that the reverse non-enzymatic gluconeogenesis can happen too, just as enzyme driven metabolic reactions are reversible in living organisms,' he says.

If I read all this correctly, Ralser is really not disagreeing with Larry’s enthusiasm for “Metabolism First” and also does not disagree with Larry that “Metabolism First” emerged in the absence of enzymes but instead emerged in the presence of mineral catalysts. At the same time, Ralser also adresses the primacy of gluconeogenesis vs glycolysis.

At this point, I actually find it difficult to determine where the two disagree.

I do agree with Larry that Ralser et al could have done a much better job of distancing themselves from a naïver version of “Primordial Soupism” which was too random, accidental and dilute.

I hope I have not made too bad a hash of this and do in fact understand the finer points of this debate.

Thanking in advance, I welcome correction from any and all.

Tom Mueller said...

@ Raul Félix de Sousa

Oh wow - I wish I had read your post through before posting my recent one above!

If I understand you correctly, my notion of a metabolic "chemical clock" oscillating between catabolism and anabolism is not far off the mark.

You state that : Even the most exergonic of these sequences, the tricarboxylic acid cycle, has been shown to be used by many organisms in the "reversed" sense.

Even today? Really?!

I presume these would include prokaryotes under reducing conditions such as thermal vents. Could you please explain by providing specific examples?

Thanks in advance.

Tom Mueller said...

Hi Gary

I wish I knew what was going on... I am guessing slower diffusion of molecules from interiour of the egg yolk is making it to the surface of the coacervate where encounter with the lower pH is changing the surface charge on the surface of the coacervate. Like charges repel - i.e your "propulsion" and this phenomenon dissipates and is replenished at different rates depending on the size of the coacervate.

I am guessing here... I really do not know. I never did the experiment, but now I fully intend to.

Gary Gaulin said...

And Hi Tom!

When there is only one or two parts of indicator solution to swim around in they swarm in place. The air/liquid boundary layer around the bubble (under cover slip) helps show what is going on at a surface, and at a good viewing angle. The color change along the depth of the surface layer (parallel to light direction) would indicate whether there is a DC polarity as in a capacitor, or not.

It's hard to describe how colorful they are. If you have access to a video microscope with broad spectrum light source or use sunlight then it should be easy to get great pictures that I would need to see. Could then view a video frame by frame or slow down coacervate speed with temperature, many days of use, maybe indicator dilution and less light.

This is a case where I quickly learned that I needed help figuring out this one, and you're the first to show interest in trying. I'm already certain this is a clue to the origin of life. With propulsion like this flagella scaled up to the size of the coacervates would only get them all tangled up in each other. It's hard to say how fast they go in normal (primordial) sunlight but from what I have seen they don't need much to propel them.

Larry Moran said...

I don't have time to describe the citric acid cycle in detail but let me make a few points.

The traditional citric acid cycle consists of a series of near-equilibrium (ΔG = 0) reactions where a two-carbon moiety (acetyl group) is oxidized to CO2 producing ATP equivalents and reducing equivalents. In fact, however, the intermediates in the reactions form a pool of metabolites that are involved in many different pathways. (This is true whether they are confined to the mitochondria, as in eukaryotes, or are present in the cytosol, as in bacteria.) It's wrong to say that this is an "exergonic" pathway.

Intermediates in the citric acid cycle are constantly depleted by anapleurotic reactions and resupplied by catapleurotic reactions. Entry and exit of any intermediate results in immediate equilibration of the entire pool of intermediates indicating that the reactions proceed readily in either direction.

The vast majority of species with a complete citric acid cycle also have a glyoxylate pathway that's used to build 4-carbon molecules from two 2-carbon molecules.

The citric acid cycle is the classic example of an amphibolic pathway. It is both a catabolic pathway and an anabolic pathway depending on circumstances and, to some extent species and tissues.

Most species of bacteria do not have a complete citric acid cycle. Most of them have a reductive branch (left side of the traditional "cycle) leading from oxaloacetate to succinate or αkg. Many of them have an oxidative branch (right-hand side) allowing synthesis of citrate and isocitrate. The forked pathways (i.e. not a cycle) supplies all of the precursors of amino acids, porphyrins, and fatty acids.

Many obligate and facultative anaerobes (e.g. E. coli) use the forked (noncyclic) versions of the pathways to grow in the absence of oxygen.

Quite a few species of bacteria have a complete set of citric acid cycle enzymes but they use them to run the pathway in the opposite direction in order to fix CO2 and produce acetyl moieties.

