Yearly Archives: 2013

MERS-CoV, The Haj, and the remote chance of a killer global pandemic

It seems to me that the science of epidemiology is a lot like being in shoe sales in a country on the pacific rim. You never know when the other shoe is going to drop, but you know it will. Our species (humans) is numerous, contiguous, and dense (in more ways than one). This means that a highly virulent pathogen could spread across the globe and kill a gazillion people before we could do anything to stop it. Yet, such a thing has not happened in modern times, meaning, since the widespread and easy flux of population provided by the airline industry at several scales of space.

At the present time we (humans) are faced with yet another threat of pandemic disease, this time from the coronavirus MERS-CoV. Spoiler: It is very unlikely that MERS-CoV is going to be a major pandemic because it does not seem to be all that virulent, in the sense that it does not seem to spread easily from one person to another. When it shows up in a population, it does not seem to spread around quickly. On the other hand, it is human-spreadable, similar coronaviruses are virulent so maybe this one could evolve to be so, and the mortality rate is so far an alarming ~50%. And, there is another complication. MERS-CoV is very likely to be carried from its homeland in the Middle East to several other countries by the mass movement of pilgrims returning from The Haj.

A recent study in PLoS Currents Outbreaks (yes, that’s a clumsy phrase, not a typo) looks at the situation. Researchers use reasonably good (but limited) data on air travel to estimate the number of people who will return-travel form the major Middle Eastern pilgrimage sites between June and November. They look at relative rates of return-travel to each area, and at health care expenditures per capita as a way of estimating the ability to address an influx of deadly disease-carrying return visitors, in each country.

16.8 million travelers on commercial flights departed Saudi Arabia, Jordan, Qatar and UAE for an international destination between June and November 2012. 7.5% had final destinations in countries that were low income, 47.4% lower-middle income, 17.3% upper-middle income and 27.8% high income. 51.6% had final destinations in just eight countries: India (16.3%), Egypt (10.4%), Pakistan (7.8%), the United Kingdom (4.3%), Kuwait (3.6%), Bangladesh (3.1%), Iran (3.1%) and Bahrain (2.9%; see Table). Individual cities with the highest travel volumes include Cairo, Kuwait City, London, Bahrain, Beirut, Mumbai, Dhaka, Karachi, Manila, Kozhikode, Istanbul and Jakarta, each of which received more than 350,000 commercial air travelers from MERS-CoV source countries between June and November 2012. Furthermore, an estimated 8.7% of foreign Hajj pilgrims in 2012 originated from countries that were low income, 56.4% lower-middle income, 27.3% upper-middle income, and 7.6% high income. 60.7% of foreign pilgrims originated from just eight countries – Indonesia (12.4%), India (10.1%), Pakistan (9.9%), Turkey (7.8%), Iran (6.5%), Nigeria (5.7%), Egypt (5.5%) and Bangladesh (2.9%). A bubble plot depicting the volume of international travelers departing Saudi Arabia, Jordan, Qatar and UAE from June to November 2012, the estimated number of foreign pilgrims performing the Hajj in 2012 and estimated healthcare expenditures per capita in 2011 is shown in Figure 1.

Fig. 1: Country-Level Destinations of Air Travelers Departing MERS-CoV Source Countries*, Origins of Hajj Pilgrims†, and Healthcare Expenditures per Capita‡ * Final Destinations of Air Travelers Departing Saudi Arabia, Jordan, Qatar and the United Arab Emirates via Commercial Flights between June and November 2012† Estimated for 2012 ‡ Sizes of the circles are proportionate with healthcare expenditures per capita as estimated by the World Bank, 2011
Fig. 1: Country-Level Destinations of Air Travelers Departing MERS-CoV Source Countries*, Origins of Hajj Pilgrims†, and Healthcare Expenditures per Capita‡
* Final Destinations of Air Travelers Departing Saudi Arabia, Jordan, Qatar and the United Arab Emirates via Commercial Flights between June and November 2012† Estimated for 2012 ‡ Sizes of the circles are proportionate with healthcare expenditures per capita as estimated by the World Bank, 2011

The researchers note that MRS-CoV has the potential of being a pandemic disease, and that understating population movements that could underly its spread is essential. The key points here seems to be that there is an intersection between countries that have a lot of pilgrims returning from MERS-CoV source areas and a low probability of detecting and containing cases of international spread because of inadequate health care systems. Related to this, they also identify possible blind spots in the global health care industry. For example:

The four countries with confirmed cases in returning travelers…the United Kingdom, France, Italy and Tunisia…account for an estimated 7.1% of the final destinations of all international travelers departing the MERS-CoV source countries since September 2012 (each of which are high or upper-middle income countries). By comparison, India, Pakistan and Bangladesh represent the final destinations of an estimated 27.7% of all international travelers over the same time period (each of which are low or lower-middle income countries), but have not reported cases of MERS-Co. Although not definitive, these findings could indicate the presence of epidemiological “blind spots” to MERS-CoV as a result of limited infectious disease diagnostic and surveillance capacity.

