Tag Archives: Uncategorized

Polar Vortex Begets Baby Boom?

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Nine months after the Polar Vortex covered a good part of American with freezing cold, there appears to be a baby boom, according to one unverified news story:

MINNEAPOLIS (WCCO) – It’s been nine months since our bitter cold winter ended.
Now, delivery rooms are bracing themselves for a Polar Vortex baby boom.
All 39 maternity rooms and the NICU are full this weekend at a Des Moines hospital.
Doctors believe the baby bonanza is a result of the polar vortex last December and January.
In case you forgot, it was one of the snowiest and coldest winters on record.
August and September are usually the busiest months for maternity wards, draw your own conclusions why.

I’m holding out for more data.

Titanic Fearless Dinosaur Unearthed

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I’m sure you’ve heard. The most complete skeleton of a titanosaur, a newly named species, Dreadnoughtus schrani, is being reported from Argentina.

It is not a bird. I mention that because we’ve been talking about how birds are dinosaurs lately (see:”Honey, I shrunk the dinosaurs” and “Flying Dinosaurs: A new book on the dinosaur bird link.”).

Dreadnoughtus schrani is a sauropod. Brontosaurus, if it existed, would be a sauropod. These are the dinosaurs with the little heads, long necks, and long tails. In cartoons they are sometimes called “long-necks.” Dreadnoughtus schrani is, as mentioned, a titanosaur, a particularly large long neck.

How does this relate to the other dinosaurs? The dinosaurs are part of a really big group of organisms that includes crocodiles, pterosaurs (those flying things) and so on. Within this group are the proper dinosaurs which you can think of as being divided into three groups. One group is the Ornithischia, named from the greek for “birdlike.” These are not birds either, but their hips somewhat resemble bird hips. (Birds are “lizard hipped” dinosaurs, which completes the paleoirony.) The Ornithischia are separate from the other two groups which are the Sauropods and the Theropods. The Theropods include Tyrannosaurus rex and pigeons. The Sauropods includes the Brontosaurus-like dinosaurs, though of course, there is no such thing as Brontosaurus. Because people who name dinosaurs are, essentially, sadistic.

Anyway, Dreadnoughtus schrani is estimated to have been about 26 meters (85 feet) long. So if you live in a typical city lot it could eat the bushes on your front lawn while knocking over your garage out back with its tail. It would have weighted about 59 metric tons. That’s about 65 regular tons. Nobody really knows what a ton is unless you are in certain professions, so that’s about 33 cars, or about 70 head of cattle. So, the average American could replace the usual meat in their diet with meat from one well fed Dreadnoughtus schrani for about two centuries. Give or take. This is all based on the one specimen found in Argentina. But, that individual was not full grown. So, wow. I’m not sure if Dreadnoughtus schrani is the biggest sauropod, as there are others in this size range.

The specimen is about 45% complete as a skeleton, but about 70% of the bones in the body are represented. Unfortunately the head is missing. But really, where could it be? I’m sure they’ll find it if they keep looking!

Titanosaurs were the major large dinos during the Mesozoic (252 – 66 mya) in the southern continents. This particular find dates to the Upper Cretaceous, the latest part of the Mesozoic.

From the paper:
srep06196-f2

(A) Reconstructed skeleton and body silhouette in left lateral view with preserved elements in white. (B) Left scapula and coracoid in lateral view. (C) Sternal plates in ventral view. (D) Left forelimb (metacarpus reconstructed) in anterior view. (E) Left pelvis (ilium partially reconstructed) in lateral view. (F) Left hind limb in anterior view (metatarsus and pes partially reconstructed and reversed from right). (G) Transverse ground thin section of humeral shaft, showing heavy secondary remodelling (arrow indicates extent of dense osteon formation), a thick layer of well-vascularized fibrolamellar bone, and a lack of lines of arrested growth or an external fundamental system. Abbreviations: acet, acetabulum; acf, acromial fossa; acp, acromial process; acr, acromial ridge; ast, astragalus; cc, cnemial crest; cof, coracoid foramen; cor, coracoid; dpc, deltopectoral crest; fem, femur; fhd, femoral head; fib, fibula; flb, fibrolamellar bone; gl, glenoid; hum, humerus; il, ilium; ilp, iliac peduncle; isc, ischium; isp, ischial peduncle; lt, lateral trochanter; mtI, metatarsal I; mtII, metatarsal II; of, obturator foramen; pop, postacetabular process; prp, preacetabular process; pu, pedal ungual; pub, pubis; pup, pubic peduncle; rac, radial condyle; rad, radius; sc, scapula; scb, scapular blade; sr, secondary remodelling; tib, tibia; tpp, tuberosity on preacetabular process; ul, ulna; ulc, ulnar condyle. Scale bars equal 1?m in (A) to (F) and 1?mm in (G). (Skeletal reconstruction by L. Wright, with G. Schultz.)

The name means “Fearless-creature guy-who-funded-expedition.” According to the authors, this is specifically where the genus name comes from:

Dreadnought (Old English), fearing nothing; genus name alludes to the gigantic body size of the taxon (which presumably rendered healthy adult individuals nearly impervious to attack) and the predominant battleships of the early 20th century (two of which, ARA [Armada de la República Argentina] Rivadavia and ARA Moreno, were part of the Argentinean navy). Species name honours the American entrepreneur Adam Schran for his support of this research.

For more information:

The Scientific Report article (which appears to be Open Access): A Gigantic, Exceptionally Complete Titanosaurian Sauropod Dinosaur from Southern Patagonia, Argentina

An open access paper on how this type of dinosaur even walked: March of the Titans: The Locomotor Capabilities of Sauropod Dinosaurs.

Michael Balter with Science Mag: Giant dinosaur unearthed in Argentina

Mr. Dinosaur Brian Switek: Enormous New Dinosaur as Formidable as Its Namesake Battleship

Ian Sample at The Guardian, including a video: Battleship beast: colossal dinosaur skeleton found in southern Patagonia

Francie Diep at Scientific American: New “Dreadnought” Dinosaur Most Complete Specimen of a Giant

Important new meta-study of sea level rise in the US.

