Large Alligators, explained.

I've now seen several reactions to this video shouting questions like, "Why aren't they all dead?!", "Why aren't they running for their lives!?"

Well, sit yerself down my friend, I'm going to be brief.

1. Telephoto lens makes that ol' gator look bigger and closer than it is.

2. Gators rarely attack people unless fed by people, or defending nests. Average is less than one fatal attack a year in the US.

3. Gators are aquatic ambush predators. They don't run down large prey on land.

4.  Florida has well over a million gators. Spend time there, you learn not to worry about them.

5. I stepped on a live, submerged gator while working in the Everglades. It moved away. So did I.

6. Florida, outside Miami Beach, is the deep South. Somebody, possibly everybody, in that crowd is armed.

7. If they had all run away there would be no video of it.

 "Video: Large Gator Spotted in Florida" isn't quite fake news, but it certainly isn't news.

The Case of the Incomprehensibly Big Super Volcano

The Yellowstone Super Volcano is every American's favorite geological Apocalypse-in-waiting.* Every 700,000 years, give or take a few hundred thousand, this buries a significant portion of the western US in various astounding superlatives. But this article on the recent 4.8 earthquake at Yellowstone has the biggest (and silliest) superlative I've come across in a while. The article states that,

"Late last year a new study into the enormous super volcano found the underground magma chamber to be 2.5 times larger than previously thought — a cavern spanning some 90km by 30km and capable of holding 300 billion cubic kilometers of molten rock." 

Now, 90*30=2700, and 300 billion over 2700 is 111,111,111.1111, or a bit more than 110 million. So for the volume of the cavern to be 300 billion cubic kilometers, the cavern would have to be 110 million km deep, or roughly 8700 times the diameter of the earth, about 2/3 of the distance to the sun. That is one deep hole. With the utmost respect to the Ragnarokian prowess of the great and powerful Super Volcano, I question whether its magma chamber is roughly one third of the entire Earth. Rather, I suspect that this is another case of innumeracy (or at least i-unitacy) on the part of a reporter. 300 billion cubic kilometers of molten rock is not likely, but 300 billion cubic meters of molten rock is quite plausible. A cubic kilometer is a billion cubic meters, so 300 billion cubic meters is 300 cubic kilometers, which is about how big you would expect a 90*30 km cavern to be. Still figuratively, but not literally, astronomical.

The fact that reporters often don't understand units and don't do the basic arithmetic to check numbers is nothing new, but it has only just occurred to me that there is a systematic bias in this. As when NPR casually mentioned the "240 mile deep water" off Alexandria, or when I heard on the radio that a local bank was receiving a bailout in the hundreds of trillions of dollars, reporters always seem to get the numbers wrong in a way that grossly exaggerates the claim. If the magma cavern was stated to be 300 billion cubic millimeters (equal to 300 cubic meters) instead of 300 billion cubic kilometers, a reporter or editor probably would have found that unsatisfying and therefore caught the mistake. If it was instead 300 Sextillion cubic meters, it would look sexy and nobody would likely question it. But there is probably another bias at work. Once a number is really big, substituting another really big number generally doesn't change the impression much, and if one doesn't understand what the numbers mean, it is therefore equivalent. Incomprehensibly Big = Incomprehensibly Big. So overstating your case by a factor of a billion isn't go to raise nearly as many alarms as understating it and thereby eliminating the hugitude.


*You only think you prefer that tired old tectonic fault.

Article in The Scientist

http://www.the-scientist.com/?articles.view/articleNo/37154/title/Why-Women-Lose-Fertility/

Immortaly Tomfoolery

Their is a saying among scientists that the more you know about the scientific subject a journalist is writing about, the less of what he writes makes any sense. There is a long new article in the New York Times magazine about a hydrozoan jellyfish, Turritopsis dohrnii, which the author claims holds the key to immortality. As someone who happens to work on hydrozoans, and on aging, I can assure you that not a bit of it makes any sense. The title, "Can a Jellyfish Unlock the Secret of Immortality?" should be a dead giveaway that this is magical thinking with a whitewash of pseudoscience. The argument behind the article, striped of its misunderstandings and untruths,  goes something like this:

1. There is this jellyfish that can develop back from the medusa phase, which we normally think of as the adult, to the polpy phase, which we normally think of as the juvenile. It can then develop into the medusa phase again.
2. We are going to assume that this is the only know case of an organism that does not show a human-like pattern of aging.
3. We are going to assume that this non-human like pattern is equivalent to immortality.
4. We are going to assume that if we understood the mechanisms behind this assumed immortality, we would know how to make humans immortal.
5. We would know by now what makes them immortal except that we are going to assume that the one researcher I talked to extensively for the article who studies the species is the only one doing so.
6. We are going to assume that this one researcher is unfunded and working alone not because he is considered a crackpot, but because the rest of science is just too blind and lazy to see the importance of this man and his work.
7. We are going to assume that when he has learned a little bit more, we will achieve immortality.

