Monday, April 30, 2012

Bio-Art: Find A Happy Place in Glowing Bacteria.

Two exams over. Two more due on Thursday. One next week Monday. An interview and volunteer thing this week.

Find a happy place. Find a happy place. Find a happy place...

...ooh, glowy! :D

That cute little beach scene was done entirely in glowing bacteria, probably Escherichia coli. These particular bacteria glow only under blacklight, but is is possible to make bacteria really glow in the dark as well. Since I have actually done this process, I know a few things about how they make bacteria glow in any color you choose.

First, you need to isolate the gene that makes the protein you want. Most blacklight-sensitive bacteria will be using jellyfish ( Aequorea victoria) genes. Some pigments, like the red up there, probably came from an anemone that glowed red in its lifetime. There are even genes isolated from protists that really do glow in the dark! There are special enzymes out there that cut DNA strands at certain sequences, and you need to find the right tool to cut out the ones that glow in the dark. We did not do this in class, but what we did do was pretty cool.

After being isolated, the glowing gene is integrated into something called a plasmid ring. Bacteria aren't like more complex organisms in that their DNA is fixed; instead, they are constantly recombining DNA from their environment and from each other! There was a whole temperature-changing process (I recall ice being involved) to make sure the bacteria took their extra DNA.

Also on the plasmid ring was an antibiotic; this ensured that only the bacteria with the glowing plasmid ring survived and multiplied. We needed a lot of them, after all. We selected the glowing ones out by putting smears on petri dishes laced with antibiotics. This is also how scientists test for antibiotic resistance in bacteria. If they can survive on that plate, watch out!

We had to wait a bit for the bacteria to grow, but after that, we put them under blacklight and practiced painting with them. Yes, painting. With brushes. There were no special scientific tools involved with drawing on a petri dish. By the end, we had a few good practice cultures of bacteria that glowed green under blacklight - just like Alba and GloFish!

Finally, after getting a good, pre-made culture of glowing bacteria, we took out paintbrushes...and just started painting on petri dishes. This has been done with other organisms since at least Alexander Fleming (the guy who discovered penicillin) using E.coli and other microbes, including fungi.  We've been painting with germs for a while, and here's the end result:

I look too sober for my own good. -.-;

Sunday, April 29, 2012

Let's Go Spelunking: Mexican Tetra.

Just when you thought cave animals could not get any weirder, this happens:

Those are both the same species of fish, the Mexican tetra (Astyanax mexicanus). It ranges from the Rio Grande in Texas to Central Mexico, both in caves and in surface rivers. The main (but not only) difference between them is simple: One has eyes and one does not.

The eyed and eyeless Mexican tetras have several differences. While the Mexican tetra's surface form looks like, well, a normal silvery fish, the cave form is albino, almost see-through, and, most obviously, eyeless. On the slightly less noticeable side of things, cave tetras store more energy as fat and have much better senses of smell and hearing than their sunlight-dwelling brethren. If you want to see how stuff that evolved in caves is different from its counterpart on the surface world, Mexican tetras are a great place to start. 

Love is blind! (c) Richard Borowsky.

When the blind specimens are born, they have eyes. As the fish grows, opaque skin grows over the eyes, rendering the fish completely blind. The eyes themselves also degenerate as the fish grows older. The coding for eyes is there, it just gets overridden as the fish matures. Nobody knows precisely why, but theories such as protein conservation and sheer dumb luck have both been tossed around.

The exotic pet trade loves these fish, particularly the blind ones. They recommend putting natural rocks into the tank and keeping them in semi-aggressive schools. The appeal is obvious: pet hobbyists, regardless of what sort, like different things.  It's hard to get more different than a blind fish with a see-through body. 

Creationists also love picking on this fish as evidence against evolution. Without factoring in the extensive adaptations this fish has made to cave life, it seems weird that an animal would develop eyes, then suddenly lose them. Clearly they are not familiar with the sheer amount of junk traits humans have retained over time, like our ill-adjustment to something as basic as being bipedal.

