Jupiter and Jenner: Real Science Controversy and Vaccination.

“Scientific controversy,” as we often hear of it, is neither real controversy nor scientific. Usually it is a squabble within and among laypersons ultimately based in ignorance and emotional bias.  In the scientific community, on the other hand, such issues either have been decisively settled or never were an issue to begin with. As a person doing research in a field that actually does have scientific controversy, I see the difference. Actually, I have seen the difference for a long time. And I am losing more and more patience each passing year with the notion that our society should coddle people who’s opinions and stances that are not based on mainstream scientific findings when these people are unable to contribute to the development of the knowledge.

Caveats here: Note I said those unable to contribute to the development of the knowledge. What I mean here are folks that have no expertise in the mainstream science expressing their contrarian opinions and even advocacy against the mainstream scientific findings.

Another caveat: Coming up with alternative views and explanations are actually useful. Some may call this conspiracy theories and indeed may ultimately arise from a distrust of whatever institutions are involved – religion, media, government, paid scientists. However, it is the idea that matters. Ideas are the first step towards scientific revelation. But you know what? Most ideas, hypotheses, in the proper vernacular, turn out to be wrong. Hypotheses are like anuses, everyone has one.

What makes an individual embarking on actual science is going beyond the hypothesis and into observation, experimentation, and ruthless, cold, testing of the idea. Also, a person needs to understand a lot of the field in which they are proposing or supporting an idea – contrarian or otherwise. Now, to be clear, it doesn’t mean you have to be PhD in some scientific area but the expertise to use the scientific method for activities beyond most everyday use (such as diagnosing a car engine failure), takes a lot of education and hands on work. Why? Simple.

We have learned a lot in the few thousand years of civilization. And every bit of that knowledge came with a price of either lives, money, or time. Sometimes all three. It takes a while to bring a curious individual up to the state of knowledge in a particular field. It also takes hands on work to train a person to act and think like a scientific and time to learn the particulars of a given field of inquiry.

The “University of Google” can only get you so far. Having the ability to read journal articles in a given field can only get you so far. It really also takes knowing the community of a field of inquiry as well. Let me explain a real scientific controversy and link it to my own experience at this stage of my dissertation.


This is Jupiter:


Take a good hard look at it. You are positioned thousands of kilometers above the equator. You probably first notice the alternating bands of brown and white. Next you probably see a number of spots including the reddish-brown Great Red Spot in the low latitudes of the southern hemisphere.

People have first noticed these bands since Galileo first pointed a telescope at Jupiter in 1610. Professional and amateur astronomers have been fascinated and puzzled by these cloud formations for centuries. Meteorologists have likewise been interested in these. Why? Jupiter (and the other gas giant planets) are an example of fluid flow and meteorology that we simply have no direct experience on Earth. We live on one planet that is very different. In some ways, our weather is more complicated and we have come a far way in understanding it. But fundamental questions remain unanswered. Between these bands of brown and white are jet streams. These are relatively narrow streams of fluid (liquids, gases, plasma are all fluids) that move at a relatively high speed. We have them on earth and everyday you hear weathermen discuss the position on the jet stream and how that brings us our weather here in the mid-latitudes.

Our jets on Earth meander, split, have high speed regions within them, called jet streaks, and are guided manly by mountain ranges, oceans, and ultimately by temperature contrasts on the surface. Jupiter has no solid surface that is influencing its jets. Any solid surface that does exist is small and lies tens of thousands of kilometers below what is essentially a bottomless atmosphere. Likely the core is also in a fluid state of molten metal, rock, and liquid metallic hydrogen. The upper atmosphere grows increasingly dense, like any atmosphere, until we start to see hazes. These hazes are in the stratosphere and upper troposphere. In the troposphere we have clouds. A whole planet covered in them. The visible cloud deck are mostly ammonia ice clouds and some other compounds. Beneath them are a deck of water clouds down at a pressure ten times our own surface pressure here on earth. Beneath them, the pressure increases until the border between a gas and a liquid no longer have a distinction. The atmosphere becomes more dense and with greater pressure than our deepest spot in our ocean but still flows like a gas. Eventually, at millions of pounds per square inch, the hydrogen forms a strange liquid like form but otherwise has the properties of a metal. For most of the depth of the planet, we have a deep bottomless fluid. No mountains, no major temperature contrasts, no continents, no oceans.  This is an idea place to study fluid motions that we cannot study on Earth!  A natural laboratory.

