Tuesday, August 25, 2015

Starchy stable isotopes? I don't think so!

Have a read at this statement from Hardy et al 2015:

“…stable isotope analyses indicate a mainly carnivorous diet for Neanderthals; a wider range of isotopic values have been observed in contemporary Middle Pleistocene H. sapiens (Richards and Trinkaus 2009), indicating that considerable differences in the levels of starch consumption existed between these two species.”

Now, if you read this I think you might be led to believe that stable isotope analysis indicates that Neanderthals were carnivores and H sapiens ate a different amount of starch to a carnivore. I feel the implication of this sentence is that H sapiens ate "more-than-zero starch" during the Middle Pleistocene.

You would believe wrongly. Did you check the reference? No? Naughty. Richards and Trinkaus (2009) actually say this:

“As the method only measures protein intake, many low-protein foods that may have been important to the diet (i.e., high caloric foods like honey, underground storage organs, and essential mineral and vitamin rich plant foods) are simply invisible to this method.”

The data do not deny starchivory. But the data equally do not in any way support its occurrence. Starch, fruit and honey are invisible on stable isotope analysis. This is a gross mis-citation of Richards and Trinkaus by Hardy et al. Never believe stuff like this without checking the refs. Easy when it is a freebie in PLOS. What do Richards and Trinkaus actually say about diets of carnivorous Neanderthals vs H sapiens? Try this:

“There are now enough isotopic data to see patterns in the data, and they show that the Neanderthals and early modern humans had similar dietary adaptations, obtaining most of their dietary protein from animals, although some of the early modern humans obtained significant amounts of their protein from aquatic, and not just terrestrial, sources.”

You can tell H sapiens ate fish because aquatic food chains are long. The longer the food chain the greater the effect visible in stable nitrogen isotopes. They make fish eating carnivores look like hyper-carnivores. That's how they show up in the paper. Had humans eaten any significant amount of protein rich plants (hazel nuts get cited as a possibility) it would show a lower stable nitrogen ratio. There is no evidence for this.

Did early humans consume starch to grow their brain size? Stop laughing! No one knows, certainly to the point where a starchivorous paper has to mis-cite a completely non-supportive paper as being actually supportive of their rubbish hypothesis.

I love it.

Did you hear the one about Jennie Brand-Miller? Passthecream linked to this gem in the comments of the last post. Some things are just too funny not to share. Have a giggle. J B-M is second author on the starch-is-needed-to-grow-brains paper...


Monday, August 17, 2015

Sweden's dietitian advice? No thank you.

Hot off the press from Uppsala and Stockholm:

A high energy intake from dietary fat among middle-aged and older adults is associated with increased risk of malnutrition 10 years later.

"Contrary to what was expected, a high energy intake from total fat, saturated fat and monounsaturated fat among middle-aged and older adults increased the risk of exhibiting malnutrition 10 years later. However, this applied only to individuals with a BMI < 25 kg/m2 at the baseline. In conclusion, these findings suggest that preventive actions to counteract malnutrition in older adults should focus on limiting the intake of total fat in the diet by reducing consumption of food with a high content of saturated and monounsaturated fat."

Repeat after me. Association does not prove causation. How anyone dare suggest an experimental intervention on a large subpopulation of their nation based on an observational association within a subgroup of the target population is beyond me. How dare they?

It must be embarrassing to be a dietitian in Sweden nowadays but this sort of intervention recommendation is not going to decrease the stupidity index of mainstream dietary advice.

Hopefully sensible people will continue to ignore them!