So, we’ll see how this goes.

Above I note that despite the obvious risk of a global pandemic of something spreading across the human population there really hasn’t been one, but I think this should be put in context. We have had widespread and multi-layered (in terms of economic and other strata) air flight for less than fifty years, but that air travel has probably not penetrated all regions of the world until the last 25 years or so. Pandemics with really large death tolls, however, are very rare. The HIV/AIDS pandemic is a slower moving but very deadly one, and is the largest in modern times, and it started in 1981 and was certainly facilitated by the ability of humans to travel. The previous large pandemics that could possibly have been facilitated by air traffic in a major way were two flue pandemics, in 1968 and 1957, each very small compared to HIV/AIDS but effective at a much higher temporal rate. The previous pandemics that were very large, but prior to major air travel effects, most likely spread internationally with boat traffic, were the famous 1918 flu pandemic and the less famous 1889 flu pandemic, and a handful of near-million death level cholera pandemics, in 1899, 1881, and the 1850s.

So, during the 163 years from 1850, worldwide pandemics that killed 6 figures and above happened about 8 times. That’s about every 20 years. So, when we look back at the history of air travel, which has allowed the ready movement of large numbers of people across a wide range of social and economic categories living in most populated areas, we should not be surprised at the number of pandemics. It is hard to put a year on when humans became as internationally mobile as they are today, but the east-west divide was a major factor dampening movement until the 1990s. One could say that the current highly mobile situation dates to about 1990, and is thus, just over 20 years long. In other words, the rough time scale of the emergence of diseases with the ability to spread widely and quickly, using cholera and flu as a proxy for “disease” is once every 20 years, and the situation in which the Giant Killer Pandemic in which human population is measurably reduced because of a disease we can’t control for several years could occur is recent. I quickly add that Cholera is a lousy proxy for such disease because it is readily treated these days and its initiation and spread is only partly related to human movements. It may well be that the frequency of the evolution of a spreadable pandemic disease is much longer than 20 years.

There are shoes. They can drop. They seem to drop slowly, infrequently, but as time has passed over the last few decades the potential severity of such an event has clearly gone up in some ways while our ability to control disease through treatment and vaccination has probably stabilized or even gone down.

MERS-CoV is probably not the next pandemic. But the idea of there being such a pandemic, and even a pandemic with previously not seen qualities because of our denser than ever, larger than ever, and more connected than ever population is nothing to sneeze at.


Khan, Kamran, Jennifer Sears, Vivian Wei Hu, John S Brownstein, Simon Hay, David Kossowsky, Rose Eckhardt, Tina Chim, Isha Berry, Isaac Bogoch, Martin Cetron. 2013. Potential for the International Spread of Middle East Respiratory Syndrome in Association with Mass Gatherings in Saudi Arabia. PLoS Curents Outbreaks. July 17, 2013. Full Text here.

Reproductive Rights: FtBConcience On Line Conference Session

This was one of the many great panels at FtBConscience, this panel hosted by Miri of Brute Reason and organized by Biodork.

A panel of reproductive rights activists come together to discuss access to abortion in current events , clinic escorting and some common religious and non-religious arguments against abortion. Our panel consists of clinic escorts – including one panelist who volunteered before FACE laws went into effect (Freedom of Access to Clinic Entrances), health care professionals, an author and several bloggers who write about reproductive rights. Our panelists hail from Minnesota, Kentucky, Virginia and Ireland.


Photo Credit: Morten Watkins via Compfight cc

Thinking Rationally about Climate Change: FTBConscience Conference Session

Climate Scientist John Abraham and I just finished a session of FtBConscience on Climate Change and during that session we promised to provide some useful links. We also used some graphics during the session. Below are the links and the graphics!

First, here is the video of the session:

Climate Change Science Twitter List

I created a twitter list of people (or organizations) that tweet about current climate change science. If you check this list at any given moment you’ll know the latest climate science news. If you have a suggestion as to who should be added to this list, send me a tweet!

The list is: Climate Change Science

Climate Consensus The 97%

John Abraham and Dana Nucitelli’s blog at the Guardian, mentioned during the session, is HERE. John mentioned his post “Global warming and economists-SuperFreakonomics is SuperFreakingWrong.

A gazillion posts on Climate Change

I’ve written a few hundred posts on Climate Change over they years on this blog, which are HERE.

I have a question about climate change …

If you have a question about climate change, one of the best places to find out a good answer is the web site Skeptical Science. John mentioned this during our session. Pretty much any question you’ll ever hear from anyone about climate change is addressed here, often at multiple levels.

