The Bats Have Left the Belfry

In this run-up to Halloween season, I have to confess that I am puzzled that bats feature so prominently in Halloween iconography. In this part of the world, the bats are hibernating when Halloween rolls around. I have always been a big fan of bats. I am not a fan of Frank Miller, the asshole fascist who ruined the "Batman" franchise by making it all angsty and shit (and by "shit", I mean shit). My opinion of the "Batman" mythos can be summed up with a simple couplet:

The "Batman" that's the best,
Is the one with Adam West.

I can't decide which "Batman" villain is the best... whether it's Egghead (Vincent Price, W00T!) or King Tut. I love King Tut's supervillain origin story:





I suspect Bruce took pity on him because the good professor gave him a "Gentleman's B".


Post inspired by some yuks in the comment section at TBogg's place. Post title taken from one of the founding documents of "Goth" music.

Bat Dance

I am fortunate enough to work at some genuinely beautiful sites, and I get to see a lot of unusual things. Being bummed out by the general state of the world, I was able to find some solace around sundown.

I've always been enchanted by bats, ever since I was a small child. Well, as the sky was darkening, I noticed that an unusually large number of bats were flitting around the property. They weren't shy at all, often swooping close enough to me that I could hear the "whirring" of their wings. It was a really magical moment, especially considering all the mosquitoes they were devouring.

While I was enjoying the aerial dance of these cute chiropteran cutups, my friend and co-worker Fred was being driven... uh... batty by these unholy bird/mouse hybrids. Hilariously, I caught him jumping a couple of times, in an ambitious effort to catch one of these aeronauts. Poor thing, he was so out of his element.

What were you expecting? Huh?

Pokémon Patrolman

Tonight is my first night on Pokémon Patrol, I'm here because one of the guys in my department had a big conference for his day job, and the two other guys in the department were needed for regular shift coverage. It's a pretty cushy gig, and a rare opportunity for overtime. It also took me to the site where I work the least, so it was great to see people I haven't seen since the big all-staff meeting in the Spring. Like all of our worksites, this is a very pretty area of the world. I don't have any funny feline co-workers here, but there are two golf carts on which I can zip around... I really shouldn't talk about how fun this particular job is, though I'll be the first person to admit that the job is very cushy, except when it's not, even to my bosses.

Right now, the sun is going down, and there is an aerial shift change going on- the birds are retiring for the night, while the bats are heading out on their insect-abatement assignments. I've long had a fondness for bats, and I enjoy their aerobatics. This site also has a lot of deer- pretty, shy ones unlike the bolder deer of other sites. I chalk their shyness up to a greater coyote presence in this area.

All told, I can't complain about Pokémon Patrol, I haven't even had any Pokémongers show up- maybe the 'Site Closed' sign and the presence of a parked car is inspiring them to turn away. The only people that I've had interactions with so far were an exterminator who was responding to a call about a large hornets nest onsite (I should have told my boss that I could deal with it- knocking down hornets nests after dark, when the insects cannot function, is one of my specialties), a contractor who had done work for us in the past who was just driving through the vicinity with a friend (I had a nice conversation with the guy, and told him to call our main office to ascertain whether there was any need for his services), and a woman who was asking for directions, but didn't want to drive on any of the main roads to get to her destination...

"I don't live around here, but I would suggest you take the *REDACTED* parkway."
"I don't want to drive on the parkway."
"Then you can take Route *Redacted*."
"I don't want to take Route *Redacted*"
"Then you can take Route *Redacted-B*."
"I don't want to take Route *Redacted-B*."
"Then I can't help you, there aren't any alternatives that I know."
"I'll take Route *Redacted*."

I think I would have preferred a Pokémonger. A 'squirtle' is less elusive than a mystical highway that this woman would have wanted to drive.

Now that the sun has gone down, things should be real quiet. It's a Monday night, the site is pretty remote, and I think that the 'navigation' system of the game is a bit screwed up now, so people have a harder time locating their Pokémon sites. I haven't received word of the site being removed from the system, so the 'patrol' is going on until the end of the week, when we will re-assess the need. It's not a bad gig, and at this point in time, everyone in the department has gotten overtime.

I'm not complaining, things are pretty sweet.

Weaponization of the DOJ Against Leftist Activists?

Perhaps I'm being a bit paranoid, but I found this tweet from Vulgarmort very disturbing:

Consideration is being given to declaring ANTIFA, the gutless Radical Left Wack Jobs who go around hitting (only non-fighters) people over the heads with baseball bats, a major Organization of Terror (along with MS-13 & others). Would make it easier for police to do their job!

— Donald J. Trump (@realDonaldTrump) July 27, 2019

The characterization of antifascist activists as terrorists follows upon a similar proclamation by Ted Cruz. It is particularly sinister in light of the proposed end of the moratorium on the federal death penalty. It is not inconceivable that the Trump Maladministration would label political opponents 'terrorists', with the threat of a potential death sentence hanging over their heads.

In three weeks, a coterie of far-right figures from around the country plans on staging an armed rally in Portland. They have threatened violence, but in the current media climate, the gutless commentators will probably cling to the narrative that the Portland natives who protest this invasion are the villains.

The current regime is exhibiting the fourteen characteristics of fascism, and this current push to label their opponents on the left as terrorists may signal that their policies might take a turn for the worse.

Clark WolverAshton Smith

I have long been a big fan of teller of weird tales Clark Ashton Smith, whose stories combine a highfalutin' vocabulary with a detached-yet-macabre sense of humor. One of Smith's best known stories is The Vaults of Yoh-Vombis, a creepy tale of an archaeological expedition on a Percival Lowellesque Mars. Smut Clyde clued me into a comic book adaptation of the story by Richard Corben. Poking around the intert00bz, I found a comic by legendary cartoonist Basil Wolverton which is eerily similar to CAS' tale of terror:

The Brain-Bats of Venus is available in its entirety at Archive.org. It's a fun-yet-creepy comic by a legend, who looks to be ripping off inspired by another legend.

They Grow up so Fast

I don't know anyone who doesn't instantly fall in love with barn swallows (Hirundo rustica).  They are attractive birds which eat flying insects and have a particularly aerobatic flying ability.  I enjoy watching them flitting about the property, admiring their athleticism and thinking of all the mosquitoes they must be eating.  As the evening draws near, there's a shift change, and the equally aerobatic bats take over the flying insectivore niche.

We have one particular building with an overhang, and the swallows love to build their nests underneath this structure, plastering their mud nurseries under the beams.  Whenever we check on this building in the course of our job duties, we are greeted by the enchanting young birds:

Soon, these little beauties will be joining their parents on the wing, zipping about in zig-zag fashion, gobbling up mosquitoes in a particularly balletic fashion.  They are sure to enchant me for a few more weeks, before flying south to Central or South America, and for that (and the pest control work), I am grateful.

Old Friends, New Friends, Ancient Friends

Today was an awesome day. I made plans to meet up with a co-worker, a friend of hers from Melbourne who is in the midst of a cross-U.S. motorcycle odyssey, and Major Kong at the American Museum of Natural History, which is my beloved Temple of Science!!! Unfortunately, my co-worker had to bail, because she was suffering from a migraine and a bad flare-up of her allergies.

After a bit of a "hiccup", which saw me circling around the Kingsbridge section of the Bronx looking for parking near the "1 Train", I met Major Kong and our antipodean friend, who I will dub P.J. in the interest of brevity and his privacy, at the parkside entrance of the museum around twenty minutes past eleven o'clock. We made a bee-line for the fourth floor, to the halls of vertebrate paleontology, where I paused to explain how I made peace with the Hall of Vertebrate Paleontology being named after David Koch. The last time the good Major had graced these halls, the Tyrannosaurus rex was in its "Godzilla" posture, rather than the more accurate stalking posture in which it is now displayed. We then high-tailed it to the pterosaurs exhibit- longtime readers will know that the Major is the go-to authority on aviation. Ancient fliers, meet a current flier! I'm going to have to put up a post specifically about the pterosaurs exhibit. Right now, suffice it to say that the new reproductions of pterosaurs are a lot more colorful than the older ones- rather than the leathery lizard-bats of yore, the current depictions are of colorful, fuzz-covered (pterosaurs have been known to have fur since the early 70s) lookers. The variety of well-preserved fossils bearing all sorts of crests on their heads is a recent, lucky discovery... as I said, I'll have to compose a post solely on this exhibit.

