Sunday, July 15, 2012

Protons: Where's the pump?

This post, pictures excepted, is largely based on the core ideas presented in this paper by Nick Lane, John Allen and William Martin. It's downloadable as a pdf from Nick Lane's website and gives great pleasure in return for careful reading. There are more details on the nature of catalysis in pre protein conditions and the acetyl-CoA pathway in Michael Russell's paper (unfortunately PPV, I have the text) co-authored with William Martin here. Some ideas make a great deal of sense. These are in that category. Enough preamble, on to the post:

The Lizard Peninsula in Cornwall is an interesting place. For a variety of geological reasons a chunk of deep ocean mantle is available to visit on the Earth's surface, without getting too wet or borrowing a deep ocean submersible. We visited Kynance Cove about 10 years ago to pick up a few pebbles of serpentine. We were LC beginners at the time.

Serpentine is formed during the hydration of olivine by sea water, as it percolates in to the earth's crust. The process generates heat, produces molecular hydrogen and increases the volume of the rock by about one third, massively fragmenting it. Sorry for the lack of a hammer.

Large amounts of warm, hydrogen rich fluid are produced under pressure and enter the ocean at hydrothermal vents. The chemistry of serpentinisation also means that the fluid is alkaline. The process is continuous and occurs over geological time scales. These are alkaline hydrothermal vents. I prefer the term of White Non Smokers (rejected by Nick Lane).

Unlike the well known Black Smokers of the mid oceanic ridges/troughs, White Non Smokers generate temperatures and mineral concentrations which are not particularly aversive to the abiotic chemistry which might be considered as pre biotic.

The early Earth is thought to have had an atmosphere, like that of present day Mars, which was CO2 rich. This would have made the early oceans mildly acidic.

White Non Smokers are also structurally full of microporous vents. These have vesicle structures which have warm alkaline fluid within and cool acidic fluid without. There is, intrinsically, a pH gradient across their wall. The difference in positively charged hydrogen ions across the vesicle wall is comparable to the proton gradient across microbial, and of course mitochondrial, surface membranes.

This might be where life started.

If it is, here is the proton gradient, nowadays maintained by the electron transport chain pumping protons, pre dating the development of that chain. Under WNS conditions it is possible to generate high energy molecules using the geochemical proton gradient intrinsic to the vent vesicles. For life as a more distinct entity to leave the WNS suburb simply requires a method to maintain the proton gradient away from the geochemical reactor which initially sustained it.

ATP or, in all probability, a simpler high energy molecule could be made for free in the WNS environment. Away from any "free" proton gradient you need to do work to sustain one. Acetate (like methane) is one of the few products of the exergonic combination of molecular hydrogen (from the vent) with CO2 (from the ocean) which supplies enough energy to maintain a proton gradient in an ATP producing state, without any other energy input, no geochemistry, photons or complex organic chemicals.

There are modern, highly evolved and sophisticated bacteria thriving on this utterly primordial pathway even today. Acetate, to them, is waste. But it can be used if you are so inclined.

As you might expect, activated-acetate (nowadays in the form of acetyl-CoA) forms the basis of most modern metabolism, generating ATP in large amounts through the electron transport chain. But it's probably less primordial than the proton gradient itself.

I think that the mitochondrial inner membrane potential both pre dated life and is possibly rather important to on going life. And you can adjust it, under modern conditions, by what you do or don't eat off of your plate...

Which has some bearing on health.



Puddleg said...

Wow, that is indeed an enjoyable pdf and provides both fuel for thought on the origins of life, and a wide-angle perspective from which to ponder the mysteries of modern metabolism.
Cheaper than a Higgs-Boson, too.

js290 said...

I knew this all sounded familiar. You may have posted this link in a previous post.

Purposelessness said...

I can feel carbinsane to come up with a "debunk" of this post. Probably thinking of ways to misrepresent the formation of serpentine, discredit your theory of mineralization, constructing a strawman that acetate=vinegar and mocking you then for implying that prebiotic "life" made vinegar. Or simply stating that white non smokers show that insulin is non fattening.

xxxxxxxxxxxx said...

Ah the internet. Global exchange of valuable information for some. Excellent tool to sharpen school yard bully tatics in hopeless middle-age for others. Let the "debunking" and deriding begin!

Nick said...

My advisor is a huge proponent of metabolism comes before life. Some of the early work by Wachtershauser was done decades ago. If you want any of the PDFs I have access to the un-free ones :)
Great post!

Some good reads on the theory of how metabolism could have evolved abiotically are:

ItsTheWooo said...

@Purposelessness So frigging accurate. You win the internet!

