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? · 2021-07-21T12:11:15.162Z · LW · GW

I watched a few videos and contact improv looks great.  (Full disclosure I watched the videos x2 speed I've little patience watching most stuff). For people in a good enough physical condition, and relaxed enough to go with it,  I can see it being beneficial and a lot of fun. (5 years ago I would have hated the idea because back then movement = pain, pain, pain and I couldn't have let go to move) It looks like free-flowing movement, guided instinctively by the body rather than the brain trying to control and direct.  Support is being provided which allows increased movement (I achieve similar things by legs hanging off the bed, leaning over arm of chair, using the kitchen worktop as a bar, swinging from posts...)  Working towards a full range of natural movement means moving through all the positions possible,  the "more awkward" is easier when support is available and the 'support' is also moving which adds more randomness and further increase range of movement.  I find a similar, gentle, effect moving around in water and letting my limbs float around but if I get the opportunity I will try contact improv.

Now seems a good time to have a minor rant about our modern flat earth.....  Walking (especially barefoot) over uneven terrain flexes and stretches the whole of the body in a way that shoes and flat ground just don't allow. 

I will take some time to have a good read of bewelltuned. Are there particular bits that resonate with you? For now, pulling this quotation:

By repeating certain movements and positions over and over again (e.g. during sitting work), we involuntarily strengthen connections between movements and muscles that don't make much sense lumped together.

This fits with my distorted 'body map in the mind' that sends motor commands to the 'wrong muscles', adding to imbalance and misalignment.

What do you experience when you are focused on your body?

(body scanning? I don't know much about the methods involved)

How would you describe your sense of proprioception?

My 'conscious proprioception' skills were pretty much at zero when I started and it's been a revelation actively experiencing the sensory feedback from by body. Starting with focus on my pelvic floor and rectus abdominis 'Base-Line' muscles from where movement originates and using my midline anatomy as the reference for positioning of the rest of my body.

Active engagement of the Base-Line muscles creates a positive feedback loop, increasing awareness of :

  • Voluntary activation of muscles.
  • The body map in the mind
  • Proprioceptive feedback that is compared to the map. Seeing the sparkles. The basis of chakras and Qi?

Now I'm aware of my body in a way I never was before. I was always very clumsy...

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-21T11:23:15.244Z · LW · GW

Some comments on Dr Scott Dye's failure-of-homeostatis model:

I read the abstract "Patellofemoral Pain: An Enigma Explained by Homeostasis and Common Sense" and found myself nodding along...

overload and/or injury produces pain. Bone overload and synovial inflammation are common sources of such pain.
Patience and persistence in nonoperative care results in consistent success. Surgery should be rare"

I agree with all that. I'd classify it as common sense as they say in the title.

But after reading the article a couple of times I don't feel the authors were saying anything new.

Our Hypothesis: Loss of Homeostasis Causes Pain
We hypothesize that pain is the result when load applied to musculoskeletal tissues exceeds the ability to maintain homeostasis.  Loss of tissue homeostasis from overload and/or injury produces pain. 

Overload/injury = stresses beyond tolerable levels --> damaged tissues & inflammatory processes,

which the authors are describing as "loss of homeostasis". The use of "homeostasis" feels unnecessary.

Injury/overload = damage. simples.

However, the inflammatory processes are anything but simple. Inflammation is a rabbit hole I avoid looking to deeply into, I'd be lost for a very long time!

Pain anterior knee. —a consistent set of symptoms, signs, and test results—that does not exist. 

I agree with this, and it happens to fit with my 'individual trauma imprint' explanation for pain-related symptoms. What our bodies have been subjected to, the damage sustained. With innumerable positions the body has a massive capacity for adaptation. As damage builds up, patterns of symptoms will emerge throughout the body but we're all a bit different. 

Emotions play a role in pain as well, and somatization resulting in knee pain is a well-known phenomenon, particularly in adolescent women related to stress or even abuse. 

I checked the article's references for more details about somatization but found nothing listed. (I also noted the references are mostly to other articles by the authors.) Whilst I do believe emotions and the physical body are intertwined, this statement feels more like a dismissal of knee pain when reported by the young and female. Adolescent women being told "it's all in your mind" when nothing shows on exam or standard imaging.  I wonder how often adolescent men with knee pain are told it's due to their emotions too, or do they get a "diagnosis" of patellofemoral something or other? I didn't find anything to back up this as a "well-known phenomenon".