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This is not a peer reviewed meta-study, but a meta-study nonetheless. Reuters has engaged in a major journalistic effort to examine sea level rise and has released the first part (two parts, actually). It is pretty good; I only found one paragraph to object to, and I’ll ignore that right now.

There are two reasons this report is important. First, it documents something about sea level rise that I’ve been trying to impress on people all along. The effects of sea level rise do not end at one’s perceived position of a new shoreline. Here’s what I mean.

Suppose you are standing on a barrier island, and your feet are on a grassy sandy knoll 10 feet above high tide. You are standing next to a climatologist who says “some projections say that the sea level will rise by one foot more than it already has by 2100. You breath a sigh of relief because you are standing 10 feet above high tide, and you realize that one foot of seal level rise is easily accommodated by the sea you see in front of you.

But you would be a fool to not be worried for several reasons. First, you are standing on a 10 foot high sea cliff. The sea cliff represents erosion that happened since the last bout of sea level rise (and is actually an ongoing process). When the sea rises by one foot that sea cliff will erode away. The land many hundreds of yards behind you may be fine, but the place you are standing will be gone. It is hard to predict how much land will horizontally erode with a given rise in sea level, but it is generally a positive number, rarely zero (there are places where it effectively can be zero but not along the sandy shores). Second, as you stand there looking at the sea, the restaurants and businesses along the road behind you and the residential and commercial properties all across the nearby hinterland are busy lowering the ground water by taking water out for their own use as if it didn’t matter. So, while the sea may rise up one foot by 2011, it may also drop a foot because of the groundwater removal. Third, if the sea rises only a little across certain kinds of sediments, the weight of the sea may further suppress the land. Fourth, if this bit of land you are standing on is along the US Atlantic coast, you probably get more than one foot of sea level rise if the global sea level goes up by one foot. This has to do with the shape of the oceans, wind and water currents, etc. Fifth, one foot of sea level rise means many feet of extra storm surge when that rare tropical storm comes along. The chance of a hurricane hitting a given beach along the Atlantic is low. But we’re talking about the year 2011. Between now and then a hurricane with enhanced storm surge will come along and remove the land you are standing on. Sixth, the climatologist you are standing next to is an optimist. He is referring to “some estimates.” The funny thing about sea level rise estimates, as well as polar ice sheet melt estimates, is that they keep changing over time, always in one direction. Ten years ago the estimate was one foot by 2200. Now, it’s 4 feet, and some estimates suggest 6.6 feet. Also, looking at the paleo record, the last time atmospheric carbon dioxide levels were at their present level plus what we expect to put in the air over the next few decades for good measure, sea levels were so high we used meters instead of feet! Figure 25 feet, maybe 40. The town behind you will eventually be gone, buried deeply in the sea, a nice fishing ground. That probably won’t be by 2100, but is it really your job to throw every human that exists after 2100 under the climate change bus because it is a nice round number? No. No, it isn’t.

The Reuters report deals with most of those issues (though in a different way), chronicling numerous cases of actual current and ongoing encroachment of the sea on the land. And this brings us to the second key thing about this report. Reuters documents that the humans are running around like chickens with their heads cut off. Local business leaders who want to preserve their short term profits are controlling supposedly long-term-thinking state and federal agencies so nothing gets done. Big Science (in the form of NASA) is busy studying glacial melt and sea level rise from rocket-launching bases that are being washed away by the rising ocean, and acting as though they can somehow stop that. Congress. It does nothing. And so on.

This is the first in a series of reports, it is excellent, and I look forward to the rest of them. You can read it here. By the way, a lot of what is documented by Reuters was covered earlier in this book: Hot: Living Through the Next Fifty Years on Earth, worth a look!

(The graphic above is from the National Climate Assessment report of 2014.)

Scrivener on Linux: Oh Well…

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UPDATE (January 2, 2016): The makers of Scrivener have decided to abandon their Linux project. Kudos for them for giving it a try. The Scrivener on Linux users were not many, and almost nobody donated to the project, and as far as I can tell, the project was not OpenSource and thus could not have attracted much of an interest among a community of mostly OpenSourceHeads.

So, I’m no longer recommending that you mess around with Scrivener on Linux, as it is no longer maintained. Back to emacs, everybody!

Scrivener is a program used by authors to write and manage complex documents, with numerous parts, chapters, and scenes. It allows the text to be easily reorganized, and it has numerous ways in which the smallest portion of the text, the “scene,” and larger collections of text can be associated with notes and various kinds of meta-data. It is mainly a Mac program but a somewhat stripped down beta version is available for Linux.

In some ways, Scrivener is the very embodiment of anti-Linux, philosophically. In Linux, one strings together well developed and intensely tested tools on data streams to produce a result. So, to author a complex project, create files and edit them in a simple text editor, using some markdown. Keep the files organized in the file system and use file names carefully chosen to keep them in order in their respective directories. when it comes time to make project-wide modifications, use grep and sed to process all of the files at once or selected files. Eventually, run the files through LaTeX to produce beautiful output. Then, put the final product in a directory where people can find it on Gopher.

Gopher? Anyway …

On the other hand, emacs is the ultimate linux program. Emacs is a text editor that is so powerful and has so many community-contributed “modes” (like add-ins) that it can be used as a word processor, an email client, a calendar, a PIM, a web browser, an operating system, to make coffee, or to stop that table with the short leg from rocking back and forth. So, in this sense, a piece of software that does everything is also linux, philosophically.

And so, Scrivener, despite what I said above, is in a way the very embodiment of Linux, philosophically.

I’ve been using Scrivener on a Mac for some time now, and a while back I tried it on Linux. Scrivener for the Mac is a commercial product you must pay money for, though it is not expensive, but the Linux version, being highly experimental and probably unsafe, is free. But then again, this is Linux. We eat unsafe experimental free software for breakfast. So much that we usually skip lunch. Because we’re still fixing breakfast. As it were.

When you create a Scrivener project, you can chose among a number of templates. The Scrivener community has created a modest number of alternatives, and you can create your own. The templates produce binders with specific helpful layouts.
When you create a Scrivener project, you can chose among a number of templates. The Scrivener community has created a modest number of alternatives, and you can create your own. The templates produce binders with specific helpful layouts.