Arctic Sea Ice melt interactive graphics

The really cool interactive graphic we used during the session, showing arctic sea ice melt (surface area) over several years, is HERE. I also talked about this graphic in a blog post HERE.

Other climate change links of interest (please add your favorite non-denialist sites in the comments section below if you like!)

There are a lot of sites, here is just a sampling.

Climate Change Graphics

I have a category for climate change graphics here and Skeptical Science has a page of graphics here. These are both science based graphs and memes (which are also science based as well, of course, but in the form of something you can put on your Facebook Page!) The graphics we used during the session are here:

Nuccitelli_OHC_Data

bau_future_warming

We also showed the jet stream and orital geometry driven delta–18 cycles but those were randomly drawn from the internet and not vetted so I’m not going to include them. To get a jet stream graphic, just google “jet stream” but also, check out this post on the nature of the jet stream and weather: Why are we having such bad weather? which also has a video with Jennifer Francis, mentioned during our session.

Revision


I want to revise/modify something I said during the session. I referred to the fact that we have yearly data over the last several hundred thousands of years. Most of the data that we use that goes back over long periods of time averages many decades or centuries, or is look at at 1,000 year intervals. Even if we had annual data for every year, we’d probably average it out over centuries of time anyway. What I was referring to, however, is the fact that for many time blocks over this period we have segments of data that can be looked at on a year by year basis, or often, on a quasi seasonal basis with a nearly year-long signal and a smaller winter or spring signal (depending on the data source). This includes lake varves and tree rings as well as other data sources.

I have other questions about global warming!?!!?

If you have other questions, just put them in the comments below.

Reproductive Success and Fitness are not the same thing

Reproductive Success (RS) is defined in many ways in different places by different people, but one of the most common definitions is simply the number of offspring an individual produces. This definition is further modified in most cases to mean only those individuals that will be fertile, i.e., capable of producing further offspring. RS is important in understanding Natural Selection (NS). In the simplest model, a heritable feature that increases RS will be selected for over time in a population because individuals with higher RS will contribute more offspring to future generations and this, in turn, causes the frequency of the RS-enhancing allele (gene variant) to become more common over generational time in that population.

Fitness is a property of an allele that refers to its relative likelihood of representation in future generations in a population. An allele with higher fitness will be more likely to be represented in future generations within a population than an allele for the same gene with lower fitness. The important thing here is that the likelihood of future representation has to be due to a feature of that allele, and not random effects.

At first glance RS and Fitness are the same, or similar, but one might immediately notice that RS is a feature of an individual (that has offspring) while fitness is a feature of an allele. So, it is possible that a given individual will have a relatively high RS but contain a particular allele with low fitness. Presumably the higher RS of that individual is due to high-fitness alleles of other genes. In this way, fitness and RS are different, but when considering large scales of time and large populations, the two can be (perhaps) safely conflated because things average out over time and the different alleles are being independently assorted over generational time, so each allele gets to have its day, sometimes, independently of other lower-fitness alleles. By this way of thinking, RS and fitness can be safely considered as measures of roughly the same thing, but with caveats.

RS is usually measured, in actual experimental work or field observations, as the number of offspring observed for an individual, but to make sure that RS is correlated with fitness, one might measure grand-offspring in order to factor out infertile offspring and other factors that may affect one generation but that do not apply over the long term. Again, RS and fitness are then, it would seem, equatable but with caveats.

RS is the number of offspring or grand-offspring but kin selection may apply as well. This is where an individual foregoes some of its own reproduction for the benefit of a relative, causing indirect fitness, a measure of this contribution devalued by the probability of the two individuals sharing the same allele by common descent. One can state that a measure of RS is still a measure of fitness because over the long term, again, things average out, but equating fitness and RS is done, again, with caveats.

There may be an optimal number of offspring an individual may have, above which longer term reproduction is reduced. A litter that is too large may result in a set of adults that are smaller than ideal and will thus have fewer offspring, or in the case of serial reproduction, if parental investment is spread out over several offspring, having too many offspring in a row may cause a deficit for all of the offspring, or for the later offspring that get less care because less energy is available, or earlier offspring may get short changed by being left on their own sooner. Putting this another way, the ultimate long-germ fitness strategy may be to have X offspring, where having more or fewer than X results in a suboptimal outcome. In this way, increasing RS from zero towards X increases fitness, but increasing RS beyond X decreases fitness.

So, RS equals fitness except:

  • RS is a measure applied to an individual while fitness is ideally applied to alleles for a gene or some other genetic construct;
  • The offspring-fertility link can be misleading. A queen bee with an allele that allows her to produces more sterile offspring may also produce more fertile offspring;
  • RS is fitness plus or minus random effects;
  • RS usually does not consider indirect fitness;
  • RS is selected to be optimized while fitness is selected to be maximized.