I say: The knees are joints that are under a lot of stress with little slack so problems appear here first when the body is not aligned and fully balanced. Stress/abuse affects positioning of the body.

Poor positioning can be subtle but it takes its toll.    Knee pain - slight adjustments in the joints above and below i.e. hip and ankle to avoid the pain.  It affects the whole leg, which then affects the body-whole over time.   The body is very adaptable, able to cope with a lot of misusage and abuse but the imbalance and misalignments are cumulative.

The treatments listed: activity modification, cold therapy, anti-inflammatories, physical therapy. are (or at least should be) standard protocols. I'm cringing at the thought that surgery might be pushed in some parts of the world (without good reason), and thankful I wasn't prescribed opiates as a teenager.

I was going to comment more on cold therapy but I thought I'd check some things I'd always been told, turns out it's an another rabbit-hole to go down.

Cold - good or bad? It does numb the area for a while but what's the deeper effects on the tissues...

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-19T13:44:24.002Z · LW · GW

I hope your Dad is doing OK. No worries with timeframes - less than immediate responses are one of LW's strengths IMO.

Abs, butt, quads, traps. I'll try being more mindful of those,

Fricking awesome! Feel for positioning, freedom to move, and balance in left and right. Just to expand a little ...

abs. All good. Imaging extending the linea alba between the rectus abdominis every in-breath. Pubic symphysis to sternum.

butt. fair enough. Big ass muscles - gluteus maximus.

quads. What makes you say "quads" here? It would be very useful for the insight. Focus on the rectus femoris, shin to hip bone. The quadriceps share a distal insertion (common ligament of quads.-patella-patellar ligament-tibial tuberosity) but the rectus femoris is only one of the quads to cross both hip and knee joints. image here. or in the post main muscles made easy. I think of the rectus femoris as the guide muscle of the quadriceps, positioning the leg so the 3 vasti muscles 'fall into line' (I don't like that phrase - but have nothing better).

traps. Excellent. The trapezius muscles should free to support the head and arms through a full range of movement. Movement starting from lower trapezius.

(coughs) Pelvic floor. The base foundation of the body.

It would be useful to me to know how much is "the pelvic floor muscles being important" common knowledge here?

This honestly sounds amazing. Is there a way for a civilian to get access to large mammal [human?] dissections?

Commenting here got me thinking about who has the opportunity to handle really really fresh tissues like I've had. It's not a long list: Anyone who turns animals into meat. Anyone performing autopsies on the freshly dead. Euthanasia and immediate post-mortem is possible in the veterinary world but human corpses are likely to be older when examined and it doesn't take long (1-2 hours) for connective and adipose tissues to change consistency - temperature and humidity dependant. A certain class of serial killer (skip over that one). Anyone who turns animals into meat. Surgeons, especially those dealing with mass trauma injuries. Removing dirt out of fuzzy connective tissues is a bitch...

I imagine most human dissections aren't fresh enough to really appreciate "live" tissues. So, how to get in on the action? If you can find a farmer/small-holder type willing to let you watch a butchering, a hunter that processes the carcass, a fresh meat butcher. Or a friendly large animal/equine vet that's willing to call you when the chance to do a fresh post mortem arises.

I've been fortunate with the opportunities I've had to increase knowledge and understanding of mammals 'in the flesh', something I appreciate a lot more now that I've stopped to think about it.

I have quite a lot to say about the link you provided, so will be back with a separate comment. Have you worked through "DAMN-IT" (from one of my previous comments) and seen where that gets you?

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-07T10:47:13.351Z · LW · GW

Yes, there are a lot of ways to get sensory feedback. I listed some to increase awareness of the relative positioning of the midline anatomy here.

imagine a string attached to the top of your head, towards the back. "

The "imagine a string" example is great - if it works for an individual and they engage the 'right' muscles to improve posture. It didn't for me, my body was too restricted and misaligned, my 'myalgia of imbalance' too advanced for imagining a string to be of any help.

To take the string idea further, think of the linea alba and nuchal & supraspinous ligaments as part of this string. To straighten the string the main muscles are the rectus abdominis and trapezius muscles. The "attached to the top of your head, towards the back" I'd replace with the external occipital protuberance.