The crown jewel of the exhibit is a reproduction of Quetzalcoatlus northropi, a giant with a wingspan of about ten meters (approximately 33 feet). Major Kong dubbed it "the B-52 of pterosaurs"- that pretty much sums it up. The exhibit also features interactive displays, in which one can "pilot" a pterosaur. Major Kong took a turn at piloting a Pteranodon longiceps, explaining the conditions leading to a stall. P.J. told us anecdote about his childhood home in Queensland- the conventional wisdom in this cyclone-prone region of Australia was to build houses with flat roofs, but certain winds would actually create lift, ripping off a flat roof, so his father built a new roof, pitched to create "stall" conditions.

After a good long time with our pterosaur buddies, we returned to the Hall of Vertebrate Paleontology, this time spending time with the mammalian fossils. We then headed to the planetarium where we strolled around the sphere for a while until we decided to bring things back to Earth, checking out the hall of earth science. We then made our way through the hall of North American mammals, the hall of human evolution, and eventually to the famous blue whale sculpture, which has been renovated to reflect a better knowledge of blue whale anatomy. The changes are minor enough so I could quip to Major Kong that some things haven't really changed since his last visit. We ended up our visit by checking the hall of meteorites and the hall of gemstones- the Star of India star sapphire being the most notable of the gems on display.

After our museum tour, which lasted over four glorious hours, we headed to the venerable Grey's Papaya for their famous hot dogs and fruit drinks. Fortified, we strolled east on West 72nd St, past the Dakota, and entered Central Park near Strawberry Fields- there were several acoustic guitars in evidence. Protip for emo college types, get your asses their now and play renditions of Beatles tunes, and you may be fawned on by cute tourists of whichever gender you wish to attract. A turn around the park, toward the Loeb Boathouse, and we were winding down the day. We parted ways at the "B,C" station at 72nd St.

It was a day well spent, hanging out with old friends, new friends, and ancient friends. Here's to friendship!

Secret Scince Club Zoom Lecture Recap: Mind and Music

Tonight, my great and good friends of the Secret Science Club are presenting a Zoom lecture with neuroscientist Dr David Sulzer of the Psychiatry, Neurology, and Pharmacology departments of Columbia University Medical Center.  Dr Sulzer is also a musician and composer, and an early SSC lecturer (sadly, before I started blogging).  He is cofounder of the Thai Elephant Orchestra, and the author of Music, Math, and Mind: The Physics and Neuroscience of Music.

Dr Sulzer told us he would be asking two broad questions:  Do other species hear music like we do? Can other species play musical instruments?  First, though, we would have to get some math and physics out of the way.

Sound is a wave in the air.  The wavelength is the length of a wave from corresponding parts, amplitude is the height of the wave.  Molecules are pushed together and pulled apart (water can't be compressed, when squeezed, it's amplitude rises  air can be squeezed.  The speed of a recurring wave is the frequency.  Humans can hear sounds of a frquencye of about 20 Hertz (waves per second)  an elephant can hear sounds at 1 Hz.  Human teenagers can hear up to about 20000 Hz, while adults lose some hearing ability and hear up to 15,000 Hz).

Dr Sulzer illustrated waves in the air by describing the workings of a siren, originally a rotating, perforated wheel on which compressed air is blown.  He used the Audacity program to illustrate frequency, and the harmonics which 'spice' a sound.  He also used a piano to play notes corresponding with frequencies.  He also gave us an experiment to perform, setting up a speaker in a hallway, then walking toward it to hear the amplitude change of the waves as a change in volume.  

Musical notes and harmonics are whole note multiples of frequency.  Pythagoras (Dr Sulzer joked that he is Christ-like because he wrote no books but his followers did) opined that the universe should make sense.  The universe should be explainable in recurring series of multiples.  From the quantum level to the cosmic level, these recurrences exist.  An octave is twice the frequency of the lower octave.

Dr Sulzer displayed a photo of a replica of a swan-wingbone flute (35,000 years old) that employs a pentatonic scale.  He then returned to Audacity, to demonstrate that adding harmonics always produces a periodic wave.    He assured us that this was all leading to something.  He then played a dissonant note, which messes with the period wave.  Notes that aren't harmonic can make beats, using interference to alter amplitude, cancelling out sounds.

Dr Sulzer then moved on to the neuroscience of music, where we recognize consonance and dissonance.  Dr Wilder Penfield, a pioneer in the surgical treatment of epilepsy, also studied the cortical regions which determine muscle movements and sensory inputs.  Nima Mesgarani studies the role of the cortex in analyzing sound,  mapping where plosives, fricatives, and nasals are analyzed.  Even ferrets can distinguish these sounds in human speech.

Do other animals hear like we do?  The frequency ranges can be very different (bats can hear up to 200K Hz, elephants hear about an octave lower that humans), but noise and consonance are built on physics.

Can other species play musical instruments?  Caged zebra finches can trigger musical sounds, even with no training or reward.  Would wild birds play musical instruments?  Mockingbirds have a wide musical vocabulary, and might be more likely to do so than, say, pigeons.  Susan Savage-Rumbaugh has studied bonobos interacting with musical instruments.  He then featured the Thai Elephant Orchestra, noting that the instruments provided to the elephants were chosen due to their popularity among the locals, such as the marimba-like ranat ek.  He also noted that elephants love harmonicas.

Dr Sulzer ended his lecture with a note about Asian elephant conservation.  In 1900, there were 100,000 domesticated elephants in Thailand. They were working animals.  Now, the population is about 3,700, since the elephants are not needed for work.  Logging was banned in 1989, so tourism is the only work.  

What other species play musical instruments?  Some songbirds, bonobos, elephants, but we are only scratching the surface.  Instruments must be ergonomic for other species, and must produce attractive sounds for those species.  Bad instruments are not appealing. 

The lecture was followed with a Q&A session.  Dorian started the process by asking if animals began by playing sounds in their own voices- zebra finches did, but developed musical tastes, playing other songbirds songs, and human music (but they avoided canary sounds because canaries are big and scary).  Regarding the Thai elephants' taste, they prefer 'hillbilly' music, the pentatonic music of the Northern Thai musicians who use fiddles- this is the music of their mahouts and caretakers, and the elephants are used to it.  Elephants are social animals, and this is the music of social gatherings of both humans and elephants.  African elephants are no longer domesticated, but they once were, such as Hannibal's famous elephants, so their musical tastes are unknown.  Why is some music scary?  How does the Devil's Interval work?  In consonant music, the notes reinforce each other.  While some dissonance is acceptable, it can be resolved.  If the frequencies are divided exactly in half, an irrational number results- according to legend, the Pythagorians drowned the person who discover.

Some bastard in the audience asked about the neurology of audition among different animal lineages- the auditory cortex is pretty well known, but the areas of the brain that interpret sound need to be studied better.  Other animals with a cortex have similar auditory areas, even though their ears may be radically different (such as insects which have ears on their knees).  Even among insects and crustaceans. the mechanisms are similar Marta Novotny, Lisa Olson of Columbia study bush crickets and katydids.

Another question involved animals which hear low-frequency sounds, such as whales.  It is possible that fin whales, before the noise of mechanized shipping, could have heard each other from hundreds of miles away.  Certain animals, such as frogs, have limited frequency ranges at which they hear.  Hearing is really the detection of vibrations, so even moths can 'hear' each other moving.

Another question involved people who love dissonant music- people love to add noise to their music, overblowing saxophones, using guitar feedback, adding additional noisemakers to instruments.  Synth pioneers such as Wendy Carlos immediately set about finding ways to 'dirty up' synthesized sounds. 

Another questioner asked if animals sounds also followed pentatonic scales, Dr Sulzer recommended the Cornell Laboratory of Ornithology's sound analyzing Raven app, and said that some bird songs have the octaves built in, he urged her to study this topic herself.