On Jupiter, the jets are straight, nearly uniform speed, and have remained like that for decades and maybe even millions or billions of years. Some flow east and some flow west. They are stable in that they don’t meander (Saturn has a few that do but nothing like what ours do on Earth), and they violate many known stability theorems governing fluid flow. Almost every theory about the stability of fluid flow when it comes to jet streams comes unglued when applied to Jupiter and Saturn, with the exception of maybe one.


But one of the major controversies is the origin of these jet streams. When the Pioneer and Voyager spacecraft flew by in the 70’s, detailed images were taken as well as radio probing of the atmosphere. We learned a lot about the position, speed, and remarkable stability of these jet streams. What we didn’t learn is their origin.

Are these jets are manifestation of processes going on deep down, far below the visible cloud deck? Or are they ultimately near “surface” phenomena? To this date, there are these two schools of thought. Both of these schools have evidence that both supports their ideas as well as refutes them. In other words, no one really knows. The Deep School and the Shallow School (my terminology) are hoping to unravel this mystery. Both are actively publishing and both are explaining various observations well but also failing quite a bit in others. I’m not going into detail except to say that neither has figured it out and both keep plugging away at it and each other as well as within their own Schools.

This is an example of everyone has a hypothesis. And these hypotheses have condensed into two main schools of thought. But where the venture beyond a curious idea and shrug of the shoulders is what is needed next. Both schools know that we need more observations (the Juno spacecraft on the way to Jupiter may help give us more hints) and more numerical simulation including the development of new atmospheric models that can join the physics of the deep with those of the shallow regions.  Both have a good idea of what to do and where to go next and generally, even if opinionated at times, are in the same boat in that everyone wants to answer this question.  It is a friendly debate compared to many issues that we experience outside the scientific community.

I can tell you from less than a year of working with “an older code but it checks out” (thank you, I did go for the Star Wars reference here), this is hard ass work. And I’m not even going to venture into a dissertation trying to unite these schools of thought with a new computer simulation code. I was told that is something that will likely take a group of tenured professors with a lot of grant money some years to develop.

Understanding how the weather works on Jupiter and the other gas giant planets brings us closer to understanding weather, period. Weather and fluid flow anywhere in the Cosmos from Earth to the exotic Exoplanets we have discovered can be understood the more we understand weather on Earth, Venus, Mars, and the Gas Giants. We may also even unravel one of the greatest mysteries that still remain from classical physics – turbulence, that chaotic motion of fluids that can only really be understood and predicted from a statistical viewpoint.

Oceans and atmospheres are very similar and both are governed by a complex system of equations, called the Navier-Stokes equations (N-S).


They look complicated and even from someone that is educated enough in this field to explain them, they are complicated. As a matter of fact, you cannot, in general, solve these by hand. It isn’t that they are too complex to solve by hand, it is just no “closed form analytical solution” exists! We don’t have the math and maybe it doesn’t even exist. To add insult to injury, they are “non-linear” which means that the solutions get really funky even when the numbers aren’t that big. Waves like you might see when you drop a stone in a pond are easily predictable when the water is deep. They get ugly fast when those waves lap the shore line! Also you can’t just add up a bunch of simple linear solutions and get the total complete solution. That trick, called “superposition” often used in other areas of math and physics cannot work with the full N-S equations. Only in special simple cases sometimes found in engineering needs can we actually solve these. And those are so few and far between, they have become classic case studies. I even gave some of those classic cases to my students to solve just like I had to do. Many of the terms simply drop out.

So how do we solve them? Answer: Numerical methods. Computers and coding. Now you know why math and computer coding is so critical in the physical sciences. But even that isn’t enough. This guy, Lewis Richardson first tried it in 1920.


He had a bunch of weather stations take measurements and he set out to make a weather “forecast” six hours in the future for a few locations in Europe. This was before the days of computers so it took him six weeks to do it. When he compared his results to the actual six hour weather observations, they were an abject failure. There were several reasons but mostly it dealt with solving the correct physics along with some unknowns that come about when solving physics in a numerical analytical approach.  Some new discoveries were made in numerical approximation math as well as in weather.