Let's Go Spelunking: Cave Shrimp + Crayfish

(Apologies: I went to take a nap and wound up sleeping longer than intended. Come hither, Hell Week...)

Remember when I mentioned that cave creatures had a strange aesthetic to them? Well, to be more specific, creatures that spend their lives exclusively in caves tend to have a few features in common.  These include pale skin, poor or absent eyesight, reduced size, and enhanced senses of hearing, touch, and smell. In human terms, 3/4 isn't bad, nerds.

Lincoln approves of cave shrimp?

Enter the Kentucky and Alabama cave shrimp (Palaemonias). They are both native to the Southwestern U.S. as their names imply. Yes, apparently the South has a lot of neat cave life. They eat anything that washes into the sediments underground. (FYI: Since several kinds of shrimp do in fact eat dirt like this, they are probably not the healthiest seafood in the world.) As the picture above demonstrates, they are smaller than a penny.

Cave shrimp are a prime example of what happens to 'normal' animals once they adapt to cave life. These shrimp are not just blind - they're completely eyeless. They're pure white with translucent skin. If they ever left the safety of the caves, they would die in a heartbeat. Even as they are, they have predators in other cave creatures such as salamanders, raccoons, and equally-blind cave crayfish (a case of the blind eating the blind).

Yes, crayfish live in the caves, too. There are several species (Cambarus pecki in Alabama; Procambarus elsewhere), several of which live in Florida and all of which are endangered. They look a lot like cave shrimp, only bigger, nastier, and with pincers. Like the shrimp, their skin is so light you can see through it - who needs melanin when you live in depths in which nothing can see? It's amazing; we could have saved so much mess in biology if some smart soul had bred translucent crayfish for us to study.

Both species of cave shrimp and all cave crayfish are endangered. The main cause for this classification is poisoned groundwater. As we've said before, freshwater ecosystems are fragile. So are species that are highly adapted to one environment. Cave shrimp will probably not be around much longer, so enjoy them while you can.

Friday, April 27, 2012

Let's Go Spelunking: Dismalites.

As you all probably know, I'm a huge fan of things that glow in the dark. Bioluminescent animals are of particular interest to me. Go figure that caves have some creatures that glow in the dark. Bioluminescence occurs wherever there's darkness - you just need to know where to look for it.

If fireflies and mushrooms are not your cup of tea and you still want to see something glow in the dark on land, look no further than the caves in Dismals Canyon, Alabama. The caves there are chock full of glowing worms called dismalites (Orfelia fultoni). They are related to the Arachnocampa of New Zealand. They make the inside of a cave look covered in cyan stars. 

Beware, looks are deceiving! That light show looks like a starry sky for many invertebrates flying into the cave, too. The glowing spots are just a trap to lure in tasty moths, larger flies, and other creepy crawlies, including mosquitoes. The glowly spots conceal an intricate web of mucous strings that works almost like a spiderweb, snatching prey in mid-air. Although we may be big enough to avoid getting caught in the web, other insects are not so bright and get stuck in the sticky strands. The larvae then feed on the helpless bugs to their hearts' content. If other bugs are not available, they resort to eating their own pupae.

These enchanting, yet vicious, little glow-worms are members of the family Diptera, which also contains the ever-popular fruit flies and garbage-eating houseflies. The adult form of these glowing larvae is a type of fungus gnat. They stay a long time in their larval form, however - if Arachnocampa are any indication, anywhere from 6 months to a year, which is like eons to a fly. Beelzebub would be so proud to see humans ogling his not-as-repulsive familiars.

As one may have suspected, there are a lot of larvae up there. This is an immense gathering of flies that just so happens to look attractive to us humans. They need very specific conditions to gather in such numbers. Along with keeping cave water clean for human use, let's preserve cave ecosystems to keep the second starry sky alive.

Wednesday, April 25, 2012

Let's Go Spelunking/They Actually Eat That: Bats.

It was difficult to pick a "They Actually Eat That" for this week. One, this week is Hell Week, meaning that a lot of tests and reports are due this week. Two, humans don't live in caves, so we haven't had that much time to turn the life there into cuisine. Three, umm, people eat bats, even if they aren't necessarily the cave-dwelling kind.

