Emergence of the 2009 Swine-Origin Influenza Pandemic
Paul Hoffman: Our next presenter is Michael Worobey. He’s an ecologist and an evolutionary biologist at the University of Arizona. He is part of a team of researchers that have a very important paper published just last month in “Nature,” about the evolution of the swine flu virus. And what he basically found was that it has circulated undetected in swine for perhaps up to a decade. Michael Worobey.
Michael Worobey: Thanks, Paul.
I’m going to talk about the emergence of the swine flu epidemic. But I thought first I put it in the bigger context of the emergence of influenza virus in general.
So here is the kind of tool that I used. It’s an evolutionary tree and all I want you to notice is for this H1 variant here, there is a nice human lineage, the Spanish flu is on that. There is a swine lineage, and there is a bird lineage. And these are the major players in the emergence of human influenza.
And most of the genes, as Peter [Palese] said, of this new variant come from pigs.
So here is a picture from the paper that we published. And just in case this doesn’t mean much to you, all these lines and dots, I want to take you through what we found here.
So coming from British Columbia, I’d like to use the saguaro as the teaching tool. I actually work in Arizona now, so it makes some sense.
With viruses, they evolve so quickly that you can actually see evolution happen, not just on the time frame of years, but in this instance, in the time frame of weeks. And this was a bit of surprise with just a few weeks of sequences that were produced as this pandemic was unfolding, we were able to calibrate the molecular clock.
So let me just use this analogy, if you want to find out how old your saguaro was, you might not be able to do it just by counting tree rings or something. But if you have a photo from 1999 of this cactus in your yard, and you were able to compare it to how much it has grown in the ten years since that time. You start to have a grasp on how quickly this thing grows. And you can make some estimates from the different branches of the percent of that centimeter per year of growth rate, and that can allow you to work back to when the thing originated.
So we do the same thing with viruses. If you have a small observation window like this, you can often make really robust differences about things much deeper in time. Okay now as an analogy, I just want to show you an evolution tree that you are more probably familiar with here. So we do the same sort of things for primates, and if you did an evolutionary tree of primates, you will have a human branch on the tree, or more closely related species, or chimpanzees and bonobos, and then you have the more distantly related species here.
And you can place the date on the most recent common ancestors of all humans and that might be around a hundred years ago. You could also ask, what’s the most recent common ancestor of humans? And whatever is most closely related to them, and that’s all the way back here, around 5 million years ago. So for this swine origin flu pandemic we did exactly the same thing.
So two questions: What is the timing on that ancestor of the virus once it jumped into humans? So when that jumped take place and if you go gene by gene and asked what’s the most closely related species for each gene? It’s actually a pig virus. So we also ask for each gene, when that broke off from the rest of the sample of pig viruses. Okay, so now we’re back to this, and what you see for each gene is the human sequences go less quite recently in time, but nowhere near the March and April  timeline that this thing first emerged, to our knowledge. And for each of the genes, the most closely related sequences are from pigs. Now Peter [Palese] mentioned that some of them ultimately are of avian origin, and some are human origin. What you see when you go gene by gene is that, even for the ones that are ultimately an avian or human origin, they traveled through pigs. And in each case, we find that there’s been a timeline of about 10 years where this virus has been in pigs but has gone totally unnoticed--which says something about our surveillance.
And for the human outbreak, what you see is a timeline of about somewhere around October to December of last year  that the virus was probably in humans. So it took several months to actually spread to the point where the tip of the iceberg became apparent to us.
And here is a rather complicated looking slide that shows while you have genes from an avian pool, and from a human pool, each one of those actually travel through a pig before it got into this new swine origin influenza virus.
One other interesting detail when you look gene by gene and Peter showed a nice picture of the individual segments. So these are actual physically separated chromosomes. You can actually place a date for each one of those as to when it got to humans. When you do that, and you line it up against the answer you get if you take all of the genes together, you get a little bit of a discrepancy. And this discrepancy, it turns out, you get an earlier date with each gene than you do with the entire genome. And we think what’s going on there is once this virus jumps into humans, it actually started evolving at a more rapid phase, and it looks like it goes at about 1.5 times the rate that it evolves in pigs.