Our understanding of these pathways in bacteria leads to a simple model of how an irreproducibly complex pathway like the citric acid cycle could have evolved ]Blown Out of the Water] ]Metabolism First and the Origin of Life].

Incidentally, you can possibly win one million dollars if you find a website with a correct depiction of the citric acid cycle [WikiPathways] [Biochemistry on the Web: The Citric Acid Cycle].

Unknown said...

Hi, Larry

I certainly did not wish to go into that level of detail about the citric acid cycle, but I agree that I should have been more accurate and specify that I was referring to the fact that the Krebs cycle, or the citric acid cycle, in its catabolic, or oxidative direction, constitutes the core of the most important energy-yielding process in organisms. The reversibility of each of its steps and the reequilibration that follows the depletion or resupply of intermediates, justifies, in my opinion, the interest in studying the properties of metabolic sequences that, although used by modern organisms preferentially in the catabolic direction, may illustrate more general aspects of that particular type of reaction, such as mechanism and kinetics.
In this specific case, I do not agree that the mere fact that a generally catabolic route is being focused necessarily implies the belief that early life relied on the heterotrophic consumption of energy-rich organic compounds supplied by abiotic sources, as proposed in the prebiotic soup model.

Gary Gaulin said...

I can add: With the large number of possible interactions happening in the coacervate experiment it would not surprise me that there are very interesting proton gradients, but of course pH is not a direct measure of the number of protons and what is changing membrane pH can be sodium, potassium, or other specific ion exchange across the membrane through molecules found in yolk (and whatever membrane loving molecules are found in the indicator solution). Some of the reactions can be influenced by light, which is why I had to mention the possibly of that changing their velocity. Even where the amount of propulsion is insignificant photoactivity is still a part of what the coacervates already developed, or may later develop after the system chemically settles down to some equilibrium state (without being eaten by bacteria).

Where what causes what to make a chicken is followed back we first have an egg containing a yolk sac filled with the chemically stable raw ingredients needed for development to the hatchling stage. Before animals and bacteria a similar mixture could fill a tidal zone and be safe from consumption. Whatever membrane forming molecules were around would be at the water/yolk interface. Having more than is needed for a thin monolayer (in favorable conditions) allows mobile vesicles (coacervates) to form. Whatever later developed in the primordial yolk was free to consume it until the new life covered the habitat or planet then increasing scarcity of the easy food had to be the mother of invention that utilized other food sources.

It's hard to say how close chicken egg yolk is to primordial nutrients and the cabbage broth is to primordial water conditions but both have a good collection of what it takes to get something started. Then add the once common minerals with metals that cause all sorts of other things, including development from back and forth reactions from a light cycle.

To go with this (could call it) coacervate world is the home/classroom OOL model that predicts: In even a very watery oceanic primordial soup protein skimming will at the tidal zones serve up a nutritious yolk-plasma dumpling stew with monstrously long egg noodley appendages stretching the length of its sometimes foamy shorelines:

Origin Of Life Aquarium

And to go with egg yolk is this published by a National Science Teachers Association journal for self-assembly:

Idea Bank: Demonstrating the Self-Assembly of the Cell Membrane
As published by NSTA in The Science Teacher

With there being no way to exactly know what life chemically started from whatever is in an egg is a good starting point. What's sold by the dozen at any grocery store at least works for chickens. The cause of that can be a chemically simpler but similar primordial-biomass that was deposited in certain habitats as in the soup to stew OOL Aquarium experiments.

Roberto Aguirre Maturana said...

Larry, hope you can comment this publication any time soon:

High-energy chemistry of formamide: A unifiedmechanism of nucleobase formation

Opus7 said...

Now its quite some time ago so that debate could cooled down a bit; so I would like to comment on this blog. All living cells use a conserved network of biochemical reactions to catalyse their metabolic reactions. This network, called the metabolic network, had an origin in early evolution, but this origin not understood. One of the main questions in this field is about how did the first catalysts about two conserved pathways, called glycolysis and the pentose phosphate pathway, looked alike. Where these RNA molecules? Or where these minerals or other molecules? That's what we test in our paper. We joined up with Earth Scientists at the University of Cambridge. They told us what they think was abundantly available in the Archean oceans. And we tested systematically with very advanced mass spectrometry methods whether these molecules can catalyse reactions observed within the most conserved part of metabolism. We got a hit in the metal ions. And that's very remarkable, because it shows that the first catalysts capable to catalyse the reactions as found now in modern cells central metabolism, did not need to have a complex enzyme fold structures for a start. This makes it much easier to explain the origin of the metabolic network. Nobody, really nobody, claims here that the ocean was a soup full of ribose 5-phosphate. But its fun to read Larrys calculation, but I have to admit it would not have hurt him to read a bit about what is known and not known about the origin of the metabolic network structure before starting shouting out lout against the work of others

Larry Moran said...

