Sorry about the delay. The last couple months have involved some major changes and frenetic activity, and this post also expanded considerably in scope from what I originally had in mind, evolving (if you will) from a straightforward explanation of Linnaean taxonomy to an extremely detailed answer to the question "how do we know that we are descended from apes?" Since the post was so gigantic, I've split it in half. Here is part one. Read it, get some sleep, the next will be up in a couple days. I have one or two posts on taxonomy I want to do after this one, and then we should move right into evolutionary theory.

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The first scientist to call human beings animals and primates was a Christian creationist.

Carl Linnaeus (1707-1778) was a Swedish biologist, and like most Western natural scientists of his time, he was a Christian who believed all life was divinely created by God, more or less in its present form (he suggested that there might be little changes due to hybridization). He was also the inventor of what is usually called "Linnaean taxonomy" (remember that " . . . More

Happy Valentine's Day!

In celebration for this day where people give candy and Hallmark cards to the ones they love, I decided to share a few of the weirdest and wildest animal mating strategies I have ever come across. It almost make you feel lucky to be a Homonid!

Animals have been around much, much longer than us, and will most likely persist long after we are gone. So, animals are the true senseis of sex. They’ve been doing it longer, and are far better at it than we could ever be (yes, even better than the fabled Wilt Chamberlain).

And now, on to the main event!

I have combed through everything I have ever learnt about animals, and I have come up with a list of the five most bizarre, yet still interesting, animal mating strategies. Now, this is by no means a complete list, just the weirdest and most interesting. Believe me, there is a LOT more. If you like it, I’m sure I could be persuaded to write more.










5) Well, it IS stuck

Banana slugs look exactly as their name suggests, are about eight inch slugs the colour of a banana. The interesting thing about these animals is that since they are hermaphrodites, when mating time arises, they both possess female and male sex organs.

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This week's guest blogger is Joe Hanson. He is currently working on his Ph.D. in Cell and Molecular Biology at the University of Texas at Austin, where he works on things far less interesting than the work you are about to read, specifically mobile genetic elements and ancient introns. He blogs at It's Okay To Be Smart and runs an awesome Tumblr page of the same name (updated ten times as often). Joe can be found on Twitter @jtotheizzoe.

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I was on a little bit of a post-vacation downer this past week. Only, I didn’t actually go anywhere. Instead, the SXSW music (and arts and interactive and style) festival came to me, right at home in Austin, TX. It was a week of uplifting musical and artistic expression emanating from every street corner and bar in town, and much of could even be classified as good! As I look back on the last week, two things jump out at me: 1) Tall cans of cheap, hipster beer and 2) BEARDS.

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Last time, we introduced the nested classification of Linnaean taxonomy originally created in the mid-18th century by Christian creationist Carl Linnaeus. Using this classification system, we established that human beings are not only animals, but vertebrates…even if we completely avoid saying the word “evolution” and just look at our overall anatomy. Vertebrates, you make recall, are eukaryotes (they have cells with a nucleus), animals (mobile multicellular eukaryotes which eat the cells of other organisms), eumetazoans (animals with organized tissues), bilaterians (eumetazoans with bilateral symmetry), deuterostomes (bilaterians in which the opening for the anus develops before that for the mouth), chordates (deuterostomes which have a notochord, pharyngeal pouches, and a tail), craniates, and vertebrates (chordates with an internal skeleton protecting the brain and spinal chord).

Vertebrates include things that we call "fish," as well as amphibians (like frogs and salamanders), "reptiles" (like lizards, snakes, and crocodiles), mammals, and birds. However, several types of "fish" lack a couple of features possessed by most: notably jaws and a . . . More

Parents screamed, children cried and I looked on in horror at the scene unraveling around me in the Shamu tank at the San Diego Sea World in February 2010.

Death was up to his usual tricks.

The stadium was packed and the trainers were putting the whales through their paces. Birds circled above, eyeing the fish the trainers were using as rewards for Shamu and his pals performing their tricks

But then, a lone brown pelican, about the size of a poodle, landed on the far side of the tank to take advantage of the bounty.



The trainers didn’t notice. But Shamu did.

In an instant, Shamu dove under the water, swam up under the bird, opened his mouth and, with a splash, dragged it down. The trainers realized what happened when the carcass floated to the surface and the whales began fighting over the prize. They immediately stopped the show.

Instinct had trumped training, and Shamu was sent for the killer whale equivalent of a time-out.

A week later at Sea World in Florida, instinct won over conditioning yet again. Only this time, the victim was a female trainer. According to news sources, while the trainer lay down in a shallow area leading into the tank, her ponytail was floating and attracted the whale’s attenti . . . More

A genus is a group of very similar species (the plural is genera). The practice of naming genera and species is called alpha taxonomy. When we name a species, we say both the genus and species names together. For Tyrannosaurus rex, “rex” is the actual species. “Tyrannosaurus” is a genus (notice that both words are italicized; genera and species names can also be underlined). This means that you could have a bunch of closely related species which are all grouped under Tyrannosaurus. In fact, there is a form from Mongolia called Tarbosaurus bataar, which lived just a few million years before Tyrannosaurus rex, and which is almost identical to it. Some paleontologists think should be considered a species of Tyrannosaurus: Tyrannosaurus bataar. It is acceptable to give the genus name as just the first letter followed by a period, for example T. rex (but not as T-rex, T-Rex, as it is sometimes given). So, we could say that there are two species of Tyrannosaurus: T. rex and T. bataar.