See, with equations as complex as the N-S, you have to simplify them even when using a modern powerful computer. These equations solve for all kinds of fluid motions including sound waves that travel really fast and have no influence on the weather. Things that we really want to know, like how jet streams move and form and how wave like motion that is thousands of kilometers long and takes days to move around a planet are also found from solving these equations. We have to find a way to manipulate these equations to solve for what we want so we can ignore what isn’t important. If we do that right, we can drop out some things and get a simple set, called the Shallow Water equations and from that we can further simply things to what is called the Quasi-geostrophic Potential Vorticity Equation. One equation is much easier to solve and from that solution we can then get our fluid speed and position and all those good things we need to understand and forecast the weather.

But it is a simplified set of equations and does a decent job at a number of things of interest. But not everything. Like my code I’ m working with, I cannot model thunderstorms directly. I cannot model the bubbling, percolating nature of the fluid thousands of kilometers down in Jupiter’s guts. I can only model the shallower stuff.

I cannot fuse the link between the Deep and Shallow Schools with this code. I know my limitations of my tools and my knowledge of the physics. More critically, I am learning what the limits are in the scientific community. I’m learning where the gaps are and what we know, what we have a pretty good idea of what we know, and where we are really fuzzy. I even know many of the players, by their publications, and how some are professing to know things but they haven’t yet convinced their colleagues. In other words, I’m learning the “tribal nature” of this community. I’m working my way to being able to contribute to advancing the state of knowledge in this field and some closely related fields.

—————————————- RESUME HERE: ————————————————————

That being said, becoming an expert on atmospheric simulation and fluid flow or a current expert on certain facets of the engineering world doesn’t make me an expert in accounting, economics, or medicine. Here I have to rely much more on the knowledge from those that are experts in those fields. I also know that their prevailing thoughts may turn out to be wrong. A mainstream view at any time may turn out to be wrong. Science is filled with these. However, what makes me have a measure of trust in those that are the experts is that it is almost always experts in that same field, whether in the near future, or decades later that find the actual right answers. I also know that in some critical issues facing our society, the data may be hidden, twisted, laden with vested interests, or otherwise unavailable and then values-based factors come into play. I also know that my chances of making a smart decision are those that have largely “proved” their case with the most relentless process available – science. And I also know, I may be dead wrong on supporting the mainstream viewpoint. But I’m willing to accept that risk. Here I’m going to be talking of mainstream views.

I dive into one of my pet peeves of the science-based world. Vaccination. I’m not a doctor. I haven’t practiced medicine nor play a doctor on TV or the internets. But, I have been able to do more than just attend the “University of Google” to learn about it. I understand the peer review process and have been involved with it. Mostly with rejection! LOL. I know that certain sources are more likely to be correct because they go through a detailed process of review that although not foolproof, is more likely to uncover mistakes. But this is a human endeavour and not perfect. Mistakes will be made but I can bet you my paycheck that a mistake is likely to be uncovered and corrected by a fellow expert employing the scientific method rather than a talking head. Rush Limbaugh or John Stewart isn’t going to discover a super secret goof by the CDC or WHO (World Health Organization). Oh, they will report on it, lampoon those involved, and rail against a particular vest interest…but they will not be the discoverer.

Neither will you or I (unless you, the reader, are an expert in medicine in this field). We have to rely, however uncomfortably, on someone else that has a stance different than our suspicion, assuming we have a different stance at all. And trust in any institution these days seems to be waning. This is understandable. I do think this is one of the main reasons why why we have so much anti-science nonsense spewing around. The other reasons are the internet has made for effective (loosely using the word) echo-chambers and some interesting findings about human psychology as it related to political affiliation.

This echo chamber effect is rather sad. I wonder when the internet was first being declassified if anyone thought that there would be a dumbing-down effect? We have a lot of knowledge at our finger tips but we have seen a tremendous and baffling combination of science denialism coupled with an intense interest in science simultaneously!

Sometimes the “discussion,” putting it mildly, has to do with how vaccines were incorrectly purported to cause autism, a hypotheses that was rejected almost as soon as it appeared in the now retracted 1998 study of a dozen kids that started that whole mess. It has been rejected over and over and over again with ever increasing larger sample sizes. As one autism expert stated, we don’t yet know what causes it but we know some things that don’t and vaccines including the various ingredients used most certainly do not.

Just because I can’t tell you what doesn’t cause something should not make you think we have no decent leads. I don’t know what causes both the number and direction of all the jets on Jupiter, but I can assure you it isn’t vaccines, aliens, or solar burps on a Tuesday. I do know it has a lot to do with the planetary rotational speed, deep fluid atmosphere, weak temperature gradient in latitude, Rhines length scale, Rossby deformation radius, and a bunch of other things. And, in the medical field, I can look up what the prevailing medical opinions are even if that takes some time and actually talking to medical experts. It isn’t hidden knowledge and it isn’t kept away from the unwashed masses.