Can elephants maintain a steady beat?  They tend to be better than humans at it, but we have to be careful about anthropomorphizing their behavior.  Also, is this spontaneously play or training?  It's a combination of both.  The zebra finches weren't trained at all, but learn their songs from their fathers, and the elephants were trained for about five minutes.

As an added bonus, SSC alum Dr Diana Reiss chimed in during the Q&A to note that a lot of dolphin 'hearing' takes place through the jawbone after lauding Dr Sulzer's lecture.  It was a fun instance of Secret Science Synergy in action.

Once again, the Secret Science Club delivered a fantastic lecture, and Dr Sulzer managed to sneak in math and physics along with the fun stuff about musical elephants, kinda like making us eat our vegetables before dessert.  He added musical flourishes to illustrate his

For a taste of the SSC experience, here's a video of Dr Sulzer talking about the subject of his book:

Pour yourself a nice beverage and soak in that SCIENCE!!!!

Chupacabra Sighting

Tonight, as a nearly full moon was climbing the celestial vault, and the setting sun painted the western welkin a lovely orange, I had a rare treat... I saw a chupacabra. No, this wasn't the chupacabra of urban legend, but a real old-school goatsucker... and no, it wasn't Mickey Kaus.

In the deepening twilight, I had the pleasure of seeing two common nighthawks (Chordeiles minor) in flight. These birds are easily identified (if rarely seen) by long, narrow wings, each marked with a large white patch. They are very graceful in flight- more aerobatic than a jay or a crow, but less than a swift or a swallow- as an aside, my mind was damn near blown the day I learned that the swifts and swallows are not-closely related... this is a really beautiful example of convergent evolution. The nightjars have a feeding style similar to that of the swifts and swallows (and bats)- snapping up insects on the wing. Their aerial dance was something to behold.

Secret Science Club Post-Lecture Recap: Caves and Crocodiles

Last night, I headed down to the beautiful Bell House, in the Gowanus section of Brooklyn, for this month's Secret Science Club lecture. Last night's lecture marked the triumphant return of Dr Evon Hekkala, evolutionary biologist at the American Museum of Natural History and biology professor at Fordham University. Dr Hekkala lectured back in 2013, so this wasn't her first time at the Secret Science rodeo.

Dr Hekkala began her lecture with a simple declaration: Surprises should be part of science. She noted that sometimes things will be what you don't expect, citing the unexpected discoveries of Rosalind Franklin, Luis and Walter Alvarez, Raymond Dart, scientists whose discoveries upended prevailing conventional wisdom. She noted that life is full of good accidents, citing her own PhD woes, when she was unable to study lemurs, and settling on crocodilians as a field of study instead. She noted that ideas come from everyone and everywhere because people start out with curiosity... she joked that a child who overturns a container of milk is performing an experiment. In her case, she started out studying art history and anthropology.

She characterized art as depicting hypotheses, specifically citing the dioramas at AMNH, each of which depicts a particular moment in space and time. Museum collections are archives of the natural world. Museums started off as curiosity cabinets, collections of wonders from around the world. Most museum specimens are not on display- there are vast collections of preserved specimens behind the scenes. Archives are specimens, Dr Hekkala cited a 1930s-era letter in the AMNH archives concerning the danger of extinction faced by the indri, a letter she described as 'a smoking gun for a changing planet'. Dr Hekkala also noted that museums besides natural history museums have important scientific evidence- for example, the Metropolitan Museum of Art has a crocodile mummy.

Dr Hekkala's particular specialty is the study of crocodiles. Two decades ago, it was thought that Nile crocodiles (Crocodylus niloticus) were well known, but people were wrong about a lot of things, especially by thinking that crocodiles were 'living fossils'. One mystery about the crocodiles of Madagascar is whether there are separate species on the island. Back in the 1970s, African crocodiles were in danger of extinction, but were brought back by the introduction of sustainable crocodile leather production- economic value was an important factor in conservation. Alligators are approximately as closely related to crocodiles as humans are to bats, having split from each other approximately sixty-five million years ago- they have a similar form because this particular submarine predator physique works well. The extant crocodile populations of African can be divided into two species, with Crocodylus suchus inhabiting West Africa and Crocodylus niloticus inhabiting East Africa. The crocodiles of the New World are more closely related to the East African crocodiles than to the West African ones, with the lineages splitting between three and six million years ago. C. suchus and C. niloticus were long considered the same species, until Dr Hekkala ran DNA tests on samples of Egyptian crocodile mummies, finding them to be a distinct species, C. suchus. She joked that she was 'scooped' by a couple of centuries by French naturalist Étienne Geoffroy Saint-Hilaire who noted differences between the two species. Saint-Hilaire was inspired by the works of Herodotus, which described two separate, distinct populations of African crocodiles. Dr Hekkala is at the forefront of a new era, extracting ancient DNA from old specimens... she has been responsible for mummy genomic projects, extracting DNA from temples and museums full of crocodile mummies. She noted that the Egyptians could distinguish between niloticus and suchus, even without the benefit of DNA sequencing. Crocodile mummies are also being scanned, with one mummy actually containing almost fifty crocodile hatchlings and two larger specimens.

Dr Hekkala noted that crocodilians were considered important by many cultures that were in contact with them throughout their range- Egypt, Australia, Mexico, Madagascar. People observe the animals they live with, and crocodiles were considered to have various powers. The apothecary alligator crops up in art throughout the ages, and crocodilians were considered to have healing powers. Crocodilians' blood has antibiotic properties.

Dr Hekkala then narrowed her focus to the crocodiles of Madagascar. Once considered a separate species, Crocodylus madagascariensis, the Malagasy crocodile is now considered a subspecies of Crocodylys niloticus. Prior to the arrival of C. niloticus to the island, there was an endemic crocodilian species, Crocodylus robustus or Voay robustus (also known as the horned crocodile), which is now extinct, along with other Malagasy megafauna such as gorilla sized lemurs, dwarf hippopotomuses, and elephant birds. The extinction of Madagascar's megafauna is a big whodunit- was it people or pathogens or environmental change? What happened to the endemic horned crocodile of Madagascar? The Nile crocodile only arrived on the island about two thousand years ago. Humans started sporadically colonizing the island about twelve thousand years ago, with a sustained human habitation being achieved about two thousand years ago. Did the two crocodile species coexist? Up until the 1860s, explorers described two types of crocodiles. Did the horned crocodile succumb to human overexploitation? The horned crocodile is allied with the dwarf crocodiles, but only seven complete specimens are known. Did the Nile crocodile outcompete the horned crocodile? Did it 'swamp out' the horned crocodile through hybridization (if they were closely related enough). This being a whodunit, she went to the archives for clues, perusing the account of shipwrecked sailor Robert Drury for descriptions of wildlife.

In a stroke of luck, while watching a video of cave divers collecting lemur bones in a flooded Madagascar cave, Dr Hekkala noted a crocodile skull:





It turned out that PBS wanted to produce a program on the crocodiles of Madagascar, which led to what Dr Hekkala comically referred to as 'In Search of Lost Crocodile Lineages of Madagascar, or What I Did on my Summer Vacation'. I have to note that it just wouldn't be a Dr Evon Hekkala lecture without a generous dose of globetrotting adventure. She had twelve days to head to Madagascar with a film crew which would visit four locations on the island. She joked that it seemed impossible for this expedition to be pulled off in such short time, but a local 'fixer' was able to sort things out for them. They started off at the Croc Farm, then visited some sacred crocodile lakes (in local legend, crocodiles are ancestors of the populace- they were inhospitable people transformed into crocodiles because of their nastiness). While she and the crew weren't able to touch the crocodiles in the sacred lakes, where zebu are sacrificed to the crocs, they were able to collect DNA from traces in the water. They then traveled via boat and zebu cart (Dr Hekkala quipped 'planes, trains, and automobiles') to the spiky karst landscape of Ankarana Special Reserve. All the while, she was obtaining evidence- DNA from footprints, signs of 'robustus' among the crocodiles at Croc Farm. She kept the audience enthralled with pictures of lemurs, of giant baobabs, of rugged landscapes. The cave which the team visited was accessible by a forty foot ladder- originally, spelunkers would have to climb down a banyan root into the cave. There are numerous birds in the cave- raptors, kingfishers. The water in the cave is about 80F. The expedition was headed by Dr Laurie Godfrey, who Dr Hekkala photographed holding a lemur femur.