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-07T10:36:26.084Z · LW · GW

From the link you provided:

"A very recently reported third discovery demonstrated a previously unknown tissue component-'interstitium'-a networked collagen bound fluid-filled space existent in a number of human organs."

I read that and thought:

"What? The interstitium? I learned about that 30 odd years ago.  Wasn't that one of the things I had to label when sketching from a histology slide, wow that was so long ago ....  "

What has been recently noted and publicised is the interstitium in its form in living tissues.   From this article:

The researchers said these fluid-filled spaces had been missed for decades because they don't show up on the standard microscopic slides that researchers use to peer into the cellular world. When scientists prepare tissue samples for these slides, they treat the samples with chemicals, cut them into thin slices and dye them to highlight key features. But this fixing process drains away fluid and causes the newfound fluid-filled spaces to collapse.

Histology 101.  Tissues are distorted when prepped for slides.  I was taught that at vet school (if not before).  I'd assumed / never thought about it, that it was common knowledge amongst medical folks.

I've handled a lot of 'fresh' mammalian tissues (canine, feline, bovine, equine, ovine, caprine and various others). I'll go out on a limb and say it's all the same stuff - bone and muscle fibres all wrapped and blended in a web of connective tissues ... in humans too.  (This could be a major error.  I've not handled enough human flesh to really know....)

Seeing live/freshly dead tissues, feeling them in your hands, is a very different experience from learning from a textbook, histology slides or studying bodies prepared for dissection.  They can't compare in giving understanding of how a body is put together, of what it really consists of.  These experiences give me lot of confidence in what I say about the role of connective tissues, also the knowledge that defining and delineating is very difficult so I'm sticking to the covering term of 'connective tissue' which I wrote a bit about here.  I don't know the precise pathology of 'physical restrictions in connective tissues'. (Is it collagen fibres cross-linking? Is it interstitial components hardening from fluid to gel to the palpable lumps I can feel subcutaneously? Is it a combination of many factors?!) A good question is how to sample and examine these tissues without distortion.    

Putting aside the issue of levels of certainty here,

Phew, much appreciated. : )

I'd agree with ChristianKl that I'm a bit unclear what the implications of your model are, except perhaps, "pay attention to your posture and movement" which I already do a fair amount.

I've been side-tracked by "posture".

My model is about learning to use your body better. I believe the 5 main muscles of movement are key to this, leading to:

  • Better physical health. 
  • Better mental health.
  • Less pain and tension in the world.

The level of knowledge about the structure and location of the anatomy I share is at a sufficient level for me to use the word "fact" ( grinding my teeth as I type this,  I don't like to use "fact" for anything).

Muscle tissue blending with connective tissues is very hard to describe in full detail but, ignoring the pelvic floor for a minute, the other 4 main muscles are big and easy to palpate. We know their attachment points to bone and connective tissue structures (minor variations in individuals have been noted and no doubt there are more that have not). 

The is enough information for someone to find the muscles on their own body, to touch them and increase conscious awareness of them. 

There is much still to learn, to put together, to figure out.  I believe Base-Line Theory increases understanding of how we could better use our bodies, of why there is so much unexplained pain -and how to fix it.  

As a simple experiment if you are willing, find the 5 midline markers and feel for their relative positioning.    As you move through your day, pause to take a few deep breaths and try to be more aware of your midline anatomy.  Use it as a reference for the positioning of the rest of your body.  See how it feels, what you experience.

Thank you for the interaction! It's very useful.

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-07T09:58:48.312Z · LW · GW
Posture it's where the body naturaly without effort. For a muscle to hold something in a specific position it has to fire constantly which costs energy. It makes sense for the body to save that energy by using fascia to hold the posture.

This is an issue of definitions then. I agree that it is the connective tissue system that provides passive support for the body, minimising muscular effort. I also believe it is the location of 'physical restrictions' that cause tension, alter positioning and restrict range of movement.

My definition of posture: The position of the body - all of it, at any time.

(I checked a few sources for a definition of posture. Lots of options out there, pretty much saying what I am calling posture and several mentioning the role of muscles.)

I'm not advocating attempts to get muscles to hold a specific position - in any shape or form. Think gentle movement and relaxation ...