Methyltransferase in methanogens

The archaea developed rather differently from the Ech driven bacteria. I want to look at them from the energetic point of view so it seems reasonable to start with this image from the first of the Life series posts, back in February:

This has CH3-SH (used at two points in the process) driving acetate formation for cell carbon generation. We know this works because Huber and Wächtershäuser demonstrated the abiotic generation of activated acetate from CO and CH3-SH in the presence of an FeS/NiS slurry. No enzymes, no cofactors, no structure. Energetically, it works. I now want to speculate wildly about other uses of CH3-SH in the development of methanogens and the evolution of methyltranseferase, the archaeal alternative to Ech. Let's get rid of the carbon fixation doodles. The location of CH3-SH might need to change as ideas develop:

In the background to the following speculation we still have a FeNi hydrogenase "visiting" a proton channeling pore to generate reduced ferredoxin using a localised low pH region just inside the cell. In the archaea I'm assuming there is no preformed Na+ pump because the protein translocating precursor never jammed up so never pumped Na+ ions. There was no drop in intracellular Na+ and the FeNi hydrogenase never attached firmly to the proton pore in the membrane. Interestingly the methanogens do still have a cytoplasmic FeNi hydrogenase (or NiFe in this illustration) passing electrons down FeS wires. Instead of dropping them straight on to ferredoxin to generate reduced Fd2- using the proton gradient of the cell wall conducted through a membrane pore (as per proto Ech), pairs of electrons are split at an FAD. Half do the up hill job of generating Fd2- and the other half tumble down hill to the easy target of heterodisulphide. Energy from the latter down hill reaction is used to allow the up hill Fd reduction and gets you out of the need for a membrane proton gradient. I do wonder if this is the same FeNi hydrogenase of proto Ech but here diverted to electron bifurcation. This is from Buckel and Thauer's fantastic paper Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation:

That's what happens today. What might have been the core process when metabolism was less refined? Here's a scheme with FeNi hydrogenase (in Hdr, heterodisulphide reductase) using CH3-SH as the electron acceptor for a crude version of electron bifurcation:

Under circumstances of freely available CH3-SH there is no need to conserve sulphur.

The Ni is shown associated with the enzyme which generates all of the biological methane ever produced on earth, methyl coenzyme-M reductase. Nowadays the Ni is bound in the lovely and highly complex coenzyme F430 (an interesting read if you have access):

Here it is in the step producing methane:

Sulphur is no longer a disposable commodity and it is recycled via CoM as a loop in combination with another sulphydryl based coenzyme, CoB.

CoM provides the -CH3 and CoB provides the -H to generate methane. The reaction joins the two coenzymes together to give the mixed, disulphide bridged, heterodisulphide. This is the modern electron acceptor in the Hdr electron bifurcating hydrogenase. It actually accepts a pair of electrons to give CoM-SH and CoB-SH:

The CoM-SH is regenerated to CH3-S-CoM by the methyltransferase shifting a -CH3 from CH3-H4MPT. Ultimately the energetics of the cell is determined by the availability of CH3-SH analogue CH3-S-CoM controlling electron bifurcation at Hdr:

Next let's take out the electron bifurcation system having established a central role for CH3-S-CoM to energetics control and add in the proton port being used to generate Fd2- using the vent H+ gradient:

And add in the antiporter for Na+ ions:

At this point there is some benefit to converting a protein-translocase to a Na+ driven ATP synthase. Consider that it is Na+ ions that are stabilising the membrane section of the translocase so it seems logical to accept a sudden Na+ gradient as the force pushing inwards to reverse the translocase to generate ATP. So we need the A1-A0 ATP synthase adding in to the diagram:

Now a proton gradient is once again driving a Na+ coupled ATP synthase and all is hunky dory for the cell. Excess ATP synthesis can be regulated by CH3-S-CoM inhibiting Na+ antiporting:

When the vent proton gradient fails all that is needed is for CH3-H4MPT to take over from the vent proton gradient. The transfer of the methyl group from H4MPT to CoM is exergonic and is used to drive a conformation change in B12 which ejects the Na+ ion. Lots of detail from Thauer again at The Na‡-translocating methyltransferase complex from methanogenic archaea.

Which simplifies to this:

Giving a speculative journey leading to how we might have ended up here:

In modern methanogenic archaea Na+ energetics have been carried forward to today. Protons still look like an add on to me. Of course the question posed from here is how similar is the Na+/H+ antiporter of the methanogens to the NouH and NuoL combination in the bacteria, incorporated in to the base of complex I.