The cave was a trove of bones- four extinct lemur species could be found in one meter of sediment, and the bone collectors hit their specimen limit in four hours. The Madagascar Cave Diving Association provided the divers for the expedition. Dr Hekkala related a funny anecdote about falling in the mud in the cave, whereupon it took twenty minutes to extract her. To make matters more unpleasant, in order to maintain 'continuity' for the filming, she had to wear the muddy clothes the following day.

The cave dive was productive, a small 'robustus' skull was quickly found. The divers eventually found thirty crocodile skulls 'grinning' from the cave walls, though only two skulls were removed from the cave. Unfortunately, the team only had permits to collect lemur bones, not crocodile skulls, so Dr Hekkala took a tooth from one skull in order to obtain DNA samples. DNA testing will resolve the question of whether these crocodiles were a relic population with low genetic diversity or if they hybridized with the newly arrived Nile crocodiles. The two skulls examined by Dr Hekkala increased the diversity of known 'robustus' specimens by almost thirty percent. The twelve day trip was an accident, a happy one, and left Dr Hekkala resolved to obtain cave diving certification (as if she's not 'Indiana Jones' enough as it is!).

Dr Hekkala wrapped up her lecture by noting that, in order to understand the future, sometimes we have to visit the past. The study of biodiversity is crucial to our human survival. Also, outreach to children is crucial to the future success of humanity. so she is dedicated to teaching little kids as well as graduate students and, on occasion, barflies.

The lecture was followed with a Q&A session. Regarding the relationship between New World crocodiles and East African crocodiles, the divergence took place between the two lineages took place three to six million years ago. In a somewhat macabre aside, Dr Hekkala ruefully noted that the crocodiles probably drifted along the same currents that slave traders ended up using. The Nile crocodiles of Madagascar probably originated from the Zambezi River. Saltwater crocodiles have been encountered seven hundred miles from shore, so crocodiles are capable of long sea voyages. Since the construction of the Aswan Dam, crocodiles have gone extinct in Egypt, so no DNA is available for comparison.

Another question involved the cave ecology- pollen trapped in speleothems can provide clues about conditions in the cave, whether it was wetter or drier at various times. The crocodile remains are intact and articulated, so the crocs died in situ. Banyan trees near the cave entrance tend to attract animals, but perhaps the crocs came in through another entrance.

Another question involved the diversity of crocodilians- along with the birds, crocodilians are one of the great surviving archosaur lineages. There are two alligator species, several true crocodile species, dwarf crocodiles, caimans, and slender snouted gharials. These lineages diverged about sixty-five million years ago.

Another question regarded the suchus/niloticus divide in Africa- the suchus crocodiles are smaller and less aggressive than their eastern counterparts. It's possible that some hybridization occurs, but the extent is unknown.

Another question involved the antibiotic properties of crocodilian blood. Croc blood plasma was effective in killing staphlococcus, E. coli, and streptococcus bacteria. Additional testing is needed to gauge the extent of croc plasma antibiotic properties.

Some bastard in the audience asked Dr Hekkala to speculate why New World crocodiles haven't penetrated into the territory of the American alligator while the Chinese alligator has a tiny geographic distribution... could alligators have better cold tolerance? Dr Hekkala noted that there are crocodile populations at high elevations in Madagascar where the crocodiles are exposed to cool temperatures.

One again, Dr Hekkala knocked it out of the park... she hit what I call the 'Secret Science sweet spot'- a heavy dose of hard science with revelation of new discoveries, combined with adventure narrative and science/conservation advocacy, the whole shebang leavened with humor. Kudos to Dr Hekkala, Dorian and Margaret, and the staff of the beautiful Bell House. Now, here's a video of Dr Hekkala giving an overview of the 'Crocs' exhibit at AMNH:





Pour yourself a nice beverage and soak in that SCIENCE!!!

Fabulous Fossil Finds

I was happy as a clam when I saw bit on the BBC website about fossil finds in Wyoming that detail the early explosion of mammal species after the extinction of the non-avian dinosaurs. Further poking around the t00bz uncovered an interview on Chicago Tonight with Dr Lance Grande of the Field Museum, the University of Chicago and the University of Illinois. In the course of the interview, Dr Grande displays some gorgeously preserved fossils:





I am especially intrigued by the bird fossils which show the early evolution of parrots and the hummingbird/swift divergence. Also fascinating to me are the fossils of long-tailed, day flying bats and a carnivore with the earliest appearance of a prehensile tail.

Dr Grande's book, The Lost World of Fossil Lake: Snapshots from Deep Time, looks gorgeous. Hopefully, he'll be conducting a book tour that will bring him the NYC in the near future... I know some people who'd want to have a word with him.

Secret Science Club Post Lecture Recap: This Indecision's Bugging Me

Last night, I headed to the beautiful Bell House in the Gowanus section of Brooklyn for the latest Secret Science Club lecture, featuring neurologist Dr Anne Churchland of the Cold Spring Harbor laboratories. Dr Churchland seeks to bridge the gap between our knowledge of sensorimotor reflexes and more complex behavior. Specifically, she studies the decision-making process.

Since time immemorial, humans have wondered what makes us who we are and what makes us decide to do what we do. Disease states and drugged states played some role in elucidating the mysteries of the brain, but the brain was largely unknowable. Now that we have the ability to measure neuronal activity, and to perturb neuron groups, we can begin to understand the neural circuits which give rise to behavior. The ability to understand the brain's "circuitry" can also help us solve clinical problems, such as depression, which has a major cost. Approximately one in seventeen individuals in the U.S. suffers from severe mental illness.

Dr Churchland covered the topic of reflexive behavior, ranging from such simple, easily understood behaviors as the knee-jerk reflex to the more complex vestibulo ocular reflex, which stabilizes images when one moves one's head. Dr Churchland ran us through some tests to demonstrate the vestibulo-ocular reflex, having us move our fingers in front of our eyes and asking us if the image were blurred (she joked about how the beer-guzzling audience would naturally see blurred images).

She then showed us some headlines from the popular press which made a butchery of neuroscience, including the embarrassing NY Times Headline "You Love Your iPhone. Literally.", which cited activation of the insular cortex as evidence of "love" when one handled one's iPhone... though the insular cortex plays a role in disgust responses as well as love.

Dr Churchland posed the question, "Why is understanding the brain so hard?" One reason for this difficulty is the complexity of the brain- the brain is composed of eighty-six billion neurons, which form various structures within the brain. Another difficulty is that introspections about brain function are misleading. Dr Churchland used the game of chess as an example of incorrect intuitions about brain functions... while most laypersons believe that understanding the various chess moves is more difficult than understanding how the actual pieces are physically moved- in 1997, a computer was able to outplay a chess grandmaster , but the development of artificial intelligences which can manipulate objects is in its infancy (Dr Churchland showed a tragicomic video of a robot hand trying to pick up a coffee cup). Additionally, brains do different things in different animals. Dr Churchland cited bats and mice as two mammals with very different brains. One can look to see how problems are solved in animals- this works well for kidneys and hearts, which are very similar in different animals, but brains are much more diverse. A model system has to be chosen carefully due to the evolution of brains to serve different needs for different ecological niches.

Dr Churchland's major goal is to bridge the gap between sensorimotor reflexes and complex behaviors. Reflexes are "locked in" timewise- when one's knee is tapped with a mallet, the reflex occurs in an inflexible timeline. Complex decisions take place on a more flexible time scale, and integrate many systems of sensory input. Dr Churchland cited the purchase of a car as an example- one uses various sensory inputs to evaluate a vehicle, and there is no stereotypical time scale on which a final decision is made.

