Pulse Oximetry & the Oxygen–Haemoglobin Dissociation Curve 2020-03-22T07:05:53.483Z
Physical alignment - do you have it? Take a minute & check. 2020-02-05T04:02:49.886Z
Chakras & Qi - Old Stories for the Base-Line Experience. Improve your physical & mental health by connecting body and mind. 2019-12-08T04:22:11.111Z
The '5 Main Muscles of Movement' Made Easy. 2019-12-07T09:17:50.359Z
A Good Posture - Muscles & Self-Awareness. 2019-11-15T09:19:11.580Z
Fibromyalgia, Pain & Depression. How much is due to physical misalignment? 2019-10-29T14:58:17.652Z
Does the body have an almost infinite number of potential positions? 2019-10-19T05:39:26.883Z
Conscious Proprioception. 2019-10-04T04:33:14.317Z
The Five Main Muscles for a Full Range of Natural Movement, Dynamic Alignment & Balance. 2019-09-01T03:22:38.247Z
Body Alignment & Balance. Our Midline Anatomy & the Median Plane. 2019-08-22T10:24:59.156Z


Comment by leggi on What are good resources for gears models of joint health? · 2021-06-14T11:45:02.844Z · LW · GW

I hesitate to use the word "posture" due to the various models it conjures in people's minds (slouching, pictures of the spine etc.) Put these images aside for a moment.

Posture = Position of the body.

All the body, at any time.

Good posture = good positioning - the body works well.

Poor posture = bad positioning.

(Bad positioning could be structural or due to inappropriate usage)

Bad positioning is bad for moving parts. Inappropriate tensions, misalignments, friction, stress.

Bad things in the body - detected by sensors, information transmitted by nerves, brain says PAIN!

The body adapts over time. Pain progresses if bad positioning is not corrected.

(One adaptation I propose - physical restrictions in connective tissues form in a response to inflammation, which can be triggered by a multitude of things. Over time these restrict range of movement, apply tension, generate pain. The body is very adaptable. It can take a lot of stress and abuse. The mind can ignore a lot of pain signals. An individual's awareness levels and tolerance affects when issues are noted/treatment is sought i.e. become clinically significant.

I'm about 60% confident that this gait alteration may be involved in the idiopathic foot pain

This is a good example of what I mean by "poor posture" causing pain.  Gait alteration = changing how you move =  altering posture/position.  If these alterations have resulted in pain, I'd classify it as postural pain i.e. pain due to poor positioning. 

Consciously changing your gait involves the activation of different muscle fibres to what you have been using.  Either this is "corrective" (improving positioning with activation of the 'right' muscle areas) or it's detrimental to positioning with increased use of the 'wrong' areas of muscle (causing stress on muscles and a progression of issues.  Myalgia, spasms, fatigue, trigger points → tensions in tissue,  pulling on periosteum "joint pain" which stimulates bone remodelling/osteophyte formation ... ) 

If you are at 60% in thinking a gait change and your foot pain are connected, then I hope you'll give real consideration to my model for otherwise unexplained pain.  (I've taken a very sudden active dislike to the word idiopathic, it's not idiopathic pain - anymore.)

My model fits with all the information I've seen over the years - quote and link to any studies you find relevant and I'll explain how. I joined LW with a "please rip to shreds" about my Base-Line theory of health and movement so please do!  I am p>99.999 confident that what I propose is right.  I'd like that rigorously tested.    Break me, crush me.  Release me from the frustration of knowing (with every fibre in my body) that I'm right ; )

I'm also looking to better understand my PF pain.

Keep studying the anatomy.

Focus on where the pain is coming from. Deep breathing, explore with your mind. 

Bear in mind, dissection photos of pre-prepared specimens are usually designed to demonstrate components rather than showing the natural state of a joint.  Schematic diagrams are just that, ligaments look like strings or ribbons crossing joint spaces at specific points, they don't show that most connective tissues aren't discrete parts, they blend from one named structure into another.  Ligaments being thickened bands within a web of connective tissues around a joint, closely associated with fascia, joint capsule and periosteum, which then blends to tendons and aponeuroses to connective tissues containing myocytes ("muscles").

Have a look at dissection videos of the knee joint. (preferably fresh rather than pickled tissues). After removal of the skin it's obvious how much of everything is encased in connective tissues - a bright white 'bandage' of fibrous tissue (mostly collagen). The ligaments of the knee are thickenings in this web of connective tissue.  A bit of tension somewhere pulls on surrounding areas.

The experience of handling a (skinned) knee brings another level of understanding. Seeing the layers.  Feeling where bits attach tightly to bone. Feeling the bits that glide as the knee flexes and extends.  The change in tension of various thickenings in the tissues around the bones.  The trochlear groove for the patella. There is much to experience.  Goat or sheep knees (known as the stifle) are a reasonable approximation if you do want to really get to know the knee. 

