Guess values, Priors and Science

Wikipedia defines Guess value as

“In mathematical modeling, a guess value is more commonly called a starting value or initial value. These are necessary for most optimization problems which use search algorithms, because those algorithms are  mainly deterministic and iterative, and they need to start somewhere.”

I am not an intuitive mathematician (nor an unintuitive one for that matter), but I have appreciated the importance of good guess value or nominal value developing software that uses computational geometry.

Yesterday I read this excellent long piece- The 60-Year-Old Scientific Screwup That Helped Covid Kill . Personally, I had been convinced by the Aerosol spread theory since I read these two pieces back in the Summer of 2020.

How Coronavirus Infected Some, but Not All, in a Restaurant

How coronavirus spread from one member to 87% of the singers at a Washington choir practice

As a result, I have spent the better part of the previous 14 months wondering “why is the scientific community so slow in accepting potential aerosol dispersion of coronaviruses”. They say science progresses one funeral at a time, but since Jan 2020 we have had far too many funerals that should have sped up the progress. Ever since I read this piece – The “noble lie” on masks probably wasn’t a lie I had been spending limited time I had, browsing through old papers on the spread of respiratory illnesses to disappointing results. The wired piece helped deepen my understanding of how we may have got here. Where the 5-micron boundary for aerosols came from is an extremely fascinating story. Maybe we can expect some Netflix documentary or a long-form book on this issue in the near future.

This entire episode appears exceedingly similar to the Dietary Fat is the villain dogma. Gary Taubes in his books – Good Calories, Bad calories and A Case against Sugar, has described this debate extremely well. As a video suggestion, I would recommend the youtube channel – What I have learned. In retrospect what seems appalling is how the scientific community basically accepted the faulty and weak fundamentals of the Fat theory – as initiated by Ancel Keys and propagated by hundreds after that. Ditto for the demonization of cholesterol and numerous other food items – including milk.

7 country study of Ancel Keys.

From these two examples at the very least, I would conclude the disproportionate importance of Priors and the outsized impact they have on the journey of academic and peer-reviewed science. Hopefully, the pandemic will correct some bugs in this mechanism, though this is by all accounts a slow and arduous process.

Incidentally, I was chatting with Kushal Mehra about his latest discussion with Shrikant Talageri and Kushal pointed out that he thinks the 1500 BCE dating of Rgveda is also one such Prior which has had an outsized impact on the journey of the Aryan Debate. Prima facie I found this point fair – thought I must say, the 1500BCE date has held up quite well over the centuries (especially since the recent genetic results). But has the date 1500 BCE anchored the research around it, making 1500 BCE appear the best fit for composition of Rgveda and the beginning of consolidation of the Arya into the Indian palimpsest ?

Post script:

I know this place has had a lot of AIT/OIT pieces including this one by me and lot of readers might be fed up by it (even I am to an extent). This isn’t aimed at AIT/OIT but is merely a passing reference to it.

I don’t know how Max Mueller and others came up with the date myself – but it would be an interesting story to research notwithstanding the current research. I would also highly recommend Razib’s podcast with Mallory which delves into the history of the larger indo european question.

 

Monkey see – Monkey Do ?

This is not a well-thought-out piece but a sort of rambling rant of thoughts in my mind for a year.  My previous writing on Covid is here and Ayurveda.

I have no medical/biology/medicine background nor am I am a scientist nor do I claim to understand statistics. Read this as some thoughts of a layman.

It’s been a year since India went hard into the lockdown. And after trying N things for over a year, we are back on the verge of lockdown in Maharashtra. (at least the CM keeps threatening a lockdown). Unlike initial predictions of respite from Covid in warm weather, it appears both Covid spikes in India have occurred in the considerably warmer weather while mysteriously getting low during the winter months. While I am yet to find a convincing argument that explains several strands associated with mechanisms of spread of Covid19, some aspects of the challenge, namely public reaction needs to be assessed as we get into the second year of the pandemic.

A question to ask here is – how different would the global reaction to covid19 have been without the world witnessing the Chinese state response in the first place? Did it act like a guess in an optimization algorithm – which eventually decides the outcome in some cases no matter it’s value? The European nations first chose to ignore and when they acted they acted in echoes of China. While totalitarian states like China or the gulf countries have been able to reign in the pandemic, no significantly sized country has. What would have been the Italian reaction had they First Guess been other than China? This is not to condone any herd immunity strategies – but at least in a country like India, the cost-benefit analysis needs to be done.

Additionally, should we ask if how much did lockdown work? Dr. Watve, a scientist based in Pune has some good blogs on the topic. While I am not convinced by Dr. Watve’s reasoning yet, its opposite doesn’t appear convincing too.