And there is some interesting reason why that might be. If you take that into account, and do a little correction for the rate of change, these gene by gene estimates actually starts to overlap the entire genome estimate, and they kind of converge on this timeline of the late autumn, possibly into the very first few weeks of January  that this virus in humans is spreading.
So aside from the actual findings, I just want to spend a couple of moments talking about how this happens. So when the sequences first came out, they were published by places like NCBI [National Center for Biotechnology Information] and GISAID [Global Initiative on Sharing Avian Influenza Data]. And what was great about this situation was that information was made publicly available by pretty much all the parties in real time. So as soon as sequences are available, I started analyzing them, I started firing off emails to colleagues around the world who are doing the same sort of thing. And we set up a Wiki where we can all post our results and critic them, and people that are in competing groups worked together around the clock. We have some people n Arizona, people in the UK, people in Hong Kong.
So for a period of couple of weeks, we were working 16 hours a day and when you fell asleep, you knew that when you woke up in the morning, the research would be advanced another 8 hours, and pretty quickly came to grips with the timeline of this thing.
That kind of open access mentality flowed right through the publication in “Nature.” So “Nature” published this even though we’ve had some press coverage. They also made the paper open access so anyone can download it and look at it.
And I think it’s probably time to open up to the rest of the discussion and I’ll leave the rest of it for them. Thank you very much.
Recorded on: July 14, 2009.
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As bad as this sounds, a new essay suggests that we live in a surprisingly egalitarian age.
- A new essay depicts 700 years of economic inequality in Europe.
- The only stretch of time more egalitarian than today was the period between 1350 to approximately the year 1700.
- Data suggest that, without intervention, inequality does not decrease on its own.
Economic inequality is a constant topic. No matter the cycle — boom or bust — somebody is making a lot of money, and the question of fairness is never far behind.
A recently published essay in the Journal of Economic Literature by Professor Guido Alfani adds an intriguing perspective to the discussion by showing the evolution of income inequality in Europe over the last several hundred years. As it turns out, we currently live in a comparatively egalitarian epoch.
Seven centuries of economic history
Figure 8 from Guido Alfani, Journal of Economic Literature, 2021.
This graph shows the amount of wealth controlled by the top ten percent in certain parts of Europe over the last seven hundred years. Archival documentation similar to — and often of a similar quality as — modern economic data allows researchers to get a glimpse of what economic conditions were like centuries ago. Sources like property tax records and documents listing the rental value of homes can be used to determine how much a person's estate was worth. (While these methods leave out those without property, the data is not particularly distorted.)
The first part of the line, shown in black, represents work by Prof. Alfani and represents the average inequality level of the Sabaudian State in Northern Italy, The Florentine State, The Kingdom of Naples, and the Republic of Venice. The latter part, in gray, is based on the work of French economist Thomas Piketty and represents an average of inequality in France, the United Kingdom, and Sweden during that time period.
Despite the shift in location, the level of inequality and rate of increase are very similar between the two data sets.
Apocalyptic events cause decreases in inequality
Note that there are two substantial declines in inequality. Both are tied to truly apocalyptic events. The first is the Black Death, the common name for the bubonic plague pandemic in the 14th century, which killed off anywhere between 30 and 50 percent of Europe. The second, at the dawn of the 20th century, was the result of World War I and the many major events in its aftermath.
The 20th century as a whole was a time of tremendous economic change, and the periods not featuring major wars are notable for having large experiments in distributive economic policies, particularly in the countries Piketty considers.
The slight stall in the rise of inequality during the 17th century is the result of the Thirty Years' War, a terrible religious conflict that ravaged Europe and left eight million people dead, and of major plagues that affected South Europe. However, the recurrent outbreaks of the plague after the Black Death no longer had much effect on inequality. This was due to a number of factors, not the least of which was the adaptation of European institutions to handle pandemics without causing such a shift in wealth.
