Sunday, February 07, 2021

Just an announcement

The World Nutrition Summit is coming soon as a virtual meeting based in South Africa. The organisers kindly asked for a presentation based around the ROS hypothesis of obesity. I haven’t tried to make it particularly user friendly, Mike Eades has already done that, this is more of a brief whirlwind tour of the many technical papers which went to make up the Protons thread and spawned the idea.

Thee's a lot more information from the Nutrition Foundation here.

I bought a microphone.


Sunday, January 31, 2021

Hall and CICO part 3

Okay, this is the image I missed on my first read through the results/methods of Hall's latest offering:

I have to apologise for failing to pick this up possibly because I would never read the discussion or conclusion of a Hall paper. My interest in what Hall thinks is distinctly limited. The image shows a delay in the onset of fat mass loss with LC which then proceeds at a remarkably similar rate to the fat loss in the LF group.

But clearly, the changes in fat mass under LC trend upwards (ns) initially before trending downwards, (also ns) compared to fat mass at initiation of the diet.

As David Ludwig has pointed out, appetite suppression on LC can be delayed and shows most reliably from 2 weeks onwards. This might well be related to the rising levels of ketone bodies providing enhanced energy availability as ketosis develops using the concept outlined here:

This brings to mind a very short term study from some time ago looking at ketogenic diets based around saturated vs polyunsaturated fats.

Differential Metabolic Effects of Saturated Versus Polyunsaturated Fats in Ketogenic Diets

Both diets were individualised to be weight maintaining, so we can say nothing about spontaneous food intake (ie appetite, ie weight/fat mass changes). The main point of interest is the very right hand end of Figure 1:

which shows calculated insulin sensitivity. Under high PUFA intake insulin sensitivity, after an overnight fast, is clearly enhanced.

We have no information about the FFA levels so assessing the "blood energy content" is impossible for either diet. However we can look at the relative changes in glucose vs beta hydroxybutyrate (BHB). They look to be reciprocal, but this is simply an artefact of percentage change.

Glucose drops by 10% from normal fasting levels in the PUFA group, measured as 79.2mg/dl, a sizeable number. Ketones in the PUFA group rise by 10% over the same period. But this is 10% of 1.34mg/dl, a vanishingly small amount, physiologically. There is no ability for this modest rise in BHB to offset the fall in glucose. The energy content of ketone bodies and glucose are approximately equal, per gram. Free fatty acids would be the unknown confounder.

That study looked at high (10% energy) vs very high (42% energy) from PUFA intakes, both under modest ketogenic conditions.

Hall's study looked at a mildly ketogenic diet with around 15% of energy from linoleic acid, a pathologically high intake, in comparison to a carbohydrate based diet deriving around 3% of calories from linoleic acid, ie a physiological linoleic acid intake. 

Linoleic acid at 3% of calories, ie very low, will have no blunting effect on the ability to limit caloric ingress in to adipocytes ("loss") in the peak-absorptive period (so will not generate the need to eat more food to offset this loss in to adipocytes) and will not facilitate pathological insulin sensitivity to allow hypoglycaemia in the post-absorptive period (with subsequent hunger).

I think we can sum Hall's study up in the words of the abstract section:

"One participant withdrew due to hypoglycemia during the low-carbohydrate diet."

translated as

"One participant withdrew due to hypoglycemia during the high-polyunsaturated fatty acid diet."

The other participants had to (spontaneously) eat more to successfully avoid these problems during the first week. 

The effect diminished through the second week of the study as ketones rose further to compensate for the hypoglycaemic effect of excess PUFA.


Saturday, January 30, 2021

Hall and CICO part 2

I have to say that I have enormous respect for Tucker Goodrich's self restraint in not commenting further on the single largest confounder in the latest Hall study:

Effect of a plant-based, low-fat diet versus an animal-based, ketogenic diet on ad libitum energy intake

which starts its abstract with:

"The carbohydrate–insulin model of obesity posits that high-carbohydrate diets lead to excess insulin secretion, thereby promoting fat accumulation and increasing energy intake."

If the simplest CIM model of obesity was correct then eating a diet which raised insulin, like this:

to a peak of 120microU/ml and kept it elevated for three hours, should result in marked sequestration of lipid in to adipocytes with subsequent weight gain.

It doesn't.

The question is how this occurs.

Over the years I have had a couple of attempts to understand "carbosis", which this low fat group appears to be demonstrating. None of my attempts have been particularly satisfying from the metabolic point of view. Let's try again.

In the immediate aftermath of the low fat test meal glycolysis is very active. This is facilitated by the elevated insulin translocating GLUT4s to the cell surface, which will facilitate the ingress of glucose.

Insulin will also facilitate the ingress of FFAs via CD36 translocation to the cell membrane but, at the same time, insulin will simultaneously lower FFAs:

With plasma FFAs at around 0.1mM it doesn't matter very much how many CD36 receptors are present on the cell surface, fatty acid oxidation will be a limited source of both NADH and FADH2 supply to the electron transport chain.

In addition to facilitating glucose ingress in to cells, insulin also drives the activation of the pyruvate dehydrogenase complex. This increases the translocation of pyruvate via its proton gradient coupled transporter in to mitochondria and ensures its metabolism to acetyl-CoA.

Glycolysis to pyruvate generates two molecules of cytoplasmic NADH for each molecule of glucose utilised. Much of this NADH will be reconverted to NAD+ by the malate-aspartate shuttle, passing the electrons to generate NADH within the mitochondria. If the rate of generation of NADH exceeds the capacity of the malate-aspartate shuttle, cytoplasmic NADH levels will rise and, secondary to this, the level of lactate will rise to resupply NAD+, using lactate dehydrogenase.

We can get an idea of how much the cytoplasmic NADH levels rise from the output of lactate in to the bloodstream of the study subjects after the low fat test meal. Like this:

I find a post prandial lactate of just under 3mM quite impressive. I would suggest that the NADH:NAD+ ratio is high.

So the next question is, what might an elevated cytoplasmic NADH level do to the glycerophosphate shuttle?