No, not like that! If you look up bat recipes, you get a million fake Halloween bat cupcakes, "bat wings" (black chicken wings made by Martha Stewart. May contain some seasoning from hell, but still not real bat), and so on. In America, we love eating bat-shaped things around long as no actual bats are involved.

Actually, a lot of places eat bat. If a place has bats, specifically flying foxes, someone will find a way to eat them. This restricts chiropteran cuisine to Africa, India, and Southeast Asia. China eats everything; no surprise that bats are on the menu. Sometimes, you can even find bat in Australia. A few places may eat microbats, but by and large, it's only flying foxes on the menu.

(This does not look like a flying fix to me...but there may be a scale issue.)

Eating flying foxes may not be particularly good for you. There is at least one flying fox species that has become endangered due to over-hunting. Flying foxes have also been linked to a number of diseases, including, but not limited to, SARS, Ebola, and Nipah virus. No offense to the cultures that regularly have bat on the menu, but there is a perfectly logical reason that some of us avoid it. Not that beef is really good for you, either...but that's for another entry.

As for what it tastes like? Rumor has it that bat meat smells, but otherwise tastes like chicken. It can be roasted like chicken, seasoned like chicken, and thrown in a stir fry like chicken. There really not much special about bat meat to most people except its sheer oddity.  It's mostly a big treat for foodies.

Tuesday, April 24, 2012

Let's Go Spelunking!: Waterfall-Climbing Cave Fish.

As hinted at in yesterday's entry, cave creatures can get pretty darn creepy. They often have pale skin and no eyes- usually enough to create a terrifying effect by themselves. They use senses that are either diminished in humans or completely absent. Troglobites (creatures that live in caves) are about as close as we can get to aliens on earth.  The deepsea abyss is a close second, of course.

Enter the first of the animals this week that will both terrify and fascinate you: the Waterfall Climbing Fish (Cryptotora thamicola).  It makes its home in a special type of limestone cave called a karst. It eats biofilm (i.e. that grimy stuff you might find in pet dishes) off of rocks in the darkness. Native only, and we mean only, to Thailand, it is darn near impossible to see in the wild. I don't think there are any captives, so very little is known about these fish indeed. It is also called the "cave angel fish."

The Waterfall Climbing Fish exhibits many traits common to most animals that spend their lives entirely in caves. It's blind. Its skin is white and slightly translucent. It sends chills through your soul because it looks so much like a regular fish, but not. Welcome to cave life!

Then the Waterfall Climbing Fish takes the weirdness up a notch by making Christians commit mass suicide: It climbs with its fins. Although not truly lobed like the fins of lungfish or coelacanths, the waterfall fish's fins are indeed able to move like feet. In that light, it's also interesting how these not-limbs are positioned (the actual 'body' of that fish isn't that long - on most fish, the hind fins would be way farther back). Give it a few millennia and we may well get an eyeless lizard that has evolved completely independently from all other reptiles. Darwin was right.

There is no endangered status for this fish, but it's so rare that it's listed as vulnerable. There is likely not enough data to truly classify it as endangered. However, nearly all freshwater ecosystems are extremely fragile; there's no reason a single cave in Thailand should be an exception to that. It probably does deserve to be on the endangered list if it's that rare.

Monday, April 23, 2012

Bio-Art/ Let's Go Spelunking: The Descent.

In a move expected by hopefully no one, the last week before finals will be a Theme Week! Thisweek's theme will be subterranean life. Although this may sound cheesy, life underground can be just as terrifying as life in the deepsea abyss...only it's on land, so one wrong evolutionary move and we may well have a monster on our hands with easy access to meat. This threat has not gone unnoticed by filmmakers.