I do not recommend that you read it, and mention it only because I have been asked about it, and because I would like to speak briefly about the word immortality. Immortality is defined as immunity from death. Immortal beings cannot be killed. Turritopsis dohrnii can very easily be killed. Put one out of water for a few minutes, feed it to a predatory snail, heat it, freeze it, slice, dice or frappe it, and it will be dead. Ergo not immortal. However the journalists are not to blame for the misuse of the word. A very good recent paper in PNAS from a very good careful research group is titled, "FoxO is a critical regulator of stem cell maintenance in immortal Hydra." They use the word immortal as many people in bio-gerontology do, to mean that the risk of death does not increase with age. My general impression is that using the word in this way is misleading, but that it is a lot flashier than 'nonsenescing' and therefore widely used.

Context

It is a real challenge to write papers that say, "here is what is wrong with this body of work I am reviewing" in a way that doesn't make the people who wrote that work feel like I am a nit-picky asshole. So I go back through my drafts multiple times, looking for things that are poorly stated or abrasive, and trying to fix them without losing the meaning. Then I send the draft to colleagues and ask them to look for anything I missed. I may still come across as a picker of nits, but I have minimized the insult as much as possible.

I am scheduled to give an interview to a radio reporter who wants comments from a not-involved scientist on a recent paper. I happen to know the senior author on that paper very slightly. In this situation I have none of the ability I would normally employ to go back and make sure the things I am saying aren't abrasive, overstated or unfounded. Rather the reporter has both the ability and the motive to find the most dramatic and controversial thing I say and put it in a context of her choosing.

Imagine that I say to the reporter, "This is really an excellent paper, that greatly increases our understanding of poodles and how fancy they are.  I'm not much of a poodle-fancier myself, and hadn't known there were so many kinds, let alone that they could do back flips so successfully. I would have worried that I would break their necks doing these experiments, but these guys clearly knew what they were doing. I may have to go out and get a couple of poodles."

The reporter could reorganize as follows: "A new study out of Paris has concluded that poodles are the fanciest dogs around. The authors compared the fanciness of a wide range of dog breeds on a variety of measures, and poodles took the cake, paws down. But not everyone in the field is fond of poodles. Dr. Daniel Levitis of Rostock, Germany is, 'not much of a poodle-fancier myself.' In fact, he says, 'I may have to go out and get a couple of poodles' What would he do with them? 'I would break their necks.'  So clearly there is still great scientific controversy regarding the worth of poodles."

I've been advised to avoid saying anything the least bit critical about the paper in question, myself, the authors or the weather, and instead to try to talk as much as possible about my own work. We'll see how that works out.

Genus species

When writing the genus and species of an organism, the genus name is capitalized, but the species name is not. Also note that both are usually italicized to differentiate them from common names.

Right: Homo sapiens
Wrong: Homo Sapiens, homo sapiens, Homo sapiens

This is a long established rule that is consistently followed by scientists but generally ignored by many science reporters and other non-scientists. It becomes very useful when taxonomic level could be unclear.

For example, the extant members of Bison are bison (the American bison) and bonasus (the European bison, or wisent). While bison has been out of immediate risk of extinction for some decades, bonasus populations remain small and have started to rise only recently in captivity and intensely managed reserves. Commercially available bison meat is bison. It is more commonly sold as buffalo meat, although the term buffalo is more properly used for Syncerus and Bubalus, rather than Bison.

It is prefered, but not in all contexts, that in scientific writing one put the abbriviated genus name ahead of the species name. This is done in part because many genera have identically named species. For example, Dendrocopos major, Parus caeruleus and Parus major are all birds of Europe. While P. major is clearly in Parus, P. caeruleus is sometimes placed in Cyanistes.

Scandal! Scientists find error in their own results!