One of the main questions in this field is about how did the first catalysts about two conserved pathways, called glycolysis and the pentose phosphate pathway, looked alike.

There are lots of species of bacteria that don't have a traditional glycolytic pathway and some that don't have the complete pentose phosphate pathway. All of them have a gluconeogenesis pathway suggesting the the most primitive pathway is the one where glucose is synthesized from one- or two-carbon precursors.

Your initial assumption about the most primitive pathways was incorrect and that makes the entire paper useless.

I think that the first catalysts were responsible for reactions leading to the synthesis of two-carbon compounds like acetate and simple amines. As the concentrations of these compounds built up in a restricted environment it became possible to synthesize more complex molecules like three-carbon sugars and sugar-phosphates.

According to this model, there was never a time when complex sugar phosphates existed in a primordial soup at concentrations that made any sense. (This is Metabolism First.)

Now, you don't have to agree with this popular model that has been described many times in the scientific literature. But you do have to acknowledge it and recognize that it conflicts with the basic assumptions you made in your paper.

Larry Moran said...

But its fun to read Larrys calculation, but I have to admit it would not have hurt him to read a bit about what is known and not known about the origin of the metabolic network structure before starting shouting out lout against the work of others

Thank-you for the advice.

Opus7 said...

"There are lots of species of bacteria that don't have a traditional glycolytic pathway and some that don't have the complete pentose phosphate pathway."

Details are important here. The pathways differ just in a few reactions and the basic chemical structure is the same. So its common sense they have the same or similar evolutionary origin. What is missing about the PPP is usually just the oxidative part, that are two reactions. By the way, we have also not seen these oxidative part reactions in our experiments. Also here there comes a caveat however, evidence for absence in some bacteria comes solely from the absence of a sequence homology. However we have seen in our paper that the reactions are quite fast non-enzymatically. Absence of the enzyme does thus not necessarily mean the pathway is really absent.

" All of them have a gluconeogenesis pathway suggesting the the most primitive pathway is the one where glucose is synthesized from one- or two-carbon precursors".

Agreed, in fact we also write clearly in the paper that gluconeogeneis was probably before glycolysis - the detail is important also here however: Its the same catalysts for most of the reactions that allows both glycolysis and gluconeogenesis. Without glycolytic enzymes (and their precursors), cells couldn’t do gluconeogenesis either. So its chemically and catalytically not two different pathways.

" I think that the first catalysts were responsible for reactions leading to the synthesis of two-carbon compounds like acetate and simple amines."

This does not remove the question that glycolytic enzymes need an origin in evolution!

"As the concentrations of these compounds built up in a restricted environment it became possible to synthesize more complex molecules like three-carbon sugars and sugar-phosphates.'

Agreed, but just reaching a concentration is not enough. For forming the metabolic network, you need a plausible origin for the enzymatic catalysts. These can't in the beginning have been complex enzyme folds as in modern species: They are all longer then 200-300as and posess complex folds, and this would need that everal of them would have come into being at once (Evolution can only select for the functional product, so they cant come into being one rection at a time, at least not in the absence of anon-enzymatic precursor). RNA can't do the job for these reactions either. We found Fe(II), and to a lesser extend other metals, in our experiments, thats much more primordially plausible.

"According to this model, there was never a time when complex sugar phosphates existed in a primordial soup at concentrations that made any sense. (This is Metabolism First.)"

I'm confused now – above you said that reaching the concentration was the most important of all, and now you said reaching the concentration was not possible? Please note that without enzymes, life is not possible. Enzymes as catalysts follow the same laws of thermodynamics as other catalysts (i.e. Fe(II)), means they will always convert a product into the thermodynamically favourable form. So I don't see why there is a problem with the origin of life if we show that Fe(II) can replace a glycolytic enzyme!

Opus7 said...

Still missing my other reply, hope Larry approves it to be online. By the way, you list quite a few papers above... but none of them deals with the origin of glycolytic enzymes. Could it be that, by being primed against certain theories about the origin of life, you simple missed the point of our paper, that deals with the origin of glycolytic enzymes?

Larry Moran said...

You deal with the origin of some of these enzymes by invoking a scenario that involves substantial concentrations of complex sugars in the ancient ocean. I challenge that assumption and point out that there's another hypothesis on the origin of life that does not require a primordial soup.