Not surprisingly I haven't found anyone crazy enough to float this idea. This is what Thauer has to say about Na+ translocating pores and aspartic acid within the pore channel:

"The second reason for the proposal is that only MtrE has a transmembrane helix with an aspartate residue (Fig. 1), the sequence of this helix in the MtrE subunit from all methanogens being highly conserved: 168-IWGITIGAIGSSTGDVHYGAER-191. An aspartate residue in a transmembrane helix has been shown to be essential for sodium ion translocation as catalyzed by the L-subunit of oxaloacetate decarboxylase from Klebsiella pneumoniae [62]. An aspartate residue is also conserved in the transmembrane helix of the sodium ion-translocating glutaconyl-CoA decarboxylase from Acidaminococcus fermentans and of the sodium ion-translocating methylmalonyl-CoA decarboxylase from Veillonella parva and Propionigenium modestum [63]".

Here is NuoH from complex I with the aspartic acid at D213 picked out in red:

Which rather implies that NuoH, rather than NuoL, was the Na+ part of the antiporter, assuming the membrane portions of methyltransferase and Ech derivatives are distant relatives of the same ancestral protein...


Cholesterol reflectivity at 400nm

I'm interested in paleobiology at the moment, readers might have noticed. Mostly how we might have gotten to where we are now without a Sky Pixie. The ancient past is fascinating. Not only single carbon chemistry under far from equilibrium conditions but big stuff like dinosaurs and cardiologists.

People love dinosaurs. If it's not LDLc levels, it's particle counts or apoB numbers. Am I going to die (yes!)? Will it be from CDV or cancer? Let us examine the entrails of a lipid hypothesis which lies eviscerated here before us. Messy.

How many apoBs can I see???? Do they have purple spots (i.e. does the apoB particle under the microscope have focal regions which are hyper-reflective to photons of 400nm wavelength when irradiated by full spectrum bullshit?).

I think we have to think have to respect the views of the president of the ACC. ACC is the American College of Cardiologists. These folks are wildly intelligent, free thinking, adventurous, swashbuckling promoters of new ideas. The newest idea on view from the president of the ACC is this one:

‘Some prominent cardiologists have questioned the 2013 guidelines, but the ACC and AHA have shown little appetite to return to LDL targets. “LDL may or may not correlate to cardiovascular outcomes,” Dr. Kim Allan Williams, president of the ACC, told Reuters last week1.’

Malcolm Kendrick has an excellent post up on this quote. But let's just say it again, it really is so good:

 “LDL may or may not correlate to cardiovascular outcomes”

By whom?

Dr. Kim Allan Williams.

Who is?

President of the ACC.

Which is?

The American College of Cardiologists.

Of course, the statement does leave open the possibility that cardiovascular outcomes MAY correlate to LDL levels. More likely not.


Sunday, August 16, 2015

When low fat wins

I think I’ve said before, I’m a calories-in, calories-out sort of person. Nothing as simple as losing a kilo of stored fat for every 9000kcal deficit in dietary consumption (or increase in exercise) of course. This is, as we all know, incorrect and of absolutely no use whatsoever in planning an attempt to generate a normal bodyweight.

I am also very aware that, outside a metabolic ward, it is very difficult to even approximately assess a given person’s level of energy output, assuming they are fully compliant with a fixed composition, fixed caloric input. Which they probably aren’t, much of the time. But calories out will be reflected in many more outputs than can achieved by the limited exercise opportunities afforded during the restrictions of an in-patient metabolic ward study.

As Hall commented, the repeated superiority of weight loss by carbohydrate restriction has always been achieved in outpatient studies, never in tightly controlled metabolic ward studies. He didn’t mention that the advantages from carbohydrate restriction were always achieved under calorically unrestricted circumstances in comparison to calorically restricted alternative diets. I’ll just mention that now.