Anyway, here’s what Scrivener does. It does everything. The full blown Mac version has more features than the Linux version, but both are feature rich. To me, the most important things are:

A document is organised in “scenes” which can be willy nilly moved around in relation to each other in a linear or hierarchical system. The documents are recursive, so a document can hold other documents, and the default is to have only the text in the lower level document as part of the final product (though this is entirely optional). A document can be defined as a “folder” which is really just a document that has a file folder icon representing it to make you feel like it is a folder.

The main scrivener work area with text editor (center), binder and inspector.
The main scrivener work area with text editor (center), binder and inspector.
Associated with the project, and with each separate document, is a note taking area. So, you can jot notes project-wide as you work, like “Don’t forget to write the chapter where everyone dies at the end,” or you can write notes on a given document like “Is this where I should use the joke about the slushy in the bathroom at Target?”

Each scene also has a number of attributes such as a “label” and a “status” and keywords. I think keywords may not be implemented in the Linux version yet.

Typically a project has one major folder that has all the actual writing distributed among scenes in it, and one or more additional folders in which you put stuff that is not in the product you are working on, but could be, or was but you pulled it out, or that includes research material.

You can work on one scene at a time. Scenes have meta-data and document notes.
You can work on one scene at a time. Scenes have meta-data and document notes.
The scenes, folders, and everything are all held together with a binder typically displayed on the left side of the Scrivener application window, showing the hierarchy. A number of templates come with the program to create pre-organized binder paradigms, or you can just create one from scratch. You can change the icons on the folders/scenes to remind you of what they are. When a scene is active in the central editing window, you can display an “inspector” on the right side, showing the card (I’ll get to that later) on top the meta data, and the document or project notes. In the Mac version you can create additional meta-data categories.

Scrivenings Mode
Scrivenings Mode
An individual scene can be displayed in the editing window. Or, scenes can be shown as a collection of scenes in what is known as “Scrivenings mode.” Scrivenings mode is more or less standard word processing mode where all the text is simply there to scroll through, though scene titles may or may not be shown (optional).

A lot of people love the corkboard option. I remember when PZ Myers discovered Scrivener he raved about it. The corkboard is a corkboard (as you may have guessed) with 3 x 5 inch virtual index cards, one per scene, that you can move around and organize as though that was going to help you get your thoughts together. The corkboard has the scene title and some notes on what the scene is, which is yet another form of meta-data. I like the corkboard mode, but really, I don’t think it is the most useful features. Come for the corkboard, stay for the binder and the document and project notes!

Corkboard Mode
Corkboard Mode
When you are ready to do something outside of scrivener with your project, you compile it. You can compile it into an ebook, a file compatible with most word processors, a PDF file, a number of different predefined manuscript or script formats, etc. Scrivener does all sorts of magic for writing scripts, though I know nothing about that. There is also an outline mode which, in the Mac version, is very complex and powerful. In the Linux Version it is not. So I won’t mention it.

The compile process is cumbersome, esoteric, complicated, and requires training, so it is PERFECT for the average Linux user! But seriously, yes, you can compile your document into a pre-defined format in one or two clicks, but why would you ever do something so simple? Instead, change every possible option affecting formatting and layout to get it just the way you want it, then save that particular layout for later use as “My layout in February” or “This one worked mostly.”

The Powerful Compile Dialog Box.
The Powerful Compile Dialog Box.
One might say that one writes in Scrivener but then eventually uses a word processor for putting the final touches on a document. But it is also possible that you can compile directly to a final format with adequate or even excellent results and, while you may end up with a .docx file or a .pdf file, you are keeping all the work flow in Scrivener.

This fantastic and amazing book was compiled in Scrivener directly into ebook format.

You have to go HERE to find the unsupported and dangerous Linux version of Scrivener. Then, after you’ve installed it, install libaspell-dev so the in-line spell checking works.

A scrivener project file is a folder with a lot of files inside it. On the mac, this is a special kind of folder that is treated as a file, so that is what you see there, but in Linux you see a folder, inside of which is a file with the .scriv extension; that’s the file you run to open the software directly from a directory.

Do not mess with the contents of this folder. But if you want to mess with it you can find that inside a folder inside the folder are files that are the scenes you were working on. If you mess with these when Scrivener is using the project folder you may ruin the project, but if Scrivener is not looking you can probably mess around with the contents of the scene files. In fact, the Mac version gives you the option of “syncing” projects in such a way that you work on these scenes with an external editor of some kind while you are away from your Scrivener base station, i.e., on your hand held device.

Since this data storage system is complicated and delicate, it is potentially vulnerable to alteration while being used by the software, with potentially bad results. This puts your data at risk with cloud syncing services. Dropbox apparently place nice with Scrivener. I’ve been trying to figure out if Copy does, and I’ve been in touch with both Scrivener developers and Copy developers but I’m not sure yet. I use Copy for the masses of data on my computer because it is cheaper, and I use a free version of Dropbox for Scrivener files, just in case.

I would love to see more people who use Linux try out Scrivener, and maybe some day there will be a full Linux version of it. As I understand it, the Linux version is a compiled subset of the Windows version code base (yes, there is a Windows version) and the Windows version is a derivative of the Mac version.

I should also add that there are numerous books and web sites on how to use Scrivener, and Literature and Latte, the company that produces it, has developed an excellent and useful manual and a number of useful tutorials. Literature and Latte also has an excellent user community forum which is remarkably helpful and respectful. So be nice if you go over there.

Should it be "math" or "maths"?

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Do the math:

There are actually two answers to this question.

First, “maths” looks plural and is preferred by some because “mathematics” is plural. The problem with that is “mathematics” is no more plural than “physics” or any other compound noun. It is a rational sounding utterly incorrect argument. If we said “mathematics are cool” then there might be a case. But we say “mathematics is cool.”

Second, some people say maths and some people say math, and that’s how language works. That is a valid argument, but if you are walking around in the US saying “maths” instead of “math” be aware that you are demonstrating an anglophile affection, which is fine, as long as you know you are doing it. Please remember to demonstrate other anglophile affections such as referring to “English Muffins” and “Crumpets” and telling your friend “I’ll knock you up in the morning” when you merely intend to come by to walk to work together. Most importantly, if you have switched to “maths” from “math” because of some rational argument you once heard, just know there isn’t a rational argument. It is just a matter of usage. It is arbitrary. There is no readon. And if you are in the US you are using the non-standard usage. If you are in England or somewhere fine, talk funny all you want!