The Descent is a British 2005 horror film about a group of ladies who go on a spelunking trip. Unfortunately, they wander into the wrong cave and come face to face with a number of problems - the least of which is that they do not have a map. Their equipment starts to malfunction as they wander deeper into the caves, one of their party breaks a leg, and they find hundred-year-old equipment. Oh, and they meet these guys:

Meet the crawlers, the monsters of The Descent. They appear at roughly 50 minutes into the movie, but their presence is preceded by a series of clicks and occasional flashes of humanoid figures in the caves. These are not aliens - they're cavemen who never really left the caves and evolved over millennia. As per the director Neil Marshall: "I didn't want to make them aliens because humans are the scariest things." So true.

Right off the bat (ha ha), it is easy to tell that a ton of effort went into making these things not only creepy, but also well-adapted to their environment. Like many cave creatures, they have pale skin and are completely blind. They hunt entirely by sound (as confirmed both by their clicks and a rather annoying alarm clock), just like microbats. Although hard to catch, I'm pretty sure their limbs are not only adapted to scale walls, but also slightly longer than those of an average human. Basically, the women were doomed as soon as they wandered into the wrong cave...but they put up one helluva fight until the end. (No, it does not end well - the 'happy' American ending was a hallucination in the original British version.)

Besides making them perfect cave hominids in terms of adaptations, the directors were careful to show that these creatures had families very much like humans do. Female and child crawlers can be seen in the film as well. Unlike Clover, who was meant to illicit sympathy on some level but never really made it, The Descent's crawlers touch a human nerve. Even with the fear factor going, once one sees that these things have lives of sorts, one can't help but wonder who the real monsters are. There are a few jarring scenes that make the parallel between humans and crawlers particularly close - for example, when one of the women stabs a crawler to death, then immediately goes nuts on a fellow party member. A natural reaction, but ouch. (I'll snap one tomorrow, K?) 

The Descent is definitely one of the better horror flicks I've seen in my lifetime. A lot of thought went into the monsters, the characters, and the setting - my summary is extremely condensed. I'll be rewatching it at least once because I likely missed something (And owe you all a cap.) . Still deserves the relatively good ratings from online critics like Rotten Tomatoes and IMDB, so give it a shot if spelunking horror is up your alley. Avoid the American knockoff, The Cave, like the plague.

Sunday, April 22, 2012

Creature Feature: Blue Garter Snake.

Back in the world of the living, the author of these posts sometimes wonders exactly how people can be afraid of snakes. It's not just her weird definition of 'cute' talking - put simply, exactly how is a bright pink boa terrifying?

Garters are already pretty neat snakes. Along with boas and vipers, they are among the serpents that have live babies. They are the ideal pet snake for someone who hates handling mice; they can eat worms, fish, and other things neither cute nor fuzzy. They have some very mild venom in there, but don't worry about it - it's only toxic to things much smaller than a human.

Oh, and did I mention that they come in electric blue?

There are a number of blue garter snakes, but the most coveted are the Florida bluestripe garters (Thamnophis sirtalis similis). They are native to, go figure, Florida, and are a subspecies of the Common Garter Snake (T. sirtalis). They prefer to eat other aquatic things, e,g. frogs, fish, and worms, as opposed to mice.

Starting with the obvious yet again, no, that snake was not Photoshopped. The bluestripe garter really is electric blue, which is one of the few colors that corn snakes could never manage. They are being selectively bred for more and more blue. Hopefully, the breeders have enough artistic sense that we will eventually end up with electric blue stripes on a velvety black background.

(Not mine.

If you happen to live in Florida, it is possible for you to catch these snakes in your on backyard. It can be found from the Gulf Coast inland. Look for it in pinelands, hammocks, prairies, and marshes - basically, anywhere that isn't urbanized to hell and back. They're not a rare snake at all, and they look awesome.

To a degree, I can understand some people's severe fear of snakes. As a friend of mine aptly pointed out, however, can you really take a snake seriously when it has a bright, multicolored neon display for a color palette? I think bright colors are cool, especially when black is used as contrast. The more ways we herpers have to eliminate the fear of snakes, the better.

Saturday, April 21, 2012

Creature Feature: Sinonyx.