We can also say, with some degree of certainly, that under very tightly controlled in-patient conditions, extreme dietary fat restriction (less than 8% of calories) produced more stored fat loss than a modest reduction in carbohydrate restriction, provided both groups are rigidly forced to cut calories and to limit their exercise to a specified level, for six days. My own feeling is that this is probably true under the circumstances of the study. It provides a very small piece of data of very limited application to the real world. As Hall writes:

"Translation of our results to real-world weight-loss diets for treatment of obesity is limited since the experimental design [and model simulations] relied on strict control of food intake, which is unrealistic in free-living individuals".

I am very lucky.

I don’t live in a metabolic ward. If the weather is cool outside and I feel warm enough to not need my jacket when I let the chickens out in the morning, so be it. If both the air and water temp are 4degC but there is a four foot swell with clean waves shaping up in First Bay I’m going to be thinking about the roof rack, my playboating kayak and my drysuit. I’m guessing that there are few near freezing surf opportunities in a metabolic ward.

People might also be aware that I rather like fatty acids, especially free fatty acids. These uncouple respiration. Uncoupled respiration, at the mitochondrial level, generates heat and so increases metabolic rate. For people with a heathy interest in cold water kayaking, this has its advantages. Sitting in a metabolic ward eating 140g of carbohydrate per day is not going to increase my free fatty acids to a level were uncoupling is going to feature in my metabolism.

The average person with a BMI of 35 is probably going to be running their metabolism under the Crabtree effect. Increased dependence on glycolysis at the expense of reduced utilisation of mitochondrial beta oxidation. While it is quite possible to immediately and markedly increase fatty acid oxidation, there are limits set by how many mitochondria a given cell possesses. The moderate carbohydrate group did increase their fatty acid oxidation, but not enough to compensate for the loss of carbohydrate available from the diet. This is perhaps most clearly seen in Table 3 where a significant drop in sleeping metabolic rate occurred in the moderate carb group and an actual increase was seen in the very fat restricted group. It's probably why the moderate carbohydrate group had a suggestion of increased protein degradation compared to the very low fat group.

Even thought it was nearly 15 years ago, I can still recall Atkins Flu™ as I switched to deeply ketogenic eating from a fairly reasonable modern diet. The "flu" lasted about 6 days (apologies for exactifying my recall to fit with the study duration!) with further acclimatisation over the next few months. There should be no such problem with increasing glycolysis in the very low fat group if you are already running your metabolism on starch combined with HFCS. It is no major problem to up regulate carbohydrate metabolism when it is your normal metabolic fuel source.

So for the first six days of an enforced, calorically restricted, non-ketogenic diet, cutting fat rules provided the restriction is very, very extreme. Do this long term and you will, of course, fail.


Wednesday, July 29, 2015


When I draw my doodles of early energetics my standard protocol is to have low pH, high H+, oceanic region at the top. The ocean is above.... I have the vent derived, geothermal, low H+ region at the bottom, that's were the rocks are.

Once people start looking at modern membrane complexes there is no need for such conventions and figures are usually produced the other way up. So when we want to look at modern Ech and derivatives I think I have to turn my proto-Ech doodle upside down like this:

I have, very naughtily, butchered a cartoon of a modern Ech (out of the lovely paper from Efremov and Sazanov) to produce this image of my concept of proto-Ech. As in the doodle, this must use a geothermal proton (not Na+) gradient and does not look to be reversible:

Note that I've altered the black arrows to match my red arrows, showing the generation of reduced ferredoxin from oxidised ferredoxin and the consumption of (primordial) H2 under the influence of oceanic proton flow through the brown membrane protein labelled EchB but which I will refer to from here onwards as NuoH, or a homologue there-of. Their original image of a modern Ech on which I based my proto-Ech is this one:

Again, for various reasons, I will refer to the blue subunit EchA as NuoL. This modern Ech is energy converting, it pumps protons through the blue anti porter homologous to NuoL. All of the arrows are now in their modern pumping direction. The pump is powered by reduced ferredoxin (from elsewhere in the cell) and produces hydrogen as waste. Typical bacteria using this Ech might be E coli, to produce flammable flatus. The source of reduced ferredoxin is any catabolic process. Fermenting starch in the anaerobic colon has predictable results in this department.