Last September, a group of scientists in Italy got some strange results that made headlines around the world. Their results suggested that neutrinos were traveling faster than the speed of light.

I ask you to consider the following excerpt from a BBC article that came out just after their announcement:

"We tried to find all possible explanations for this," the report's author Antonio Ereditato of the Opera collaboration told BBC News on Thursday evening.
"We wanted to find a mistake - trivial mistakes, more complicated mistakes, or nasty effects - and we didn't.
"When you don't find anything, then you say 'well, now I'm forced to go out and ask the community to scrutinise this'."
Friday's meeting was designed to begin this process, with hopes that other scientists will find inconsistencies in the measurements and, hopefully, repeat the experiment elsewhere.
"Despite the large [statistical] significance of this measurement that you have seen and the stability of the analysis, since it has a potentially great impact on physics, this motivates the continuation of our studies in order to find still-unknown systematic effects," Dr Ereditato told the meeting.
"We look forward to independent measurement from other experiments."

I now ask you to consider the opening of NPR's article reporting the news that the error has probably been found:

Remember last year, when we reported that Italian scientists claimed to have broken the speed of light?

And this, from a blog post headed "That's Embarrassing" that one of my Facebook friends linked to:

Remember CERN's claim that they found neutrinos traveling faster than the speed of light? Weeeeeell now they want to renege, blaming a faulty fiber-optic cable and timing gear for the erroneous results. Jesus -- and we're supposed to trust these people to NOT tear open a black hole and swallow earth?

And this, linked to by another friend

Ridiculous: A Loose Cable Caused Those ‘Faster-Than-Light’ Particles

We know that Einstein always has the last laugh, but this is hilarious: the faster-than-light particles that could have wrecked his relativity theory are no more. It was a mistake in the test results caused by a loose cable.
Didn't anyone from the Genius Bar tell them about the first rule of tech support? Check your cables first! Oh, scientists!

I try not to get to whiny in complaining about the state of American science journalism, as I know it is not going to improve any time soon, but this really quite lamentable. The scientists involved were faced with data that could potentially destroy the theoretical underpinnings of their field. The wrong things to do would have been to ignore the data because they are theoretically heretical, or to make a big deal about their irrefutable and earthshaking discovery. Instead they did exactly what they should have done: They announce the situation to their peers and asked for help in evaluating the situation. They did this with full knowledge that their results would probably be shown to be in error, and that when that happened they would be mocked and insulted. This is an example of science working as it should, despite a dysfunctional press. No one, no matter how well established or well funded (or named Einstein), is the High Priest of science, and everyone's conclusions have to be reexamined and reconsidered. This responsibility to skepticism extends especially to one's own conclusions.

Their results have now been shown, by them, to have probably been an error, and the message the average American is getting is that these goofy Italian so-called-scientists were just too comical to even consider the possibility that Einstein was smarter than they are. NPR's science reporting is actually usually better than most, which is why I read their articles. In this case, they went with the invented scandal.

Could be good

A reporter has sent me a couple of questions about my review article. It hasn’t come out yet, but the Royal Society makes these things available to reporters on condition that news stories not come out before the actual article does. So anyway, I have somewhat mixed feelings about this particular email. I have written in the past about my low opinion of the general state of science journalism. The journalists generally fail to understand the science, oversimplify that misunderstanding to make it accessible, add in unrelated stuff to make it interesting and then compress it all into a few hundred words. The resulting news article is often nearly pure misinformation. I should say here that when the NYTimes covered a previous paper of mine, it was pretty well done, and some science news outlets are of course better than others, and this particular reporter is from one of my favorites, which gives me considerable confidence. The content of the questions did not. They gave me the distinct feeling that the reporter either hadn’t read, or hadn’t understood the article. He said in his email that he had read it, so that leaves the possibilities that he hadn’t understood, or that he was trying to provoke quotable explanations by pretending not to understand.

If he ends up writing about my work it will bring my mother great bragging points with her cousins whether he gets it right or not, but I would be greatly annoyed if he slaughters it.

Extinction is evolution

I often enjoy Olivia Judson's science blog on NYTimes.com. She has an actual science background, and gets the science badly wrong far less often than most other reporters of science.

Her most recent post is more in line with what I expect from science journalism. Without recapping her whole argument, she writes, "But if [evolution] has that much potential — how come organisms keep going extinct in nature? In other words, why does evolution keep failing?"