What else (if anything) could we have done differently? especially in India.  Critics of government often talk about the lack of testing as an issue in India. Personally, I feel once we get a critical mass of vectors, testing and tracing becomes merely a placebo exercise. Aping the WHO models on test, trace on Indian scale (at least with the resources we have).

Another thing that continues to bother me is the Fomite transmission theory. Going through the literature, I couldn’t find convincing research to believe it in the first place, let alone taking it to the insane level it was taken to – especially in India. Newspapers and milk delivery was turned off for months. Home deliveries of groceries were turned off initially. Shops were open only for small durations of the day. All these measures together meant that whatever essential services were available were often extremely crowded with people.  How much did these bizarre policies initially aid the transmission of covid?

I still remember vividly the most spectacularly stupid team meeting I have been part of. This meeting took place around 10-15 March 2020 to let the employees know that the company was doing everything they can to stop covid around the company premises (which was mostly a rain of sanitizers). In this meeting, the management called around 30-40 people in a closed room and talked without masks (that was early 2020, and even the scientists and WHO were maskophobic back then). Anthony Fauci who today, parades in “Rand Paul’s words” in two masks after getting two shots of vaccine, was saying a year back that masks are unnecessary (or even counterproductive). It’s perfectly acceptable for humans to make errors and correct those in the course of action – that’s something we should all try to do. But an analysis of what led us to make those mistakes in the first place ought to be done. Or was it just another example of the Sun revolves around the earth?

Local authorities (including society chairmen etc) have been on a different level of insane. After seeing city authorities sanitizing roads, pavements, trees, and even migrant laborers, whenever a patient is found in a building, the staircases, floors, and grounds continue to be sanitized. I am not even a novice on Bacterial evolution, but on my rudimentary understanding- this use of sanitizers scares the shit out of me. It is not that I am totally sure that fomites don’t spread covid, but the focus on fomites has also meant the possible aerosol spread was not focussed on. What’s worse, in my opinion – the focus on fomites and sanitization has lulled large swathes of people into the sense of false security. People wash their hands, sanitize groceries, but when talking to people often take down masks. Almost 95% of the cases I have heard have of contracting covid from a distant family member indoors or at some function. Yet people continue to focus on sanitization while attending public gatherings and religious ceremonies. At one point in my society, deliveries had to be collected at the society gate while members celebrated Diwali, New years, and Republic day inside without masks in large numbers. To this day, servants and handymen are treated with suspicions while friends and family (some of whom may have more exposure) arent. We have a separate lift for non-members – while members don’t mind traveling in lifts with unmasked members.

However, another question posed by this pandemic is, what should be the role of the state? and what should be its Aim?

  • Is the Aim to try and prevent every covid infection – at cost of the economy and livelihood?
  • Is the aim to avoid the overcrowding of medical facilities so as to avoid collateral damage?
  • Is the aim to keep pushing potential cases in the future – so as to reduce potential cases by vaccination?

When it comes to livelihoods, we need to separate two strands – the effect on the economy due to natural fear in people & and lockdown invoked economic downturn.

The mathematics of economic catastrophe is clear enough to follow – while the mechanism of spread seems to allude even the best of the minds. Every time someone comes up with reasons for why Covid stopped spreading rapidly around the end of 2020 in India and began afresh in 2021. The lockdown had ended in October and *new normal* activities had opened by November, but it appears this increased activity didn’t immediately accelerate the pandemic. Intuitively I would guess it takes time to gain a critical mass and a similar time for it to reduce. The momentum of the critical mass of vectors ought to carry on the spread (due to unavoidable contacts) in spite of overall contacts being low. Maybe once the first fuel was exhausted, it took time to gain a similar mass of vectors before it could truly explode. Add to this the new variants and reinfections (especially those who were asymptomatic the first time), then maybe the second wave starts making sense. Or maybe I am just pulling theories out of my ass which has no value – Either way I don’t mind as no one seems to have any deep insight into this.

All well-meaning people have been trying to shield the elderly for over a year. I have myself spent hours convincing older people to stay secure. But at what point does this become unbearable for a 75-year-old? Would it be wrong for an older person to be to think that they might not survive the pandemic (dying naturally amidst it) to live the end of the pandemic? Can they decide to take the risk of living a few months dangerously ahead of being condemned to a year in lockdown. (This equation has changed now with vaccines but the question still carries some weight I reckon)

Maybe this time next year we would have more answers than we have at this point. And hopefully, we would devise better strategies in countering such events in the future than acting like imitating monkeys in an experiment.

Ancient and Modern Medicine

My friend Dr Joishy is a very well respected physician (an oncologist by training, with a special interest in palliative medicine). He also comes from a family of Ayurvedic practitioners and a long time ago he wrote a small article about ancient medical systems and modern medicine. He shared it with me, I liked it, one thing led to another, and here is his note about that article (unfortunately not available in etext form, only as a scan, see link in the following note).. I hope to do a podcast with Dr Joishy one day by the way..