Equating RS and fitness is therefore only a rough approximation. When initially learning about Natural Selection students are often led to believe that RS and fitness are the same, which is only true with these (and possibly other) caveats. Equating RS and fitness in pedagogy risks skipping past and perhaps never understanding the caveats, and these caveats are very far from trivial. They are, in many cases, the point of specific evolutionary research projects.

Skeptically Speaking: War on Science

The latest Skeptically Speaking is “War on Science”

This week we’re looking at threats to science and critical thinking, and how you can sort fact from fiction. York University science librarian John Dupuis joins us to discuss what he calls the Canadian government’s War on Science. And Chris MacDonald director of the Jim Pattison Ethical Leadership Program at Ryerson University, joins us to talk about his textbook The Power of Critical Thinking, which can help you navigate the hyperbole and misinformation that happens when the media looks at science news.

Listen here.

And, I just finished recording a segment that is going to go along with an interview Desiree did with the interesting author of an interesting book. Stay tuned!

Man fishing for bluegills catches shark by hand instead

This is funny:

Just so you know, he was not fishing for “bluegills” This is a bluegill:

A nice bluegill
A nice bluegill

Bluegills live in fresh water and are like “sunfish” and “pumpkinseeds” and “crappies” etc. all of which are in the bass family.

Bluefish live in the ocean and roam along littoral regions in large schools. This is what large bluefish look like:

skip_leadingva_bluefish

Of course, when one is fishing for bluefish, there is always the possibility of catching the fish that eats them, such as striped bass. Like this:

nantucket_elistriper

The striped bass is not in the “bass family” referred to above. Striped Bass are Moronidae, bluegills, largemouth bass, etc. are Centrarchidae.

Anyway, sometimes you catch a shark.

Thinking Rationally About Climate Change, at FTBConscience

John Abraham, of St. Thomas University, and I have a running conversation about climate change … the science, communication about the science, the politics, etc. … and we are going to package this conversation in a one hour session at FTBConscience, an on line conference, Saturday Morning at 9:00, July 20th.

Details are here.

Join us as we discuss the latest news and events related to climate change, such as what is happening in the Arctic, deep in the Oceans, with the Jet Stream and weather extremes, some recent research on glacial melting and sea level rise, and so on.

And, we’ll also talk about science denialism and the latest trends in anti-science pseudo-skepticism.

There will be a chat room so you can toss us questions. See you there!

Reproductive Rights at FTBConscience

I’ll be joining a panel of amazing people, organized by my friend Brianne Bilyeu, to talk about reproductive rights, on Saturday. I expect my contribution to be relatively minimal and I’ll be listening with great interest to …

A panel of reproductive rights activists come together to discuss access to abortion in current events , clinic escorting and some common religious and non-religious arguments against abortion. Our panel consists of clinic escorts – including one panelist who volunteered before FACE laws went into effect (Freedom of Access to Clinic Entrances), health care professionals, an author and several bloggers who write about reproductive rights. Our panelists hail from Minnesota, Kentucky, Virginia and Ireland.

That will be on Saturday, July 20th, 2:00-3:00 PM. I’m guessing that’s Central time, but now that I think about it … I better check on that! Details here.

Evolutionary Psychology Panel at CONvergence 2013

There is now a video and a transcript of the Evolutionary Psychology Panel at CONvergence 2013. Many of you, when you watch this, will become enraged at things said by the panelists. Rumors of what was said had already been spread around on the internet and as I understand it Jerry Coyne and Stephen Pinker have already become enraged. Or maybe the loved it. I’m not sure.

If you want me to respond to any of your enraged rage regarding anything that was said, or for that matter, if you have anything at all … negative, positive, informative, whatever … to contribute to the conversation please put it in the comments below. Of late I’ve been engaged in a handful of projects that curtail my web surfing activities so if you put comments somewhere other than below this post I’m very unlikely to ever see them. This thread will not be moderated unless you post secret launch codes or whatever. (Comments are typically held in moderation until I release them unless you are a prior-trusted commenter, but I’ll put whatever you’ve got here that is not spam … or launch codes.)

Here’s the video:

The transcript is here.

Has global warming stopped?

No. Here’s a handy graphic for you to enjoy and share, courtesy of Climate Nexus.

1005209_538549109538050_11633400_n

Also, you might want to ask the question: What has global warming done since 1998?

That question is addressed HERE, where this handy graphic is available showing the importance of ocean warming:

Total-Heat-Content

So, has global warming stopped? No, I’m afraid not.


Other posts of interest:

Also of interest: In Search of Sungudogo: A novel of adventure and mystery, which is also an alternative history of the Skeptics Movement.