I completely agree with you that having a preference for certain hypothesis affects how one interprets and designs experiments. That's why it's such a good idea to mention alternative hypotheses when you publish and discuss whether they are consistent with your results. It's especially important to note whether your results help to choose between competing ideas.

In your case, it's highly unlikely that some of the glycolytic enzymes arose because the ancient oceans contained significant quantities of sugar phosphates that formed spontaneously. However, if these sugar phosphates began to accumulate in a restricted environment (cavities in hydrothermal vents) because they were synthesized from more simple compounds by primitive enzymes, then the scenario becomes feasible.

You should have discussed this possibility in your paper and pointed out the problems with having an ocean full of sugar phosphates.

Opus7 said...

“You deal with the origin of some of these enzymes by invoking a scenario that involves substantial concentrations of complex sugars in the ancient ocean.”

No, we did not make this statement. We used Fe(II) and metal concentrations as revealed from sediments that are plausible for the majority of the Archean ocean. So average concentration is related to the metals and salts we tested. This is clearly stated in the paper.

For the sugar phosphates, we used 7.5uM because that is a good concentration to conduct the experiment: Its lower than its concentration in cells, but can still be perfectly detected on our masspecs. Catalysis is not limited by substrate concentration, Fe(II) can perfectly catalyse the reaction even at much lower concentration. So this result is concentration independent.

“I completely agree with you that having a preference for certain hypothesis affects how one interprets and designs experiments. That's why it's such a good idea to mention alternative hypotheses when you publish and discuss whether they are consistent with your results. It's especially important to note whether your results help to choose between competing ideas.”

The papers you cite above do not contain alternative hypothesis about how the first glycolytic enzyme could have looked alike. Please be more specific which papers you refer to.

“In your case, it's highly unlikely that some of the glycolytic enzymes arose because the ancient oceans contained significant quantities of sugar phosphates that formed spontaneously.”

Our paper does not deal with the question how carbons reached life compatible concentration. This is important, fully agree, but another problem not addressed in the paper. Glycolytic enzymes exist in living cells – so doesn't matter which theory of life you prefer- at one point glycolytic enzymes started in evolution. The question we address is how its first structures could have looked alike. Some textbooks believe it could have been ribozymes, but attempts to create ribozyme mimetics of glycolytic enzymes have failed so far (except with RNAs that bind metals).

Perhaps, its not certain as you say that spontaneous reactions did allow carbon fixation, its very well possible that inorganic catalysts were involved.

“However, if these sugar phosphates began to accumulate in a restricted environment (cavities in hydrothermal vents) because they were synthesized from more simple compounds by primitive enzymes, then the scenario becomes feasible. You should have discussed this possibility in your paper and pointed out the problems with having an ocean full of sugar phosphates.”

We did, and on several places in the paper! Please read for instance this part (and its not the only one) in the discussion...”This seeming paradox of the universality of
sugar phosphates and their low stability in the prebiotic world might
be solved by accepting different reaction sequences for carbon
fixation and the first forms of metabolism: Carbon fixation could
have occurred through non-metabolism-like events, including the
so-called formose reaction, which is, in a series of condensation
steps, able to convert several formaldehyde molecules into complex
carbohydrates structures (Breslow, 1959; Maurer et al, 1987),
or through alternative/parallel scenarios that include mineral- or
photochemically catalysed reactions, as well as microcompartmen-
talization, that allowed the accumulation of first biomolecules

Opus7 said...

A question to you Larry then: Ok you do not believe me that Fe(II) catalysis could have helped to explain the origin of glycolytic enzymes. Fair enough.. Saying no is however always easy, but what is your alternative explanation then how glycolysis could have started? Spontaneous reactions can't do all of the reactions (we tested that), RNA can't either. So you have other catalysts in mind?

Larry Moran said...

I don't object to your claim that iron could be involved. In fact, I think we have strong evidence that most of the primitive oxidation-reduction reactions used ferredoxin cofactors.

What I object to can be summarized as two points. I list them here and then I'll let you have the last word. It's clear that you aren't listening.

1. Your claim (see the title of your paper) that these reactions evolved in the ocean where there were significant enough concentrations of reactants to get life started.

2. Your insistence on referring to the primitive pathway as "glycolysis" (see your question above) implying that there was an abundant supply of glucose available when the degradation reactions evolved. I think the reactions evolved in the other direction and the first pathway was gluconeogenesis. That scenario does not require the presence of spontaneously formed sugar phosphates in the primitive ocean.

