Now that I'm finally The Dread Zoologist Roberts, I feel a need to help the people. The confused people. People confused about wives tales, folk taxonomy and poorly researched news stories. People confused about whether the appropriate short form of Charles Darwin's name is Chas D, Char Dar, or Chuck D (in fact, all three are acceptable, along with "Charwin").

But as my first order of business, I'd like to demolish some zoological misconceptions I commonly come across. I hate zoological misconceptions! Let's begin:

1. Assuming you live in the New World, honey bees are not your friends. Nor are they friends with your true bee friends, the native bumblebees. Honey bees were introduced to the Americas by European apiculturalists, making them an ALIEN/INVASIVE species. So, it shouldn't be any wonder that they are "declining", given that they didn't belong here in the first place (OH SNAP).

2. Daddy Long-Legs are not spiders, nor are they poisonous. They are harvestmen. Also, check out the weird pro-harvestmen science bias in the Wikipedia article:

Because they are an ubiquitous order, but species are often restricted to small regions due to their low dispersal rate^{[citation needed]}, they are good models for biogeographic studies^{[dubious – discuss]}.

Indeed! Dubious!

3. Polar bears are not a distinct biologically species, separate from grizzly bears and brown bears (which themselves are not biologically distinct). In other words, polar bears, grizzly bears and brown bears are in fact all the same (biological) species, and hybridization is possible!

4. Monkeys and Apes are different things! Chimpanzees, Bonobos, Gorillas, Orangutans, Gibbons and Humans are apes. Apes, I say! Monkeys are things like Tarmarins, Capuchins, Owl Monkeys (above), etc. So, next time your esteemed associates say "Humans are descended from monkeys!" you can say "That statement is incorrect, associates! They are descended from, and still are, apes!".

5. Killer whales are oceanic dolphins, not whales. Similarly, Koala bears are not bears.

Do you feel informed? I have many more such facts, stay tuned!

Most people agree that owning a poofy kitty or a slobbery poochie can be extremely rewarding. Companionship, pre-warmed furniture, a lap-full of shedded fur...the list of pet benefits is both long and heart-warming.

However, it is really moral to keep animals locked in our houses, mostly for our own enjoyment? Furthermore, is it moral to genetically alter (i.e. breed) animals to look "cute" or "handsome", even if that means creating in serious health risks for the animals?

Based on the picture above, I'm inclined to say that the moral risks are well-worth the hilarious pet-wig payoffs. For the sake of argument, here's a run-though of the various moral justifications I've heard from pet-owners, along with my zoological retorts:

1. "Pets live much better/more comfortable/longer lives in human homes than they would in the wild."

This one is tough to defend. It rests upon the anthrocentric idea that humans, being all-mighty, must know what's best for animals and how to give them the most fulfilling lives possible. But how can you ever know whether or your dog is truly better off in your house versus the lush woods?

2. "Dogs and cats have been selectively bred to enjoy the company of humans. My dog loves it at home!"

The problem with this that is assumes that the behavior the animal has been selected to express (amicability to humans) is truly reflective of the animals thoughts/"feelings" (i.e. that they really do enjoy the company of humans, rather than simply behave that way).

3. "Working animals, such as seeing-eye dogs, increase the owner's quality of life dramatically."

This is probably true. However, it doesn't change the fact that the animal is born into a life of servitude.

4. "It has been suggested that dogs may have domesticated themselves. They've got themselves into this mess, they can get themselves out."

I haven't thought of a clever response to this yet. I was thinking about using "Its only a theory!", but we all know where that leads.

So, it seems that the keeping of animals as pets is, at least in some ways, difficult to defend from a moral standpoint. In spite of all my zoological musings, Chris sent me the following video that blew my arguments to smitherines:

Evolution can be a tricky (but by absolutely no means impossible!) process to observe. This can make teaching students about the theory of evolution somewhat difficult compared to more readily demonstrable concepts such as magnetism or acid-base chemistry.

Computer simulations of evolution offer an excellent solution to this problem. Using these simulations, students and scientists can explore the process of evolution and get (in some cases highly visual) results in a matter of minutes. Luckily, thanks to intrepid biologist/programmers, many of these sexy in silico simulations of evolution are now freely available for download! Here are a few, at a glance:

Breve Creatures

Gene Pool

Java Evolution Simulator

Java Biomorph (Java implementation of the Dawkins Biomorph program)

Mushroom Life

(OK, its not a true evolution simulator, but I have a soft spot for Conway's Game of Life. And mushrooms.)

See also:

Dr. Saul's Evolution Lab
Evorunners
Flow in games
Maxis 1990 computer game Simlife
Discussion of the validity of computer simulation to provide evidence for evolution.

Ever since I saw the painting shown above, I've wanted to suffocate birds in my very own home laboratory. As I got older, the desire to destroy life subsided, but the desire for a home laboratory remained. People have home studios, why not home labs? Obviously, the main obstacle to realizing this dream is cost.

So how much would a general purpose home laboratory cost? Internet searches provided little help, so I decided to compile a quote myself. I aimed to make the lab as complete and general purpose as possible, without being unrealistic in terms of cost (continues after the break):

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Here are some science-themed icons and wallpaper spruce up your otherwise un-sciencey desktop! Enjoy!