I admit it: I've been a bad girl and been doing more extinct creatures than stuff one can find in the current era.Any extinct creatures besides dinosaurs, saber-tooth tigers, and mammoths tend to get shoved to the side- or even combined in the same era. *GAG.* Pardon my favoritism towards the lesser-known beings that dwell in the depths of your nightmares...and actually existed, of course.

Enter mesonychids. Oh, how I love mesonychids at this blog. Sinonyx up there was one of the first, and was found in China. It lived around 56 million years ago. Like all mesonychids, it was a rare example of a hooved carnivore. It probably lived along shorelines, snapping up fish and whatever other forms of meat it could find.

Sinonyx was a little badass. It was about the size of the modern wolf and similarly built for stamina and speed. It had hooves, so it was probably a little faster than a wolf, even though the two animals were roughly the same size. This was small for a mesonychid, but still a threat.

Found here, please don't sue.

Two words: Those JAWS! Sinonyx had a huge skull in proportion to its body, much like a pit bull (no offense pitty lovers) or Tasmanian devil. Unfortunately, every aspect of that skull was geared toward jaw power; the skull housed an extremely tiny brain.

Sinonyx was, debatably, one of the first cetaceans-to-be. There's a lot of subtle detail that goes into defending that this particular mesonychid as a whale relative, but the best and most easily-explained piece of evidence is that insane jaw. It's very long and narrow, just like the jaw of a dolphin or killer whale. There are more subtle things (like earbones) that make people think Sinonyx was the first real step towards whales.

Also, that name. Seriously, tell me that that name doesn't sound like it should belong to the fursona of a teen trying to be goth and cooler than they actually are. In all seriousness? It means "Chinese claw." Still a cool name for a metal band or something, which I would totally listen to if they used the animal as their mascot.

Thursday, April 19, 2012

Creature Feature: Tiger Mosquito.

Y'know what's really ironic? Humans are so good at killing other species that there have been movies and anime series devoted to how humanity's recklessness will wreck the planet. We eat literally everything that is edible.We should be able to kill any species we want.

Yet we suck hard at killing invasive species. There are a number of reasons for this. Sometimes, we introduce extremely fertile species by accident through the pet trade. The main carrier for invasive freshwater species is, get this, ballast water - excess water that ships take in to adjust their weight, then dump as soon as they hit port. Invasive species can get in anywhere and establish themselves thanks to the globalization of humanity...and we can't do a thing to stop them.

So when we introduce a non-native mosquito? Shoooot, we already have problems killing the bastards.


The Asian tiger mosquito (Aedes albopictus) is actually pretty cool-looking for a death bug. It's native to the tropical areas of Southeast Asia. If you don't already know what a female mosquito eats, I feel sorry for you...and envy your location in a mosquito-free area. They're pretty much vampires.

The strangest thing is how these mosquitoes got here: via an international trade in used tires. Stagnant water had gathered in the tires at tire dumps, allowing mosquitoes to lay their eggs in a completely undisturbed environment. The larvae then got shipped to 28 countries around the world, including the United States, Australia, and the Middle East. Unlike most tropical species that only stick to hot, humid regions, these mosquitoes are able to handle cooler, dryer environments as well. We're frightened, and we haven't even gotten to the bad news yet.

The really bad news? Name a disease and these guys probably carry it. West Nile, yellow fever, and even heartworm in dogs and cats are all carried by the Asian tiger mosquito. The only good news is that, obviously, it can't carry things that don't use a mosquito as a vector (so no AIDS or cancer). Let us remind you that we suck at getting rid of these things, not for not trying.

It's ironic. We're so good at wiping out species that human-driven extinction is touted as being way faster than any other extinction event in Earth's history, and yet we fail at eradicating specific species, even if we put our minds to it. It's like the tiger mosquito, Asian carp, Burmese python, and bunnies are all laughing at us. If there is a God, it sure as hell has a weird sense of humor.

Wednesday, April 18, 2012

"They Actually Eat That:" Alligator.

