Category Archives: Uncategorized

That Facebook Book Meme Thing

September 13, 2014UncategorizedBook Meme, Books, UncategorizedGreg Laden

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My friend Iain Davidson tagged me with the facebook novel meme. Here are the rules: Oh, hell, never mind the rules. I wanted to provide links to the books so I decided to do this as a blog post which I’ll paste on my facebook page (and of course tag some unlucky facebook friend).

Here it is. I broke some rules. So what?

Moment in the Sun: Report on the Deteriorating Quality of the American Environment by Dr. Robert Reinow was my Rachel Carson’s Silent Spring. As a child I watched Reinow’s Sunrise Semester course on TV a couple of times. He would give a lecture on some manner or other by which humans were ruining the environment. Then he and his wife would put on a skit demonstrating it satirically. I especially remember the Reinow family sitting around to eat a nice dinner, and Mrs. Reinow sneaking over to the stove, opening the top of the pot in which the stew cooked, and dumping in copious quantities of DDT. “This is what we are doing to ourselves!” One day I started a project. I had just started driving and I wanted to visit every public road between Rout 9W and the Hudson River from Albany south at least a couple of counties distance. Early on during that project I came across Holly Hock Hollow Road. It sounded familiar. I drove up the road, and along it were various signs made to look like they were written by elves or gnomes, about this and that aspect of nature or the environment. Finally I came to an unoccupied (at the moment, but lived in) cottage and small complex of outbuildings. I had come to the Reinow estate. I went back a couple of times later but never managed to run into them. The book, which is the point of this paragraph, was prescient. It predicted pretty much everything that happened over the 20 years or so after it was written, from acid rain to DDT. The book made me an angry supporter of the environment, like Reinow was.

I had messed around with the Sherlock Holmes Canon here and there for a long time then one day decided to read them all cover to cover. Then I did it again. Twice. I don’t know why, I just like it.

Karl Hiassen wrote Tourist Season and then he wrote a bunch of other books, fiction, not children’s fiction, with a guy named Skink in them. I use those attributes to define the “Skink Canon” though in truth Skink himself is a relatively minor character in some of the books, and is never the main character. But he is in all of the books. The protagonist and antagonist in his novels shift though they are often similar to each other while Skink stays in place. In the swamps. Where he lives. I guess I like the Skink canon because if I lived in Florida I’d probably be Skink by now.

Everybody seems to either love or hate Anne Rice, and when they do, it is all about the vampires. The vampires are nice, and I would certainly included those stories on a longer list of books, but less appreciated but in my view better is the series related to the Mayfare Witches: The Witching Hour, Lasher, and Taltos. Creepy weird good stories. Take notes, you’ll need them. Maybe a nice genealogy program will help.

Rita Mae Brown wrote a number of novels exploring both related and unrelated themes in the same setting (though sometimes varying the century). This includes a long series co-authored with her cat. Rubyfruit Jungle is her famous, break-through, prize winning work. Amid this larger set of works is a trilogy, if memory serves correctly but I may be missing a piece (and they were written out of order but I’m giving you the historical order of the story here) that I take to represent her larger work. They are: Six of One, Loose Lips, and Bingo.

Marge Piercy’s Gone to Soldiers is an historical novel set during World War II following several different individuals of varying degrees (including zero) of connection to each other.

I read Lord of the Rings when I was too young to totally get it but I enjoyed it. (It was about the second or third “adult” thing I read). Then I read it again when I was older and then one more time. Then, when I as in the Congo with a really bad case of Malaria I read a good part of it again and the story entered my delusional state, which was … interesting. I survived both. I’ll include Hobbit in with the trilogy because it fits.

About the same time I was reading Lord of the Rings, I read The Intelligent Man’s Guide to Science (in my case, two paper back volumes, one on physical science, the other biology). It is how I got introduced to science, sort of (I was actually introduced earlier but this was my first systematic learning of science, insofar as reading a book serves in this way). The science I was reading was a bit out of date but to a kid one digit in age that hardly mattered. Black holes were a conjecture, the big bang as I recall somewhat more accepted. Many particles had not been “found” but that search was very much underway. The biology section sticks with me less probably because I’ve gone ahead and unlearned all of the 1960s biology, since I’m kind of a biologist.