In 2010, the last year covered by the essay, inequality levels were similar to those of 1340, with 66 percent of the wealth of society being held by the top ten percent. Also, inequality levels were continuing to rise, and the trends have not ended since. As Prof. Alfani explained in an email to BigThink:
"During the decade preceding the Covid pandemic, economic inequality has shown a slow tendency towards further inequality growth. The Great Recession that began in 2008 possibly contributed to slow down inequality growth, especially in Europe, but it did not stop it. However, the expectation is that Covid-19 will tend to increase inequality and poverty. This, because it tends to create a relatively greater economic damage to those having unstable occupations, or who need physical strength to work (think of the effects of the so-called "long-Covid," which can prove physically invalidating for a long time). Additionally, and thankfully, Covid is not lethal enough to force major leveling dynamics upon society."
Can only disasters change inequality?
That is the subject of some debate. While inequality can occur in any economy, even one that doesn't grow all that much, some things appear to make it more likely to rise or fall.
Thomas Piketty suggested that the cause of changes in inequality levels is the difference in the rate of return on capital and the overall growth rate of the economy. Since the return on capital is typically higher than the overall growth rate, this means that those who have capital to invest tend to get richer faster than everybody else.
While this does explain a great deal of the graph after 1800, his model fails to explain why inequality fell after the Black Death. Indeed, since the plague destroyed human capital and left material goods alone, we would expect the ratio of wealth over income to increase and for inequality to rise. His model can provide explanations for the decline in inequality in the decades after the pandemic, however- it is possible that the abundance of capital could have lowered returns over a longer time span.
The catastrophe theory put forth by Walter Scheidel suggests that the only force strong enough to wrest economic power from those who have it is a world-shattering event like the Black Death, the fall of the Roman Empire, or World War I. While each event changed the world in a different way, they all had a tremendous leveling effect on society.
But not even this explains everything in the above graph. Pandemics subsequent to the Black Death had little effect on inequality, and inequality continued to fall for decades after World War II ended. Prof. Alfani suggests that we remember the importance of human agency through institutional change. He attributes much of the post-WWII decline in inequality to "the redistributive policies and the development of the welfare states from the 1950s to the early 1970s."
What does this mean for us now?
As Professor Alfani put it in his email:
"[H]istory does not necessarily teach us whether we should consider the current trend toward growth in economic inequality as an undesirable outcome or a problem per se (although I personally believe that there is some ground to argue for that). Nor does it teach us that high inequality is destiny. What it does teach us, is that if we do not act, we have no reason whatsoever to expect that inequality will, one day, decline on its own. History also offers abundant evidence that past trends in inequality have been deeply influenced by our collective decisions, as they shaped the institutional framework across time. So, it is really up to us to decide whether we want to live in a more, or a less unequal society."
Our love-hate relationship with browser tabs drives all of us crazy. There is a solution.
- A new study suggests that tabs can cause people to be flustered as they try to keep track of every website.
- The reason is that tabs are unable to properly organize information.
- The researchers are plugging a browser extension that aims to fix the problem.
A lot of ideas that people had about the internet in the 1990s have fallen by the wayside as technology and our usage patterns evolved. Long gone are things like GeoCities, BowieNet, and the belief that letting anybody post whatever they are thinking whenever they want is a fundamentally good idea with no societal repercussions.
While these ideas have been abandoned and the tools that made them possible often replaced by new and improved ones, not every outdated part of our internet experience is gone. A new study by a team at Carnegie Mellon makes the case that the use of tabs in a web browser is one of these outdated concepts that we would do well to get rid of.
How many tabs do you have open right now?
We didn't always have tabs. Introduced in the early 2000s, tabs are now included on all major web browsers, and most users have had access to them for a little over a decade. They've been pretty much the same since they came out, despite the ever changing nature of the internet. So, in this new study, researchers interviewed and surveyed 113 people on their use of — and feelings toward — the ubiquitous tabs.