The joints of the leg - hip, knee, ankle, foot offer a lot of potential for movement.  The knee joint is mostly extension/flexion, it has very little medial/lateral movement  - there is almost no slack.   Any issues above or below the knee  (rotations, tensions etc. from the hip/ankle/foot which put the leg in a less than ideal position) will show first in the knee.   (The hip and ankle/foot have much more slack so can cope for longer with mal-positioning/misusage but it will appear with poor positioning).

This has good rather long and I'm out of time, but if you are interested - I could run through a diagnostic process for knee pain.

Comment by leggi on What are good resources for gears models of joint health? · 2021-06-13T05:45:57.662Z · LW · GW
sporadic, idiopathic pain in another joint.

Can I clarify before I spend time writing a long answer - You are looking for a model that explains why you've now got pain in your foot (with a history of knee pain)?

If that's what you want to know, it's not complicated - pain spreads over time.

How I'd briefly explain things:

We alter position to avoid pain.

Positional changes alter the stresses throughout the body (we are connected from head to fingers to toes).

Stresses are unevenly distributed when the body is not in an ideal posture.

Alterations due to pain = not good for posture.

Poor posture = Pain.

One problem area spreads to another as the body keeps adjusting to avoid pain.

I've written a fair bit about muscles, connective tissues and pain in this post.

I could write specifics about knee pain if want.

Otherwise, some good resources:

Basic bone physiology, pathology: (veterinary - think "mammalian")

Comment by leggi on Why anything that can be for-profit, should be · 2020-05-01T06:45:09.745Z · LW · GW

I was specifically asking about a vaccine for coronavirus. (I should have said covid19)

The potential profits from such a vaccine could be massive.

Weigh that against the effects of giving the world's population some sort of immunity.

If this vaccine is shown to be effective, the first round of vaccinations will be available at cost from Oxford University and AstraZeneca.:

Landmark partnership announced for development of COVID-19 vaccine

The partnership is to begin immediately with the final terms being agreed in the coming weeks.  This will allow for rapid vaccination around the world if the COVID-19 vaccine candidate proves to be effective. The vaccine candidate was developed by the University’s Jenner Institute who began trials in humans last week jointly with the University’s Oxford Vaccine Group.
.... AstraZeneca will work with global partners on the international distribution of the vaccine, particularly working to make it available and accessible for low and medium income countries.
Both partners have agreed to operate on a not-for-profit basis for the duration of the coronavirus pandemic, with only the costs of production and distribution being covered.
Comment by leggi on Against strong bayesianism · 2020-04-30T12:18:19.625Z · LW · GW

An interesting read and I'm happy to see people publishing posts like this.

The more that beliefs are questioned, the more improvements in thinking can be made. (or something to that effect, I'm struggling with the wording).

Comment by leggi on Why anything that can be for-profit, should be · 2020-04-30T09:23:12.698Z · LW · GW
Anything that can be for-profit, should be.

A vaccine for coronavirus could be for profit. Should it be? What would be the overall effects (advantages?) of:

  • having a vaccination that is sold for profit.

compared to:

  • a vaccine that is available on a not for profit basis.

- - -- ---

Money .... keeps people honest

Does it? Fraud. Tax returns ...

Comment by leggi on Poll: ask anything to an all-knowing demon edition · 2020-04-29T08:40:52.579Z · LW · GW

I would ask a different question in each case. (about unrelated subjects)

Comment by leggi on Helping Lily Make Dinner · 2020-04-27T15:26:27.956Z · LW · GW

Well done Lily!

Does Lily want to join the rota and prepare dinner again?

If so, tortilla wraps are fun to do - stuff to weigh and knead (and getting flour all over the place!)

It's a good opportunity to do a bit of math when splitting the dough into pieces (I'd suggest working in grams) and rolling the tortillas can lead to some interesting shapes and designs ...

Various fillings can be prepared to cater for vegans, vegetarians and meat eaters. A mix and match meal for everyone.

Comment by leggi on Poll: ask anything to an all-knowing demon edition · 2020-04-25T08:33:25.747Z · LW · GW

Who gets to hear the question and answer?

Just me or is there a wider audience (that also know the oracle cannot lie)?

Comment by leggi on A Significant Portion of COVID-19 Transmission Is Presymptomatic · 2020-04-24T08:54:50.725Z · LW · GW

Temporal dynamics in viral shedding and transmissibility of COVID-19

We report temporal patterns of viral shedding in 94 patients with laboratory-confirmed COVID-19 and modeled COVID-19 infectiousness profiles from a separate sample of 77 infector–infectee transmission pairs.
We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset.
We estimated that 44% (95% confidence interval, 25–69%) of secondary cases were infected during the index cases’ presymptomatic stage, in settings with substantial household clustering, active case finding and quarantine outside the home.
Disease control measures should be adjusted to account for probable substantial presymptomatic transmission.
Comment by leggi on Do you trust the research on handwriting vs. typing for notes? · 2020-04-24T07:42:51.038Z · LW · GW

Are you reproducing a text-book / full script of lecture or are you making study notes?