Working with the '5 main muscles of movement' and consciously connecting with them provides a lot of sensory feedback about the relative positioning of the torso, head and limbs. Whether it be using 5 midline markers, the linea alba or Base-Line muscles (pelvic floor + rectus abdominis) as the starting reference for positioning (whatever works for an individual). This sensory feedback provides the information needed to work towards a full range of natural movement and a body that is balanced and aligned - where all the parts of the body in the correct relative positioning and free to move, including the myofascial meridians.

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-06T09:00:54.623Z · LW · GW

I agree, biology is a realm of uncertainties. The wonder of how living organisms function blows my mind. The level of complexity phenomenal.

However, anatomy is much more fixed. Grossly examinable and recordable. Studied in detail for hundreds of years. We have accurate atlases of how the body is put together, what attaches where....

Anatomy can be complicated (I've very much skipped over a lot of details about the pelvic floor muscles and connective tissue structures) and individual variations are seen, but there is much more certainty about how we are put together than biology as a whole.

I know I am right. It has taken a lot for me to get to the point of saying that out loud. Question everything has been a motto of mine for a very long time - and it will always be with me. But I feel how I feel, and accepting that feels right - especially having facts and logic on my side (IMO at least - please someone look at the anatomy!).

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-06T08:45:50.590Z · LW · GW

Thank you for providing some background. I found it very insightful into your methods of thought and what you consider evidence. (I had to google pedagogy, I don't know what to make of "perceptive pedagogy".)

You've studied anatomy, I think great! Most people (in my experience) find anatomy intimidating but I would hope someone who has studied it would feel more comfortable giving some consideration some, fairly basic, anatomical facts.

I said something about posture being a mix of fascia and muscle and she said: “No, it’s just fascia”

And you are happy to accept that statement? That muscles, the bodily tissues that change the relative positioning of different parts of the body, don't affect the position of the body (i.e. posture)?

The state of the connective tissue system (including the ill-defined fascia) is important. The way muscles are functioning, moving the parts and repositioning, is also important. Humans have the capacity to send motor commands to "voluntary muscles". Muscles can be used to consciously alter positioning, to change posture. Anyone who says body position is just about fascia loses a lot of credibility in one swoop IMO.

Those are the kind of people I ask when I want to know something about how human anatomy works.

Have you done any independent research? Fact checking? Thought about it for yourself? Or are you relying on the opinions of others (however great you feel their experience/knowledge/credentials are)?

I don't want anyone to just believe me, I want the anatomy to be given some thought. I am constantly open to updating my model, but without feedback I can only work with my experiences. And the facts.

You didn't answer the question I asked:

Have you ever found the 5 main muscles on your body and given some thought about how they are functioning?

A simple yes or no will do at this point.

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-06T08:37:02.850Z · LW · GW

I've read Painscience over the years. It's one of the few places that attempts to cut through the BS of "pain medicine" and I agree with Paul on many things.

However, I am looking at "posture" from a new perspective. (Kind of wish I had another word for body-position - pose? A lot of bad thinking is currently applied to "posture".)

Posture = the pose you are in = the positioning of all the bits of your body, at any time.

  • Good posture = good positioning. Enabled by an unrestricted range of movement, normal tensions within the connective tissue system and the appropriate use of muscles.
  • Bad posture = bad positioning = misalignment of moving parts = increased biomechanical stress. At some point the body will start to generation warning signals - pain.

The body is an incredible machine with a massive capacity to tolerate misusage, adapting its positioning to avoid pain and spread the burden of misplaced forces. Every adaption however, reduces alignment and increases imbalance, a progression of worsening positioning overtime. The more strain/exertion/trauma the body is expose to the more misalignment develops. For the body to function at/near optimal, it much have all potential position possibilities open to it - a full range of movement - allowing whatever posture/position that is most appropriate to be used for the task at hand.

Paul Ingraham says in the article you linked to:

Poor posture is any habitual, self-imposed positioning that causes physical stress, especially coping poorly with postural challenges.

There is a big difference between “poor posture” and “postural stress,” but the distinction seems to be absent from most discussions of posture and ergonomics.

I say poor posture is when there is postural stress. Also posture can be active or passive (conscious engagement of muscles or subconscious brain to body commands to muscles - habits).