ADDED:

The conversation about “knocking up” has developed here, on Facebook and on Twitter. Interestingly a lot of Brits claim this is simply not a thing Brits say, yet it is. It may simply be patchy in its use, but it really is a British saying. More so than an English Muffin being a Crumpet (I know it is not, but I do love the reaction to the comparison among the Crumpet Sympathizers). Anyway, “I’ll Knock You Up” is defined in many places, and used by many Brits, to mean to rouse, wake up, call on, etc. another person. In American English, it means to make pregnant. In at least some forms of British, when does not “get pregnant” but one “fall’s pregnant” and if one chooses one might have the baby in the hospital, in America, or in hospital, in British-English areas.

Anyway, here’s the Google Ngram for various uses of “knocked”:

Honey, I Shrunk The Dinosaurs …

Birds, Uncategorized

There is a fantastic paper just out in Science: “Sustained miniaturization and anatomoical innovation in the dinosaurian anceestors of birds” by Michael Lee, Andrea Cau, Darren Naishe and Gareth Dyke.

I want to talk about this research but if you really want to know more about it, don’t rely on me; one of the co-authors of this important paper is Darren Naish, who happens to be a stupendous blogger, and he has written the research up here. So go read that for sure, and revel in the excellent graphics. Meanwhile I have a few random thoughts….

READ THE REST HERE

Tanganyika v. Tanzania

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Tanzania is the name of a country in Africa. Tanganyika is, among other things, the older name of that country, more or less. It is a formerly used term that should no longer be used to refer to that country.

Wikipedia has this wrong on the indicated page on August 16th, 2014. Any wiki authors out there, please feel free to fix. I recommend changing the term “Tanganyika” to “Tanzania” and deleting the rest of the sentence.

Why not change this myself? Here’s why.

#Ebola Outbreak: Rate of new cases remains high, Nigeria may now have outbreak

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It is probably safe to say that Nigeria now has an outbreak, as a handful of cases contracted in country seem to have been reported, though it is too early to be sure this will stick. Hopefully it won’t.

There is also one suspected case, a death, in Saudi Arabia, of someone who would have caught it in Liberia.

The number of new cases per unit time seems to have increased, or at least, stayed high as it has been for the last several days. The following chart based on WHO data shows the cumulative number of cases and deaths, including probable, suspected, and confirmed, as per WHO reports which come out at irregular intervals but generally every few days, though today’s report (August 6th). The mortality rate continues to hover between 50 and 60% (the drop at the end of that line is probably an artifact of the rate of new cases added and does not mean a drop in mortality rate, most likely)>

Ebola_2014_Outbreak_Aug_6_update

See this post for a more detailed look at the dat up through the previous report, where there is a discussion of some of the nuances.

More posts on Ebola:

<li><a href="http://scienceblogs.com/gregladen/2014/08/04/there-is-a-cure-for-ebola-we-have-it-we-just-dont-let-anyone-use-it/">There is a cure for Ebola, we have it, we just don’t let anyone use it.</a>

<li><a href="http://scienceblogs.com/gregladen/2014/08/04/ebola-outbreak-continues-probably-worsens-perhaps-spreads/">Ebola Outbreak Continues, Probably Worsens, Perhaps Spreads</a></li>
  • Ebola Perspective: Risks of spread to the US and elsewhere
    • <li><a href="http://scienceblogs.com/gregladen/2014/07/27/ebola-outbreak-in-west-africa-some-basic-information/">Ebola Outbreak in West Africa: Some basic information (Updated)</a></li>

    Unhappy Anniversary World War I

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    But they did not call it that then.

    This isn’t actually the anniversary of the war, but it is the wedding anniversary plus one month of Archduke Ferdinand and his wife, Sophie, and the day the two of them were assassinated by Mlada Bosna. Today, one month later one hundred years ago, the first of several declarations of war was made, by Austria-Hungary against Serbia. After that, it gets very complicated.

    By the end, the Ottoman Empire, the Austro-Hungarian Empire, the Russian Empire, and the German Empire did not exist any more. The German colonies around the world were lost to Germany. The war was fought across Europe and Asia, in many parts of Africa, and even a little bit in the New World. Had things gone slightly differently, the US and Mexico may well have resumed hostilities, and if Mexico prevailed, Texas, Arizona and New Mexico might be Mexican states today. Over forty countries were involved on the “allied” side (or affiliates of the allies) though many on paper. The “Central Powers” (the bad guys) included a minimum of seven countries, depending on what you count exactly as a country. (The Ottoman Empire included a bunch of states.)

    About ten million military personnel were killed in the war, but the number “missing” is almost as large, about 7.5 million. (over 20 million wounded). About seven million civilians were killed. It is almost certain that the Pandemic of 1918 was caused by the war. That killed between 50 and 100 million people.

    Let’s assume the worst. 18 million killed in the war plus imma add 5 million untimely deaths following it from those wounded, and 100 milli0n for the flu, to come up with a total of 123 million people. That’s close to 7% of the world’s population at the time, but concentrated unevenly. The war plus the flu in France (where the war was a much much larger factor) deleted nearly 7 million out of about 40 million, or 18%. Those numbers are very rough estimates.

    Verily, it was the war to end all wars. Except it didn’t.

    So, Unhappy Anniversary.

    Ebola Outbreak in West Africa: Some basic information (Updated)

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    LATEST UPDATE HERE

    UPDATE: The latest numbers do not indicate a weakening of the outbreak. (See list of new cases below. Several graphs have been updated as well)
    UPDATE: More detailed discussion of transmission of Ebola
    UPDATE: I note with sadness the death of my neighbor (though I did not know him) of Patrick Sawyer, of the Liberian Ministry of Finance, who died in Nigeria of Ebola contracted in Liberia. He was on his way home to Minnesota at the time.