ANCIENT MEDICAL SYSTEMS VS. MODERN MEDICINE:

BOTH CAN THRIVE TOGETHER IN THE EAST OR THE WEST

 By Suresh K. Joishy, M.D., F.A.C.h.P.M.

                 My good neighbor Dr. Omar Ali and myself were having a mutually interesting conversation on ancient medical systems and modern medicine.  I had published a paper on this topic titled “Towards Ideal Medicine: What Can Traditional Medicine Teach Us?”   This paper can be accessed by copying and pasting the following link onto an internet browser:

https://drive.google.com/file/d/1zDhnS11SFkhEKUomFVpLuPY1n4wNhEyD/view?usp=sharing

After reading it, Dr. Ali suggested I submit it to “Brown Pundits” but we did not have an electronic copy. The scan is attached above.

My paper was written in 1981, when I was practicing Hematology and Oncology  in the U.S., after a research assignment in Malaysia.    Since I am a medical graduate from India, my grandfather was a physician in Ayurveda, and as I lived in several states of India, I was able to closely observe the ancient medical systems still in practice and thriving.

I am a practitioner of modern medicine.  I believe in science and evidence-based medicine.  Then why write about ancient medical systems?  My paper addressed this very question as to why Ayurveda, Unani and Traditional Chinese Medicine were thriving despite the success of modern medicine in curing infections with antibiotics and no limits to what a surgery can accomplish to repair, replace, or transplant organs.  I have described the science of modern medicine and compared it to Ayurveda,Unani  and Traditional Chinese Medicine (TCM).

Rather than dwell on the past again, here I will give my views on what has transpired since 1981,  after which I was teaching and conducting research abroad in Malaysia, Saudi Arabia, England, Japan, and New Zealand.  I also observed ancient medical systems were still thriving over there. Continue reading Ancient and Modern Medicine

Razib Khan corona-casting in the time of coronavirus

I recently talked about coronavirus with our old friend Kushal Mehra. I decided this is probably a time where I can post all the different coronavirus related podcasts I’ve done. I started on February 17th, on my podcast with Spencer Wells. You can see all the podcasts in rough order of date recorded…

It’s not live yet, but I’m going to have an episode on Two for Tea soon (it was recorded before the two below, so I put it here).

Browncast episode 88: Phillipe Lemoine, covid-19 “optimism”

Another BP Podcast is up. You can listen on LibsynAppleSpotify,  and Stitcher (and a variety of other platforms). Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe to one of the links above!

You can also support the podcast as a patron. The primary benefit now is that you get the podcasts considerably earlier than everyone else. This website isn’t about shaking the cup, but I have noticed that the number of patrons plateaued a long time ago. This month has been our biggest traffic month ever, and I think our corona-casts have been popular (patrons also get access to one that you can’t find on the public feed).

I would though appreciate more positive reviews! Alton Brown’s “Browncast” has 30 reviews on Stitcher alone! Help make us the biggest browncast! At least at some point.

This week I talked to Phillipe Lemoine about his blog post Are we headed toward an unprecedented public health disaster? A philosopher by training, Phillipe is now working as a data scientist, and he has been looking a the patterns of fatality in Europe for the past several weeks.

The Weather, South Asia, and coronavirus

I have a post where I analyze the idea that weather has an effect on the spread of coronavirus. One thing to note is that the best models focus on absolute humidity. This means that coastal Karachi is much better placed than inland Lahore, because Lahore often has low humidity. Mumbai shouldn’t be well suited for the spread of coronavirus at any time of the year (absolute humidity too high).

The major confound here: air conditioning. This creates a bubble of low absolute humidity, so coronavirus could spread very well in these environments. If you believe these results, one might want to turn off air conditioning in offices.

The Consequences of Coronavirus

A couple years back, I spent my down time playing a video game called Plague Inc. The game starts off with you playing as a bacteria, parasite, fungus, or of course as a virus. Your objective is to spread yourself across the globe infecting as many humans as possible, eventually leading to the culling of all of humanity. To win, you must silently evolve and spread, careful to not alert too many humans nor remain too isolated. On the way, you cause travel bans, mass hysteria, political clashes, etc… Sound familiar?

Screenshot of Plague Inc – A Popular Disease Simulator Game

Now, we are seeing an eerily recognizable reality to the fantasy of that game. Coronavirus-19 has become the modern plague of our times. And while it is no where near the level of Plague Inc’s apocalyptic end game, COVID-19 threatens to upend many of our society’s given structures and force the world down a new path.

Continue reading The Consequences of Coronavirus