If there isn't stress, it's not a bad position to be in so it's not a poor posture. Examples Paul uses:

The most stereotypical poor posture of them all — a hunched upper back, with the shoulders rolled forward

Is this really an example of "poor posture"? If the shoulders can be "unhunched", if the subject has a full range of movement, hunched is just another pose. Being in a position that is classically labelled "poor posture" isn't an issue if stress is minimal, and no pain is generated (RSI in wrists much more likely with "texting hunches"). However if movement of the neck and shoulders are restricted, if "hunched" is a fixed feature, the body is less able to adjust when it needs to, so it becomes a bad posture, generating postural stresses.

“Squatting like a baby” ...... hopelessly unrealistic for most people.

I understand Paul's view on this, a few years ago I would have laughed at the thought of getting into a squatting pose and cried out loud twisting and rotating to get into an approximation of the position. I would have battled a lot of pain to stay there, fidgeting and adjusting looking for the least painful option. But I can squat comfortably now. It wasn't an aim, or something I intentionally did. It's just another position to move into and out of as I work with the whole of my body, using my Base-Line as starting reference for relative positioning of the rest of my body - to sense my posture for myself and feel how to move to improve my range of motion.

Read though my take on posture. Question the validity of each statement.

Read though Paul's take on posture. Question the validity of each statement. (I still agree with a fair bit in the article.) Check the references and consider what, who, how was studied. I'm not impressed with the quality of any studies listed. It'd be more efficient if you link to any ones you find that have some validity rather than me trying to comment on them all.

On a personal note, my patellofemoral pain started (bilaterally) when I was about 7 yrs old. I got a diagnosis of chondromalacia patellae, a label that sounded special but did nothing to reduce the pain in my knees. Walking was always painful, occasionally to the point of almost non-weightbearing. The pains shifted around and around in my knee (and the rest of my body) as my posture altered to avoid pain and keep on going. Now that use the right muscles to position my legs to torso (rectus femoris to align hip and knee joints, gluteus maximus to stabilise the posterior pelvis) my knee pains have finally gone.

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-03T12:32:03.495Z · LW · GW

There's not much in it but - based on my experiences and the anatomical facts - I am more certain about Base-Line Theory of Health and Movement that I am about the sun coming up tomorrow. There I've said it. It's what I believe. That strongly. Even so, I would be willing to change my mind and that's why I persevere with looking for feedback.

Have you ever found the 5 main muscles on your body and given some thought about how they are functioning?

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-03T09:58:54.409Z · LW · GW

I expect the sun to come up tomorrow, I am confident it will, but I am not certain of any future event. There's plenty of time between now and then for things (however improbable) to occur that mean the sun doesn't come up.

Comment by leggi on What are good resources for gears models of joint health? · 2021-07-03T09:53:20.813Z · LW · GW

My theory is based on anatomical facts, logic (feels like I'm stating the obvious) and my subjective experience. It's not complicated but there are multiple parts (split over several posts). I find myself using a lot of words in an attempt to explain clearly and simply (unsuccessfully it seems) so attempting to use as few words as possible and clarify my theory:

Base-Line Theory of Health and Movement

Use the right muscles. Balance and align body and mind. 

Anatomy of alignment

  • Linear structures: Linea alba, supraspinous & nuchal ligaments.
  • 5 midline markers: Pubic symphysis, navel, xiphoid process, jugular notch, external occipital protuberance.

The body is balanced and aligned when midline anatomy can be positioned to create the median plane. 

5 main muscles of movement, dynamic balance and alignment

The position of the rest of the body is relative to Base-Line. The body's core pillar of strength.

  • Pelvic floor - the Base foundation of the body.
  • Rectus abdominis - central Line. Supporting all movement.  Alignment of the linea alba.

Base-Line to legs:

  • Gluteus maximus. Strength and stability of posterior pelvis.
  • Rectus femoris. Align hip and knee joints.

Base-Line to upper body:

  • Trapezius - to guide the head and arms through a full range of natural movement. Alignment of nuchal & supraspinous ligaments.

Conscious Proprioception

Increased awareness of the sensory feedback regarding  position, motion and balance.  Feel how to move to increase alignment and balance, starting from Base-Line.