An understanding of the initial role for this antiporter is crucial to any logical approach to bioenergetic evolution. Equally interesting are the adaptions of subunit EchB (homologous to NuoH) to changing the activity of NuoL from antiporting to Na+ pumping.

We can now look at a NuoL type antiporter embedded in a membrane without any power supply. It will consume membrane proton potential by allowing protons to move inwards and expel Na+ ions outwards in exchange, like this:

It can do this in a modern bacterium because there is a proton gradient, created by complex I (or any other energy converting complex/hydrogenase), i.e. protons are available to travel down a concentration gradient in to the cell, much as they might have done in primordial times. Na+ ions are forced out against a concentration gradient, in this case because this particular microbe lives in an extremely high Na+ environment. If you delete the Mrp genes for subunits MrpD and MrpA you cripple its antiporting ability. Engineering back in homologous proton translocators from a modern complex I restores the full antiporting ability.This tells us that the modern proton translocators of complex I are still antiporters but their antiporting is kept suppressed. I would suggest by NuoH.  Note that the Mrp antiporting complex has no NuoH subunit.

NuoL does appear to be distantly related to NuoH, possibly by very ancient gene duplication. The conservation of form can be seen in these lovely images from Marrreiro et al. The gold ribbon is NuoH and the grey one is NuoL. The channel form is clearly visible. I consider NuoH to be homologous to the original proton ion channel from my proto-Ech doodle and its relative NuoL to be homologous to a prototypical Na+/H+ antiporting derivative.

I think that the initial gene duplication/modification would probably have produced an uncontrolled antiporter which would have produced a dramatic fall in intracellular Na+ concentration. This activated ATP synthase, making it function as an ATP generating rotor turned by Na+ re-entering the cell. This would generate ATP as fast as the proton gradient could produce a Na+ gradient. Very fast.

Possibly the first priority after the generation of a Na+/H+ antiporter would be to work out how to stop it. Here's how:

Proto-Ech is essentially sidelined as a source of high energy compounds by the novel Na+ energetics system. Mutations in NuoH or the NiFe hydrogenase would no longer be fatal, so there is the scope for the now redundant proto-Ech to be converted to a metabolic sensor and switch.

Excess reduced ferredoxin indicates a surplus of energy supply, almost certainly driven by over zealous antiporting. If this excess reduced ferredoxin is allowed to drive through proto-Ech, pushing electrons towards the FeNi centre and beyond to reduce protons to H2, this sign of excess could easily be adapted to produce a conformational change in NuoH.

NuoL is stuck on the side of NuoH. Changes in the shape of NuoH produce changes in both shape and function in NuoL. All that is needed is for excess reduced ferredoxin to produce a conformation change in NuoH and it could shut off the antiporting in NuoL. Having the antiporter (NuoL) glued to the side of NuoH allows the switch to function effectively.

Summary so far: Excess reduced ferredoxin stops/reduces antiporting and so controls ATP over-synthesis derived from exuberant Na+ energetics.

So here is the next question: What happens when the geothermal proton gradient fails? For a start, the free lunch from antiporting disappears. We still have the back up of ferredoxin energetics from electron bifurcation but nothing to compare to the glut of ATP from the now diminishing Na+ energetics.

What is needed is some way of pumping Na+ out of the cell which could replace the simple and exceedingly easy antiporting system. I've already got reduced ferredoxin acting through redundant proto-Ech as a brake on antiporting, as part of a control system on Na+ energetics. If we were to generate a change with allowed us to "over-apply" the ferredoxin brake we could, plausibly, go so far as to do more than simply stopping Na+ entering the cell, we might actually start to reverse Na+ ion flow and pump it outwards. Na+ pumping by using the energy derived from reduced ferredoxin.

Proto-Ech is now running in reverse and pumping Na+ ions. It is conserving energy as a Na+ gradient and so is now a true Ech, there no longer anything "proto" about it. It's reversible. Na+ energetics are restored and the core power supply to the cell is electron bifurcation supplying power to drive Na+ energetics.