Dr Churchland went on to demostrate multisensory integration, and the differences between our processing of stimuli. Auditory stimuli are not very good in a spatial sense- it is often hard to pinpoint where a sound is coming from. Visual stimuli are very good at spatial resolution. As an example of this disparity, Dr Churchland cited a ventriloquist, who is able to exploit our poor auditory special recognition by providing a deceptive visual stimulus- we are "fooled" by the dummy's mouth moving, so it seems like the sound is emanating from the dummy. As a more glaring example, she pointed to the speakers around the room, from which her voice was emanating, and noted that none of us had any problem perceiving her as the source of her voice.

The visual system is not particularly good at timing, while the auditory system is much better at it- by flashing a dot once, but sending out two "beeps" in rapid succession, she was able to "fool" the audience into believing that two dots were flashed.

Subjects weigh incoming information according to its reliability- Dr Churchland cited a 2002 paper by Ernst and Banks (PDF) which dealt with the integration of visual and haptic (touch) stimuli- when deceptive visual stimuli are presented, a subject can use touch to correct perception. The brain can change from one stimulus to another moment-to-moment, with regards to environmental statistics- multisensory integration is geared towards a statistically optimal condition.

In her lab, Dr Churchland uses rodents as subjects- rodents are able to judge stimuli rates to be high or low. A subject was confronted by an array of LEDs and speakers and would respond to the auditory and visual stimuli in order to gain a reward, a drink of water. A low stimuli rate would indicate that the rat would be rewarded by placing its snout in the left-hand dispenser, a high stimuli rate would indicate the right-hand dispenser. Twelve "events" per second was chosen as the arbitrary "cutoff" between high and low rates. While the task that had to be performed by the rat was unnatural, it nevertheless tapped into natural neural pathways. A rat could be trained to shape its decision making behavior (at this point, Dr Churchland showed a hilarious "training" montage accompanied by the song The Eye of the Tiger). After showing video of the rat performing the necessary tasks, Dr Churchland called for a volunteer from the audience, and a game fellow named Issac was brought up to the stage to undergo the same "test" as the rats. He scored a whopping 85% success rate, better than any rat. For his efforts, Dr Churchland awarded him with a packet of string cheese.

Of course, studying behavior is only the first step in the "journey"- imaging of the brain was conducted while the rat was engaged in the decision making process. To supplement brain imagine, tetrodes fifteen microns in diameter were placed in the rats' skulls to measure neural activity. There was evidence of neurons firing in the posterior parietal cortex, which is imaged in this video, which indicates that the PPC plays a role in decision making.

In the Q&A some bastard in the audience asked Dr Churchland how the rats dealt with conflicting stimuli, say a high rate visual stimulus combined with a low rate auditory stimulus. She indicated that, in the case of conflict stimuli, the more reliable stimulus was the basis of the decision- a bright visual stimulus would be weighted more heavily than a low auditory stimulus. Another questioner in the audience asked about the role of glia in the brain, and Dr Churchland indicated that the glia play a "scaffolding" role- they help to define the structure of the brain.

Once again, last night's lecture was another triumph of the Secret Science Club. Dr Churchland gave a great presentation about the workaday aspects of a scientist's research, and gave a wonderful view into the efforts to increase our knowledge about the "divide" between simple reflexive behavior and complex behavior. For a brief taste of the subject of the lecture, here's a video of Dr Churchland discussing research that she had conducted using primates as subjects:

Gloaming

I often describe one of my jobs as "very cushy, except when it's not"- today has been the perfect exemplar of my little conundrum. My department is very small, so the slightest irregularity in scheduling can play hob with my circadian rhythms. I had to work "split" shifts today- both the midnight to eight A.M., and the four P.M to midnight. I watched the sun rise at 5:22, and watched it set at 8:30. In a cruel caprice of fortune, I had to address some issues midday with another job when I should have been ironing my ears. That being said, the schedule is a killer, but the actual workday has been wonderful.

This morning, I saw a thrilling little drama play out, as two mockingbirds mobbed a crow unrelentingly- at one point, they were joined by a red-winged blackbird, and the little passerines drove the crow across an open area, where it flushed a half dozen noisy killdeer out of hiding. The barn swallows were engaging in their marvellous aerobatics, and a catbird, looking quite saucy in its jaunty black cap, gave me a good-natured scolding.

This evening, as the sun lowered in the west, I sat outside to watch my beloved bats take over the aerobatic show as the swallows called it a day. The killdeer were still piping in the twilight, as multitudes of fireflies rose from the tall grass, looking like embers rising from a bonfire. In a low-lying area, where my favorite nettle patch gives way to cattails, another variety of firefly- a quicker, more nervous variety, with a rapid display reminiscent of a camera flash in color and duration- could be seen. These fireflies aren't easily caught and, by frequenting nettle patches and marshes, would pose all sorts of perils to any child dauntless enough to attempt such a capture.

I love the transition from day to night, and the changing of the faunal guard, so this tiny bit of doggerel I wrote years back is a lie, a bit of poetic license in service of a silly muse, too undignified to be numbered among the Nine:

Crepuscular critters
Give me the jitters.

With almost two hours of work to go, I'm tired, but my mood is good (in fact, I feel as jaunty as a catbird). In honor of the fireflies, here's a song which came to mind, even though it expresses a mood which is completely at odds with how I feel:





WARNING: Before you watch the video, please be warned that the song may turn you gay. Also, check out the video for Ennio Morricone's The Ecstasy of Gold at the link- pure bliss!

Postscript: I could have substituted a "T" for the "M" in the title, now that I re-read the post.

Secret Science Club Post-Lecture Recap: Sneaky Ebola, Sneakier Antibodies

Last night, I headed down the the beautiful Bell House, in the Gowanus section of Brooklyn, for this month's Secret Science Club lecture featuring microbiologist and immunologist Dr Kartik Chandran of the Albert Einstein College of Medicine. The topic of Dr Chandran's lecture was 'Unraveling and Counteracting the Infection Strategies of Emerging Viruses', with a specific focus on the Ebola virus. Dr Chandran researches how emerging viruses invade cells, and how medical practitioners could use 'jujutsu flips' to counteract their takeover strategies. Viruses such as Ebola emerge for a variety of reasons: clear-cutting forests, herding livestock which can allow viruses to change hosts, and climate change. Viruses can jump from various animal hosts into human populations. It takes a long time to figure out strategies to combat viruses when they jump to humans.

The Ebola virus was named after the Ebola River in the Democratic Republic of Congo. The Ebola virus was discovered in 1976 in a remote missionary station run by Belgian nuns. The events behind the emergence of the Ebola virus were the topic of Richard Preston's bestselling thriller The Hot Zone, which will be dramatized as a National Geographic miniseries which Dr Chandran ruefully predicted will probably be 'a hot mess'. The Ebola virus is lethal but rare, and strikes in remote places. For a long time, charities such as the Gates Foundation did not consider Ebola to be a major healthcare problem compared to infant mortality and malaria. That changed with the 2013-2016 outbreak of Ebola in West Africa, which set healthcare in the region back by a decade. A lot of healthcare personnel died in that outbreak. Currently, there is an outbreak of Ebola in the Democratic Republic of Congo, in an active warzone. A lot was learned during the West African outbreak- there is an urgent need for vaccines, but where do we begin?

The Ebola virus is a filovirus, a virus that forms a filament, a single strand of RNA. Viruses can be likened to molecular machine assemblies, they reproduce by taking over cells and turning them into virus factories. Viruses have an 'invasion machine' which gets them into cell cytoplasm and a 'payload', a genetic code which turns the cell into a virus factory. Dr Chandran is primarily interested in the delivery system of the virus, which is a glycoprotein. This large molecule sticks to the cell and enters the cell's lysosome in order to reproduce more viruses.

Dr Chandran posed a darkly jocular question: how do we study viruses without losing grad students? The invasion mechanism of Ebola can be attached to the vesicular stomatitis virus, a cattle pathogen which only causes minor illness in humans. In effect, this altered VSV is a 'sheep in wolf's clothing'. This invasion mechanism could then be used to develop antibodies to fight the Ebola virus. This therapy, named ZMapp, was dubbed by Newsweek magazine 'The Secret Serum that Could Cure Ebola'. Antibodies are 'tailor made' by the immune system to bind to viruses. Viruses evolve rapidly, though, and Dr Chandran compared harnessing antibodies to pin down the Ebola virus to burly wrestlers trying to pin down agile ballet dancers.