She then goes on to make a big deal about how evolution fails each time a population fails to evolve. But in so doing she fails to admit the distinction between evolution on the one hand and adaptation on the other.

Evolution is genetic change in lineages with time. Adaptation is the process by which the genetic makeup of a population is altered in a way that helps individuals of that population be more successful in their environment. Adaptation is one mechanism, and result of, evolution. It happens to be the best known mechanism, and the one that in the popular imagination defines evolution. But evolution has lots of other mechanisms. Genetic drift for example. Imagine you have a small population of squirrels on an island, some gray, some black. A disease comes through and kills a significant portion of the squirrels, and even though they are all equally susceptible to the disease, through the randomness of epidemiology more grays than black catch it and die. After the disease, the population has a higher proportion of black alleles than before. The population has evolved, because the proportional genetic makeup of the population has changed. But this is not an example of adaptation, because the genetic change was not caused by one version of the color gene conferring a selective advantage over the other. The allele frequencies "drifted" without being pushed by selective considerations. The next time the disease comes though more black squirrels could happen to catch it, and the allele frequencies could drift back.

So adaptation is not the be all and end all of evolution. Much of the evolution that happens is non-adaptive. And another important mechanisms of evolution is extinction. Imagine now that the disease killed not just some, but all of the squirrels on the island. That population is extinct. They are no longer represented in the genetic diversity of squirrels more generally, of rodents more generally, of mammals more generally. The remaining diversity, through the removal of that population, has changed. The extinct population has ceased evolving, but through their removal the larger group is left genetically less diverse. The genetic makeup of the larger lineage has changed, so evolution has occurred. It is also possible that the residual populations are more fit than the pre-epidemic average, because they are resistant to that particular disease. Whether or not this qualifies as adaptation depends on the fine details of the definition of adaptation you prefer. There is no standardly accepted definition, or rather different groups of biologists prefer different definitions. But all evolutionary biologists, save those who have crossed over into journalism, agree that extinction is an example of, not a failure of, evolution.

Ego boost of science.

There is a very flattering article in tomorrow's New York Times science section, by Natalie Angier, about our article on the definition of behavior. (There is also an online quiz associated with it.) It has, to be honest, many fewer errors than I generally expect from science journalism. The main one that will jump out at most of my peers is her statement that, "neither that textbook nor any other reference he consulted bothered to" define behavior precisely. We found lots of definitions, they just didn't agree with each other, or with what we or other biologists thought the word meant. That said, I think this NYTimes article is much better than most science reporting on the accuracy front. And of course, it is nice to have one's work described as "provocative and crisply written" in a large circulation newspaper.

She did neglect mention my two favorite things about the article; the title is, "Behavioral biologists do not agree on what constitutes behavior," and; in a biological article in a peer reviewed journal, we quote both Supreme Court Justice Potter Stewart's opinion on pornography and Conan-Doyle's Sherlock Holmes mystery of the dog that did nothing in the nighttime. I amuse myself heartily.

Persickity-Split

I've often vented about how terrible science journalism in this country is. The journalists never seem to understand the science they are writing about, and the more I know about the topic, the less they seem to know. I am finding now that as I gain greater expertise in particular topics, large portions of the scientific papers on those topics, written by scientists and published in peer-reviewed journals, strike me as incorporating significant misunderstandings. I many cases, I feel these misunderstandings are significant enough to call the value of the papers into question. By the time I retire, I will undoubtedly think even my own work is crap. I begin to understand why the practitioners in some fields seem to be primarily interested in trashing each other's work.

Carnival of Science!

The lead story on the BBC New's Science and Environment page is on the research of one of the post-doctoral researchers in my professor's lab. The idea is rather simple, the process was complex.
We know that climate changes over time, and that where one can find a particular type of habitat changes with the climate. Recently, using a wide range of data sources, scientists have been constructing both a detailed history of how climate has changed over time and what climate parameters limit the extent of particular habitats, such as South America's Atlantic Rainforest. My lab-mate, Ana Carnival (along with several collaborators) combined the climate history data with the climate requirement data to make maps of how the extent of the Atlantic forest has changed over the last 20,000 years. She found that there were a few relatively small areas that had been rainforest the whole time, even when climate shifts caused the rest of it to change to other habitat types, such as grassland. She identified these as 'rainforest refugia,' areas where rainforest species could survive through the millenia when the climate was inhospitable elsewhere. She then predicted that these refugia should be the centers from which genetic diversity spread to the rest of the forest once its borders once again grew. To test these predictions, she gathered genetic samples from three species of frogs which can survive only in the rainforest. Sure enough, the frog's DNA told the story she had predicted, confirming the refugia she had identified based on climate models. This is not only cool science, it has significant conservation implications. These refugia should house a large portion of the diversity found in the rainforest, because at some points in the last 20K years, all the rainforest species lived there. This suggests that if we are forced to make choices about which land to preserve (which we are) we might do well to preserve these refugia. And both the methods and the conclusions are potentially generalizable to other thretened habitats around the world.