Pains & weird sensations  

  • Using the wrong muscles results in myalgia of imbalance.
  • Restrictions in connective tissues =  stiffness, physical tensions = pain and weird sensations.
    Restrictions result from tissue trauma (inflammation, injury, infection, surgery, stress etc.) and as long-term adaptation to poor posture.  Individual trauma imprints.
  • Misalignment increases with cumulative damage. Pain spreads.


Chronic pain negatively affects sleep quality,  mental well-being, quality of life.  Physical tensions = mental tensions. 

 - - -- --- -----

So, with "what is Base-Line theory?" cleared up...

What evidence would falsify your theory?

1) Anything that offers an alternative explanation for my decades of pain and subsequent recovery over the past 4 years.    I've researched my pain for decades.  I've not come across anything that would invalidate Base-Line theory health and movement.  No inconsistencies with what is "known" as far as I can see. (please anyone, tell me different.) 

2) Any evidence that what I have experienced is some existential mindfek rather than what I think of as reality.   Open to suggestions (very much a joke....)

3) No supporting evidence when  'use the right muscles to balance and align the body' is tested.  

Two parts to examine:

  • Test validity of "the right muscles".
  • Test "body balanced and aligned" is a good thing.

Many methods to test come to mind both those parts.  

  • Looking for the presence/absence of physical misalignment in chronic pain patients. (Chronic pain patients that can align their midline anatomy to create the median plane would disprove me).
  • Assessing levels of pain in those who's body is balanced and aligned.  (Full range of natural movement with high pain levels would disprove me).
  • Studying those with no pain and their state of physical alignment. (Finding grossly physically misaligned people with no/little pain would be evidence to disprove me).
  • Biomechanical studies as the body as it goes through a full range of natural movement looking at the  condition and positioning of the 5 main muscles. The trapezii have the most potential movement and are responsible for the alignment of the upper body, so if I had to pick one muscle pair to study I'd start with them.

For the assessment of chronic pain there is a lot to consider. Technology will bring better recording methods of aches and pains.  More specific location, duration, intensity, frequency, type of pain. I've plenty of feedback to give on how to record pain more accurately. 

One easy assessment for clinicians is to examine the condition of the nuchal ligament. Minimally invasively accessed and should be easily palpated. (I'd like clinicians to have examined a "free neck" to appreciate how much movement there should be and how the nuchal ligament aligns when the head is dropped forward).

Clinical trials.

I'm drooling at the thought of access to motion capture and digital analysis.  How many dots would I get? I'd start with the 5 midline markers, hip bones, tibial tuberosities, C7, spine of scapulae ... Precise placement of markers is crucial.  

Computer analysis allows detailed, blind assessment of movement and state of alignment of participants compared to the calculated potential range of movement for each individual. Assessment at 0, 3, 8 and 16 weeks as rough figures. 

Or simpler testing,  subjects stand with their back to column/wall.  How does it feel/measurements. Then take a few deep breaths and think of aligning your midline to the column.  Relax and allow the rest of the body to move as feels natural.  Note what moves where. body parts, pain...  Use a long, straight stick ...

Potential early testing participant groups that spring to mind:

  • Medical students from several schools. Broadly similar age range. Should have no trouble understanding the anatomy.   1/2 the schools told to focus on the 5 main muscles and how they move. 1/2 no instructions.   Attendance of movement classes for all participants?
  • A group who do regular exercise classes together to minimise variables to what exercises are used.  Take half a class, provide resources (intro. session, videos, pictures) to the relevant anatomy.  Encourage focusing on using the main muscles as they move and feeling for the alignment of their midline anatomy.  Ask them not to tell the other half of the group acting as the control.
  • Chronic pain suffers.   1/3 told about the 5 main muscles, 1/3 told to increase movement, 1/3 nothing.

That'll have to do for now. 

Comment by leggi on What are good resources for gears models of joint health? · 2021-06-22T13:54:11.287Z · LW · GW

Muscles move bones. Muscles do determine posture, along with connective tissues. I did edit my "posture post" after you'd read it. Originally I'd not mentioned the condition of connective tissues affecting posture (a glaring omission!). I find "fascia" too restricting as a term, I'm sticking with connective tissues.

  • Muscles alter positioning/posture in an active manner. 
  • The condition of connective tissues affects posture in a more passive manner.
factors that are involved in getting it unstuck in more complex

Could you provide details about these factors? This is the stuff I'm looking for.