Dr Kent Brantly, an American doctor infected by Ebola while serving in Liberia, was treated with ZMapp. Dr Ada Igonoh of Nigeria contracted Ebola virus, was left for dead, but survived the infection (as an aside, I have to mention Nigeria's Dr Ameyo Adadevoh who quarantined Liberia's 'patient zero', containing the outbreak, and died of the disease). The ZMapp antibodies 'lasso' the Ebola virus' glycoprotein and targets it for destruction. The problem with ZMapp is that it only works on the Ebola Zaire strain (other strains are Bundibugyo, Sudan, Reston and Taï Forest). The Zaire strain is the most common Ebola strain, but epidemiologists cannot predict which strain of Ebola virus will jump out of nature.





Dr Chandran likened the interaction of viruses and antibodies to a lock and key- not all antibodies can be useful to all viruses. Viruses mutate to be resistant to antibodies- they 'bob and weave' so the antibodies can't bind. The search is on for a 'Rainbow Unicorn Antibody', an antibody which could recognize proteins that a virus cannot change and act on those proteins, effectively beating Ebola and other viruses at their own game. Viruses stick to certain receptors, they 'figure out' what sort of cells they need to affect. For example, the polio virus cannot bond to mouse cells unless the mouse receives the human receptor gene. Ebola has a 'homing beacon' on the lysosome, the NPC1 gene (Niemann-Pick, type C1). The NPC1 gene transports cholesterol from the lysosomes, and is present in eukaryotes from yeast to humans. Dr Chandran likened NPC1 to a janitor working in the basement who is coerced by the Ebola virus to allow a break-in. If the NPC1 gene can be knocked out, Ebola is ineffective at invading the cell. The NPC1 gene is rapidly evolving in 125 African bat species. Usually, 'housekeeping' genes such as NPC1 evolve slowly. It appears that bats are evolving to disallow Ebola's use of NPC1 as a receptor, which suggests that Ebola is a bat virus, new to primates. The most promising treatments for Ebola would target the virus' ability to dock with the NPC1 gene in human patients.

The Ebola virus glycoprotein uses a staged invasion strategy. Dr Chandran quipped that he is not a rocket scientist, but he likened the invasion strategy to a multi-staged rocket. The NPC1 gene is not located on the cell's surface, but is sequestered within the cell membrane. The virus must be 'eaten' by the cell, and once inside the lysosome, it 'takes off its disguise' and multiplies. All primates have the same NPC1 gene, it is the perfect site to put an antibody which can prevent the Ebola virus from docking in the lysosome. Combining antibodies increases their effectiveness, and one antibody, mAb-548, binds to the NPC1 gene better than the virus- it beats the virus every time. Other antibodies dock with the virus better than the NPC1 gene does. Combining antibodies blocks the binding sites of both virus and cell. Antibodies need to be in the right place at the right time- Ebola viruses can sneak into lysosomes without either antibody tagging along. Antibodies typically can only bind to one thing- there is an effort to develop antibodies with 'second arms' that can grab onto two sites. Such a 'two armed' antibody could bind to either the virus or the NPC1 gene. These bispecific antibodies were tested on mice infected with the Ebola Sudan strain, and two shots of the antibody were sufficient to protect the mice. Eventually, the virus was beat at its own game and mice could be protected from multiple Ebola strains.

Dr Chandran then shifted the subject of the lecture to the Rainbow Unicorn Antibody, a naturally occurring antibody which could work against all Ebola strains. Blood obtained from an Ebola survivor was tested, and the antibodies were 'gold that has to be fished out' of the sample. Memory B cells function as a library of everything than an individual has survived- if Ebola antibodies are sought, they must be fished out of these cells. The B cells are sequenced, the Ebola antibodies are obtained, and injected into yeast cells to produce additional antibodies. The yeast cells are then screened to obtain the desired gene sequences. The entire process takes about a month to complete. Using this technique, 350 antibodies were found from one Ebola survivor and twenty of them turned out to be 'Rainbow Unicorn Antibodies'. The task then is to make cocktails, starting with one antibody, then adding additional antibodies and testing them on monkeys. These cocktails are effective up to day seven of an infection.

In the field, administering medications is difficult, considering the protective gear that medical personnel need to wear, and the hot conditions that prevail in the regions where Ebola outbreaks occur. A intramuscular injection delivered cocktail would allow more people to be treated quickly. Such a cocktail is now being developed for human use, and it has the potential to be used to treat multiple viruses: filoviruses, hantaviruses, nairoviruses, pneumoviruses, alphaviruses, and flaviviruses.

Dr Chandran ended his lecture by mentioning his participation in an organization called the Prometheus Group, which was formed to transform human antibodies into antiviral treatments in three years. He likened the group's approach to 'jazz improvisation' to develop many tools to fight viral diseases.

The lecture was followed by a Q&A session. The first question concerned the unintended consequences of turning off the NPC1 gene... when the gene is turned off, cells can get clogged with cholesterol and cause neurological damage. This naturally occurs in individuals with Niemann-Pick Disease Type C. Turning off the NPC1 gene will cause cholesterol to accumulate over the course of several years, while Ebola can kill a patient in two weeks. Turning off one of two copies of the NPC1 gene can prevent Ebola infections while not leading to Niemann-Pick. Another question concerned the reasons why the West African Ebola outbreak died out- it was mainly due to quarantining patients and treating them with IV fluids. Individuals infected with Ebola must be isolated for 28 days in order to ensure the safety of others. Another question involved the lysosome... lysosome delivery systems are used by many viruses. Regarding the effects of different strains affecting different primates, it seems that crab-eating macaques are particularly vulnerable to the various Ebola virus strains. A question regarded Africa's genetic diversity, which is the greatest on the planet, and the possibility that it is a result from evolutionary responses to emerging viral outbreaks- the human genome contains a lot of genetic sequences from viruses. There was a question regarding the vulnerability of antibodies to viral mutation- if one antibody is involved, there is a good chance that the virus will evolve and thwart it, so multi-antibody cocktails are necessary. There was a question regarding using the same approach to combat HIV- therapies are under development, and it is possible that one will be available in the next two years or so.

Some bastard in the audience decided to ask a sociopolitical question- what is the role of conflict in Ebola outbreaks? The recent Ebola epidemics took place in regions wracked by civil war. Dr Chandran noted that conflict prevents responses by medical personnel, it destroys or degrades infrastructure, increases distrust of government. One necessary strategy to deal with outbreaks is to find influencers who can combat anti-medical social media memes, to convince people to get treatment. Trusted voices are needed to convince people to seek aid, not just voices from people in 'space suits'.

The last question concerned Dr Chandran's 'origin story', how did he end up studying Ebola. Dr Chandran indicated that he had been studying HIV early in his virology career, but was drawn to study Ebola by reading The Hot Zone. How's that for the power of books?

Once again, the Secret Science Club delivered the goods. Dr Chandran knocked it out of the park- he delivered an informative lecture on a topic which has been sensationalized by the media, conveying hard science fact in terms accessible to the layperson, discussing terrifying topics with just enough humor to leaven this heavy topic. I left the lecture more hopeful about humanity than I was when I entered. The 'good guys' are out there, and Dr Chandran is one of them. I also have a personal interest in Ebola, my brother Vin was deployed to Liberia in 2014 to build a medical infrastructure in the early days of the Ebola outbreak. It's good to know that scientists such as Dr Chandran are working to protect people who live in these 'hot zones', and people going to the hot zones to combat the disease, and other emergent diseases. Kudos to Dr Chandran, Dorian and Margaret, and the staff of the beautiful Bell House.

Here's a video on this topic by Dr Chandran, which showcases the fantastic imagery he displayed while he delivered his lecture. My recaps are mainly black-and-white, which isn't always up to the colorful, animated presentations utilized by the speakers:





Pour yourself a nice, refreshing beverage and soak in that SCIENCE!

Post- Lecture Recap: No Crocodile Tears in Brooklyn!

Last night, I headed down to the beautiful Bell House in the Gowanus section of Brooklyn for the latest Secret Science Club lecture, featuring evolutionary biologist Dr Evon Hekkala of Fordham University.