You don't have to agree with these views but since they challenge the main assumptions of your paper you did have to discuss them and include references to these other legitimate scenarios. I'm pretty sure form what you've written here that you weren't aware of these issues so I'll attribute the mistake to ignorance.

Opus7 said...

Dear Larry,

great, than please allow me to finish by wrapping about what is in the paper and what is not, after all I feel qualified about making this statement having written it.

There is something special about glycolysis and the pentose phosphate pathway. These pathways provide the most essential metabolites for the synthesis of RNA, lipids, amino acids and the TCA cycle, are thus the most central ones in the metabolic network in modern cells. They are evolutionary ancient, and despite chemistry would offer many more possibilities about how carbohydrates could be inter converted (and since divergence of first species enough time has passed which would allow to evolve alternatives) found with some minor variation (I.e.the Entner-Dourdoroff pathway) across all living species.

Despite comments in this blog try to put these into our paper, what we do not study, test, or measure in our paper is a) the average sugar and sugar phosphate concentration in the Archean ocean b) the total carbon presence on the Archean world expressed in megatons, c) mechanism how the first biomolecules accumulated, d) which biomolecules first accumulated and when, e) in which compartments the first biolomecules accumulated, f) by which energetic mechanism they accumulated, g) which were the first chemical reactions leading to live, neither do we propose an order which order reactions became important for life. The paper is also not an example of sleepy reviewers and Editors; the paper was insensitively reviewed and is published in one of the most prestigious scientific journals in the field; its also not a Review article forgetting several citations when comparing different theories with each other.

What it is, that it discovers in an enormous attempt of measuring nearly 3000 samples obtained in Archean ocean simulations by advanced mass spectrometry, that 28 chemical reactions, which in modern organisms are catalysed by enzymes within glycolysis and the pentose phosphate pathway, can be catalysed by simple molecules, mainly Fe(II), in concentrations that are found in the average Archean sediment. Thus, even before the event of RNA, genetic selection and proteins, requirements to select for enzymes, there was everything available in large parts of the Archean ocean which allows to catalyse glycolytic and pentose phosphate reactions, efficiently and with high specificity.

Torbjörn Larsson said...

This was useful, thanks all! I was just listening on Steven Benner's latest web seminar where he asked for an alternative pathway to ribose than his borate pathway, and I was thinking of Keller et al 2014. Googling criticism of the latter brought me here.

Since I want to respond, I note that Tom Mueller has made the heavy lifting on placing this in context. I do think battery theory is the strongest in the darwinian sense, because we share many traits with Hadean alkaline hydrothermal vents. It is also here that chemiosmosis _had_ to evolve. [ ]

So I share the concern that papers tend to ignore the contenders to the soup theory consensus. (Consensus according to NASA's Astrobiology Strategy 2015 roadmap; ) And I congratulate Ralser et al to removing Orgel's theoretic problem of side reactions. [“The origin of life – a review of facts and speculations”, Leslie E. Orgel, TIBS 1998; ]

So I think the criticism and problems can be summed up like this:

1. There is no pyruvate source, so no gluconeogenesis. [Moran]
2. There is no energy coupling, so no gluconeogenesis. [Szostak]
3. These pathways makes "tars". [Benner]

In that order, pyruvate is now known to be produced in the vents. A recent proof-of-principle work that shows how redox driven processes like Russell et al alkaline hydrothermal vent metabolism should be able produce hydrocarbons up to and including pyruvic acid in alkaline hydrothermal vents, with a modicum of efficiency (~ 8 % faradaic efficiency) . [ ]

I think Luisi's editorial (already linked to in the comments) together with the above energy coupling demonstrates that Szostak is half right, it is cells that do the necessaru coupling and product separation.

Finally, Benner's objection. His seminar discuss similar metabolic-like networks, and even if they didn't his timescale of "tar" (side or breakdown products if I understand correctly) is "years". [;jsessionid=F662A8DEE69B0D2489FE7F304177FF25?talkid=4772&parent=1 ] RNA strands has a halflife of ~ 4 years at the edges of the vents. If vents produce ribose on timescale of hours, and eventually putatively nucleotides from ribose on similar timescales, there is no "tar" problem.

On the contrary, a supply of glucose at the colder boundary to the ocean would constitute a natural feedback loop and supply against variations in pyruvate metabolite production. And, I would like to ask the biochemists, isn't it there that a later RNA world could start to use the now irreversible steps of glycolysis to regulate the pathway and extract energy (polyphosphates)?