The anatomy is as near to "fact" as it gets but "restrictions in connective tissues" is my weak spot.  I don't have any specific histological results or evidence past my experience and reasoning based on available knowledge. (What I've seen incidentally in various studies over the years does fit with "sticky connective tissues" - inflammation's a bitch)

I've felt the restrictions, heard them, seen them as I've moved and released tissues, regaining a little more movement each time. Something is giving, releasing.  Connective tissues/ECM is the only tissue it could be (other suggestions welcome).  Body wide releases.  I can feel my myofascial meridians, where the lines of tension are. I can 'see' them when I close my eyes and focus on how my body is moving - proprioceptive feedback from my body giving me a visual representation of the state of my body in lights and colours, flashes and streams.

I'm not saying you have to have strong muscles, I'm saying you have to use the right muscles.

Comment by leggi on What are good resources for gears models of joint health? · 2021-06-22T13:41:07.966Z · LW · GW

Well blushing a lot at my typo. I went from % to <p> and apparently forgot about the decimal point.

I'm not one to put numbers on things but it's popular on LW and my fingers spat it out as I was typing.

I am certain.

I've never been so certain of anything in my life.

What confidence level would be acceptable?

Comment by leggi on What are good resources for gears models of joint health? · 2021-06-22T13:34:24.507Z · LW · GW
Why? How many times, for how long? What evidence do you expect this practice to give me in support of your theory? If I don't feel anything, will you count that as evidence against your theory, or will you explain it as somehow supporting your theory, like Freud would claim that a patient was in denial if they claimed not to have some desire that his theory predicted that they would have?

I can answer each of those questions if you want me to. I am willing to spend the time if you ask but what value are my words to you?

I am offering you a map.

If you want to explore your territory it is up to you.

I will still be back with the big question of anti-theory evidence.

I would be very interested in your prior regarding me passing this test.  Even if you don't want to share, pick a number now. ; )

I'm finding it a valuable exercise, so thank you for the interaction.

Comment by leggi on What are good resources for gears models of joint health? · 2021-06-21T10:33:40.349Z · LW · GW

Thank you for the comment, there's a lot of questions in there to deal with.

My theory is not not just "position = pain" as you put it.  There's a bit more to what I am saying, but at its shortest:

Chronic malpositioning causes pain. (This pain is currently either labelled as idiopathic, or may have a label/syndrome but it's cause is still not understood - i.e. still technically idiopathic.) 

To break it down:

(As I see it) there are two options with "pain". Either: 

  • Signals are generated somewhere in the body and we end up experiencing "pain" . (Pathway which involves various stimuli activating 'tissue sensors',  electro-chemical transmission of information via peripheral nerves to central nervous system (spinal cord to brain) .


  • Something occurs in the brain that makes us think "pain".

Malpositioning = increases stress on body.  (Misalignment, imbalance. Basic biomechanics.) (Inappropriate/excess) stress is bad.  "Pain signals" occur where something bad is occurring.

Why would your assessment of a patient do anything other than figure out which of your Big 5 muscles are involved in the pain? If the answer is, "Strengthen the glutes and your pain will stop," then how is any pain ever properly characterized as degenerative?

It's not a matter of "figuring out which of .... 5 muscles are involved in the pain" or of "strengthen" a muscle and stop the pain.  I would like to know what I've written that led you to these thoughts so I can edit and clarify so others don't make the same mistake.

As I stated full history and clinical exam are important for a full assessment. Gather all the information/evidence, consider all the possibilities. Lots of things can go wrong in the body. 

I was sharing a diagnostic process so the OP can work through the possibilities and rule things in/out.  If nothing else shows up indicating other issues, then mechanical/postural/positional/usage issues are the options left - i.e. the "idiopathic pain" my Base-Line theory deals with.

When is "degenerative" a primary aetiology? It is a pathology.  Specifically, for joint pain - "degenerative joint changes" may be post-traumatic, post-infection, mechanical 'wear and tear', nutritional issues .... Degeneration may or may not be detectable on clinical exam but is something that can be often be seen on imaging. Something for the clinician to show the patient "There, there's the source or your pain" clinician has made a "diagnosis",  but patient is still in pain and the primary cause hasn't been found. 