Most people use tabs for the short-term storage of information, particularly if it's information that is needed again soon. Some keep tabs that they know they'll never get around to reading. Others used them as a sort of external memory bank. One participant described this action to the researchers:
"It's like a manifestation of everything that's on my mind right now. Or the things that should be on my mind right now... So right now, in this browser window, I have a web project that I'm working on. I don't have time to work on it right now, but I know I need to work on it. So it's sitting there reminding me that I need to work on it."
You suffer from tab overload
Unfortunately, trying to use tabs this way can cause a number of problems. A quarter of the interview subjects reported having caused a computer or browser to crash because they had too many tabs open. Others reported feeling flustered by having so many tabs open — a situation called "tab overload" — or feeling ashamed that they appeared disorganized by having so many tabs up at once. More than half of participants reported having problems like this at least two or three times a week.
However, people can become emotionally invested in the tabs. One participant explained, "[E]ven when I'm not using those tabs, I don't want to close them. Maybe it's because it took efforts [sic] to open those tabs and organize them in that way."
So, we have a tool that inefficiently saves web pages that we might visit again while simultaneously reducing our productivity, increasing our anxiety, and crashing our machines. And yet we feel oddly attached to them.
Either the system is crazy or we are.
Skeema: The anti-tab revolution
The researchers concluded that at least part of the problem is caused by tabs not being an ideal way of organizing the work we now do online. They propose a new model that better compartmentalizes tabs by task and subtask, reflects users' mental models, and helps manage the users' attention on what is important right now rather than what might be important later.
To that end, the team also created Skeema, an extension for Google Chrome, that treats tabs as tasks and offers a variety of ways to organize them. Users of an early version reported having fewer tabs and windows open at one time and were better able to manage the information they contained.
Tabs were an improvement over having multiple windows open at the same time, but they may have outlived their usefulness. While it might take a paradigm shift to fully replace the concept, the study suggests that taking a different approach to tabs might be worth trying.
And now, excuse me, while I close some of the 87 tabs I currently have open.
Inventions with revolutionary potential made by a mysterious aerospace engineer for the U.S. Navy come to light.
- U.S. Navy holds patents for enigmatic inventions by aerospace engineer Dr. Salvatore Pais.
- Pais came up with technology that can "engineer" reality, devising an ultrafast craft, a fusion reactor, and more.
- While mostly theoretical at this point, the inventions could transform energy, space, and military sectors.
The U.S. Navy controls patents for some futuristic and outlandish technologies, some of which, dubbed "the UFO patents," came to life recently. Of particular note are inventions by the somewhat mysterious Dr. Salvatore Cezar Pais, whose tech claims to be able to "engineer reality." His slate of highly-ambitious, borderline sci-fi designs meant for use by the U.S. government range from gravitational wave generators and compact fusion reactors to next-gen hybrid aerospace-underwater crafts with revolutionary propulsion systems, and beyond.
Of course, the existence of patents does not mean these technologies have actually been created, but there is evidence that some demonstrations of operability have been successfully carried out. As investigated and reported by The War Zone, a possible reason why some of the patents may have been taken on by the Navy is that the Chinese military may also be developing similar advanced gadgets.
Among Dr. Pais's patents are designs, approved in 2018, for an aerospace-underwater craft of incredible speed and maneuverability. This cone-shaped vehicle can potentially fly just as well anywhere it may be, whether air, water or space, without leaving any heat signatures. It can achieve this by creating a quantum vacuum around itself with a very dense polarized energy field. This vacuum would allow it to repel any molecule the craft comes in contact with, no matter the medium. Manipulating "quantum field fluctuations in the local vacuum energy state," would help reduce the craft's inertia. The polarized vacuum would dramatically decrease any elemental resistance and lead to "extreme speeds," claims the paper.
Not only that, if the vacuum-creating technology can be engineered, we'd also be able to "engineer the fabric of our reality at the most fundamental level," states the patent. This would lead to major advancements in aerospace propulsion and generating power. Not to mention other reality-changing outcomes that come to mind.