Personal experience:

For me, letting go of my need for everything to be neat and complete was a bit step in making notes to learn from. They don't have to be perfect, they need to be useful. A summary in short form, including the key words/points, missing out the rest.

For example, all this text taken from Wikipedia - (no need to actually read it all)

Diabetes mellitus (DM), commonly known as diabetes, is a group of metabolic disorders characterized by a high blood sugar level over a prolonged period of time.[11] Symptoms often include frequent urination, increased thirst, and increased hunger.[2] If left untreated, diabetes can cause many complications.[2] Acute complications can include diabetic ketoacidosis, hyperosmolar hyperglycemic state, or death.[3] Serious long-term complications include cardiovascular disease, stroke, chronic kidney disease, foot ulcers, damage to the nerves, damage to the eyes and cognitive impairment.[2][5]
Diabetes is due to either the pancreas not producing enough insulin, or the cells of the body not responding properly to the insulin produced.[12] There are three main types of diabetes mellitus:[2]

Type 1 diabetes results from the pancreas's failure to produce enough insulin due to loss of beta cells.[2] This form was previously referred to as "insulin-dependent diabetes mellitus" (IDDM) or "juvenile diabetes".[2] The loss of beta cells is caused by an autoimmune response.[13] The cause of this autoimmune response is unknown.[2]

Type 2 diabetes begins with insulin resistance, a condition in which cells fail to respond to insulin properly.[2] As the disease progresses, a lack of insulin may also develop.[14] This form was previously referred to as "non insulin-dependent diabetes mellitus" (NIDDM) or "adult-onset diabetes".[2] The most common cause is a combination of excessive body weight and insufficient exercise.[2]
Gestational diabetes is the third main form, and occurs when pregnant women without a previous history of diabetes develop high blood sugar levels.[2]

Prevention and treatment involve maintaining a healthy diet, regular physical exercise, a normal body weight, and avoiding use of tobacco.[2] Control of blood pressure and maintaining proper foot and eye care are important for people with the disease.[2] Type 1 diabetes must be managed with insulin injections.[2] Type 2 diabetes may be treated with medications with or without insulin.[15] Insulin and some oral medications can cause low blood sugar.[16] Weight loss surgery in those with obesity is sometimes an effective measure in those with type 2 diabetes.[17] Gestational diabetes usually resolves after the birth of the baby.[18]

Reduced to this:

DM = G  PU/PD ↑hunger

 --> ketoacidosis.   heart, kidney, foot ulcers, neuropathy, eyes, cognative probs. 

Type 1 - insulin production  (idiopathic autoimmune beta cells pancreas)

Type 2 - insulin resistance body cells. --> progress to type 1.  ( assoc. factors weight  exercise)

Type 3 - gestational. no prev. hx.  resolves post-partum. 


diet, exercise, X-smoking (obesity sx.)

BP, foot + eye care,

insulin, oral tx 

By reading the text and then condensing it I've spent time considering the words, assessing what the key points are and absorbing along the way (using common notation that I know exactly what it means e.g. PU/PD = polyuria polydipsia = increased urination and increased drinking)

I now have an easy to scan summary to be able to reproduce the full text in an exam. I'm aware that adding words such as "normally" and "most cases" provides the caveats and cover that very little is 100% in medicine.

If you know something there's no real benefit in writing it out in full again but I still found myself adding "beta cells pancreas" to the above notes for completeness.

Whether I take notes this way by handwriting or keyboard doesn't made much difference to the learning/absorption process, but typed notes are much neater, which I like!! And more formatting options are available - easy bold, bigger fonts. Rather than the old highlighter pen.

I've found drawing flow and other diagrams and spider maps by hand is invaluable in some situations though.

Comment by leggi on How strong is the evidence for hydroxychloroquine? · 2020-04-24T06:55:45.050Z · LW · GW

A study, not peer-reviewed:

Outcomes of hydroxychloroquine usage in United States veterans hospitalized with Covid-19

HC= hydroxychloroquine,

HC+AZ = hydroxychloroquine and azithromycin

no HC = no hydroxychloroquine

RESULTS: A total of 368 patients were evaluated
(HC, n=97; . HC+AZ, n=113; . no HC, n=158).
Rates of death in the HC, HC+AZ, and no HC groups were 27.8%, 22.1%, 11.4%, respectively.
Rates of ventilation in the HC, HC+AZ, and no HC groups were 13.3%, 6.9%, 14.1%, respectively.
Compared to the no HC group, the risk of death from any cause was higher in the HC group (adjusted hazard ratio, 2.61; 95% CI, 1.10 to 6.17; P=0.03) but not in the HC+AZ group (adjusted hazard ratio, 1.14; 95% CI, 0.56 to 2.32; P=0.72).
The risk of ventilation was similar in the HC group (adjusted hazard ratio, 1.43; 95% CI, 0.53 to 3.79; P=0.48) and in the HC+AZ group (adjusted hazard ratio, 0.43; 95% CI, 0.16 to 1.12; P=0.09), compared to the no HC group.