If we assume that high cytoplasmic NADH activates the glycerophosphate shuttle we will have the transfer of electrons from cytoplasmic NADH to the intra-enzymic FAD of the mitochondrial component of the glycerophosphate shuttle, mitochondrial glycerol-3-phosphate dehydrogenase.

From here the input is from the outer surface of the inner mitochondrial membrane directly on to the CoQ couple. From the mitochondrial point of view, that cytoplasmic NADH never arrives (it should have entered using the malate-aspartate shuttle). Instead it is "seen" as an FADH2 input, with all of the implications that has related to the FADH2:NADH ratio intrinsic to the Protons thread.

Under the influence of insulin there is clearly a great deal of cytoplasmic NADH generated from glycolysis and it is this action of insulin which must be limited to avoid excessive caloric ingress.

With glucose at 120mg/dl (sorry for the quaint units):

and insulin at 120microU/ml there are lots of calories entering cells. With FFAs at or below 0.1mM they will not be a significant source of either NADH or FADH2.

Fatty acids are out of the equation. So the signal for cellular satiety, driven by ROS, is going to come from the rising FADH2:NADH ratio generated by the glycerophosphate shuttle converting NADH to FADH2.

Ultimately the sensing of a cellular "satiety" level of substrate ingress will be signalled the generation of high-physiological levels of superoxide and hydrogen peroxide, facilitated by the glycerophosphate shuttle. I won't mention negative feedback from complex III but it will contribute too.

What will not be involved to any significant degree is beta oxidation. FFAs are low at the time of peak calorie availability/storage. And of those FFAs there will be very, very little linoleic acid.

A very low fat diet side steps the problems caused by linoleic acid failing to allow satiety-facilitating levels of ROS to be generated. Linoleic acid is simply out of the equation, what little there is of it from the diet being squirrelled away in adipocytes during the period of peak calorie availability. It is simply not there to interfere when cellular satiety is being successfully signalled.

Couple that with the fact that the low fat meal plans provided a linoleic acid supply limited to 3% of calories, it is quite easy to see how a group of 20 slightly chunky young Americans (BMI 27ish, 32% body fat, not the Arnie look for the slightly high BMI!) might be suffering from chronic linoleic acid toxicity. Dropping to 3% energy from linoleic acid is going to be markedly less fattening than the level which might be found in any version of the SAD.

Low fat is synonymous with low linoleic acid. High carbohydrate/high insulin has its own satiety mechanism, more dependent on the glycerophosphate shuttle, which is impervious to small amounts of linoleic acid. And with a diet of 2000kcal supplying LA at 3.1g/1000kcal, then just over 6g/day is not a lot to worry about.

I'll stop here to keep it simple. Obviously the tendency to normalise weight in the low carb period is directly related to low insulin, facilitating lipolysis. Once insulin is low enough, ie once carbohydrate intake is low enough, then linoleic acid, even at a total of around 40g/d (as was eaten during the LC phase), becomes unimportant.

EDIT, missed the lack of fat loss on LC! I guess 40g/d of linoleic acid with low but not basal insulin is too much! The is an update on this here. END EDIT.

Until you get just a little bit of carb creep of course... As carbohydrate and associated insulin rises then that approximately 13% of calories as LA is going to facilitate weight regain with a vengeance.


Saturday, January 23, 2021

Hall and CICO again

I have no free time at the moment so no real chance for blogging. Apologies for the undoubtedly multiple typos and grammatical errors in this hastily written post.

Raphi and I had a chat which is up on Youtube here

Peter & Raphael talk about fatty acids, mitochondria, the origins of life, covid, vaccines & keto

and I also picked this thread up on twitter, again via Raphi

which sums up why I don't do twitter. To join this discussion would take weeks of careful thought and reference trail following. However this review (DO NOT download it from SciHub!!!!!! Or if you do, make a donation. I didn't say that) came out of it:

Free Fatty Acids and Insulin Secretion in Humans

which has a core, absolutely correct statement:

"In fact, they [FFAs] increase insulin precisely to the degree needed to compensate for the fatty acid–induced insulin resistance."

After that it's all about ROS and double bonds, a concept which Boden (who sounds a really interesting chap) lacked at the time. The basic CIM (Carbohydrate Insulin Model) of obesity is undoubtedly incomplete and, nowadays, is a straw man for people like Hall to use to facilitate career enhancement. As in

Note: There are buzz-words even in the title of this paper which make me uncomfortable!

As Raphi and I discussed, studies do not arrive out of the blue. Hall knew exactly how to set this latest CIM "destroying" study up. The rival camp (Ludwig's group are current torch bearers here) have pointed out that in short term studies that CICO applies quite well. In longer term studies (over two weeks, and yes, of course Hall knows this) low carb has a significant ameliorating effect on the fall in metabolic rate associated with caloric reduction/restriction. As in:

Do Lower-Carbohydrate Diets Increase Total Energy Expenditure? An Updated and Reanalyzed Meta-Analysis of 29 Controlled-Feeding Studies

People may recall I've looked at Hall vs Ludwig in the past. Of the two camps I personally favour the one with the most honest approach to the data. My thanks to David Ludwig for updating me on this latest interchange within the on-going process.

Anyhoo, time to get the children's breakfasts and keep working on the house before the builder arrives on Monday, while working towards various deadlines off blog.


Monday, January 18, 2021

ROS (01) Insulins are ubiquitous in eukaryotes

I've had this paper lying around for years:

Role of Insulin-Induced Reactive Oxygen Species in the Insulin Signaling Pathway

Figure 4, shown below, sums up why it interests me

Brief aside: The role of glucose in generating ROS from mitochondria is, to me, extremely dubious. It certainly can occur but it needs the activation of the glycerophosphate shuttle, which doesn't get a mention. But the GPS is how we convert cytoplasmic NADH in to mitochondrially inputted FADH2, with ROS generation resulting from the raised FADH2:NADH ratio intrinsic to this conversion acting on the CoQ couple. It will apply in the presence of insulin, not isolated hyperglycaemia. If you slog through the refs trail (not good) you need to realise FBS = insulin/IGF-1. Also few people even think of fatty acids in this respect, a serious omission. Enough of mitochondria, back to the cytoplasm. End aside.