Peter said...

Nick, thanks. I think it is reasonable to view Russell and Martin's WNS-land as pyrites based metabolism with a continuous supply of basic chemicals and a way of concentrating reaction products. Steps in understanding. I completely agree, without metabolism, what can drive the processes we call life? "Life" didn't just happen and then look around to find a way to power its replication!!!

George, yes, some interesting insights. Glad you enjoyed.

js290, several of those papers to revisit still.

Purposelessness, keto and Woo, LMAO.


Brian H said...

Hello, Peter

First time to comment, love your blog. Sure didn't expect to see an ophiolite there, though. Posting to rec'd to any ophiolitophiles out there John McPhee's literary paen to all things serpentinous:his Assembling California. Which is included in his geological omnibus Annals of the Former World. A sheeted dyke will never look the same.

BTW, I have used Atkins to lose weight in the past, the only thing that ever worked. Protein coming out of my ears. Had a devil of a time staying in ketosis,though, and my weight would not budge unless I was. However, your breakfast of egg yolks fried in lots of butter inspired me to lowball the protein and amp up the fat (especially butter). Now I'm purple all the way, it doesn't waver, and the pounds are melting off. I think a lot of people are aware of their intolerance to carbs, but are unaware that things may go better for them metabolically if they moderate their protein intake. Or not. But it's something to experiment with.

Bill said...

Interesting post Peter, I kind-of-get-it. is this the first post in a new series you’re planning?

Peter said...

Hi Brian, Someone gave me a hand mineral faceting/polishing kit for Christmas when I was about 12 years old, I've been fringe interested in geology ever since. Even here in Norfolk, on an ephemeral ridge of glacial terminal moraine, you can pick up all sorts of northern European pebbles on the beach... And I remember walking the Water of Leith in Edinburgh with my kayaking brain functioning to assess if it might be paddle-able, with a local geology guide in my hand. This dyke gives this whitewater rapid... I think I may be a bit weird.

Protein, yes. There are studies showing LC doesn't work for T2DM. You just have to get protein high enough and restrict carbs by total calorie restriction, plus be of a mind set to preserve the staus quo! Luckily the word is getting around, mostly through Jimmy Moore and Tom Naughton at the moment.

Bill, yes, you can't think about the ETC without some idea of why it's there, where it came from, what it does and why the superoxide free radical might just be the ultimate satiety hormone, as well as the primary cause of both physiological and pathological insulin resistance. I've not dared think about nitrogen derived free radicals yet... All from the ETC, all function/dysfunctional


Marnee said...

Very nice. The universe & life are truly a fractal and if you look for it you can see the parallels all around you. This is a really cool one. Cheers.

Brian H said...

"I think I may be a bit weird"

I've done the same thing, only with white water streams in Arkansas. Our name is Legion.

Margaretrc said...

Great post. I've downloaded the PDF and look forward to reading it. I loved Nick Lane's book "Ascending Life: The ten great inventions of evolution." and especially remember the chapter on this topic.

Puddleg said...

To get energy from sugars you need an improbable array of enzymes and half the B vitamins; to do the same to fats involves repeating the same step over and over with FAD-NAD; beta-oxidation is modular, repetitive.
Even the modern version of beta-oxidation seems more primitive and less refined than glycolysis.
It's like a pit pony beside a Lippizaner.

Sam Knox said...

@purposelessness, woo

It's not been a good summer for Evelyn. Low-carb diets shown to have a metabolic advantage and Jimmy Moore is losing weight.

Not much for her to write about, I'd think.

LeonRover said...


"Not much for her to write about, I'd think."

It seems Jenny Diabetes might be coming into view . . . .


Puddleg said...

What was the primal co-enzyme in the dawn of metabolism?
This is my candidate:

Unlike other antioxidants, the exceptional molecular stability of PQQ allows it to carry out thousands of electron transfers without undergoing molecular breakdown
PQQ is 30 to 5,000 times more efficient in sustaining redox cycling (mitochondrial energy production) . . . than other common [antioxidant compounds], e.g. Ascorbic Acid (Vitamin C)

Purposelessness said...

Sam Knox

Yes, to us, it may appear that way. But think about it, anyone who can go "Taubes didn't mention ASP so his hypothesis is wrong and he is only in it for the money trolololo" will always find stuff to rant about. Even if it comes to one overweight women mocking other overweight people. I mean look at her go - multiple blog posts per day? I don't even have that much time to read blogs, let alone actively read many blogs I disagree with, trying to construct strawmen, or googling pictures of Taubes all day long until I find one where his shirt bulges.
I cringe every time I think about the fact that she actually seems to teach at college level. But then again, I have had my share of horrible professors, so it wouldn't be too unusual.
Maybe I should stop my habit of skimming her blog every few weeks, but it's kind of a guilty pleasure for me. Provides me with a mix of amusement and pity when I look at some of the obvious mistakes she makes. I just feel bad for her readers who never took a biochem class, you couldn't possibly pick up all of the errors she makes then...

xxxxxxxxxxxx said...