Another closely related argument somewhere out in the “batshit crazy regime”, is that vaccines don’t work or are generally harmful. Ok. Then explain how we conquered this:


This is a child from 1973 with smallpox. A disease, untreated, with a 30% mortality rate. Survivors often were scarred for life or blinded. How was this stopped? Vaccination. Forceful at times and places; completely necessary to destroy this scourge. It has one reservoir: humans. This horrific disease had the possibility only once dreamed of by millions of victims of being eradicated. And the cleverness of man found a way. And in the last of the countries left where it was endemic, it probably was viewed as “controversial” to forcefully eliminate it by vaccination. But it was done and the last wild case of smallpox was in 1978 or 1979. The killer exists now only in controlled labs (and hopefully will stay put there).

Sometimes the argument is the number of vaccines or schedule of shots. Again, this is a cop out because now we have the “vaccines aren’t bad but the rate or schedule is.” Ok, so now the argument sounds a lot less batshit crazy. However, what makes the layperson think they know better than the medical community about the schedule or number of vaccines? Maybe the schedule of vaccination or number is still a problem after all. But who is going to discover if that is true? Jenny McCarthy? Nope. It will be a doctor or someone in a very closely related field.

Also, there is the whole ignorance of risk involved. Yes, I know when it is a loved one, emotion overcomes math. “My loved one or my baby is the most important thing. If there is one chance in 100,000, I’m not subjecting my baby to that risk” (of some vaccination related harm). Ok. Well guess what? Public health considerations for a functional society cannot be guided by that level of emotional bias. Furthermore, do the math.

Before the discovery of inoculation by Jenner (and maybe others unknown previously) came along, huge fractions of people worldwide came down with smallpox and it killed hundreds of millions before the 20th century. Most of the population of North and South America died from smallpox and other diseases in which there was no natural immunity in those populations.

The stuff we vaccinate against these days are typically far worse killers such as measles, rubella, and mumps. But these are nasty, dangerous, and are lethal albeit less so than smallpox. In the 1860s, thousands of soldiers, mostly country boys joining the army with many urban recruits died of these diseases. In those days, that was the way it was. Diseases killed twice as many solders as battle wounds. There was no preventive vaccinates available. If you lived, great. If you died, that was how it was.

Then we learned how to prevent them and another scourge our parents remember: Polio. You know, this thing:


Again, it is a risk management thing. Even in the face of doubt about the safety or effectiveness of vaccines, it is a mere (although perhaps difficult in the face of doubt and peer pressure) question of which evil do you wish to worry about occurring. The disease or the possible vaccine side effect (assuming this is even a serious risk)? Most of the industrialized west has gone with the idea of taking out the disease and accepting a small risk of the latter.

I wonder just how many more facets of our knowledge will be challenged, foolishly, because we are victim of our own success. Few people of my age (early 40s) in the United States remembers anything more than a case of a fever with a childhood disease like measles or chickenpox. I never knew a classmate that died of measles or crippled from polio. Smallpox? What was that? It was nothing more than a strange looking inoculation scar on my mother’s left arm and some scary looking bad drawings or black and white photos in an encyclopedia.

Somehow the norm of vaccinating kids became challenged from after the time I was entering elementary school in the mid 1970’s and much later became a rallying point for a libertarian cause – individual rights…possibly at the expense of the well being of an entire community. This is the bane of the public health sector and indeed a basic question of the role of both individuals’ responsibility as well as the role and responsibility of The State. Who decides?

48 states have exceptions for religious reasons against vaccination. However, recently a low court said challenged this in a limited region (New York Public Schools). Here is one link to the story:


I wonder if this will hold up in higher courts. It will be an interesting example of how the courts decide between the ever-present battle between an individual’s right (presumably to do bad risk assessment) and The State’s right and role to protect all its citizens. But more importantly, it may be more interesting to see how science’s hard earned victories against ignorance and microbes play out in the years to come. Until then, enjoy some photos of how microbes don’t give a damn about coddling your feelings or your precious baby’s bodies. You want to be pissed at me for being snotty in this blog, fine. Be pissed. I’d rather be pissed and wanting to do the proven best thing to fight the little microbe bastards that do this:




Categories: lessons for life from science., politics

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