Welcome to another delicious little installment of "They Actually Eat That." Here, we aim to prove that humans are so omnivorous that goats look at us the same way food critics do regulars at McDonald's. We are the absolute last species that other species should be copying or stealing the garbage of. Our ability to eat anything is only a small part of why species die around us, but it's a part nonetheless. (More species actually die from people conforming to 'standard' foods.) We're so omnivorous that it's sick, is the point.

Humans do one thing that absolutely no other species does: we eat apex predators. Apex predators, by definition, have nothing native to their ecosystem that eats them (keyword being "native," as we'll see later). It's what makes being a big predator good.

Then you add humans, and even apex predators are on the menu. Things get even nastier when that apex predator happens to be under threat already.

Enter alligator meat. It's classified as seafood, even though alligators are strictly freshwater reptiles. It is quite popular in southern states, particularly Louisiana and Florida. I can only assume that this is yet another good reason for gator farms to exist.

Gator meat is so popular, apparently, that there are a million websites and recipes for it. There are charts like the one below showing exactly how many parts of the gator can be eaten. There are almost as many ways to cook gator meat as there are for chicken. 

Disclaimer: We at "They Actually Eat That" do not advise you to go out into the Everglades and hunt a wild alligator. If you absolutely must have gator, please buy farmed gator. You don't know what the big guys in the wild have been eating; remember, concentrations of things like mercury are super-high in apex predators. Is it still kinda cool to be able to say that you've eaten alligator once? Sure.

Alligators also have the rare instance of being eaten in their natural habitat, albeit by an invasive predator. Florida is a hotbed of exotic pet smugglers. It happens to have an environment quite a lot like Southeast Asia, a place with giant pythons like Burms and retics. Snakes eat gators and gators eat snakes. Currently, the two mega-reptiles are in an arms race as to who will emerge victorious in the Florida Everglades; place your bets now and stay tuned.

Tuesday, April 17, 2012

Creature Feature: Palm Cockatoo.

Aww, parrots! Pirate references aside, there are few things that have the charm of a rainbow-colored, bright-eyed hookbill. There is very little bad to be said about parrots (unless you try owning one - then you get dust issues). Overall, they're happy, brightly-colored, intelligent, fun-loving birds.

Then you remember they have beaks. Parrots have strong, heavy beaks that can crush nuts with ease. Seriously, your finger is screwed if a large parrot bites it. If only they had the aggressive look to match that badassery...

(From thepetwiki.)

....yep, perfect candidate for "heavy metal parrot," there.

The Palm Cockatoo (Probosciger aterrimus) is probably the best parrot-y logo for a band ever. It crushes nuts for food, which is a good threat to anybody's masculinity.  It is native to Indonesia, New Guinea, and northern Australia. Unlike many of the creatures in that range, the palm cockatoo is nowhere near endangered. This is somewhat of a miracle, but more on why later.

Palm cockatoos are in a class all their own. No, really; they're the only members of their genus. Molecular testing says that they're distantly related from most other cockatoos.  If any cockatoo is an ancient cockatoo, it's probably the Palm.

Genetics talk aside, palm cockatoos are impressive birds to look at. They're the largest species of cockatoo in the world. Those red patches get brighter if the cockatoo gets stressed, making them one of the few birds that can change color. Their bill size is second only to that of the hyacinth macaw. Again, please think about that before you piss one of these birds off. (Is this guy nuts?)

These cockatoos have one of the neatest-sounding behaviors in the world: they drum. As in, they take a seed pod or heavy stick and drum it against a dead tree. Nobody really knows why they do this - dress rehearsal, perhaps? Their vocal repertoire isn't lacking, either, sporting a large vocabulary, a variety of whistles, and a call that sounds like a human's "hello." These guys truly are the rock stars of the parrot world!

You lookin' at me?

Palm cockatoos are available in the exotic pet trade with a price tag over 5,000 USD (I've seen snakes worth more). I'm honestly surprised they are not worth more; one of the candidates for "good pet" is a relatively fast breeding rate compared to humans. Some palm cockatoos do not breed until their 30's or 40's. They also live into their 80's, so if you do happen to be able to afford one, be sure to provide for it in your will.

Also...they can eat meat.