When people ask me what novel to read, I often say “Hey, did you read The Egyptian by Mika Waltari yet? No? Read it!

If you haven’t gotten around to Mastering Regular Expressions yet than you are missing out.

I read One Day in the Life of Ivan Denisovich in the seventh grade, and it was quite life changing.

I read Deschooling Society (70 Edition) in the ninth grade. It was quite revealing.

I dropped out of school in the 10th grade. But that’s another story and there is no book.

One day my sister said, “You’re kind of a freak, here, read this,” and handed me Welcome to the Monkey House. It was my first adult fiction. I didn’t find it freaky. That must prove I was a freak. Soon after I read Fahrenheit 451, then everything by Bradbury and Vonnegut (available at the time) along with, as mentioned Lord of the Rings. So that is how I got my start on literature.

A Naturalist’s Voyage Round the World: The Voyage of the Beagle is the most revealing of Darwin, within a reasonable volume of words. I don’t know if it changed me but it has stuck with me and I refer to it often.

Although A Perfect Spy might be a perfect Le Carré book, I wouldn’t wish it on anyone who hadn’t already read the Smiley canon. And, really George Smiley is where it is at: Call for the Dead, A Murder of Quality,The Spy Who Came in from the Cold, The Looking Glass War, Tinker Tailor Soldier Spy, Honorable Schoolboy, Smiley’s People, and so on (there are about three others).

Sungudogo, the story of a pair of adventurers traveling across the Congo in search of an elusive primate that may or may not exist, reminds me of a lot of things I’ve done myself. Brilliant novel.

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Giant Semiaquatic Predatory Dinosaur

September 11, 2014Uncategorizeddinosaur, dinosaurs, Paleontology, Spinosaurus aegyptiacus, UncategorizedGreg Laden

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It is called Spinosaurus aegyptiacus but it sounds a bit more like Godzilla. Spinosaurus is a theropod dinosaur (that’s the groups birds evolved within) found in what is now NOrth Africa, between about 112 and 97 million years ago. It was first discovered about one century ago, though those bones were destroyed during WW II. Spinosaurus aegyptiacus might be the only species of this genus, or there may be two. It is probably the largest carnivours dinosaur, up to 18 meters in length. Up top of the post is the picture from Wikipedia. Although the head looks a lot like a crock, you can see the overall Godzilla-esque body.

A paper out today in science presents a detailed analysis of Spinosaurus aegyptiacus‘s aquatic adaptations. Writing for Science, Michael Balter notes:

Researchers have long debated whether dinosaurs could swim, but there has been little direct evidence for aquadinos. Some tantalizing hints have appeared, however, in claimed “swim tracks” made by the bellies of dinos in Utah and oxygen isotopes indicating possible aquatic habitats in a group of dinosaurs called spinosaurs. Now, a research team working in Morocco has found the most complete skeleton yet of a giant carnivore called Spinosaurus [which] confirm that Spinosaurus was bigger than Tyrannosaurus rex, but also show that it had evolutionary adaptations—ranging from pedal-like feet to a nostril far back on the head to high bone density like that of hippos—clearly suited for swimming in lakes and rivers.

The scientists describe Spinosaurus aegyptiacus as “semiaquatic.” It’s pelvis is small, hind limbs short, and as mentioned, its limb bones are solid to act as balast. It’s hind limbs may have acted as quasi-flippers while in water. The dorsal sail “may have been enveloped in skin that functioned primarily for display on land and in water.” They say nothing about its ability to exhale nuclear fire-breath. Perhaps that will be ascertained with further study.