There is a lot of cross-over with the DAMNIT list.  It is diagnostic tool to run though aetiologies - for any health issue, not just pain.   It's not perfect but it is useful.

How many things induce inflammation?!   

.You say you came to LW to get your theory disproven.

What I actually said was "please tear to shreds". I meant think about what I say, pick apart bit by bit.  There's several threads to pick at. Some real consideration of the anatomical facts I present and how the body is put together. Pointing out any errors.

especially when your model takes eight disorganized posts and has many irrelevant images in it

I'm disappointed that you consider my posts disorganised, but good to know. Thank you. I was hoping they were a progression from facts, definitions and logic to my experiences and updated thoughts. Seems like I failed there.

Feedback is what i want. Some consideration of what I am saying.  Pointing out any errors. Some examples of issues with my posts would be great.  How much did you read? Where did I lose you?   I'll freely admit that presentation isn't my strong point and it's hard to know what level to pitch at.   I want to provide accurate anatomy, without it being overwhelmingly wordy.  And to provide enough background information for anyone who isn't familiar with human physiology.   When I realised I wouldn't be publishing a couple of drafts I was working on I did slip some bits into other posts, which might account for a disorganised feel.  There is a fair bit of repetition because it does all come down to the anatomy of alignment (midline structures able to align, the body balanced either side) and the 5 main muscles: pelvic floor, rectus abdominis (either side of linea alba), gluteus maximus, rectus femoris. trapezius (either side of nuchal and supraspinous ligaments) that are key to achieving dynamic alignment and balance and having a body that is well-positioned.

I find anatomy easier to understand in pictures rather than words hence many images. And it is all about the anatomy.  Which images do you consider irrelevant? 

I would really appreciate your thoughts in more detail.

I will be back with a response to what evidence would falsify my theory, it's more than I can just rattle off.

If you are genuinely willing to give some thought to Base-Line theory then spend some time thinking about the anatomy, finding the muscles on your body and breathing with your Base-Line.

Lie on the floor and take a few deep breaths. Touch your pubic symphysis, navel and xiphoid process in turn. Imagine the line (the linea alba) that joins them extending as you breathe. Close your eyes and focus on the sensory information your body is providing. Give that a go. More than once.

Comment by leggi on What are good resources for gears models of joint health? · 2021-06-18T12:55:20.087Z · LW · GW

A diagnosis should focus on finding the aetiology. i.e. knowing why there is an issue (not just naming the problem. Anything idiopathic isn't a diagnosis, it's a label IMO).

{IRL I'd want a:

  • Full history including details of all other ache and pains you experience - location, duration, severity, type, frequency, initiating actions etc. The good reason for you suspecting increased muscle tone?  Do you physically feel tense?  Spasms? Restricted movements?  Other health issues, history of injuries etc.
  • Thorough clinical exam.  Of the primary problem areas checking for heat, swellings, areas that are painful/tender in palpation. Bruising, scarring etc. Testing range of motion and response to movement in various positions.


This "DAMN-IT" mnemonic can used to work through possible aetiologies of any body issue. There is some cross-over between categories ("inflammatory" is a common response to something wrong) and it may not be a totally inclusive list (but I can't think of anything that doesn't fit somewhere). It's very a useful tool:

D = Developmental, Degenerative.

A =   Autoimmune, Atrophic, Allergic, Anomalous.

M = Metabolic, Mechanical,  Mental.

N = Nutritional,  Neoplastic.

I = Inflammatory, Infectious, Ischemic, Immune-mediated, Inherited, Iatrogenic,  Idiopathic. 

T = Traumatic,  Toxic.

- - -- ---

So first steps are history & exam. Depending on what shows up:

Possible imaging - radiographs, MRI, ultrasound

Possible other tests - blood work, joint tap (if indicated).

If a clinician finds nothing remarkable on exam, a kind of "you say there's pain but I can't find anything specific" the usual process is prescribe rest, anti-inflammatories. +/- ice, physical therapy (some exercises to do) and come back in 3-6 weeks if not better. If you do go back, imaging would be the next step (gotta do something if they come back....)

- - -- ---

Think about the anatomy and were your pain is coming from.

Run though the aetiology list - what categories would you consider possible sources of your symptoms? I know which ones I'd pick out without other clinical signs, but I don't know your situation so it's over to you!

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.