It's worth pointing out that the insulin receptor is thought to act as a G-protein coupled receptor which signals to an NADPH oxidase (probably NOX4) using a specific G protein. The NADPH oxidase generates H2O2 extracellularly (this becomes important in future posts) which re-enters the cell (some papers suggest there is a specific transporter) to oxidise cysteines on protein tyrosine phosphatases, disabling these enzymes. Without PTPases maintaining the suppression of insulin signalling both the insulin receptor and insulin receptor substrates autophosphorylate and so signalling takes off.

That's all pretty straightforward and is verging on textbook.

Nothing happens without ROS generation.

This led me down a rabbit hole, thinking about how primordial insulin signalling might be and how primordial the ROS generation might be. Is insulin core, with ROS as a second messenger? People may have noticed that the most basic signalling is what interests me.

How far back does insulin go? If we have a look at this review

Insulin-like signaling within and beyond metazoans

we can see that there is a recognisable insulin like receptor stemming from the common ancestor leading to both ourselves and sponges. That's pretty far back, marked by the blue lineage arrows in Figure 1 from the review:

Insulin signalling is thought to be present in most, but not quite all, metazoans (blue circle).

The review looks at the evidence for insulin signalling in yeasts, plants and a ciliated protozoan.

Sacchromyces has no suggestion of an insulin receptor. However it responds to exogenous human insulin with a response remarkably recognisable as the response of human cells to insulin.

Plants are more straightforward. They produce an insulin-like cysteine rich peptide which interacts with an insulin-like receptor to induce the effects typically seen in mammalian cells under insulin. In fact using this peptide on adipocytes produces exactly the same effects as human insulin.

Neither the "plant insulin" nor its receptor have anything in common with metazoan insulin/receptor protein amino acid sequences.

Except they have common "shape".  They are immuno-related. They look similar enough (shape/charge distribution) that they can be recognised by the same binding antibody.

Exactly the same findings are duplicatable in the ciliate protozoan T pyriformis as for the Sacchromyces yeast.

So. Different insulin-like hormones, different receptors. Genetically completely unrelated, but causing the cell to respond in the same way.

The simplest answer is convergent evolution, as suggested in the review. I think this is correct. But there is a deeply insightful comment towards the end of the discussion. Almost insightful enough, but ever so slightly not quite there:

"The convergent evolution of ligand-receptor pairs alone cannot explain however the biochemical similarities in the intracellular response to insulin observed outside metazoans, as illustrated above. One way to overcome this seeming inconsistency is by considering that independently evolved upstream components of pathways devoted to processing environmental information may have been tied to evolutionary conserved core metabolic and cellular growth signaling networks".

The most obvious metabolic signalling molecules which adjust core metabolic function and cell growth are the ROS.

Metazoans, plants, yeasts, protozoa; all will use ROS signals to control metabolism and growth. This is the evolutionary conserved process on to which various environmentally responsive ligands and receptors have been co-opted to respond. On at least four separate occasions. My opinion.

A eukaryote is a derivative of a bacterium living inside an archaeon. Information about archaea is remarkably thin on the ground. I expect them to use ROS. Bacteria are more rewarding once you turn to Pubmed.

Perhaps bacteria are where we should be looking to find the origin of the primordial ROS signal.


Thursday, January 14, 2021

Where the UK is heading perhaps (or not)

From January 13th 2021, early in Lockdown 3, UK.

This is Dr Mary Ramsay, head of immunisation for PHE (Public Health England, UK government). She is reiterating exactly the manifesto of the Great Barrington Declaration. I think it was April 2020 that I heard Prof Sunetra Gupta first advocate this concept. Now, in the early days of Lockdown 3, suddenly there is a voice of reason from a government department. It's echoing Vallance/Whitty from March 2020, before they both had all of their immunology knowledge, presumably with most of the rest of their brain function (sarcasm warning again) removed, sometime during Lockdown 1.

Here it is! (I can't see any way to embed and preserve Dr Ramsay's interview clip), it's in a Great Barrington Declaration tweet here

This is the text from the tweet because I always worry tweets may be ephemeral:

"Head of Immunisation for @PHE_uk -Dr Ramsey announced to the Science & Technology Committee that England may follow a focused protection strategy, where protection is given to the vulnerable and the disease is allowed to circulate among the young where its not causing much harm."

The text is true to the verbal narrative in the short clip.

While I'm on the subject of brain removals, people may be aware that daily COVID-19 deaths are currently exceeding those in the spring epidemic in the UK.

at a time when all-cause mortality is absolutely normal for the time of year, as mentioned in the last two posts. As in:

April was something exceptional. If anyone thinks December is in any way comparable to April you can head to the Funny Farm now. That's you, Prof Whitty.

Current COVID-19 death "data" are being used as an excuse for our government, particularly Matt Hancock (the UK Health Minister), to personally incite supermarket store managers to bully and harass people with mask exemptions into wearing masks in-store, if they want to buy food to eat. Apparently further measures are under consideration, god only knows what they will be.

Disgust is too mild a word.

I wonder whether Dr Ramsay will last at PHE? Perhaps the Guardian could run a hatchet job on her.


Tuesday, January 12, 2021

Just an update

Here is the right hand end of the graph from the last post, showing the partially adjusted all cause mortality for the UK in week 52:

Clearly the down tick at the end is the result of PHE struggling to adjust for the incomplete data from a week with a bank holiday followed by a week with two bank holidays. Paperwork, such as registering deaths, tends not to get done at weekends or on bank holidays.

So, theoretically, we could have had any of the red dashed line corrections:

EDIT We now have the 2021 week 2 report with more delayed registrations included. Looks like all cause mortality is now on a par with 2017/18. Still watching...