Dr Hekkala started her lecture with a brief autobiography. She had a personal statement, "doing" is better than "believing"- the process of scientific inquiry is what is important, not reliance on authorities. She then chronicled her rambling career, as she became disenchanted with the graphic design she studied as an undergrad, then progressed to a study of evolutionary theory, with a desire to study lemurs. Her study of lemurs was derailed when she discovered that the residents of the villages she visited had eaten the lemurs in the vicinity, but she came to the realization that one can't tell someone whose child's belly is distended with malnutrition to refrain from eating bushmeat. She was determined to return to Madagascar, and changed the focus of her studies to the native crocodiles. When she returned to Madagascar, she had to act as a courier for a team of researchers who had run low on funds. In a plot worthy of a "James Bond" movie, she detailed getting a transfer to her bank account, purchasing bundles of travelers' checks, then cashing them in Madagascar, where the exchange rate was so lopsided that she had to hire porters to help her carry the cash.

Dr Hekkala then gave a quick overview of the crocodiles. There are 12 recognized species of extant true crocodiles, genus Crocodylus (compared to two species of extant alligators). Crocodiles have been hunted for their skins, which can be made into a fine leather. They also face danger from wetlands development , chemicals which interfere with the development of their endocrine systems, and, perhaps most alarmingly, from global climate change, which can determine which gender hatchlings will develop in the nest.

Most of Dr Hekkala's work with crocodiles involved the East African "Nile" crocodile Crocodylus niloticus, which inhabits various ecological niches in Madagascar, including karst caverns and "sacred" lakes, such as Lake Ravelobe. Again, her work comes across as an action film (and was immortalized in a "National Geographic" documentary, Man-Eaters of Madagascar- in the space of a year, nine humans were killed by the crocodiles of Lake Ravelobe. Traditionally, the humans in the area coexisted peacefully with the crocodiles- women could wade into the waters of the lake with cans of worms on their heads while they fished. Unraveling the mystery of the crocodile attacks, Dr Hekkala determined that the lake was being fished by persons unfamiliar with the area, and runoff from slaughterhouse located upstream from the lake caused the crocodiles to become more aggressive (I am reminded of a case in Brazil where sewage runoff attracted aggressive sharks) while water management efforts by the government caused the level of the lake to rise and destroy crocodile nests and the lack of younger crocodiles (crocodiles are cannibals) removed an important food source from the lake. As an aside, I have been looking for Man-Eaters of Madagascar on the web, but have not been able to find the video, much to my chagrin. It really sounds like it has the makings of a great action/mystery flick.

Dr Hekkala then proceeded to discuss her efforts to collect DNA from crocodiles, both living and dead, and to sequence their genomes. Again, she was confronted by a mystery- ever since Herodotus wrote his histories, the crocodiles of the Nile were divided into aggressive, dangerous monsters and more docile crocodiles sacred to the ancient Egyptians, who often mummified them. The mummies were often wrapped in documents, and the possibility that such mummies were used as fuel would represent a tragic loss.

In 1807, the French naturalist Étienne Geoffroy Saint-Hilaire noticed differences in the skulls of the "sacred" crocodiles and the larger Nile crocodiles. Sadly, the two types of crocodiles were lumped together as C. niloticus and Saint-Hilaire's proposed species name Crocodylys suchus went largely forgotten. In her study of the DNA of various crocodile mummies and preserved specimens from museums around the globe, Dr Hekkala was able to determine that the crocodiles of the Nile belong to two distinct, distantly related species. Crocodilus niloticus is actually more closely related to the New World crocodiles than it is to the "rediscovered" C. suchus. Yet another instance of "sleuthing" on Dr Hekkala's part- is her career better than a movie, or what?

Dr Hekkala, no stranger to preserved crocodiles, then went into a brief digression into the tradition of scholars and apothecaries hanging crocodiles in their shops. In a case of truth being stranger than fiction, it turns out that crocodile blood has antibiotic properties... maybe those old quacks were onto something after all!

In the Q&A, some bastard in the audience asked Dr Hekkala about the contrast between the diversity and cosmopolitan (in the tropics and subtropics) distribution of the true crocodiles vs the relatively limited ranges of the two extant alligator species. Why are the crocs so much more successful? While Dr Hekkala didn't have a direct answer for this question, she noted that the alligators and crocodiles diverged about 65 million years ago, in the Cretaceous period, so alligators and crocodiles, despite superficial similarities, are about as closely related as bats and humans. The Nile crocodile, far from being "primitive", is about as old as humanity.

All told, this was another incredible Secret Science Club lecture... it hit the sweet spot between adventure narrative and hard science, and Dr Hekkala came across as a supergenius action star. She totally knocked it out of the park.

On an unrelated note, I met an old friend, handsome Johnny C., native of Ireland, but long-time Brooklyn resident, at the Bell House for the lecture. He coaches soccer for the same program I coach judo for- I had a big blond 'fro when I first met Johnny C. It was good to be able to hoist a few pints with an old friend and, more importantly, to win another convert over to the ways of the Secret Science Club.

Secret Science Club Post-Lecture Recap: This Lecture's Gone Viral

On Wednesday night, I headed down to the beautiful Bell House, in the Gowanus section of Brooklyn, for this month's Secret Science Club lecture featuring evolutionary biologist and virologist Dr Paul Turner of Yale University. Dr Turner titled his lecture Viruses: Good, Bad, and Ugly, in homage to his favorite spaghetti western.

Dr Turner began his lecture by addressing the amazing biodiversity of the planet, displaying first a list of North America's 'big five' charismatic megafauna- grizzly bears, caribou, moose, bighorn sheep, and wolves, contrasting it with an invisible 'big five' of North America- the Giardia protozoan, the influenza virus, the HIV retrovirus, a bacteriophage, and the Cordyceps fungi. He posed the question, are microbes nasty? His answer was that this was not necessarily true, that microbes can benefit human health. In humans, the microbiome, the community of bacteria, fungi, and viruses within the body, outnumbers the body's own cells. The microbiome can affect one's risk of heart disease, cancer, and other illnesses- it also plays a role in an individual's weight. It is currently believed that childhood exposure to microbes may help prevent autoimmune diseases, a concept known as the hygiene hypothesis. In experimental helminthic therapy, irradiated hookworm eggs are introduced into subjects in order to reduce autoimmune diseases. Dr Turner summed up this part of the lecture by noting that we live in a microbial world.

He then posed the question: What is a virus? After repeating his theme of ugly, good, and bad viruses, he posed another question: Might a virus save your life someday? Cellular life can be divided into three broad categories- bacteria, archaea, and eukaryotes... all of which form cells enclosed by a membrane. In contrast, viruses do not form cells, they characteristically have genetic material, DNA or RNA, surrounded by proteins. Viruses come in many forms- typical bacteriophages have tail vanes (Dr Turner facetiously compared them to the lunar lander). Influenza viruses contain RNA in the center of a protein shell. Viruses have a non-cellular life cycle. In order to reproduce, a virus enters the proper cell type, injects its genetic material, the viral genetic material hijacks the cell metabolism to copy itself, and the viral offspring are released from the cell.

Viruses are biodiverse, most are sub-microscopic... an electron microscope is needed to observe them. Influenza viruses and rhabdoviruses come in many shapes. Virus size does not correlate with host size- a whale can be infected by small viruses, a bacterium by large ones.

The evolutionary origin of viruses is a mystery- viruses appeared billions of years ago. Dr Turner posed a multiple choice question. A. Did viruses evolve before bacteria, being inhabitants of an RNA-based world that existed before DNA evolved? B. Did viruses evolve as parasites within cellular organisms? C. Are viruses 'devolved' cellular information? D. Did viruses arrive to Earth from space? Dr Turner jocularly illustrated these last two options with a picture of Devo and a picture of the lunar lander juxtaposed with a bacteriophage. Dr Turner indicated that A, B, and C are the three leading ideas.