    There is an Ebola Outbreak currently underway in several West African countries, mainly Sierra Leone, Liberia, and Guinea. This is the most extreme known Ebola outbreak to date. The first known outbreak of this virus was in 1976, and there have been several instances since then ranging from single cases (which by definition are not outbreaks) to 425 confirmed cases (with 224 deaths in that instance, in Uganda, 2000-2001). The current outbreak is significantly larger with about double that number or more.

    There is some confusion in the press (most notably in CNN) about the nature of Ebola and perhaps about some of the details of this outbreak. Here, I want to provide some basic data to help clear some of this up. CNN reported at one point that you can get Ebola only after a person is symptomatic, and (in the same story) at any time a person is infected even if they are not symptomatic. It is probably the case that as long as Ebola is in a person’s system, they can spread it. It is only spread through contact with bodily fluids, but that is not such a hard thing to do; mucus membranes can absorb the virus, as well as cuts or other injuries. It is probably sexually transmittable. It does not appear to be airborne, but bodily fluids that are in or on needles, hospital equipment, etc. can carry the disease to another person.

    Another issue with reporting is the difference between suspected cases, likely cases, and confirmed cases. Even within the health community these numbers are all over the place because they are always changing as cases go from suspected to either eliminated or confirmed. Wikipedia and CNN both recently stated that there have been 1,093 human cases with 660 deaths so far. However, this includes both confirmed and suspected cases. There is a good chance that the total number of cases is in fact close to this, but the data are of lower than ideal quality. If we want to look at mortality rates and changes over time in this outbreak, it is better to look at a smaller subset of the better confirmed data. That’s what I’ll do here. But, when looking at the numbers, keep in mind that although most of the data I show in graphics below show several hundred fewer cases than being widely reported, the actual number of people affected by the disease over the last four months or so is probably not only higher than the cleaned up data set but also, likely higher than the reported 1,093. Furthermore, the data I’m using here only go up to July 24th.

    One of the most egregious errors at CNN is the frequent statement that Ebola has a 90% death rate, but that the current outbreak has a much lower death rate. This is rubbish. Ebola simply does not have a 90% mortality rate, and stating that the current outbreak is much lower in mortality gives the impression that this particular form of Ebola, or this particular outbreak of the disease, is somehow not as bad as usual. In fact, this outbreak is worse than any previous outbreak for several reasons. For one, it is larger. Also, it seems to be not burning itself out like most previous outbreaks did. Ebola outbreaks in the past have tended to happen in relatively isolated areas, because the population that includes victims is in close proximity to the presumed reservoir of the disease (probably fruit bats) and interacts directly with the intermediate hosts (eg. primates or other mammals that picked up the disease from fruit bats*). But there is plenty of reservoir and intermediate reservoir in some areas near major population areas. Apparently, Ebola broke into the human population in one or more areas of high population density, and this density together with relatively high mobility is allowing the disease to persist.

    The following graphs are based on data I collected from the WHO reports. For March, I use only very likely cases, for April through July, I use only confirmed cases (not available for March). And, July does not include the last week for that month (a few more days have been added to this information bringing us to July 23rd, added on July 30th).

    The following charts show the total number of cumulative cases conservatively estimated, and total number of cumulative deaths. When the outbreak starts to weaken, we would see a leveling off, but that is not indicated here (UPDATED).

    UPDATED_EbolaCumulativeCases2014

    The last several reports from WHO (including confirmed, probable, and suspect cases) are as follows:

    July 21st through July 23rd: 108 NEW
    July 18th through July 20th: 45
    July 15th through July 17th: 67
    July 13th through July 14th: 18
    July 08th through July 12th: 85
    July 06th through July 08th: 44
    July 03rd through July 06th: 50

    The exact time spans for each of these reports may not be the same, but I believe the number of cases do not overlap; each listing is a separate set of new cases. Clearly, for the last several days of available information, there is variation in, but no let up in, the number of new cases.

    Looking at the number of new cases reported (and for the most part confirmed) and the number of deaths (the same data as used to make the cumulative graphic above, but by month) we have this (Updated):

    EbolaConfirmedCasesAndDeaths2014

    Keep in mind that the data for July are short by several days.

    Another area where MSM, and for that matter, Wikipedia, could do a better job is in reporting the mortality rate for the disease. Wikipedia states that “The disease has a high death rate: often between 50% and 90%.” This is misleading because the outbreaks with 90% mortality rates are not typical, and the statement seems to be based on a set of data that includes a lot of data points one would do better to ignore. I assume CNN is taking this information (from Wikipedia or elsewhere, which perhaps repeats the Wikipedia claim) and exaggerating slightly when they say that Ebola normally has a 90% mortality rate.

    The Ebola affecting people right now in Africa is one of a handful of similar viruses known over a larger geographical range. Some of the deaths found in the larger data set of all known outbreaks are from individuals who showed up in a hospital nowhere near where they got the disease, or laboratory workers. The best way to estimate mortality rates related to the present outbreak in West Africa is to take only field cases — actual outbreaks in normal populations — in Africa only, and to not count “outbreaks” that are not outbreaks because only one person is in the sample.

    The following chart compares mortality rates for all of the “outbreaks” listed in Wikipedia page regardless of size of sample, geography, or circumstances, with only those that are African Ebola in the field. The latter set also excludes the present outbreak.

    Ebola_Mortality_Rates

    Notice that the clean data are bimodal; some outbreaks have mortality rates between 0 and 90%, others between 40 and 60%, and not much in between. Also, there are several in the all-data set that have a mortality rate of zero. This bimodality is not necessarily a persistent statistical characteristic of the sample; I could make it go away by changing the histogram intervals. But it is a convenient place to break the sample into “more severe” and “less severe” outbreaks.

    The zero cases in the full data set are all odd cases. Seven are not in Africa and include in some cases lab workers or animal handlers, and most are not African (Zaire type) Ebola. One is a scientist who caught the disease from doing a necropsy on a chimp in the Ivory Coast, examining an outbreak among the non-human primates there. There is one case where the fatality rate is 100%, but this was only one person, and the case was discovered post hoc. We don’t know if anyone else there had the disease. A 90% mortality rate occurred in a remote part of the Congo, with 143 people affected including health care workers. It appears that several individuals contracted the disease butchering non-human primates. This occurred during suboptimal conditions during the Second Congo War. One case of 88% mortality occurred early on in the history of the disease (the second known outbreak) also under very poor conditions. Although the data are too sparse to draw firm conclusions, it seems that the more severe outbreaks in terms of mortality tend to have occurred under more difficult conditions.