What happened when the majority (most, though not all, comes through within a week) of data were added in? On the 7th of January an update was posted so here is the original graph directly alongside the new graph. Again, ignore the downstroke:

If anyone is struggling to see the difference I've circled the important areas in red:

To put the current situation in to perspective I've pulled the curve from the last years during which we had a significant winter flu epidemic, 2017/18:

and just to make it even clearer, here's a line to show peak all cause mortality from 2017/18 vs end of Dec 2020:

It's also worth noting, again on a terribly parochial UK basis, that the winter peak in all cause mortality is almost always at the end of the first week of January. As in now, though the numbers will take a week or two to fully come in. This year may be typical, it may not. So far it's typical.

I have absolutely no doubt whatsoever that work in the ITUs (which are busy but not full, on a national basis) is hell at the moment. In hot-spots, worse. Given the level of barrier nursing needed, staff shortages because people are not allowed back to work until they eventually become PCR-ve (which can take months), social distancing within wards etc life must be awful and exhausting. 

I absolutely stand ready to accept that there is a catastrophe ongoing at the moment. It is quite possible that this winter's peak deaths will exceed that of 2017/18.

So far it hasn't.

I would suggest that the Guardian and the BBC may not be the most reliable sources of information about the current situation in the UK.

Just sayin'.


Another (as so often!) addendum:

Here are the ITU admissions for COVID-19 from ICNARC (which I consider to be unbiased reporting) up until just before Christmas:

which looks pretty grim, despite UK ITUs being at under 100% occupancy. But these are just COVID-19 patients. I don't have a similar curve for non-COVID-19 patients, but I do have this graph which includes both groups (and the rest of England), should they go on to die:

The last column is too low in both death categories due to delayed reporting, as always.

It's quite clear that for every death from COVID-19 there is nearly one less death from anything else. It could be that the virus is so lethal it is impossible to die quickly enough from anything else before it gets you.

Or it could be that managing to get a SARS-CoV-2 PCR-ve death certificate is becoming harder and harder to achieve in a hospital setting when PCRs are still being run to 45 cycles during a winter of endemic COVID-19.

Monday, January 04, 2021

Sarcasm Warning

Thank goodness for the lockdowns in 2016, 2017 and 2018. What would have happened without them?

Edit, corrected the dates on the image, apologies. Mea culpa. End edit.

The real, un-scribbled-upon data from Public Health England are here:

Please, please, please be aware that the week 52 data are only ESTIMATED.

The real value might be higher. Equally, it might be lower.

Hat tip to Mike Yeadon.


An afterthought: How do you explain the 2020/21 curve?

I don’t know. However: most “COVID-19 on the death certificate” deaths occur in hospitals and are reputed to be registered very promptly compared to community deaths. There is a massive need for the numbers of COVID-19 fatalities in the current situation, the government needs (and demands) these numbers fast to drive policy. This will inflate the uncorrected data through early December. However non-COVID-19 deaths are currently massively and exceptionally below normal for the time of year and these will only be incorporated in to the data more slowly than the rapidly registered COVID-19 deaths. So through early December the overall value has been correctly reported as being higher than normal because the low number of COVID-19 negative fatalities from the community (or even from hospitals) aren’t yet included. Now they are now coming in. I doubt PHE are remotely interested in assimilating this anomaly in to their estimating process (which will be based on previous years normal delay patterns of registration) but eventually the EuroMoMo absolute death data will have the truth out. Not that it will make any difference.

Why are non-COVID-19 deaths so low? People, sadly, die in some excess during the Winter. If you are hospitalised for anything at all leading to your death, the chances of you reaching your end without achieving a +vePCR test are very low. You will be a COVID-19 death and so you will be missing from other datasets.


End afterthought.

Thursday, December 31, 2020

Great Barrington Declaration (2)

Sorry folks, more COVID-19, more anger. Again a screen shot from part way down this page here, published by the UK government.

It looks like this:

That dark blue, slightly wavering, rising line is the deaths of the over 60s with a positive PCR. Some really will be COVID-19. They should never have been exposed to the virus. Should they have wished to, they should have been allowed to stay shielding and they should have been helped financially and practically to do so. Anyone, of any age, who became seropositive in the first wave could safely be in close contact with them today, no need for loneliness this winter. This course should have been offered as an option.

It wasn't.

The lower, paler blue line is the deaths of the under 60s. This line runs along the x axis. Very, very few people in London under 60 years of age have died with a positive PCR this Winter. Not many in the Spring for that matter either.

Shutting down much of the country, including London, in to Tier 4 lockdown (welcome to my world) has done nothing to protect the vulnerable over 60s and wasn't needed for the under 60s.

This is exactly why I signed the Great Barrington Declaration, to avoid this. Focused protection for those who need/want it, lots of it. Throw money at them. Let the rest of us get on with life.

Boris Johnson and Matt Hancock are politicians. I expect nothing from them, they're not exactly bright. But Whitty and Valance have no excuse. They must know what the above graph looks like. They know. Both of them were taught immunology once upon a time (implausible though that seems nowadays).

The lockdowns have done nothing to protect Norfolk from our Winter catch-up. We have no focused protection for the elderly. It's wrong.

Sorry for the rant.

Happy New Year.


Monday, December 21, 2020

IgG IgA and sniffing a virus which stinks

Just a quick post, possibly the last for a while as I have quite a lot going on off-blog at the moment and time will be scarce over the next couple of months.

I have downloaded this graph from the UK government website which can be accessed at

Obviously it will be out of date within 24h but, unless you are Whitty or Vallance, you will not be expecting the line to suddenly spike upwards to give (sarcasm warning) 4000 deaths per day for the whole of the UK next week.

These are the figures for London:

London is at herd immunity. Even with the second wave.

I'd like to perform a thought experiment. Let's imagine Fred. Fred lived in Lewisham and was a typical victim of the lipid hypothesis, but had not progressed to frank diabetes or significant metabolic syndrome. He contracted SARS-CoV-2 in mid February, coughed for three days and recovered. He wasn't tested, didn't go to A and E and was not a Spring peak statistic. He has 1) T cell mediated immunity 2) mucosal surface IgA immunity and 3) possibly some antibodies, neutralising, though these may not be at a level detectable in routine serology. He is, absolutely, not on the graph for the April peak in deaths.