That's how it stays until cytochromes come along.


Sunday, July 26, 2015


Let's begin with electron micrographs of the structure of the precipitates in Nick Lane's hydrothermal vent simulating bench top reactor.

At low power by scanning EM we have:

At high magnification by transmission EM we have:

I've sketched what I think might be happening within the latticework of these amorphous precipitates. As the fluids mix it's not simply linear. There will be channels, eddies and incomplete barriers.

You have to bear in mind that this is all completely made up. It's a thought experiment. This might be true, it might not be. Here's my guess:

What we do know is that this reaction is taking place:

We know because the CO goes on to reduce to formate and Nick Lane picked this up in respectable amounts from the fluids flowing through the structures shown in the electron micrographs.

The horrible slide below is the above reaction turned on its side to fit in with the first sketch:

The green ovoid shows the sort of place where I think the reaction might be taking place, but actually all over the doodle I've produced:

I would suggest the precipitate might be rather high in FeS and only doped with Ni in places. The structures in the micrographs are a lot bigger than one Fe atom across. Let's show an FeS crystal structure doped with Ni. This allows the low redox potential electrons from H2 at pH 10 from one FeNi cluster to be conducted through FeS clusters to another FeNi cluster on the other side of the crystal, where a second catalytic reaction can take place. CO2 was common in the ocean and vents so we can have step two as CO2 reduction:

I would view the second FeNi cluster on the right hand side as the potential origin of CODH/ACS, separated off in to the cytoplasm and of no further interest in the development of a proto-Ech. I've flipped back on to a more normal orientation for the rest of the pictures as reading on one side does horrible things to my brain. In the next picture I've got the first FeNi centre accepting low potential electrons from H2 at pH 10 and donating them, not to a structural FeS cluster as previously but to a ferredoxin, a soluble version of FeS, at pH 6 to give a an FeS moiety with a redox potential capable to reducing CO2 to CO, but in transportable form. Able to wander off elsewhere in the cytoplasm as the core power unit of the cell, to where ever CODH/ACS has ended up. Ferredoxin is one of the most ancient and simple peptides, possibly worth a post in its own right. Below shows the need for a low pH region close to the FeNi moiety to allow this conservation of reducing power:

The above diagram is getting rather cluttered so I thought it would be useful to simplify matters in to an enzyme based around a (not shown) catalytic centre converting the energy of H2 to reduced ferredoxin using a localised area of pH 6. This is the logical origin of the type 4 FeNi hydrogenases which are still in ubiquitous use today:

The hydrogenase is core to Ech but we need another step to get us from a hydrogenase using the pH gradient to a true proto-Ech. That step is the formation of a protomembrane. The protomembrane is freely conductive to both protons and hydroxyl ions but will stop the FeNi hydrogenase getting close enough to the inorganic cell wall structure to get a decent look at a pH of 6, needed get ferredoxin reduced.

What is needed is a protein structure within the protomembrane which can channel protons tightly through from the inorganic wall across the leaky protomembrane to allow the FeNi hydrogenase to get a decent look at a pH close to that of the ocean:

By this time the inorganic cell wall is no longer strictly needed but the protocell is clearly still completely dependent on an external pH gradient to generate reduced ferredoxin. I would call this port/enzyme combination a proto-Ech:

I think it is a reasonable assumption, if this thought train is correct, that there is no way that a gradient of Na+ ions can replace a gradient of H+ ions, you simply wouldn't get the pH 6 within the enzyme by translocating Na+ ions. The modern Ech has a second membrane protein built in to its structure, an anti porter. That will transport Na+ ions, and is reversible.


PS, for Passthecream: One way H+ but no Demon in the channel!

Saturday, July 25, 2015

Two timelines

This is for Raphi. It's a slightly rough version of the post I lost yesterday. I've been through Nick Lane's timeline for the evolution of bioenergetics in The Vital Question as carefully as I can and it's set out below. I've coloured in green the lines which are unchanged in the timeline that I would suggest and in red the sections of both timelines which I have some trouble with. Here we go:


There is a proton gradient, FeNi catalysis, activated acetate, ATP (via SLP), no membrane.