    Ebola probably has a very high mortality rate when an infected person gets no medical treatment, and a mortality rate closer to 50% when a person quickly gets medical attention. There is no cure, but when a patient is given IV solutions in a hospital setting the chance of survival goes way up. This might suggest that smaller outbreaks that run their course before intervention would have a higher mortality rate, or that the mortality rate would be higher near the beginning of the event. Similarly, one might expect mortality rates to be higher in the early years of Ebola than later, as treatment methods developed.

    There is some, but not much, evidence for these effects.

    The following chart shows mortality over size of the outbreak, using only the cleaned up data set:

    Ebola_Mortality_Rate_Over_Size_Of_Outbreak

    There is not a relationship between size of outbreak and mortality rate.

    This chart shows the mortality rate over time, for the cleaned up data:

    Ebola_Mortality_Rate_Over_Time

    This seems to show that lower mortality has been achieved in recent outbreaks, though the statistical significance of this is non existent. But, the data set is small. The above chart also indicates the average morality rate across all of these events, which is 64% across 18 outbreaks. Not “usually 90%” as CNN states.

    The following chart shows the approximate mortality rate for the current outbreak by month.

    Ebola_Outbrak_2014_Mortality_Rate_By_Month

    This is calculated from confirmed or highly likely cases. This is not a true mortality rate because people who got the disease in one month may have died the next month. But it does give an approximate indication of change over time in rates. The rate at the beginning of the outbreak could be high, or this large percentage could be a function of how cases were counted. In any event, this is an indication of higher mortality rates calculated at the beginning of an outbreak, and there are likely two reasons for that high rate, either or both applying in a particular case.

    <li>Early in an outbreak a number of people are affected, but live, and don't make it into the data  base because they are not identified; they got sick, got better, and went on their way. Those who died were all or almost all counted. </li>


<li>Early in an outbreak a number of infected people are not treated with the maximum available medical attention, so more of them die.</li>

    The current outbreak is settling in at about 60% mortality rate. There is no indication from WHO that the epidemic is slowing down.

    UPDATE: Is Ebola Only Transmitted By Symptomatic Individuals?

    According to the usual sources (WHO and CDC for example) the following is probably true. When someone gets Ebola, typically, after a while they get sick. This means they show symptoms. If they did not show symptoms they would not be “sick” even if the virus was in them and even if the virus is multiplying in them. Presumably people are infected with a sufficient number of viroids that they become a host for the disease, the virus starts to multiply above some level that makes the person sick, and we can say at that point that they “have Ebola.” This is when the infected person is able to transmit the disease to others through bodily fluids that might come into contact with wounds or mucous surfaces in the downstream patient.

    This is what the WHO and CDC literature on Ebola says, and this has lead bloggers and news outlets to state incorrectly that Ebola is only transmitted to others when the person shows symptoms. Unfortunately this is not true in one or possibly two ways.

    It appears that people who have had Ebola, live, and get “better” (i.e., their symptoms go away) can still carry Ebola for a period of time, and in this state, they can still transmit it. What has probably happened is their immune system has started to fight the virus enough that it is attenuated in its effects, but it isn’t’ entirely gone yet. Medical personnel like to send someone home only after the virus has cleared. Even so, men who are supposedly virus free by that standard, when sent home after surviving Ebola, are told to avoid sex for several weeks because there is still the possibility of sexual transmission of the virus. Meaning, of course, that the virus is still knocking around in some individuals at this point, and still transmittable. It is not clear how likely that is to happen.

    This is very important. Most people would interpret “only transmitted by people showing symptoms” (or words to that effect) when they read it in a news outlet as meaning – well, as meaning exactly what it says. But post-symptomatic patients may still transmit the disease.

    Is it possible that pre-symptomatic people can transmit the disease too? Personally I think it is possible even if it is generally unlikely. In a disease that kills over half of those who get it, “unlikely” is not comforting. A small percentage of people who never seemed to have had Ebola, or to have been exposed to it, seem to have antibodies that would probably only develop if exposed to Ebola. Some studies have shown immune reactions to Ebola in those known to have been exposed but also known to not have gotten sick. This is important but not shocking. There are a number of different situations where a normally icky disease that makes you really sick seems to have infected a certain percentage of people asymptomatically. Are these people carriers at some point, i.e., people who have the virus in them, can transmit it to others, but don’t get sick themselves? There is no evidence to suggest that this is the case with Ebola, but the total number of known human cases of Ebola is very small and the conditions for study of the disease in the field very poor, so the safest thing to conclude is that we simply don’t know, but it is also reasonable to say that asymptomatic carriers don’t seem to be a problem, or this would likely be noticed.

    The important point here is that there is not a perfect correspondence to being infected and having symptoms, and transmission post-treatment and survival is possible and of sufficient concern that WHO and CDC assume it, so it would be unwise to make too many assumptions about pre-symptomatic transmission.

    Imagine you are a health care person addressing an Ebola epidemic. An jet liner flies over a very long flight, say 10 hours long, on Monday. On Friday five people who were on the plane come down with Ebola and you have reason to believe that they were all infected before the flight. Would you determine that it was impossible for the nearly 300 people stuck on a tube with five pre-symptomatic Ebola carriers to become infected? No. You would watch those people and test them.

    An additional point to underscore; it has been touched on but not emphasized. The symptoms of Ebola include vomiting and bleeding from places one normally does not bleed. Put another way, the symptoms of Ebola include spreading around bodily fluids. This is often how diseases spread. The disease results in a bodily reaction that spreads the disease (look up “virulence”). So, no matter what, the most likely transmission by far is during the period of symptomatic reaction to the disease, or for some time after death while the virus is still viable. That does not mean that there is no transmission before or after, but it does mean that the most obvious transmission will be from symptomatic patients or recently diseased symptomatic patients.