Here comes the sad bit.

Fred has had recurrent stomach pain throughout the Summer. He keeps taking the Gaviscon and it does a bit of good but not much. The pain is never quite bad enough to go to A and E, certainly not in the face of the then current viral pandemic.

Fred's problems continue on and off until early November at which point he collapses with incapacitating stomach pain and profuse vomiting. He is still immune to SARS-CoV-2.

He is admitted to hospital and worked up for acute pancreatitis. It is difficult to describe how appalling this is as a medical emergency, and yes, it is triggered by polyunsaturated fatty acids, thank your cardiologist. After a day or so on a medical ward he is transferred to the ITU, just after his SARS-CoV-2 PCR result comes back positive.

Fred is immune to SARS-CoV-2. His respiratory system is covered in IgA. Any SARS-CoV-2 he picks up in the hospital will simply stay there, bound and unable to invade.

But if you take a swab from his throat/nasopharynx, especially in a hospital area with even minor exposure to SARS-CoV-2, the fact that that some viral particles are bound by IgA in a fully immune person makes no difference to a PCR machine running at 40 amplification cycles. He will come up positive.

Pancreatitis comes with a significant death rate. Fred dies (he's imaginary, no need to be sad, for Fred anyway) on the 28th of November 2020. What did he die of? Obviously he is in the stats for COVID-19, second wave, London. At the right hand end of the graph at the top of the post.

Here in the UK deaths at home have been running at 1000/week above normal levels since the lockdowns started in March and this has not diminished. Over 75% of these do not get COVID-19 mentioned on their death certificate. Fred made it to hospital, bound a few stray SARS-CoV-2 particles to his IgA and so died with COVID-19 by PCR amplification, which does get mentioned on his death certificate.

The chances of London not having reached herd immunity in the Spring seems vanishingly small. Certain pockets appear to have been missed and are catching up at the moment, the virus is, absolutely, still around and, absolutely, still making some people very, very ill.

But I think Fred is also common.

It is easy for anyone with a smattering of immunology and basic knowledge about PCR technology to access the data for London, which make this clear.

I'm loathe to attribute motive but SAGE has been after an extended full lockdown ever since before lockdown 2 started and they needed more than genuine infection figures, or even deaths, to get it.

I got three rapid sequential texts at 11pm on Saturday night explaining about the "new, 70% more contagious" strain of virus spreading in the South East and the essentially total shutdown of the area, just to the south of us here on the Norfolk/Suffolk border, which was going to happen at midnight.

I couldn't get back to sleep.

I was angry.

I'm well aware of the state of COVID-19 around the UK and how areas spared in the Spring are catching up now. Norfolk will be one of these. This is not trivial.

But those late night texts about a massive change in policy based around a mutation and what I guess is garbage modelling (you think that the 70% increase in transmission rate comes from some sort of data? Haha. I would bet Ferguson modelled this. It will be as good as his previous models. And then it won't be a prediction, just a "scenario", when it turns out to be bogus) are frank psychological manipulation using fear. Bullying on a national scale.

I'm left wondering if those people who control the Prime Minister and used this "tweak" to force the lockdown they so desperately wanted were actually expecting the channel crossings to be immediately closed?

They should have been, given that we are living through times of a global pandemic of stupidity. But then, they are part of the problem.


Saturday, December 12, 2020

IgG IgA and sniffing a virus

Basic immunology 101, ignoring T memory cells and cell mediated immunity..

If you contract a respiratory virus it colonises your nose/throat/windpipe. If you are unlucky it will also colonise your lungs and you might well be headed for a week or two in the ITU.

If it doesn't, you get better.

If you are re exposed to the same virus a month later you will not become ill unless you have something very, very wrong with your immune system. But might you transmit the virus still?

You can track the response of your immune system to the virus by tracking serum antibody production. The immediate effect is to generate IgM antibodies. These fade after a few weeks and are used clinically as a marker for recent infection. After a week or so you make IgG antibodies. These are present for a few months or even for life, depending on which virus we are talking about and whether there is continued exposure. If they are "neutralising" antibodies they will actually stop the virus invading cells by attaching to the cell-invasion protein of the virus. They are protective against illness.

There is another class of "poor relation" antibodies, the IgAs. These are mucosal cell surface produced antibodies. They are produced on the membranes of your nose, throat, trachea and possibly lungs if the virus gets that far and you survive.

IgA largely stops the virus becoming re-established in your nose on re-exposure. Neither IgM nor IgG, even if it is a virus neutralising IgG antibody, is going to do this.

Just to avoid controversy (and because the paper is handy) let's look at mice vaccinated against influenza using an adenovirus vector vaccine. The group used exactly the same vaccine in two groups of mice, in one they gave it intranasally, in the other intramuscularly.

Reduction of influenza virus transmission from mice immunized against conserved viral antigens is influenced by route of immunization and choice of vaccine antigen

"Here we demonstrate that transmission reduction is more effective when mice are immunized against A/NP and M2 intranasally than via the intramuscular route"

The intranasal route stimulated marked IgA production. The intramuscular route produced a minimal IgA response. Once vaccinated the group then challenged the vaccinated mice with field virus and assessed the ability of those vaccinated mice to transmit the field virus to non protected mice.

Intranasal, IgA generating, vaccination reduced transmission by 88.2%.

There is nothing surprising about this.

I fully expected the same vaccine given intramuscularly to do nothing at all to reduce transmission but it did, oddly enough, reduce transmission potential by 47%. Of course the question to be asked is whether this 47% transmission rate reduction would allow a vaccinated care worker to safely nurse your granny during an influenza pandemic.

You also still have to ask whether an 88.2% reduction in transmission might make a care worker safe to nurse an elderly person.

An adenovirus vector vaccine will induced an immune response to the protein coded for in the mRNA built in to that vaccine. If injected in to a muscle it should induce IgG in the bloodstream to that protein which, if neutralising, should protect against illness. That's good, but limited.