Unfortunately, we are even vaguer on how to recognize a genus as how to recognize a species. As with the morphological species concept, it is pretty much based on similarity. But how similar? The genus Tyrannosaurus belongs to a group of theropods (meat-eating dinosaurs) called tyrannosaur . . . More

Tom Holtz, a well-known expert on tyrannosaurs, recently posted a blog entitled "What Should Everyone Know About Paleontology?" It is worth checking out.

The next few posts will discuss the subjects of taxonomy and systematics. In biology and paleontology, the word “taxonomy” refers to a system of naming living organisms, and (more importantly for this discussion), figuring out how to classify them (group them together). “Systematics” is a broader subject which includes taxonomy, but also considers the evolutionary relationships and history of organisms.

The word “species” refers to one of the most fundamental groups of living things. Intuitively, it isn’t hard to grasp more or less what a species is: a group of living things that are the exact same “kind” of thing. Apples are one species, oranges are another. Humans are one species, chimpanzees are a different species. However, saying that all humans are the same “kind” of thing is a little vague; what exactly does that mean?

There are several different definitions which have been proposed for species, but I’ll just mention a couple here. The “biological s . . . More

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The past few days have been very interesting and filled with questions and mysteries, but the surprising thing is that none of these events happened while I was awake. For the past four nights, I have experienced some of the craziest dreams in recent memory.

Four nights ago, I had a dream that I hunted poisonous snakes in my den using nothing but a woven blanket and my wits. There were copperheads, asps, king cobras and more. And yet, surprisingly, I only had to deal with one at a time.

It was like the snakes would wait their turn to be confronted by me and my most trusted sidekick, an old friend from elementary school who I hadn’t seen in well over a decade.

Three nights ago I dreamt that I was back in my high school and had to solve calculus equations that took up all the walls in the school. I was able to ask one person for help, so I invited Sheldon Cooper from TV’s The Big Bang Theory, but as soon as he saw them he ran away.



And the brutal taskmaster, my heavily accented calculus teacher from university, said that if I didn’t solve them all perfectly by the end of the school day, the school would blow up.

No pressure, eh?

Two nights ago resulted in one of the weirdest dreams, where space aliens took over C . . . More

In 1982, Angela Cavallo of Lawrenceville, Georgia received the Mom of the Year Award. (Not a real award, but if it existed, she would probably win, hands down). Her son Tony was working on the suspension of his 1964 Chevy Impala when the car suddenly slipped off the jack and pinned him in the wheel well.

Angela dashed outside to see her unconscious son trapped under the car. She yelled for a neighbor to get help but it was taking too long, so she took matters into her own hands. Literally. She proceeded to lift the car—high enough to replace the jacks—and pull Tony out from beneath.

Yep, you read that correctly. She lifted a 3,500-pound car from the ground.

There's not much more information to be found about Mrs. Cavallo aside from this incredible story, but I'll safely assume she wasn't a body builder. In fact, I'll bet the same for the other individuals who have also demonstrated this sort of "hysterical strength." But that's beside the point—if you were placed in a similar situation, you could probably lift a car, too!

It's all thanks to the handy little hormone called adrenaline.

Activating the stress response

The kicker abou . . . More

Dr. Perry Kendall asserted yesterday that the health risks of 3,4-methylenedioxymethamphetamine—or MDMA, the active ingredient in the drug ecstasy—are exaggerated, and that pure ecstasy is not dangerous when consumed responsibly by adults.

Its lethal dangers arise, he says, when gangs pollute the drug with other chemicals.

I'm not sure when the notion came into play that anything which doesn't kill you automatically means its "safe," but I would like to respectfully debunk Dr. Kendall's remarks with a very powerful and striking study published 13 years ago.

Specifically, MDMA induces release of the neurotransmitter serotonin by causing serotonin-containing vesicles to dock and enter the synapse. Higher-than-normal serotonin levels can result in neurotoxicity in the brain.

What, exactly, causes the euphoria from MDMA is not entirely clear; other drugs that release serotonin, such as fenfluramine, do not have this effect.

Remember those old "Just Say No" PSAs from the late '80s championed by First Lady Nancy Reagan? "This is drugs." An egg cracks into a sizzling skillet. "This is your brain on dr . . . More

Aside from the dubstep pumping out of the Roche and Agilent booths, the volume of AGBT has been somewhat muted. There was no grand offering of new hardware or over the top promises of sequencing genomes on what now appear to be vaporware USB thumb drives. This is my first in person experience of AGBT, so as a virgin it seems for the most part to be rooted in the science despite the ridiculous parties and “showgirl” casino nights. The atmosphere here is unlike any other science conference I’ve attended. It’s like the bastard child of a Gordon Conference and a Las Vegas Porn Convention. I really hope that the deep pockets of Sequencing Centers are more influenced by the science than the free dinner parties and alcohol, but I have pretty low confidence in humanity. Regardless, I think everyone in attendance today was overwhelmed by a stunning talk from PacBio and the dramatic advancements of their long read technology.