In this study, we found no evidence that use of hydroxychloroquine, either with or without azithromycin, reduced the risk of mechanical ventilation in patients hospitalized with Covid-19.
An association of increased overall mortality was identified in patients treated with hydroxychloroquine alone.
These findings highlight the importance of awaiting the results of ongoing prospective, randomized, controlled studies before widespread adoption of these drugs.
However, given its increasingly widespread use, not only as therapy but also as prophylaxis for Covid-19, there is a great and immediate need to obtain insights into the clinical outcomes among patients currently treated with hydroxychloroquine, particularly because of the non-negligible toxicities associated with its use.
Comment by leggi on April Coronavirus Open Thread · 2020-04-23T19:05:07.532Z · LW · GW

Oxford COVID-19 vaccine begins human trial stage

The vaccine is based on an adenovirus vaccine vector and the SARS-CoV-2 spike protein,
Comment by leggi on Mark Xu's Shortform · 2020-04-23T10:36:27.549Z · LW · GW

Is the victory bit important in the quotation?

If it's not about the victory/winning, and rather about the path/journey ....

A first draft that springs to mind as I type:

The key to rationality.... is not to chose the label, but to choose to take every opportunity to improve/update your thinking.

(Can't ... stop ... myself ... from commenting: From what I've observed too much ego gets in the way of rational thinking sometimes.)

Comment by leggi on How likely is the COVID-19 apocalyptic scenario? · 2020-04-23T08:55:01.892Z · LW · GW

Thanks for those links. I'll need time to read properly.

I've wondered for a while about the influence of viruses on evolution (just looking at the effects of something like Zika virus for a start) or genomes picking up "new DNA" from RNA templates etc....

Comment by leggi on Jimrandomh's Shortform · 2020-04-23T08:25:41.422Z · LW · GW

It would be important information if it was true. But is it true?

(SARSr-CoV) makes the BSL-4 list on Wikipedia but coronaviruses are widespread in a lot of species and I can't find any evidence that they are restricted to BSL-4 labs.

Comment by leggi on Jimrandomh's Shortform · 2020-04-23T08:21:24.513Z · LW · GW
Whether BSL-3 labs were allowed to deal with this class of virus, is something that someone should research.

Did anyone do some research?

- --

(SARSr-CoV) makes the BSL-4 list on Wikipedia.

But what's the probability that animal-based coronaviruses (being very widespread in a lot of species) were restricted to BSL-4 labs?

- - -- ---

COVID19 and BSL according to:

W.H.O. Laboratory biosafety guidance related to the novel coronavirus (2019-nCoV)

Non-propagative diagnostic laboratory work including, sequencing, nucleic acid amplification test (NAAT) on clinical specimens from patients who are suspected or confirmed to be infected with nCoV, should be conducted adopting practices .... ... in the interim, Biosafety Level 2 (BSL-2) in the WHO Laboratory Biosafety Manual, 3rd edition remains appropriate until the 4th edition replaces it.
Handling of material with high concentrations of live virus (such as when performing virus propagation, virus isolation or neutralization assays) or large volumes of infectious materials should be performed only by properly trained and competent personnel in laboratories capable of meeting additional essential containment requirements and practices, i.e. BSL-3.

The CDC: Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)

Comment by leggi on [Site Meta] Feature Update: More Tags! (Experimental) · 2020-04-23T07:37:21.664Z · LW · GW

A good point that "health" is too generalised. I've updated my original request.

Comment by leggi on [Site Meta] Feature Update: More Tags! (Experimental) · 2020-04-23T07:34:25.710Z · LW · GW

Thanks for the full list of tags. I guess there's been a couple of changes in the lists somewhere e.g. "practical techniques" not being added when selected.

The "world optimisation/modelling" and "well-being" ones aren't on the list (page 2 somewhere??!)

To untag a post, just downvote its tag relevance

Cool. Done. A little unpleasant seeing red and and minus vote but it disappeared when I added a new tag, so all good. :)

"well-being" works for me (Christian's point re-" health" tag is well taken so I withdraw that request).

I have a sequence, lost in the depths of LW ... but since you bring it up: (cheeky smile)

An easy intro. to some key anatomy 5 main muscles made easy.

Comment by leggi on How likely is the COVID-19 apocalyptic scenario? · 2020-04-22T13:27:16.062Z · LW · GW

Some info. on coronavirus vaccines in pigs:

Vaccines for porcine epidemic diarrhea virus and other swine coronaviruses 2016

Coronavirus (and other viruses) causes severe disease in neonatal piglets. Vaccination of pregnant sows in order to confer "lactogenic immunity" i.e. antibodies in the milk is, as far as I'm aware, the main use of coronavirus vaccines in swine.

(I was a veterinary surgeon but I've not treated pigs in over a decade.)