    • Fruit bats will drop fragments, or stones, of fruit they feed on, sometimes in discrete piles. It is almost impossible to imagine a ground dwelling frugivore, such as a chimp or a duiker, not stopping to munch on this detritus. Since Ebola is spread through bodily fluid contact and can be spread via mucous membranes, and fruit bat spit counts as a bodily fluid, I’m personally of the opinion that this is how Ebola may often transfer from its natural reservoir, where it seems to exist without harm, to other animals. Of course, I figured this out after having discovered and handled several such piles of fruit bad wadge.

    Is Matt Entenza really from outstate Minnesota? No, he is not.

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    [Updated: Letter to the Editor, Worthington Daily Globe.]

    This is a followup on my earlier post (see “How do you say “Surprise” in Norwegian? The word is “Entenza.” I am not making that up” also reposted here) on Matt Entenza’s bid for the DFL (Democratic Party) Primary candidacy for Minnesota State Auditor.

    Entenza claims he is from Greater Minnesota, and thus, would do a better job representing the interests of Greater Minnesotans. This implies that highly acclaimed sitting State Auditor and candidate for re-election Rebecca Otto is not doing well in this area. In fact, she is doing very well. She is recognized for her fair and non-partisan treatment of people and local governments across the state. The previous State Auditor used the position in a more political way, implying bias, and voters rejected that approach by the largest upset of an incumbent in 112 years when Otto was first elected. It is now well-understood, here and nationally, that Otto is doing it right.

    This is similar to the misleading language Entenza is using on pensions and social security. "Too often these days, we hear stories about how folks who worked hard and played by the rules their whole lives have their retirement at risk by poorly managed pension funds and Wall Street middle-men that charge exorbitant fees. Privatization of pensions is unacceptable. Minnesotans’ pensions should not be privatized and that Wall-Street middle men have no business near our pension plans.” This, again, implies that Otto has somehow been involved in privatizing pensions. She has not. In fact, a review of Otto’s website shows that she has been leading the charge against the move to privatize public pensions, and that the Public Employee Retirement Association is stronger than ever on her watch.

    A similar thing happened in a recent news article about Otto leading a national conference of State Auditors, bringing the State Auditors from around the country to Saint Paul. A few accounting firms that work with local governments were some of the conference sponsors. Entenza said of this, via his campaign mouthpiece, that "The people being regulated should not be paying for lavish events for those doing the regulating. Attending parties and events thrown by firms the auditor is supposed to be watchdogging is not how Matt Entenza will run the office.” Again, this is a blatant attempt to mislead voters. The State Auditor does not watchdog or regulate private CPA firms in any way, and there were no lavish events at the conference. In fact, the conference was part of required continuing education classes that help auditors keep up with the latest laws, regulations and trends. So here, Entenza would have readers believe that all State Auditors from around the country are somehow having a conflict of interest. Really? He says he wouldn’t attend such conferences if elected. How then, one wonders, would his staff be able to do their jobs?

    But let’s get back to the Greater Minnesota claim. While Entenza is making a cultural and geographical claim about himself (that he grew up in Greater Minnesota), Rebecca Otto is not. Her personal growing-up history is not part of her campaign, though her education and experience as an adult is, and her background is impressive. But when I looked into it further, I found out that Rebecca Otto and Matt Entenza are roughly similar in their geographical background, and that Entenza’s claim is apparently – surprise – (or, as Wikipedia would have it, "Entenza!”) bogus.

    One of my favorite tales from Lake Wobegon, Garrison Keillor’s fictional-but-realish small town in Minnesota, is the one about the family that moved to California then returned later for the wedding of their daughter. The wandering Lake Wobegonites had changed from having lived for years in the Sunshine State. They wore sunglasses, even inside. They spoke of their lovely garden, but admitted they had a gardener. The good people of Lake Wobegon said nothing in response to this, but we know they were thinking “Gardener? Who has a gardener? That would be like having someone cut your food for you.” The joke here is based on the idea that Minnesotan life and culture, especially Greater Minnesota life and culture, is as different from California culture as any two samples of American life can be. These characterizations are, of course, humorously exaggerated imitations of American life, and to humorous effect. But it gets the point across; outsiders, represented by people from California, are suspicious. Never mind that Minnesota is a place of immigration. During the time that our Euro-American culture was forming, with the Minnesota Nice and the Upper Plains sensibility thing and all that – around the beginning of the 20th century – the vast majority of Minnesotans were not born here, or one or both parents who were not born here. The explosive economic growth just before the Bush Recession included a large number of people who moved here from the coastal regions, though we seem to focus on those who moved here from other countries. The point is, there may be a real but low level xenophobia in our state, which is a little quaint but often annoying, and not justified. I’m from New York State (which I know annoys a lot of you). In New York it is not uncommon to be represented in the US Senate by people who had to move there to run for office. This annoys some, but for most it is regarded as a good thing. New York State sometimes gets to be represented by very powerful people who have to work very little to get their voices heard. Robert Kennedy and Hillary Clinton are examples of this. Minnesota has its own history of people not born here still being claimed as strong, good looking, or above average. Elmer Anderson, the most beloved of governors, was not born here. One of our two most famous Charlies, Lindbergh, was born in Detroit. There are others. My point is this: As an outsider (though I’ve lived here as long as I lived in New York) I have noticed that “Candidate X is from this community s/he bids to represent” is a standard line in politics. Just so you know: Not everybody, across this country, does that. That’s a Minnesota thing. (And a few other places.)

    Putting all this aside, one could still argue that the people of Minnesota are so provincial, especially those who live in Greater Minnesota, that they would prefer to be represented by someone exactly like themselves, historically and demographically. Matt Entenza is making the claim that he is “one of them” apparently for this reason. This seems a bit paternalistic.

    And, paternalistic or not, he isn’t. From here.

    Matt Entenza claims he is from Worthington, a small town in Out State Minnesota. In fact, he was born in … wait for it … California. He grew up not in Minnesota at all, but in Santa Monica, and his family moved to Worthington when he was 15. He attended and completed high school there. He then moved out of state again, having lived in Greater Minnesota until he was about 18, we assume, so about three years. He did a year or so at Augustana College in South Dakota, which is not in Minnesota, an Evangelical Lutheran private college. He then transferred to a private college in Saint Paul, Macalester. After graduating from Macalaster he moved out of state again, actually out of the country, to follow Lois Quam during her Rhodes Scholarship at Oxford. The one in England. Later, he went to law school in Minneapolis. After that, he clerked for a Minneapolis-based judge. (Details from here.) He now lives in Saint Paul.