The PacBio talk came on the heels of what felt like a warm-up opening act from Jeremy Schmutz of the Hudson Alpha Institute. Schmutz has been working with a start-up that was recently acquired by illumina called . . . More

Vegans, please STFU. I'm sick of you preaching to me about what I should and should not eat. I evolved canines for a reason and will eat anything that I damn well please.

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In the last blog, I discussed the Law of Superposition. Layers of sedimentary rocks, or strata, are stacked in vertical sequences, with the oldest layers being on the bottom, and getting younger as we go up through the layers. Remember that the study of the sequence of layers of strata is called lithostratigraphy, and the study of the sequence of fossils in these same layers is called biostratigraphy. Both of these studies were pioneered in the early 19th century by a British geologist named William Smith, who was one of the very first to figure out that you could identify the same sequences of rocks and fossils in different parts of England (an excellent book about Smith and his life is The Map That Changed the World by Simon Winchester). Smith was primarily interested in the economic benefits of these observations, and was able to use his knowledge of the sequence of rocks and fossils, and how they were distributed across England, to inform land owners whether or not they could find coal or building stone on their property. What Smith did not fully appreciate during his lifetime was that he had also figured out the primary methods that . . . More

In a lab, scientists are not building a better mouse-trap, but a better mosquito.

The Anopheles mosquito's transmit malaria, which affects approximately 250 million people worldwide, and kills around one million per year. And the battle to eliminate the disease, caused by the Plasmodium parasite, is a costly one. The parasite can rapidly become resistant to the drugs used against it, and that has been the main way to combat the terrible disease.

But, scientists at University at Arizona have decided to go a different route – by creating a genetically modified mosquito (GMM) that is completely immune to the parasite. The experiment was conducted on one particular mosquito species, Anopheles stephensi, but the researchers say that it could work with all other species that spread the parasite, such as Anopheles gambiae, in Africa.

While the mosquito would be physically fine, I am sad to say that it will still bite, just not transmit the parasite during the blood-meal.

The previous development of a GMM generated 97 per cent resistance to the malarial parasite, but in science, that is not enough. I mean sure, most of the parasite would be eliminated, but what about that three per cent? With thousands of parasites, the odds (however . . . More

All are very attractive options—particularly for the aging population, and particularly for those looking for a fast, relatively painless solution with little effort on our part.

But did you know that Botox—the quick fix solicited by 6 million Americans each year and 75% of celebrities over the age of 35—is composed of the same deadly toxin responsible for botulism poisoning that can cause paralysis and respiratory failure? Let's examine the mechanism behind this potentially deadly neurotoxin and why, for goodness' sakes, Botox can be used as a therapeutic despite its dangerous potential.

Botox is the trade name for botulinum toxin, a protein produced by the bacteriumClostridium botulinum (below, left). With a relatively low LD50 of 40 nanograms, botulinum toxin (below, right) is one of the most powerful neurotoxins known today. That means that injecting just 40 ng of the toxin is lethal in 50% of the primate population in which it was tested. To put 40 ng in perspective: a gram is roughly the mass of a paperclip. A nanogram is one billionth of a gram.

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Our co-guest blogger of the week is Melissa Hughes. Her scientific interest is one that is quite unique and fairly new compared to other scientific disciplines: food microbiology and food safety. She received her M.S. degree in food science/microbiology back in 2009, and is currently employed at a private food and environmental testing laboratory in the San Francisco Bay Area. On top of being a food microbiologist and overseeing the quality operations in the lab, she also organizes and helps teach various food safety training workshops throughout the year.

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I would bet money that right now you are thinking, “What in the world does a food microbiologist do?” Don’t worry, I get asked that a lot…and then it typically leads to a discussion about a story heard on the news regarding some food-related outbreak or a product recall.

Food microbiology is quite simply the study of those microorganisms (both beneficial and harmful) that impact food and beverage products. It encompasses two major areas: general microbiology and food safety/quality. A proper understanding of microorganisms (especially bacteria, yeasts, molds, and parasites) and those factors that impact growth, survival and pathogenesis provide th . . . More

If you happened to be wondering -- or needed it explained to you -- why people get vaccinated, here is your reason.

The United States seems to be on track to have more measles cases than any year in more than a decade, with virtually all cases linked to other countries, including Europe where there's a big outbreak.

So measles is making a comeback? I wonder how that could possibly be happening.

Europe, especially France, has been hit hard by measles, with more than 6,500 cases reported in 33 nations. International health officials are blaming it on the failure to vaccinate all children.

Surprise, surprise. "But surely", the anti-vax crowd will say, "this has nothing to do with not getting vaccinated. That reason is just a canard!"

Of the 89 cases reported through the end of last week, 79 were people who were unvaccinated or who had no documentation of it, Wallace said.

You were saying, anti-vax crowd?

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24hrs or less to live. Gotta make the most of it!

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