Contrast that to a genuine field virus infection. It starts in your nose, spreads to your throat and then down your windpipe to give you a marked production of membrane based IgA throughout the airway. It is going to induce IgA production to a whole host of viral proteins, not just the one or two forms of IgGs generated by a vaccine (even if given intranasally to generate some IgA). Some field antibodies will be very useful, some less so.

It seems to me that the probability of reducing or even eliminating viral transmission might be much better from a field virus infection than from a limited antibody response generated by an vaccine, even if given intranasally.

Quite what might happen if you combined intranasal and intramuscular administration, or even gave two doses of intranasal vaccine a few weeks apart are open questions for mice in influenza models. Yes, a model is only a model.

How much of this might be generic to respiratory viruses in general I don't know but I would be amazed if it wasn't.

As always there are a slew of questions which follow on from this concept but I'll stop here with my fondness of IgA inducing vaccines and particularly of asymptomatic infections. Having said that, I would qualify it as a vet. Anyone who has had the pleasure of administering an intranasal vaccine to a 40kg aggressive dog who is voting against said intranasal vaccination with his teeth is another matter. Luckily you can get it in through a muzzle on a good day. 


Tuesday, December 08, 2020

FIP vaccines etc

This post is just some random musings about coronavirus vaccines, most clearly in cats. The rest is speculation.  As an introduction here is the abstract-like entry for a book chapter pulled up by Duckduck from 'tinternet. It sums up pretty much what I recall from back in the days when I was a clinician dealing with the horrible disease of Feline Infectious Peritonitis (FIP), derived from complications of Feline Enteric Coronavirus infection. No author is stated but if I was an editor looking to have a chapter written about FIP I would, without any doubt, send the request to Niels Pedersen, who authored this (very long and involved) review:

A review of feline infectious peritonitis virus infection: 1963–2008

The chapter abstract summarises the interesting bits of the Pedersen's review nicely:


In Fenner's Veterinary Virology (Fifth Edition), 2017

Immunity, Prevention, and Control

Feline infectious peritonitis is not controlled easily; control requires the elimination of the virus from the local environment, whether this is the household or the cattery. This requires a high level of hygiene, strict quarantine, and immunoprophylactic measures. Because kittens acquire the infection from their queens, early weaning programs have also been used in attempts to interrupt virus transmission.

The development of a safe and highly effective vaccine remains elusive, even with the availability of bioengineering approaches. The only commercially available feline infectious peritonitis vaccine contains a temperature-sensitive mutant virus, based on a serotype II virus. The vaccine is applied to the nasal mucosa to reduce virus replication and antibody formation. Under these conditions, a cellular immune response is favored, and some protection putatively is achieved. Vaccination of infected, seropositive adult cats is not effective. In addition, experimental challenge of vaccinated cats has resulted in “early death” due to feline infectious peritonitis in some cases.

A broad spectrum coronavirus protease inhibitor drug has recently shown considerable therapeutic efficacy for treatment of cats with feline infectious peritonitis, a finding that suggests the disease might in the future be treated with antiviral drugs.

What is clear from FIP vaccination is that antibody production (or the administration of hyperimmune serum or pure IgG antibodies) in the absence of a cell mediated immune response, is lethal on challenge of kittens with a field strain of FIP virus. The serum is harmless, the IgG is harmless, the vaccine is harmless. What matters is how the disease progresses when field virus meets the antibody replete host. The effect of a vaccinia virus vector vaccine was described here (you only really need to read the title, it says it all):

Early Death after Feline Infectious Peritonitis Virus Challenge due to Recombinant Vaccinia Virus Immunization

which could reasonably be described as a bit of a booboo.

To summarise: Vaccines which stimulate antibody production without stimulating cell mediated immunity are a problem. This is Antibody Derived Enhancement. It's real. It has plagued (no pun intended) certain vaccines, obvious for FIP but Dengue Fever vaccine is a similar but non-related example in humans.

I'll leave FIP alone now except for adding that work with the reagent GS-441524 suggests that FIP is no longer the invariable death sentence which it was two or three years ago. People who have worked clinically with FIP, or lost cats to FIP, will understand the awe that this drug inspires. I hope it gets used sensibly.


I was listening to Radio 4's The Life Scientific which featured an interview with Prof Sarah Gilbert from Oxford, heavily involved in the development of an adenovirus delivered vaccine for protection of humans against SARS-CoV-2.

Apart from how genuine and extremely bright she is the main thing I recall is her comment that she was very pleased that the vaccine she was developing produced a robust cell mediated immune response in additions to stimulating antibody production.

This is excellent and is all that you could ask of a vaccine where antibodies are frequently high and ineffective well before admission of patients destined to die of COVID-19 complications in the ITU.

It looks like cell mediated immunity is what matters. That antibodies are non protective is also suggested by the extremely poor results using antibody rich serum from recovered patients to treat unwell patients with COVID-19. There is no suggestion that serum treatment did direct harm, just it didn't do much good.

So the major question this poses is how much good the vaccine might do in patients who are going to become ill with COVID-19 in the future. It is not an unbelievable stretch of fantasy to suggest that the defining characteristic of people who are going to go on to become seriously unwell after exposure to SARS-CoV-2 might just be those are the ones who are unable to mount an effective cell mediated immune response.

How well might the T cells of an 80 year old, morbidly obese diabetic respond to the vaccine, assuming they are not very likely to respond to the field virus?

We can but hope that if they do fail to develop cell mediated immunity then at least their antibody response (which will still happen) does no harm. And we can hope that cell mediated immunity response has been carefully assessed in the population to which to a COVID-19 vaccine is being rolled out as of today in the UK... 

Otherwise it's a bit of an experiment on many, many people's grannies.


Thursday, November 26, 2020

Podcast with Dr Paul Saladino (2)

Part two is up, mostly about the glycerophosphate shuttle...