One final thought: This is very cool work, and very much in line with what most people in my adviser's lab study, but it is so far from my own work that I barely understand the details. This may be why I don't notice any glaring errors in the BBC article, or maybe the UK press are not as bad at writing about science as the American press.

240 mile deep water?

Listening to NPR news this morning, I heard of a break in an underwater fiber-optic cable between Europe and the Middle East, just off the coast of Alexandria in "240 mile deep water."

It struck me as odd that this was such a minor news item. After all, the previous record for deepest water on earth was only seven miles (held by Challenger Deep, off the Marianas Islands.) NPR has just increased the deepest water on earth by 3328%, an astonishing accomplishment.

I am not sure what the message was supposed to be. Perhaps the water was 0.24 miles deep? The break was 240 miles from Alexandria? There are a great many plausible options.

To anyone to whom numbers communicate anything "240 mile deep water"just off shore in the relatively shallow Mediterranean should be instantly absurd. Unfortunately, basic competence in subjects such as science and math are not expected of those in the news business. If I were king...

Public warned that lead bullets make meat toxic

In an extremely important, despite being obvious, revelation, the government of North Dakota has ordered the destruction of tons of venison, after being presented with evidence that deer shot with high velocity lead bullets are not fit for eating because of microscopic lead fragments spread throughout the body of the deer.

While the science is not new, the difference this time is that the study was done by a hunter from North Dakota, rather than by the Peregrine Fund.

Note to hunters: If you shot a deer with a lead bullet and you are planning on feeding it to your family, you are poisoning them. Throw that meat out, buy some copper bullets, go shoot another deer.

Sloppy

I've written here before about what a poor job journalists generally do in describing science to the public. I was just reading this Op-Ed piece in the NYTimes and wincing over phrases such as "sharks are very primitive living fish" and "ensure the survival of a species," which reveal a very out of date and human-centric misunderstanding of evolution. The piece includes at least half a dozen points contradictory to modern evolutionary theory. I was just considering writing yet another response letter explaining to the author that natural selection does not favor traits because they help ensure the survival of the species, and so forth, when I looked at who the author is.

The attribution:
"Neil Shubin, an associate dean at the University of Chicago and the provost of the Field Museum, is the author of 'Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the Human Body.'"

Neil Shubin knows that evolution doesn't work that way. So why is he writing like a journalist? I can only guess it is because he wants to sell more books, and someone (the NYTimes, his publicist or him) felt that one has to adopt the public's misunderstanding in order to interest them. It is sad when scientists start writing like science journalists.

"Science" "Journalism"

Even taking into account how poor the state of science journalism is in this country, and what a sorry rag the San Fransisco Chronicle is, this piece on the danger posed to San Francisco by invasive pythons is well below the curve.
To summarize, there is an introduced population of Burmese pythons in the Everglades, 3100 miles away. A USGS lab used an off the shelf climate model to predict where in the US Burmese Pythons could deal with the climate, and San Francisco (along with pretty much the southern half of the US) showed up as one potential habitat.

The idiot who wrote the article then follows this train of thought to show that pythons will be eating pedestrians on Market Street by 2020:
•One python showed up at Lake Okeechobee, 100 miles north of the Everglades, and in the same direction it would travel if its single-minded goal was to reach Fisherman's Wharf.
•Pythons can travel up to 20 miles a month, and the road to SF is 3000 miles, so it will be here in 150 months, or about 12 years.
•Pythons eat mammals.
•"Human beings - like rodents, beavers and deer - are mammals, government scientists confirmed."
•Giant snakes falling from office buildings and eating you.
•QED

The sad thing is, reading the article, I am not sure if he is joking, but I am sure there are some people who will think this is a real threat.