Research 2019 Recombinant Chimeric Transmissible Gastroenteritis Virus (TGEV)—Porcine Epidemic Diarrhea Virus (PEDV) Virus Provides Protection against Virulent PEDV

Comment by leggi on [Site Meta] Feature Update: More Tags! (Experimental) · 2020-04-22T12:41:29.631Z · LW · GW

I'm liking the tag idea!

But.. how to I remove one (added by mistake to one of my posts)?

A list of all tags currently available would be useful. (rather than seeing what appears on the drop down list when doing a search for various letters).

I'd like a "health" tag (edited to add - I withdraw the request for a "health" tag)

and would use an "anatomy" tag (but that'd mostly be for me as far as I can see).

Comment by leggi on April Coronavirus Open Thread · 2020-04-13T19:28:04.972Z · LW · GW

Test reliability:

sensitivity = number of true positives / number of true positives + number of false negatives (true positives that test negative)

specificity = number of true negatives / number of true negatives + number of false positives (cross-reactions, other infections giving positive result)

Some info. I found here about covid19 PCR test. (It might not be the test that was was used but as far as I'm aware all current covid virus testing is via PCR so the tests should be of a very high specificity - 100%?!)

A bio-optical laser sensor for COVID testing is under development.

  • Technique/testing protocol.

Contamination of swabs is a possibility for positive results in a negative patient. (e.g. test personal is positive and contaminates sample, contamination in lab.)

Poor technique on sampling, 'bad luck' just missing the virus on sampling, using the wrong type of swab, poor handing of sample will give a negative result for a positive case.

Comment by leggi on April Coronavirus Open Thread · 2020-04-13T19:02:50.238Z · LW · GW

A US study looking for recruits: NIH begins study to quantify undetected cases of coronavirus infection

A new study has begun recruiting at the National Institutes of Health .... to determine how many adults in the United States without a confirmed history of infection with SARS-CoV-2 have antibodies to the virus.
After enrollment, study participants will attend a virtual clinic visit, complete a health assessment questionnaire and provide basic demographic information—including race, ethnicity, sex, age and occupation—before submitting samples in one of two ways. Participants working at the NIH Bethesda campus will have blood drawn at the NIH Clinical Center. Other volunteers will participate in at-home blood sampling.
Comment by leggi on How to evaluate (50%) predictions · 2020-04-11T07:26:42.034Z · LW · GW

(veterinary) medically/surgically speaking:

Animal owner: ""What are its chances?"

Me: "50-50".

What I mean: Treatment's worth a try but be prepared for failure. The magical middle figures that say ' I don't know, can't guess, don't have an intuition either way, and we'll have to see what happens'.

Comment by leggi on When are immunostimulants/immunosuppressants likely to be helpful for COVID-19? · 2020-04-11T07:10:32.881Z · LW · GW

I've just come across this:

COVID-19 host genetics initiative

A project that's just starting (110 studies registered as I post) but may yield some interesting data in the future.

Being able to release the least susceptible from lock-down and increasing herd immunity. Targeting limited vaccination supplies to the most susceptible. Although a high specificity antibody test will be the game-changer.

Comment by leggi on How do you determine temperature cutoffs for women's body-temperature? · 2020-04-09T15:21:16.203Z · LW · GW

Search for "basal body temperature centigrade" (I don't think you need to add female to the search but ...) Look at images and you'll get a lot of graphs.

Knowing when an increase in temp. would be expected for your partner is valuable information.

Daily tracking will show what's "normal" for an individual - using a consistent method to take temperature.

When tracking menstrual cycles it's recommended for a woman to take her temperature first thing in morning (Basal body temperature is the lowest temperature attained by the body which happens during sleep). Temp's don't go above 37.1C on the graphs I've looked at.

Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-08T12:06:30.841Z · LW · GW

A true "live vaccine" is different from "live-attenuated" vaccine. (you're right re the link, it doesn't make the differentiation clear and is poor referencing on my part.)

Due to the increased risks of "live vaccines" (and the ability to attenuate the infective agent in the majority of cases) they are rare but they do exist and are the subject of research.

For example:

Used for military personnel: Adenovirus vaccine contains live adenovirus

adenovirus type 4 and type 7 vaccine, live

Adenovirus Type 4 and Type 7 Vaccine, Live, Oral contains live viruses that are shed in the stool and can cause disease if transmitted.
The virus strains have not been attenuated. (in section 11 DESCRIPTION)


A Study to Assess the Safety of Live Intranasal Sendai Virus Vaccine in Children and Toddlers

a live, unmodified intranasally administered Sendai virus vaccine

(for "croup" rather than disease caused by sendai virus)

Using a live unattenuated dose of COVID to stimulate immunity would fall into the live vaccination category.

Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-07T07:16:08.593Z · LW · GW
COVID and smallpox is their long incubation times, which isn't shared by something like 95% of current ambient disease

I'm not sure what current ambient disease means.