Monday, November 09, 2020

Protons (65): Fatty acids vs glucose and ROS generation

I've had this paper for some time:

The CoQH2/CoQ Ratio Serves as a Sensor of Respiratory Chain Efficiency

It really grabbed me as it was one of the earlier references to supercomplex assembly of electron transport chain components, failure of C57Bl/6 mice to manage this correctly due to a truncated supercomplex assembly protein and the deconstruction of excess complex one when electrons were fed in to the ETC via electron transporting flavoprotein dehydrogenase. So it's a great paper of enormous scope.

But there is more. Dave Speijer has a great discussion of why mitochondrial preparations are so hard to interpret because they are so far away from the in vivo situation and preparation artefacts are massively influential of results. It's in here on page 4110 if you'd like to browse.

Back to the Guarás paper. They got out of the problems of using isolated mitochondria by using intact fibroblast, treating them with a cell permeant dye which becomes fluorescent on exposure to ROS, followed by flow cytometry to assess ROS production. Then they could treat the cells with glucose or fatty acids +/- very low dose rotenone, which blocks RET without having the unacceptable off target effects of higher doses.

This is what they got. Glucose was 5mmol/l and FFAs, mixed types, were supplied bound to albumin at 1000micromol/l. Both quite physiological. Here is what they got (Fig 6, section H), we can ignore the galactose results:

So mixed FFAs produce roughly twice the ROS produced by physiological glucose. The effect is markedly reduced by inhibiting RET through complex I.

Sadly no one has done the experiment to compare saturated fatty acids, MUFA or PUFA on the generation of ROS. Still less to look at the effects of background glucose elevation to represent the immediate post prandial period, with or without insulin. But the basic proof of concept is there.

Nice paper.


Saturday, November 07, 2020

Here we go in to Lockdown 2

This is the number of daily positive PCR tests (rather than genuine cases) in the UK, via Worldometers, graphed from the UK government website data. I've added an arrow to indicate the start of Lockdown 2 for those of us living under peak incompetence.

And here are the ICU admissions for the current wave, in orange. Ignore the dramatic drop at the end of this line, it probably represents under reporting because it takes time to update the database for the last 24h and these stats come out at teatime every Friday. Again these are data for time immediately before Lockdown 2:

Will it Lockdown 2 work?

Pretty safe bet it will because PCR positive test numbers have already plateaued, ICU admissions have plateaued and are probably falling, both over the week pre lockdown.

Overall it looks like we continue to head towards herd immunity despite all attempts to stop this and in the face of minimal protection for the vulnerable. Deaths have not plateaued yet, that will lag a few weeks behind the peak in positive test results.

Any modelling scenario which did not have these data as a future possibility when it was run at the start of October should perhaps have its validity questioned. That'll be the one with the 4000 deaths per day as a possible scenario, in particular.

Listening to the modellers is like listening a cardiologist espousing the benefits and "death-preventing" effects of statins. Except for lockdowns there is no equivalent to the easy option of dropping your statin prescription in the bin.

Will Lockdown 2 end on the 2nd of December?



Wednesday, October 21, 2020

Linoleic acid makes you hungry

This paper reports what happens to hsCRP in people of differing fatty acid desaturase genotypes when you increase their linoleic acid intake from around 4% of calories to around 11% of calories. It's neutral or bad, depending on your genetics. Which is irrelevant to anyone remotely informed about what a human LA intake might reasonably be. So we can ignore the research on hsCRP.

Inflammatory response to dietary linoleic acid depends on FADS1 genotype

Two things come out that are worth noting. First is that, from Fig 4, that increased dietary LA mostly decreases the arachidonic acid in plasma phospholipids and cholesterol esters. I made a throw away comment in a previous post that I would expect supplementing any C18 PUFA would inhibit the formation of any C20 and C22 fatty acids. I got lucky on that one, AA levels mostly dropped with LA supplementation, one didn't change.

Much more interesting is the effect of the intervention, irrespective of genotype, on food intake. Like this:

"Based on food records, energy intake was significantly increased during the intervention period, which could be considered a third limitation. However, there were no changes in body weight or BMI, and an increase in energy intake was similar in both genotype groups. It is likely that the increased energy intake was at least partly related to the fact that oil consumption was carefully recorded during the intervention period."

I think we can describe this "likely" effect as ad hoc hypothesis number 3264.

A more reasonable ad hoc hypothesis is that increasing your linoleic acid intake from 4% of calories to 11% of calories makes you hungry. If this change were to have been caused by a projected loss of half a kilo of ingested lipid in to adipocytes over a year, that would be less than 50g per month. Easily masked by a number of biological variations.


Saturday, October 17, 2020

Podcast with Dr Paul Saladino

 I had a very pleasant chat with Paul Saladino.

It was quite a long chat and there were still lots of places that we did not have time to visit...


Wednesday, October 07, 2020

Great Barrington Declaration

 This is really a job for twitter but that's not my platform.

Great Barrington Declaration

I've signed.


Full blown linoleic acid deficiency: speculation

 Tucker Goodrich emailed me the link to this lovely paper from the 1930s


and included it in a blog post

Fat and Weight Gain (a Note to Peter) and the Essentiality of Linoleic Acid

TLDR, grossly linoleic acid (or the arachidonic acid derived from it) deficient mice are small, emaciated and lose a ton of water through their skin. Think superoxide.

It's an interesting situation, with a number of possible explanations and the sort of data you might expect from 1930, good for its time but we're not going to get the massive detail which people struggle to interpret nowadays.

I started off alongside the authors and caloric loss due to the evaporation of water from both the "leaky" skin and possibly from "leaky" lungs. If you have ever tried to keep a mouse warm under anaesthesia while it breathes anhydrous cold gas and is clipped and water/alcohol prepared for surgery you will sympathise. If not, you can take my word for it that without serious attention to heat conservation, their temperature drops like a stone.

The mice lose about 10ml of water per day through their skin. With a latent heat of vaporisation of 0.541kcal/g this means the 10ml of water steals about 5.41kcal per day of energy as lost heat, just to evaporate the leaked water. That's about an extra gram of carbohydrate or protein they would need.