Permeable membrane develops, Ech and ATP synthase develop and use the gradient across this membrane, both run on the vent H+ gradient

Membrane tightens to Na+.

Antiporter invented while membrane still proton permeable but Na+ opaque.

Antiporter provides a Na+ gradient in addition to the H+ gradient, this helps because Na+ (along with H+) can drive ATP synthase to produce ATP and Na+ (along with H+) can drive Ech (TVQ p144, line 10 and line 23) to produce reduced ferredoxin.

This is a pre adaptation to proton pumping, because a pumped proton drives the antiporter which maintains the Na+ gradient whenever the natural proton gradient of the vents diminishes. i.e. with an antiporter plus pumped protons a much smaller vent gradient is needed. A proton pump is developed, not specified where from but probably from Ech/antiporter.
Membrane progressively tightens to H+ and so Na+ pumping becomes progressively less important, it’s pumped protons which now return through ATP synthase.

No longer any benefit from Na+ pumping so everything uses pumped protons and these are pumped via Ech using reduced Fd- from electron bifurcation (acetogens) or via a modified anti porter powered by methylene-H4MPT (methanogens).

As I have commented before, I have trouble with the very early development of ATP synthase as a very complex nano machine providing ATP for a cell in the earliest periods of crude membrane formation. However, that does leave Ech, energy converting hydrogenase. The next few posts are on Ech but for now it is a primordial supplier of reduced ferredoxin to the protocell. It is very simple and works perfectly well on the primordial proton gradient.

However, having rejected ATP synthase I am left with the problem of ascribing the benefits of Na+ antiporting to the use of Na+ energetics by the developing Ech, this won't work. Ech, as a generator of reduced ferredoxin, is dependent on the pH gradient provided by the vents. It's a matter of redox potentials for H2 converting to 2H+ and 2e-. See next post, you can't do this with a Na+ gradient.

So that leaves me with energetic problems, no ATP synth and Ech needing a pH gradient. Hence the time line cobbled together below:

There is a proton gradient, FeNi catalysis, activated acetate, ATP (via SLP), no membrane.

Permeable membrane develops. This forces proto-Ech to develop as a protein encrusted FeNi enzyme, it runs on vent gradient to generate Fd- to generate activated acetate and ATP (still via SLP). 

Any membrane forces the development of an ATP driven translocase to allow spread of RNA/proteins through vents through membrane barriers.

Membrane tightens to Na+.

The translocase jams and ends up using ATP to pump Na+ ions rather than to translocate a protein. Modestly lowered intracellular Na+ improves proto-Ech function.

Antiporter invented while membrane still proton permeable but Na+ opaque.

The antiporter causes a marked drop in intracellular Na+ which forces the translocase-derived Na+ pump to flip in to reverse and so generate ATP from the suddenly hugely increased Na+ gradient. This is the origin of ATP synthase.

To leave the vents proto-Ech is adapted as a power supply to the antiporter (so that H+ gradient driven antiporting is no longer needed), becomes the true Ech at this stage. It always pumps Na+ outwards using Fd- from electron bifurcation either directly or indirectly via methylene-H4MPT.

Everything runs on Na+ energetics, there is no rush to generate a proton tight membrane, but no problem if/when it happens.

Cytochromes demand H+ energetics, most organisms convert to cytochromes at various different evolutionary times. Non-cytochrome microbes continue to run on Na+, even today.

The problems in this timeline, also in red, are the benefits to a protocell from lowered Na+, the limitation of Ech to pumping Na+ only, certainly until much latter and the evolution of cytochromes, and the idea that Methyltransferase, which pumps Na+ in methanogens, is a derivative of Ech. These are the subjects of my next couple of posts, along with where Ech came from and why it must have a proton gradient.


EDIT Methyltransferase is much more complex than an Ech derivative!

Friday, July 24, 2015


I have just lost a very complex post. Gone. :-(