Where do you get the figure of 95% from?

If you're talking about "colds and flu" then yes they do have short incubation times but many other viruses have long incubation times for example HIV, hepatitis causing viruses

Some figures for incubation periods for various diseases:


Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-07T07:05:33.708Z · LW · GW

I've edited the post you answered to include stuff I've posted in other comments.

Words are used to convey meaning.

I totally agree. Which is why I've been pushing the point that the meaning of variolation is not what people here seem to accept it as.

Vaccination is a word in common use for all diseases

Indeed. And it's the word that should be used here.

A starting point for increasing knowledge of the subject: live-vaccines (edit to add: not a good link for differentiating between true live and live attenuated/modified vaccines, my mistake.)

highly relevant parallel twin that refers specifically to the inoculation by the live dangerous virus, variolation.


Using a live virus is a known as a "live virus vaccination".

Can you find ANY evidence that variolation is an acceptable term for any disease other than smallpox?

Comment by leggi on What is the impact of varying infectious dose of COVID-19? · 2020-04-06T16:23:08.366Z · LW · GW

Article that might be of interest and clarify a couple of definitions:


“The viral load is a measure of how bright the fire is burning in an individual, whereas the infectious dose is the spark that gets that fire going,”
Comment by leggi on Can we use Variolation to deal with the Coronavirus? · 2020-04-05T18:55:52.803Z · LW · GW

The process of vaccination by scratching the skin is known as:

  • "scarification"


  • "percutaneous vaccination"

or simply as

  • "scratch vaccination"

(unless specifically for smallpox when variolation is appropriate.)

Via the eyes would be "intraocular vaccination".

Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-05T18:53:48.612Z · LW · GW

Thanks for that info.

It makes a bit more sense why "variolation" is the term being knocked around since the post refers to giving the vaccination by scratching the skin but variolation shouldn't be used when talking about viruses other than smallpox.

This method of administration is known as:

"scarification vaccination" or "percutaneous vaccine"

Comment by leggi on How About a Remote Variolation Study? · 2020-04-04T18:26:39.975Z · LW · GW

No it doesn't seem "pretty natural to see people re-purpose" variolation for something that would be labelled in standard and accepted medical terms as vaccination with a live virus.

Find some people in the medical profession that think it's a good idea then I may reconsider my stance, otherwise I've made my point and don't intend to post any more comments on the subject.

Comment by leggi on April Coronavirus Open Thread · 2020-04-04T18:15:25.273Z · LW · GW

Supine positioning is the easiest position for intubation but once the endotracheal tube is in-situ it makes physiological sense to turn the patient over if possible. Assuming the tube is secured in place - which it should be.

Main issues with a prone intubated patient are medical staff accessing/assessing/maintaining the tube - requiring suitable facilities or having to kneel on the floor!

Supine and immobile for days - not good.

Comment by leggi on April Coronavirus Open Thread · 2020-04-04T18:04:12.262Z · LW · GW

This is the link I was looking for (but couldn't find!) for my previous answer:

Proning the non-intubated patient

Written by Josh Farkas assistant professor of Pulmonary and Critical Care Medicine at the University of Vermont.

Comment by leggi on April Coronavirus Open Thread · 2020-04-04T07:38:25.180Z · LW · GW

Some general comments.

  • Positioning affects lung capacity and function.

Images (figure 1) and information to see the effects of gravity and compression of the lungs here and here.


supine ~ "facing up"

prone ~ "facing down"

More info: prone-ventilation-for-adult-patients-with-acute-respiratory-distress-syndrome

Proning the non-intubated patient

  • Movement is also important to help prevent congestion and keep the lungs inflated, for example post-op care for thoracotomy patients (where the chest wall has been opened which collapses the lung) is mainly about mobilisation - getting out of bed and walking around as soon as possible.

So yes, definitely worth a closer look.

Comment by leggi on How About a Remote Variolation Study? · 2020-04-03T19:21:47.797Z · LW · GW
Language use is not either correct or incorrect.

When it comes to medical issues language can be correct or incorrect. It matters.

If I went into hospital to have a debridement and someone decided amputation was an alternative I'd be pretty pissed waking up to find something had been chopped off rather than cleaned up.

It's not a matter of using variolation having a "standard usage" - it has a specific meaning. I don't think anyone will assume you want to give someone smallpox, but it does reduce the credibility of what is being said when variolation is the term chosen. (edited to add: variolation from variola = smallpox).

This website is called lesswrong, here's an opportunity to be a lot less wrong about something.

I'm not here to make friends, or get praise, or karma points and I will continue to point out errors made by people who are dabbling in subjects that they have little/no prior knowledge of.

Either people will consider what I've said and do some research for themselves. Or not.

Comment by leggi on How About a Remote Variolation Study? · 2020-04-03T13:06:34.530Z · LW · GW

"deliberate low dose infections" is a method of VACCINATION. ( or could be referred to as inoculation)

The usage of the term "variolation" is not correct. Variolation is specific to smallpox.

Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-03T08:47:53.834Z · LW · GW

Thank you for replying  and for the link. 

To quote the article by Robin Hanson:

 " Variolation is an inoculation technique whereby a scab or pus from an individual with a mild smallpox infection is introduced into the nose or mouth of healthy individuals."

Which is missing some key points about variolation.

Firstly to expand on the definition Robin used:

The Chinese practiced the oldest documented use of variolation, dating back to the fifteenth century.

 According to such documentation, mild smallpox cases were selected as donors in order to prevent serious attack. The technique used scabs that had been left to dry out for some time. Fresh scabs were more likely to lead to a full-blown infection. Three or four scabs were ground into powder or mixed with a grain of musk and bound in cotton. Infected material was then packed into a pipe and puffed up the patient's nostril.

Variolation is usually thought of in the (English-speaking) medical world as:

The procedure was most commonly carried out by inserting/rubbing powdered smallpox scabs or fluid from pustules into superficial scratches made in the skin.

Variolation is about smallpox.  A term that should not be applied to covid19 or any other virus/disease.

What Robin describes as "deliberate low dose infection"  is the process of vaccination using a live virus (as apposed to live-attenuated or dead virus vaccine).

Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-01T21:17:59.666Z · LW · GW

viral titer/titre is the technical term for "viral load" so would be more useful if looking for studies.

2 human studies I've quickly found....

Assessment of correlation between serum titers of hepatitis c virus and severity of liver disease

Dengue Viremia Titer, Antibody Response Pattern, and Virus Serotype Correlate with Disease Severity

Comment by leggi on Taking Initial Viral Load Seriously · 2020-04-01T15:31:36.502Z · LW · GW

Question - why is the term variolation being used?

Unless I am very much mistaken variolation is specific to smallpox.

Edited to add. I am not mistaken, I was just trying to be polite in some ill-attempt not to get voted down so quickly and hidden out of sight, but since that didn't work:


Shockingly poor practice IMO. I find it disappointing at how readily it's been accepted, repeated and defended without any apparent thought.


using a live (unmodified) virus to stimulate immunity is still a VACCINATION.

with a"live vaccine"

Different routes of administration have also got names.

by scratch is known as

"scarification" , or "percutaneous vaccination" or "scratch vaccination"

other routes of vaccine administration include:

intranasal, intraocular, intramuscular, subcuteneous , intraperitoneal, oral, sublingual ...

Using variolation exposes the lack of basic medical/immunological knowledge of the author/s.

IF lesswrong wants to be taken seriously on this subject using the correct terminology would help significantly.

My comments are of no benefit to me - they are for lesswrong.

And down-votes are not going to stop me wanting to help, but do provide some amusement at the rat-reactions to being challenged.

Comment by leggi on Coronavirus: California case growth · 2020-03-31T14:51:14.776Z · LW · GW

Strongly up-voted because I believe the tone of a comment shouldn't be as an important consideration as the point being made.

Interesting ideas are good, feedback for the further development should also be considered good.

I still think rationality means thinking rationally.

(And I've a couple of big doses of unexplained negative karma on the posts I've created and would have much preferred some comment/feedback whatever the tone it took and Christian was one of the few that provided some.)

Comment by leggi on Coronavirus: Justified Practical Advice Thread · 2020-03-31T11:46:50.282Z · LW · GW

The top set of links aren't working but the study to URTI rates is very interesting.

Firstly for the use of 3 doses a month apart - one dose is the standard for BCG.

I had a BCG at about 7 years old due to contact with a diagnosed TB case. Age 11 I had a positive reaction to the tuberculin skin test (Mantoux) but still got given a second dose, even though I told the school nurse it wasn't recommended - cocky little sh!t even back then and I'm sure she stamped me twice as punishment... Now thinking good for me!

Also, that there was a strong immune response in elderly subjects who tend to be considered as having a weaker immune system overall.

Testing at 6 months from 1st dose:

There were significant increase of IFN-γ and IL-10 levels in the BCG group compared to the placebo group. There were insignificant increase of IFN-γ and IL-10 levels in the pre- and post-BCG group

Memory B cells are present "for decades" so for those that have received the BCG this effect should apply.

For bladder cancer:

BCG is put right into the bladder through a catheter.

A different mode of action than a standard BCG vaccination, not so much boosting the immune system but drawing attention to the cancer cells in a localised manner.

Regarding the "cytokine storm" seen in severe patients - would previous vaccination make this worse? Musings, no idea what reality will be. But countries with vaccination programs v. those without should provide some interesting data.

Did you come across any information about any specific antibodies have been associated with COVID19?

Comment by leggi on Coronavirus: Justified Practical Advice Thread · 2020-03-30T08:40:38.736Z · LW · GW
I'd recommend getting it if you haven't, or especially for your older relatives (given that the cost/side effects is well-understood and near-zero, whereas the benefits based on the below could be serious):

I would recommend doing more research before making recommendations like the above. tb-throwaway.