Here are some of the bones and a semi-reconstructed skeleton:

Of related interest:

<li><a href="http://scienceblogs.com/gregladen/2014/09/05/titanic-fearless-dinosaur-unearthed/">Titanic Fearless Dinosaur Unearthed</a></li>

<li><a href="http://scienceblogs.com/gregladen/2014/09/03/flying-dinosaurs-a-new-book-on-the-dinosaur-bird-link/">Flying Dinosaurs: A New Book on the Dinosaur Bird Link</a></li>

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Has #Ebola Death Toll Surpassed Malaria in West Africa?

September 11, 2014UncategorizedAfrica, Ebola, Ebola, Ebola, Ebola 2014 West African Outbreak, malaria, UncategorizedGreg Laden

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In the earlier days of the West African Ebola outbreak, it was not uncommon to hear people note that we should not panic about Ebola because, after all, far more people are killed from Malaria than Ebola. This is of course an irrelevant argument. That is like telling a person who has lost their family in a tragic airplane accident that it isn’t so bad because, after all, far more people die in car crashes than aircraft crashes. For example, on August 5th, James Bell write in the Guardian, in a piece called Concerned about Ebola? You’re worrying about the wrong disease:

Since the Ebola outbreak began in February, around 300,000 people have died from malaria, while tuberculosis has likely claimed over 600,000 lives. Ebola might have our attention, but it’s not even close to being the biggest problem in Africa right now. Even Lassa fever, which shares many of the terrifying symptoms of Ebola (including bleeding from the eyelids), kills many more than Ebola – and frequently finds its way to the US.

I’m not picking on James Bell here. A lot of people said things like this, and the facts are true, though as I said, there is almost always (actually, in exactly N-1 scenarios within a given domain of scenarios) an argument that goes like this, and it really isn’t particularly relevant unless one is tasked with dividing up a fixed set of resources that will be used for a fixed set of problems. Resources rarely come that way and problems are rarely solved that way. As I pointed out earlier, consider the thought experiment where you have $10,000,000 that you want to give to either developing an Ebola vaccine, or a Malaria vaccine. Since billions have been spent on developing a Malaria vaccine and there still isn’t one, your donation would be a drop in the bucket. Retrospectively, it would be equivalent to something like the combined costs of couriers and mail by researchers working on a Malaria vaccine over the last few decades. Or the cost of coffee and donuts in the break room. Or conference travel fees. Or something like that. The point is, a bunch of millions of dollars might actually produce an Ebola vaccine given the starting point we have now, or at least, move us a good deal in that direction.

But now, we can ask if Ebola in the countries that are heavily affected right now is still “minor” compared to Malaria.

This is a matter of numbers and the numbers are hard to come by. James Bell notes that between February and July, inclusively, there had been over 300,000 malaria deaths, I assume world wide. So the comparison is not really relevant; we should be looking at what is happening specifically in, for instance, Liberia, Guinea, and Sierra Leone (or the three combined perhaps). Comparing world wide figures to a regional outbreak is a bit like reducing the Malaria death rate by shifting from numbers from countries that have endemic Malaria to include the global population.

It is hard to know how many people die of malaria every year, and the quality of the data varies considerably from country to country. A fairly recent study (here’s a discussion of it) suggests that an older estimate of 600,000 deaths per year should be doubles to 1,200,000 deaths per years. Having worked and lived in a region with some of the worst malaria (measured numerous ways) for several years, I can easily accept a doubling of numbers. If we assume that 1.2 million is right, by the way, Bell’s number of 300,000 is actually conservative.

Using data from that malaria study and WHO’s Ebola data, we can make some comparisons. I’m including all the information so you can check my work.

Here we have data from Liberia, Guinea, and Sierra Leone. The population number and malaria deaths per year are both from the aforementioned study and pertain to 2012. Then I divided malaria deaths per year by 12 to get a monthly value. I’m more comfortable working in months than years because an Ebola outbreak is normally short lived, and the number of deaths changes dramatically from month to month.