Among Pais's other patents are inventions that stem from similar thinking, outlining pieces of technology necessary to make his creations come to fruition. His paper presented in 2019, titled "Room Temperature Superconducting System for Use on a Hybrid Aerospace Undersea Craft," proposes a system that can achieve superconductivity at room temperatures. This would become "a highly disruptive technology, capable of a total paradigm change in Science and Technology," conveys Pais.
High frequency gravitational wave generator.
Credit: Dr. Salvatore Pais
Another invention devised by Pais is an electromagnetic field generator that could generate "an impenetrable defensive shield to sea and land as well as space-based military and civilian assets." This shield could protect from threats like anti-ship ballistic missiles, cruise missiles that evade radar, coronal mass ejections, military satellites, and even asteroids.
Dr. Pais's ideas center around the phenomenon he dubbed "The Pais Effect". He referred to it in his writings as the "controlled motion of electrically charged matter (from solid to plasma) via accelerated spin and/or accelerated vibration under rapid (yet smooth) acceleration-deceleration-acceleration transients." In less jargon-heavy terms, Pais claims to have figured out how to spin electromagnetic fields in order to contain a fusion reaction – an accomplishment that would lead to a tremendous change in power consumption and an abundance of energy.
According to his bio in a recently published paper on a new Plasma Compression Fusion Device, which could transform energy production, Dr. Pais is a mechanical and aerospace engineer working at the Naval Air Warfare Center Aircraft Division (NAWCAD), which is headquartered in Patuxent River, Maryland. Holding a Ph.D. from Case Western Reserve University in Cleveland, Ohio, Pais was a NASA Research Fellow and worked with Northrop Grumman Aerospace Systems. His current Department of Defense work involves his "advanced knowledge of theory, analysis, and modern experimental and computational methods in aerodynamics, along with an understanding of air-vehicle and missile design, especially in the domain of hypersonic power plant and vehicle design." He also has expert knowledge of electrooptics, emerging quantum technologies (laser power generation in particular), high-energy electromagnetic field generation, and the "breakthrough field of room temperature superconductivity, as related to advanced field propulsion."
Suffice it to say, with such a list of research credentials that would make Nikola Tesla proud, Dr. Pais seems well-positioned to carry out groundbreaking work.
A craft using an inertial mass reduction device.
Credit: Salvatore Pais
The patents won't necessarily lead to these technologies ever seeing the light of day. The research has its share of detractors and nonbelievers among other scientists, who think the amount of energy required for the fields described by Pais and his ideas on electromagnetic propulsions are well beyond the scope of current tech and are nearly impossible. Yet investigators at The War Zone found comments from Navy officials that indicate the inventions are being looked at seriously enough, and some tests are taking place.
If you'd like to read through Pais's patents yourself, check them out here.
Laser Augmented Turbojet Propulsion System
Credit: Dr. Salvatore Pais
Seek pleasure and avoid pain. Why make it more complicated?
- The Epicureans were some of the world's first materialists and argued that there is neither God, nor gods, nor spirits, but only atoms and the physical world.
- They believed that life was about finding pleasure and avoiding pain and that both were achieved by minimizing our desires for things.
- The Epicurean Four Step Remedy is advice on how we can face the world, achieve happiness, and not worry as much as we do.
Self-help books are consistently on the best-seller lists across the world. We can't seem to get enough of happiness advice, wellness gurus, and life coaches. But, as the Book of Ecclesiastes says, there is nothing new under the sun. The Ancient Greeks were into the self-help business millennia before the likes of Dale Carnegie and Mark Manson.
Four schools of ancient Greek philosophy
From the 3rd century BCE until the birth of Jesus, Greek philosophy was locked into an ideological war. Four rival schools emerged, each proclaiming loudly that they — alone — had the secret to a happy and fulfilled life. These schools were: Stoicism, Cynicism, Skepticism, and Epicureanism. Each had their advocates and even had a kind of PR battle to get people to sign up to their side. They were trying to sell happiness.