Start here: NHS Who should have BCG?.

To quote one line that you could investigate:

There's no evidence the BCG vaccine works for people over the age of 35.
Comment by leggi on Peter's COVID Consolidated Brief for 29 March · 2020-03-30T05:55:43.280Z · LW · GW
You need to practise these things

So true. I'm trained to surgical sterility and am very aware of everything I touch and when I'm contaminated but it is hard to be vigilant ....

  • Turn on tap.
  • Wash hands thoroughly with soap and water for a long time to decontaminate hands.
  • Turn off tap and recontaminate hands.

Although my constant 'helping' of others in the household to maintain standards may get me beaten to death before coronavirus gets me. : )

Comment by leggi on March Coronavirus Open Thread · 2020-03-28T07:34:28.960Z · LW · GW

The current tests are looking for the presence of a specific virus - looking at the genome using RT-PCR technology so the answer is no. (eek at being so definite)

PCR (polymerase chain reaction) is a DNA amplification technique

but Coronavirus is RNA so reverse-transcriptase (RT) is used to make a DNA 'template' from the RNA.

Some info. from Cambridge and Glasgow Universities regarding Covid-19 Genomics UK Consortium - A project to map how COVID-19 spreads and behaves by using whole genome sequencing will show if the virus is mutating.

Consider the demographics of the populations. Age, concurrent disease, levels of smoking, air pollution etc...

Levels of testing/recording/reporting....

(hope this makes some sense - written in a rush)

Comment by leggi on COVID-19 growth rates vs interventions · 2020-03-28T06:30:42.040Z · LW · GW

Some first thoughts:

  • It only takes one person to infect you.
  • You can reduce your contact, but what about your contacts contacts?
    • How many people is the person serving in the grocery store coming into contact with?
    • How strict are they all with their precautions?
  • What about other members of the same household and all their contacts?
  • The recommended distance between people may not be sufficient to prevent transmission.
  • It's easy to break the distance rule (might just be a second or two even if being v. careful).
  • Fomite transmission (inanimate carrier of infectious diseases)
  • Pre-(noticed) symptomatic transmissions. What if someone has a fever during the night, how many people would notice it/associate it with COVID? (It always amazes me the denial some people can have about their symptoms.)

QUESTION - has anyone come across data about duration of a COVID-fever? (although there's a massive potential for variability between individuals so not sure the data would actually be useful/representative/meaningful but it'd be good to have whatever information is out there...)

Comment by leggi on March Coronavirus Open Thread · 2020-03-26T16:18:51.982Z · LW · GW
virus is attacking the ACE2 molecules.

This is very interesting information. I was wondering (but not enough to actually research it) why diabetes mellitus (DM) was a bigger risk factor of severe disease than I would have associated with the "normal" increased risk with infections in patients with DM.

A quick search led me to this article in the Lancet.

The expression of ACE2 is substantially increased in patients with type 1 or type 2 diabetes, who are treated with ACE inhibitors and angiotensin II type-I receptor blockers (ARBs).
Hypertension is also treated with ACE inhibitors and ARBs, which results in an upregulation of ACE2.
ACE2 can also be increased by thiazolidinediones and ibuprofen.

(has a) functional receptor for the spike glycoprotein of the human coronavirus HCoV-NL63 and the human severe acute respiratory syndrome coronaviruses, SARS-CoV and SARS-CoV-2 (COVID-19 virus)
Comment by leggi on LessWrong Coronavirus Agenda · 2020-03-26T12:54:15.423Z · LW · GW

yellow fever vaccine is one that springs to mind that also uses eggs in production

The yellow fever vaccine is made by growing yellow fever virus in mouse embryo cells and in chick embryo cells. The final preparation of the vaccine is made in eggs. Growing yellow fever virus in mouse and chick cells over and over again weakened it. Therefore, when this "live, weakened" virus is injected, a protective immune response develops without causing illness. SOURCE
Comment by leggi on COVID-19 transmission: Are we overemphasizing touching rather than breathing? · 2020-03-25T15:42:17.692Z · LW · GW


I am in no way saying this relates to COVID19 but to give an example of a virus that can spread a long distance 'in the wind'.

"foot and mouth disease" caused by a picornavirus affects cattle, pigs, sheep, goats (+ other cloven-footed animals).

... Virus was reported to travel over water >250 km (155 miles) from Brittany, France, to the Isle of Wight, UK, in 1981, but it usually travels no more than 10 km (~6 miles) over land. SOURCE
Comment by leggi on Open & Welcome Thread - March 2020 · 2020-03-24T16:48:17.706Z · LW · GW

I'm happy to read stuff and critique. (I go harsh but hopefully fair).

General editing/formatting/readability appraisals.

I'll be of most of use on bio-medical topics (although the discussions here about vaccine development are way above my knowledge base so I'd avoid that!)