Could be the classic situation were a person finds attension and stimulation through the ancient ringleader/scapegoat dichotomy. Not sure why so many ppl get attracted to the relentless attacks, snarks, and outright lies, but the formula presents itself over and over in family, group and even national situations. *mystified*

Manythings said...

These discoveries about the nature of mitochondria are absolutely fascinating, the more so because they are so counter-intuitive - a bit like quantum physics. Yet another nail in the coffin, perhaps, of "common sense". (I mean the kind of common sense that does not require any or much observation of actual, objective phenomena).

The thing is, what's the application of this knowledge for us humans - how do we best look after our mitochondria and our health? I look forward to any forthcoming blogs on this subject!

Makro said...

More mitochondria and ketosis:

ItsTheWooo said...

@SamKnox presently the carbsane asylum is infatuated with Jimmy's 'haters make me famous shirt" so this will have to suffice in place of juicy gossip that he is getting fatter.

I have no idea why carbsane insults that dugan girl; she is more unfortunate than anything. She seems unable to stop eating junk food for whatever reason and as a result is much heavier now than she was many years ago.

Someone needs to give carbsane a memo that she herself is quite fat. It's like she is in denial about this.

She'll say she is a "BMI outlier" but then she blogs about how in the past she only weighed 110 pounds. There is NO WAY a BMI outlier could ever reach a weight that small without being extremely sickly looking and underweight. I don't consider myself a BMI outlier, when I weigh 110 pounds people constantly tell me I am underweight and emaciated and I can see bones like crazy, etc. The fact carbsane has been very small in the past w/o being notably sickly underweight automatically invalidates her "BMI outlier" justification for her size.

And, really, if it's CICO, and it's as easly as focusing on eating less...why on earth is she so fat?
...and why does she bother restricting carbs? I don't waste my time restricting things that don't matter.

@Purposelessness I am addicted to the site. I can't stop reading it, like a disorder. Everything she blogs is wrong. All of her arguments are wrong. I feel bad for the simple people there who can't see it and depend on her for "debunking'. There are so many people like that, mostly ignorant individuals who themselves do not have insulin resistance and also don't have any kind of medical background, so they have no reference point to operate from.

Just 2 days ago I argued that the increase in diabetics comes from the type 2 variety, who get it in older age and suffer miserably with sicknesses and complications related to poor blood sugar control. I explained I see this every single day as a registered nurse, and listed a few very common patients I see. When a doctor says "diabetics are living to 70 today" this is a GROSSLY misleading statement, as it is only true because we have an explosion of type 2 diabetes that did not occur several generations back.

Carbsane then proceeds to tell me as a nurse I lack education to discuss these issues (meanwhile, her profession of being a remedial community college math teacher overqualifies her to blog apparently), and I only work in a "nursing home" (she is grossly ignorant of american health care, the "nursing home" is the new medical/surgical unit, no one stays in a hospital more than a few hours before being transfered to a lower acuity rehab i.e. nursing home...).

The irony here is that I am a registered nurse, every single day I am admitting patients and giving care to patients who are actively stricken with diabetic complications, meanwhile she has the audacity to tell me I do not. Meanwhile, she sits on her ass in a junior college, and spends multiple hours per day telling people her opinions about every single disease related to obesity.

But, I forgot: Part of the carbsane self delusion isn't just that she is thin, but that she is a geeky science expert and an accomplished scientist. So naturally, a cutting edge scientist trumps the opinion of a registered nurse, lol.

Peter said...

Brian, hee hee, so there's a lot of it about!

Makro, Ta.

All, re arguments, yes it's weird. You have to look at it and wonder about what drives human behaviour. But then when I was checking at Jenny's site for the latest research links she's put up I couldn't help notice from the side bar that The Good Dr has a post up on what causes diabetes. And what to do about it. I'm running out of anti nausea pills.

It would be funny, except it's not. It's really, really, really not.


Peter Knobloch said...

Hi Peter,

The link to Nick Lane's full paper seems to be a dead link. I found his site and the download link should be one of the links here:


Peter said...

Thanks Peter,

I guess it's from when he updated his website recently. Fixed now...