But the mice were ad lib fed. They may have been pretty sick from LA deficiency but they managed to eat exactly as much as the healthy mice did each day. I find it implausible that they were so skinny because they were simply too ill to manage an extra gram of food. There is absolutely no doubt that they were very sick, but I still don't find this plausible for the emaciation.

A simple extrapolation from high PUFA diets facilitating fat loss in to adipocytes to the converse, that very low PUFA diets fail to allow fat storage is nice but seems very unlikely because the curative dose of linoleic acid seems too small to represent a supply of calories for bulk oxidation.

My core question relates to the failure to store lipid in adipocytes, with a spin off question in to the poor health of the fat free rats. This is all guesswork and speculation.

I have to accept the possibility that it might be as simply as that you cannot build a functional cell membrane or mitochondrial membrane without some bendy/fluid molecules. Given an inadequate fluidity to the mitochondrial inner membrane I can see that molecules such as CoQH2 or reduced cytochrome C, which move within/over a fluid inner mitochondrial membrane might lose electrons prematurely to molecular oxygen if they cannot reach their docking site in the next complex down the ETC. That a continuous, pathological loss of electrons from carriers to molecular oxygen, to give inappropriate superoxide and H2O2 generation, would lead to unrestrained insulin resistance and failure to grow, especially failure of adipocytes to grow, seems to be a plausible explanation.

As Burr and Burr comment, the kidney is also a very energy dependent and might well fail given a failure of insulin signalling due to excessive H2O2 generation. While the rats would lack ROS damage to membrane lipids they would not lack ROS damage to cellular proteins or DNA. The cells, if insulin signalling cannot occur due to excess H2O2 generation, would also be calorie starved as well as ROS damaged.

Quite why the tails fell of of the rats is beyond even my speculation ability.

So. The failure of adipocytes to grow suggests severe insulin resistance within those adipocytes. More generalised application of this idea would lead to explaining failure of the whole rat to grow.

Who knows what actually happened?



I've long carried the idea in my head that PUFA depletion might be protective against radiation induced injury. I think I picked this up early in my low carb journey, probably from a Ray Peat follower. But that will have been over 15 years ago and I am unable to locate where this idea came from. So I went looking on Pubmed and opened a whole can of worms. Some of which are interesting.

The first is that rats fed a completely fat free diet are at increased risk of dying from radiation injury. That was this one:




"More recently, it has been observed that the survival time of male rats, as judged by the intervals at which an LD25, an LD50, or an LD75 were reached, or by the average length of survival, was progressively improved when ethyl linoleate was given in doses of 10, 50, or 100mg daily (Cheng et al., '54)."

The same lab has produced at least four studies to support this finding.

Giving a rat 10mg of a source of linoleic acid will have no effect on substrate oxidation. But it might well allow the development of an effective electron transport chain which is less likely to release a random excess of electrons to molecular oxygen.

Of more interest is this study. It's not clear (to me) whether the diets contained 10, 20 or 30% of cotton seed oil by calories or by weight. Low PUFA diets (butter) were ineffective in small amounts but effective at 20% or 30%:

Deleterious effects of high fat diets on survival time of X-irradiated mice

"At levels of 2% or 10% of the diet cottonseed oil and margarine fat increased survival time over that on the fat-free ration. When these fats were fed at higher levels ( ie. ~ 20% or 30% of the diet), however, survival time was decreased below that obtained at the lower levels of supplementation."

My take home is that rats do, absolutely, need a few milligrams of linoleic acid. Notice that the amounts used in all of the studies are in the same ball park as found by Burr and Burr to prevent their fat deficiency syndrome. I think it is an interesting speculation that LA is particularly need to manufacture an effective membrane for the ETC, especially when electrons are going to be knocked around by x-ray irradiation over and above background radiation conditions. As the dietary dose increases then the deleterious effect of the PUFA eventually predominate, certainly in the radiation injury models.

Interesting findings.


Sunday, October 04, 2020

Prof Sunetra Gupta

I first came across Prof Gupta as an invited speaker to one of the Royal College of Pathologist seminars, now viewable on-line at

The COVID 19 pandemic: epidemiology*

*Prof Gupta is at Oxford, not Imperial College as the RCPath intro slide incorrectly shows. We all know about the Imperial College modellers.

I thought she was talking sense at the time and that impression has not changed since. I notice that she has been very active recently in the media and I happened to pick up this interview via Faceache:

The Spectator interview

I've pulled this one out from many videos because it answers the question as to what an incompetent Prime Minister says when presented with someone who is telling him that he has done everything wrong. It's near the end so I've clipped out my favourite eight seconds:

Clearly there is no way, ever, that any government is going to say that they have screwed everything up about this pandemic. Completely.

Especially if they have. And honesty is not exactly a hallmark of Boris Johnson.


NB A more competent government in power would probably have done the all wrong things too, but much more effectively. That's a scary thought. I am seriously conflicted about this.

Monday, September 28, 2020



Right. I've been back to the broken links issue and have noticed that, when you click on a link to a "search term" you get a blank Pubmed page. However in the URL of this broken link there is a complex set of gobbledygook but very close to the start is the PMID that the search term has previously pointed to. So in the post

the link to the paper by Wolever is broken. 

The URL above the blank Pubmed page from the link is this:

and 10889799 is the PMID. Pasting this in to the search box gets you to the paper originally linked to so

now gives access to the abstract as:

Dietary carbohydrates and insulin action in humans

After that it's a Sci-hub job.




Over the years I have slowly learned how not to blog.

For one thing, never use hyperlinks embedded as "here" or "these people".

Always cite the paper title, then anyone can copy paste this in to Duckduck or Pubmed and they can then side step the broken link when it goes down, as it will.

In the very early days I used the Pubmed search result URL as the hyperlink. This appears to have been fine for the last 15 years or so but recently Pubmed updated and all of those links have been lost. If a hyperlink from a simple word like "here" used to go to a search result URL it will be down and even I cannot always relocate the original paper.

Sometimes even if I know exactly which paper it was it's not always possible to find on on my sprawling hard drive.

You learn these things as you go along. Damn.