Following this we have the total number of Ebola deaths per country (summed in the right hand column as are the above mentioned data) and the approximate number of months of the outbreak. Then, the total deaths divided by the number of months. This constitutes a low-ball estimate of deaths per month from Ebola for the given expanding outbreak. Here we can see that in the comparison between Malaria and Ebola, it is not clear that one is a greater threat than the other (142:92, 49:67, 145:144).

Then we have the August-only monthly number of deaths. Here we dee that Ebola is huge compared to Malaria. So, back when people were saying “Malaria is worse,” in late July and early August, Ebola was starting to prove them wrong.

The last two numbers are calculated for all three countries combined. Here we are going out on a limb, and it is better statistically to crawl out on a thicker limb than a thinner limb. I made some estimates here, and those numbers conform to what is being talked about by WHO and others. If Ebola continues to spread at its current rate the daily number of new cases could be between 150 and 300 by the beginning of January. I state these as low vs high estimates, but actually, they are both conservative. Multiplying this by 30 days in a month, and dividing by 2 to approximate the ca 50% mortality rate, we have conservative numbers for Ebola that leave Malaria in the dust. Even if the doubling of estimated Malaria death rates should be doubled again, Ebola will be a bigger factor than Malaria.

	Liberia	Guinea	Sierra Leone	Total
Population	3,954,977	10,068,721	5,696,471	19,720,169
Malaria Deaths Per Year	1706	586	1734	4,026
Malaria Deaths Per Month	142	49	145	336
Ebola Deaths Total	508	400	461	1,369
Months of outbreak	6	6	3	–
Monthly average Ebola deaths	92	67	144	303
August Ebola Deaths	644	148	224	1,016
Estimated Janurary Ebola Deaths (low)	–	–	–	4,500
Estimated Janurary Ebola Deaths (high)	–	–	–	9,000

So that is why we should stop saying that Ebola is not Malaria, so relax about Ebola.

More on Ebola:

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Polar Vortex Begets Baby Boom?

September 6, 2014UncategorizedUncategorizedGreg Laden

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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.

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Titanic Fearless Dinosaur Unearthed

September 5, 2014UncategorizedArgentina, Dinosaurs, dinosaurs, Dreadnoughtus schrani, Paleontology, UncategorizedGreg Laden

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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:

(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

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

September 5, 2014UncategorizedClimate Change, Climate Change, Global Warming, Global Warming, Reuters Report, Sea Level Rise, UncategorizedGreg Laden

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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.)

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Scrivener on Linux: Oh Well…

August 29, 2014UncategorizedAuthoring tools, Linux, Linux, Publishing, Scrivener, Scrivener, Technology, Uncategorized, Word processing, Writing toolsGreg Laden

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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.

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.

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.

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.

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!

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.”

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.

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Welcome to the talking elevator

August 25, 2014UncategorizedUncategorizedGreg Laden

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Should it be "math" or "maths"?

August 21, 2014UncategorizedUncategorizedGreg Laden

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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”:

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Honey, I Shrunk The Dinosaurs …

August 19, 2014Birds, UncategorizedUncategorizedGreg Laden

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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

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Tanganyika v. Tanzania

August 16, 2014UncategorizedTanganyika, Tanzania, Uncategorized, WikipediaGreg Laden

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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.

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Climate Change Increases Frequency and Intensity of Wildfires

August 6, 2014Climate Change, UncategorizedClimate Change, Global Warming, severe weather, Uncategorized, WildfiresGreg Laden

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I don’t like the messaging Holdren almost always seems to start with: “While we can’t attribute a single bla bla bla to climate change” (it is not the right way to phrase what is happening, this is a good video just out:

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

August 6, 2014UncategorizedEbola, Ebola, Ebola, Uncategorized, West African OutbreakGreg Laden

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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)>

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.

Unhappy Anniversary World War I

July 28, 2014UncategorizedUncategorized, World War IGreg Laden

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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.

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

July 27, 2014UncategorizedAfrica, Ebola, Ebola 2014 outbreak, Uncategorized, West AfricaGreg Laden

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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).

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):

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.

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:

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:

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.

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.

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