    By Entenza’s standards I’m Congolese because I lived in the Congo for more time than he lived in Greater Minnesota.

    I don’t think it matters that Matt Entenza is from California, but it does matter that he claims that he is from Greater Minnesota and that being from Greater Minnesota is important. Even more importantly, perhaps, is that he seems to assume that people from Greater Minnesota would buy this.

    I respect Entenza’s background. Personally I think everybody who is in charge of anything in Minnesota should go live in coastal states for a couple of years. Being from New York, I am forever seeing things done here in Minnesota that I feel very strongly would be done differently if only people knew how the decisions they are making would play out with increase in population size and density. Boston, where I lived for several years, spent more money than has ever been spent ever anywhere at any time on a public works project to rebuild their main urban highway system, because the original system was put in place and evolved with insufficient forethought. We should be learning those lessons and avoiding those mistakes. Want proof of that? Spaghetti Junction, Crosstown X I35W and the KMart on Nicollet Avenue. On. Nicollet. Avenue. Say no more. Having people in important positions who have experience living elsewhere, and good educations (which you can get here but you can also get elsewhere) is a good thing. Good for you, Matt Entenza, for being a man of the world, who still respects and likes Minnesota. I’d vote for you in part for that reason if your other ducks were in the proverbial row.

    But no, the ducks, they are askew. Entenza had to, essentially, alter his resume to say, or at least strongly imply, that he is is from Greater Minnesota, and thus, will relate to people from Greater Minnesota. He isn’t, he won’t, and making this claim is itself the kind of misleading, pandering that one would think is subject to audit.

    The Expansion of Antarctic Sea Ice and Self Correcting Science

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    One of the things climate change science deniers say, to throw you off, is that Antarctic sea ice is expanding. They even claim that the amount of expansion of Antarctic sea ice offsets the dramatic retreat of Arctic sea ice (see this for the latest on the Arctic). I’ve even seen it argued, in that famous peer-reviewed publication Twitter, that there is an inter-polar teleconnection that guarnatees that when the ice on one end of the earth expands the ice on the other end of the earth contracts, and visa versa, so everything is fine.

    That Antarctic Sea ice is expanding has become standard knowledge. (See “Why is Antarctic Sea Ice Growing” for more.) It is a simple fact of nature that needs to be explained and addressed. The expansion of Antarctic Sea ice is one of the very few apparent reversals in climate change related trends across the world. And, there have been many explanations for it.

    Or is it?

    It turns out that we don’t know if Antarctic sea ice is expanding. A new study just released looked at Antarctic sea ice to examine the idea, which has been batted around for a while now, that there is something wrong with the data. The study, by Eisenman, Meier, and Norris, published in The Cryosphere, found this:

    Recent estimates indicate that the Antarctic sea ice cover is expanding at a statistically significant rate with a magnitude one-third as large as the rapid rate of sea ice retreat in the Arctic. However, during the mid-2000s, with several fewer years in the observational record, the trend in Antarctic sea ice extent was reported to be considerably smaller and statistically indistinguishable from zero. Here, we show that much of the increase in the reported trend occurred due to the previously undocumented effect of a change in the way the satellite sea ice observations are processed for the widely used Bootstrap algorithm data set, rather than a physical increase in the rate of ice advance. Specifically, we find that a change in the intercalibration across a 1991 sensor transition when the data set was reprocessed in 2007 caused a substantial change in the long-term trend. Although our analysis does not definitively identify whether this change introduced an error or removed one, the resulting difference in the trends suggests that a substantial error exists in either the current data set or the version that was used prior to the mid-2000s, and numerous studies that have relied on these observations should be reexamined to determine the sensitivity of their results to this change in the data set. Furthermore, a number of recent studies have investigated physical mechanisms for the observed expansion of the Antarctic sea ice cover. The results of this analysis raise the possibility that much of this expansion may be a spurious artifact of an error in the processing of the satellite observations.

    It looks like, for sure, you can’t say that Antarctic sea ice is expanding or contracting in its annual cycle. It also looks like the evidence suggests it is probably not expanding at all.

    So, science, in its self correcting way, has thrown a wet blanket … a warm and wet blanket perhaps … on the idea that the Antarctic sea ice expansion disproves everything else we know about global warming. The Antarctic sea ice is not Galileo!

    Current Status of Arctic Sea Ice Extent

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    As it does every summer, the Arctic Sea ice is melting off. Over the last several years, the amount of sea ice that melts by the time it hits minimum in September has generally been increasing. So, how’s it doing now?

    The graph above shows the 1981-2010 average plus or minus two standard deviations. Before going into more detail than that, you should look at the following graphic.
    Arctic_Sea_Ice_First_v_Second_Ten_Years

    The top chart shows the march of Arctic Sea ice melt for first ten years of the baseline data set only, and the bottom chart shows the last ten years of the same data set. This tells us that the two Standard Deviations for the period 1981-2010 hides an important fact. Since Arctic Sea ice is melting more and more every year, a proper baseline might be the first several years of this period, not the entire period.

    Now refer to the graphic at the top of the post. This is the current year’s ice extent. Notice that it is tracking right along the lower edge of the 2 Standard Deviation zone. In other words, the present year is exhibiting what we have been seeing all along: An Arctic with much less ice.

    Now look at the years that post date the baseline period, 2011 through the present, including the wildy extreme year of 2012 when a record melt was set.

    Screen Shot 2014-07-22 at 12.04.56 PM

    Here we see that collectively, the last three full years and the present partially documented year exist at the lower end of, or lower than, the 2 Standard Deviation zone. This suggests that the current trend is an extension of the previous couple of decades. More melting on average over time. One would hope this would level off, and maybe it will. But we certainly can not make that claim at this point.

    Note that it is very hard to predict the ultimate minimum for a given year, even at this point. (Even so, I did it here way at the beginning of the season). We’ll have to wait and see.