Epicurus's guide to living is noticeably different from a lot of modern self-help books in just how little day-to-day advice it gives.
Many of us are familiar with Stoicism, a topic I covered recently, because it forms the foundation of cognitive behavioral therapy. Skepticism and Cynicism have become watered down or warped variations of their original forms. (I will cover these in future articles.) Today, we focus on the most underappreciated of these schools, the Epicureans. In their philosophy, we can find a surprisingly modern and easy-to-follow "Four Part Remedy" to life.
Epicureans: The first atheists
The Epicureans were some of history's first materialists. They believed that the world was made up only of atoms (and void), and that everything is simply a particular composition of these atoms. There were no gods, spirits, or souls (or, at most, they're irrelevant to the world as we encounter it). They thought that there was no afterlife or immortality to be had, either. Death is just a relocation of atoms. This atheism and materialism was what the Christian Church would later come to despise, and after centuries of being villainized by priests, popes, and church doctrine, the Epicureans fell out of fashion.
In the atomistic, worldly philosophy of the Epicureans, all there is to life is to get as much pleasure as you can and avoid pain. This isn't to become some rampant hedonist, staggering from opium dens to brothels, but concerns the higher pleasures of the mind.
Epicurus, himself, believed that pleasure was defined as the satisfying of a desire, such as when we drink a glass of water when we're really thirsty. But, he also argued that desires themselves were painful since they, by definition, meant longing and anguish. Thirst is a desire, and we don't like being thirsty. True contentment, then, could not come from creating and indulging pointless wants but must instead come from minimizing desire altogether. What would be the point of setting ourselves new targets? These are just new desires that we must make efforts to satisfy. Thus, minimizing pain meant minimizing desires, and the bare minimum desires were those required to live.
The Four Part Remedy
Given that Epicureans were determined to maximize pleasure and minimize pain, they developed a series of rituals and routines designed to help. One of the best known (not least because we've lost so much written by the Epicureans) was the so-called "Four Part Remedy." These were four principles they believed we ought to accept so that we might find solace and be rid of existential and spiritual pain:
1. Don't fear God. Remember, everything is just atoms. You won't go to hell, and you won't go to heaven. The "afterlife" will be nothingness, in just the same way as when you had no awareness whatsoever of the dinosaurs or Cleopatra. There was simply nothing before you existed, and death is a great expanse of the same timeless, painless void.
2. Don't worry about death. This is a natural corollary of Step 1. With no body, there is no pain. In death, we lose all of our desires and, along with them, suffering and discontent. It's striking how similar in tone this sounds to a lot of Eastern, especially Buddhist, philosophy at the time.
3. What is good is easy to get. Pleasure comes in satisfying desires, specifically the basic, biological desires required to keep us alive. Anything more complicated than this, or harder to achieve, just creates pain. There's water to be drunk, food to be eaten, and beds to sleep in. That's all you need.
4. What is terrible is easy to endure. Even if it is difficult to satisfy the basic necessities, remember that pain is short-lived. We're rarely hungry for long, and sicknesses most often will be cured easily enough (and this was written 2300 years before antibiotics). All other pains often can be mitigated by pleasures to be had. If basic biological necessities can't be met, then you die — but we already established there is nothing to fear from death.
Epicurus's guide to living is noticeably different from a lot of modern self-help books in just how little day-to-day advice it gives. It doesn't tell us "the five things you need to do before breakfast" or "visit these ten places, and you'll never be sad again." Just like it's rival school of Stoicism, Epicureanism is all about a psychological shift of some kind.
Namely, that psychological shift is about recognizing that life doesn't need to be as complicated as we make it. At the end of the day, we're just animals with basic needs. We have the tools necessary to satisfy our desires, but when we don't, we have huge reservoirs of strength and resilience capable of enduring it all. Failing that, we still have nothing to fear because there is nothing to fear about death. When we're alive, death is nowhere near; when we're dead, we won't care.
Practical, modern, and straightforward, Epicurus offers a valuable insight to life. It's existential comfort for the materialists and atheists. It's happiness in four lines.