Viruses reproduce very quickly, while bacteria can reproduce rapidly through binary fission, viruses can grow even faster as their progeny are formed in the cells of other organisms. Viruses are very abundant, they thrive in all environments, and they outnumber all other organisms. They are the most numerous of Earth's inhabitants. The human global population is approximately 7.2 billion, while the global virus population is estimated to be 10³¹. If the genes of all of the Earth's viruses were laid end-to-end, they would stretch to the Perseus Cluster, approximately 250 million light years away.

We live in a viral world- the bad viruses make the news, they are the viruses that are researched. There is evidence of ancient viral diseases- the Pharaoh Siptah had a clubbed foot that suggests polio, which is probably depicted on an image of a priest on a stele dating to 3700BCE. The mummified remains of Ramesses V indicate that he had suffered a case of smallpox. The polio virus is common in soil, it is usually harmless to humans, but becomes extremely dangerous when it enters the human nervous system. The smallpox virus was rendered extinct in its natural environment, the human body, and exists only in labs at the CDC and in Russia.

Dr Turner then took us on a tour of deadly epidemics- the 'Ugly' viruses. The 1918 flu killed 50 million to 100 million victims, a single flu strain managed to infect approximately 500 million individuals before the advent of commercial air travel. In our modern era, where travel is common, a flu epidemic may be just as deadly if the available vaccines don't match the flu strain. The Great Plague of the 14th century, which killed approximately 40% of Europe's population, is generally blamed on the bacterium Yersinia pestis, but other pathogens may have contributed to the death toll, hygiene and sanitation being sub-par at the time. The smallpox epidemic which began in 1520 in the New World decimated the Native American populations, but there are no estimates of the death toll. The AIDS epidemic, which is generally considered to have started in 1981, has claimed 39 million lives, with 78 million likely infected.

Virus emergence is a continual process- viruses can 'jump into' humans from other organisms. Bats commonly harbor viruses, which are often transmitted to pigs, then from the pigs to humans. HIV has jumped from other primates to humans, with HIV1 originating in chimpanzees and the less lethal HIV2 originating in monkeys. The HIV strains were probably introduced to humans between the 1920s and 1940s. Flu viruses are commonly transmitted by birds, especially waterfowl. The human immune system is 'naive' to bird flus- infection is easy, and we don't have the money and time to prevent 'fires', just to put them out. The mosquito born Zika virus was first identified in a rhesus monkey, only recently emerging in humans.

After dealing with the positively ugly viruses, Dr Turner focused his attention on the merely 'bad' viruses. Some viruses make you sick but don't kill you. He repeated the 1969-vintage quip: "We can put a man on the moon but we can't cure a common cold." Colds are caused by a variety of rhinoviruses. If an individual has respiratory problems, such as asthma, a cold can be serious, but many people are healthy enough to go to work with a cold, becoming links in the chains of contagion. Rotaviruses can kill children, but generally don't kill adults. Approximately 5% of child deaths in the developing world can be attributed to rotaviruses, which cause severe, dehydrating diarrhea.

Dr Turner then posed the question, can viruses be used in biocontrol of pests? He brought up the use of myxomatosis, the dreaded 'white blindness' of Watership Down, to control the invasive rabbit population of Australia in the 1950s. While partially successful, this introduction generally failed because the virus tended to kill rabbits before they had a chance to transmit it. Dr Turner chalked this up to yet another example of the folly of introducing invasive species to Australia.

Dr Turner then focused his attention on the 'good'- are viruses good for ecosystems? He noted that an absence of predators tends to throw biological systems out of balance, citing the absence of the wolf in most of North America, and the resultant explosion of the deer population, as a factor in the spread of the bacteria that cause Lyme disease... fewer deer, less Lyme. Viruses indirectly regulate the photosynthetic activity of cyanobacteria in the oceans. Cyanobacteria evolved about 3.5 billion years ago, and altered Earth's atmosphere by elevating oxygen levels. Cyanophages outnumber cyanobacteria by a factor of ten to one, regulating the cyanobacteria population. The cyanophages carry the genes which code for photosynthesis. Dr Turner noted that viruses infect other organisms and continually 'churn' genes. Approximately one in twenty of a person's daily breaths contain oxygen produced by virus genes.

Dr Turner then posed us a riddle: What would you trade 36 bushels of wheat, 72 of rice, 4 oxen, 12 sheep, 8 pigs, 2 barrels of wine, 4 barrels of beer, 2 tons of butter, 1000 pounds of cheese, a bed, a suit of clothes, and a silver cup for? The answer, of course, is a tulip bulb, but not just any tulip bulb, but a bulb infected by a tulip 'breaking' virus which resulted in fantastic mixtures of colors.

Dr Turner then posed the question, can viruses solve health problems? He brought up the topic of antibiotic resistence, citing MRSA and XDRTB as worrisome diseases- the drugs used to treat them pose dangers to the body. Antibiotic resistance is a global problem, and will be implicated in hundreds of millions of deaths worldwide by 2050. Bacteriophages are viruses that only kill bacteria- they could be used as an alternative to chemical antibiotics. Bacteriophages could be used as a self-amplifying drug- they multiply, find and kill new bacteria. In the mid-twentieth century, the Russians and Poles invested more heavily in phage therapy than in antibiotics. Phage therapy was used to treat field wounds and cholera. In the case of cholera, patients were rehydrated and given anti-cholera phages. Bacteria can evolve phage resistance. Dr Turner asked, can we develop a strategy that works even with the evolution of resistance? He indicated that the best strategy would be to discover phages which attack bacteria by binding to virulence factors- by binding to these sites, the phages would force the bacteria to evolve phage resistance by compromising virulence. Resistance would be achieved by becoming more dangerous. OMK01 (PDF link),a recently discovered bacteriophage, found in a Connecticut lake, effects the efflux pumps that bacteria use to remove antibiotics. OMK01 forces bacteria to trade phage resistance for antibiotic resistance. Dr Turner referred us to the 6/3/2016 edition of NPR's Science Friday. In 2006, the USDA approved the use of phages to combat bacteria which can taint deli meats.

Dr Turner then posed the question, would you be here without viruses? He indicated that 10% of our DNA comes from viruses which entered the genetic germ line- these genes are known as endogenous retrovirus genes. Syncytin, a protein produced by endogenous retroviral genes, is crucial to the formation of the placenta- the protein is necessary for the proper reaction of the immune system, which does not treat the fetus as a parasite. All placental mammals are made possible by viral DNA, which is a really good note on which to end a lecture.

The lecture was followed by a Q&A session. Some Bastard in the audience asked if viruses could be used in gene therapy to combat genetic diseases. While viruses are good at swapping out genes, CRISPRs are better tools, simple enought to use on multicellular organisms for correcting genomes. Another member of the audience asked, are viruses alive? Viruses are often conceived as 'quasi-living', but Dr Turner considers them living because they can reproduce and they are subject to natural selection. Asked whether viruses could jump from one 'domain' of life to another, Dr Turner indicated that this is unlikely, because cross-domain protein recognition tends to be rare, though it has often been attempted in the lab. Dr Turner then brought up the topic of bacteriophage prospecting becoming a growth industry- there is an illimitable supply of viruses out there, some of which may have therapeutic value. He then pondered whether or not humans co-evolved with phages to welcome them into the body. Asked about tips in case there's another dangerous flu outbreak, he noted that people should have a home preparedness kit so they can stay home until the epidemic wanes... I guess I need to download more ebooks!

Dr Turner delivered a top-notch lecture, informative and entertaining. I'm biased toward biological subjects, so this lecture was definitely in my top tier. Dr Turner, an extremely nice guy, lingered for an 'adult beverage' afterward, and I had a brief conversation with him about OMK01, which he told me was located in Dodge Pond, a polluted body of water not far from Lyme.

Kudos to Dr Turner, Dorian and Margaret, and the staff of the beautiful Bell House for yet another fantastic lecture. Here's the first of a three-part video series on viral biology by Dr Turner:





Crack open a beverage and soak in that SCIENCE! Be sure to watch the other two videos in the series- more videos, more drinking, more learning.

Oh, and this month's lecture was the annual Lasker Foundation collaboration with the Secret Science Club. Special thanks to the good folks at the foundation for their support. The foundation was giving out these great T-shirts with the slogan: If you think research is expensive, try disease.