Icons
Mac OS X
Great Minds (via Interface LIFT)
Modern Scientists (via InterFace LIFT)
Roboticons (via Mastifnet)
Bees (via Britta/arts)
Organs (by Chistophe Bouchard) (OS X, Windows)
Molecules (by Mark Magnuson)
Arthropods (by Max Fiedler)
Windows
Science Icons by ~MrMunkily (via DeviantArt)
Chemistry Icons by eponas-deeway (via DeviantArt)
Science Icons (via My Biotech Life)

Wallpaper
European Space Agency Wallpaper
NASA HubbleSite
NSF Chemistry & Materials
New Scientist
Materials Research Society
BBC Science & Nature
BBC Planet Earth

You may have heard of Craig Venter before, as his former company Celera Genomics was one of the two groups responsible for publishing the first human genome sequence. However, Craig Venter is crazy. So crazy, that Craig Venter just might kill you if you get him angry. Why, you ask? Here are five starter reasons:

5. He's infamously cut-throat

He's been called alternately "Darth Venter", "a one man superpower ", and "an asshole". But how did Venter get this reputation? It likely has something to do with him patenting human gene sequences for profit. Also, blowing up Alderaan.

4. He was in Viet-Nam

That's right, Venter was in the shit. Probably explains the 1000-yard stare in this picture.

3. He's a billionaire

Craig Venter is so damn rich that he could pay to have a piano dropped on you and your loved ones, every day of the year for the next 300 hundred years [($1,000,000,000 / $8000)/365]. Plus, he has two magic science boats, a team of brilliant lackies, and a cool rain jacket.

2. He sequenced his own genome

He really did. If you think one Craig Venter might kill you, imagine what an army of clone-Venters could achieve.

1. His lab recently created the first synthetic genome

If you thought Venter's heyday had past, think again. The J. Craig Venter Institute is has been busy creating life from scratch in the lab. While the JCVI argues that their technology could be used to create bacteria that produce electricity/oil/hydrogen, I can only think this might be the start of something bad, especially coming from Darth Venter.

Much like being a dog trying to use a computer, applying to graduate school is a stressful and confusing affair. We have it a little easier in Canada, as we don't have to write the GRE (suckers!), but the process is nevertheless taxing. Here's are some links I personally found very helpful during my graduate school application adventures (which continue to this day):

Advice on Getting Into Graduate School:

1. About.com Graduate School Tips
(excellent general resource)
2. Advice for undergraduates considering graduate school
(no nonsense tips)
3. The Grad School Application Process
(from ScienceBlogs blog "Uncertain Principles")
4. Biology Graduate School Advice
(meant for biologists, but its all the same!)
5. A graduate school survival guide
(more no-nonsense tips, this time for computer scientists)
6. Getting into Graduate School
(phds.org section on graduate school, lots of good stuff!)
7. Academic Productivity
(more of a productivity blog, but also has grad school advice)

PLUS! Two essays on being a good graduate student (but also applicable to undergraduates and real life)
1. "On being a successful graduate student in the sciences"
2. "Some modest advice for graduate students"

One of the great things about evolution are the smooth transitions that occur between different species. Since most of the transition-species are extinct, they get very little attention (kind of part of being dead, I suppose). Here I present some of these unsung heroes of evolution. Listen carefully, because we could de-evolve into any of these slick dudes at ANY TIME:

1. Ape and Human - Sahelanthropus tchadensis

When people talk about proto-humans, species in the genus Australopithecus (e.g. "Lucy") are the usual suspects. I personally prefer our friend Sahelanthropus tchadensis, pictured above. While S. tchadensis is much more on the ape side of evolution than it is on the human side, it has been suggested that it was fully bipedal (walks on two legs), making it a nice transition form from tree-swinging apes to hop-scotching humans.

2. Reptile and Mammal - Therapsids

I remember watching a movie in elementary school and being perplexed by the statement that mammals evolved from reptiles. It wasn't until my comparative vertebrate anatomy class in my sophomore year that the mystery was cleared up! Therapsids, like Lycaenops ("Wolf-face", ha!) pictured above, are quite basically mammal-like reptiles. The main features of these wolfy-lizards are: large developed jaws, a sleeker and lighter skull, and placement of the legs below the body to facilitate fast "galloping" as seen in the modern pooch. Some scientists even believe that therapsids had by this time evolved mammal-like hair (fur).

3. Fish and Amphibian - Tiktaalik

You remember the Tiktaalik, don't you? He remembers you! Just kidding, but this squirmy little guy wins the award for Most Likely to Frustrate Believers In Intelligent Design due to his existence being predicted long before his bones were even found in 2004. Also, the Tiktaalik is Canadian (found on Ellesmere Island, Nunavut)! For that, I give him a four fleshy-lobed fin salute.

4. Invertebrate and Vertebrate - Larval Urochordate

Another difficult evolutionary step to visualize is the transition between worm-like sea beasties and fish with basic spines composed of vertebrae (i.e. vertebrates) . The leading hypothesis is actually quite ingenious and satisfying, much like this blog. It goes something like this: In the fossil record, oceanic vertebrates appear suddenly 550 million years ago. Up until to this point, the sea was dominated by crazy giant insects and Urochordates, who were (and are!) invertebrate sessile filter feeders (like a sea sponge). The key fact is that the earliest life stage (larval stage, pictured above) of the Urochordate was similar to a tadpole, and even had a rudimentary spine. The hypothesis states that some natural selection situation caused the Urochordate to stay a larva for longer and longer until eventuall, the sessile adult stage was totally eliminated (this process is called neoteny in evo-devo jargon). So in the end we were left with a nice little tadpole who eventually gave rise to all the fishies in the deep blue sea. As for mollusks and the like...I have no idea!

5. Unicellular and Multicellular Life - Cellular Slime Mold

When life first arose, it was almost definitely in the form of one-celled creatures. While many of these simple organisms have persisted in one form or another to present day, others somehow made the jump from being composed of a single cell to being composed of many. This is not a trivial evolutionary step! Now, while the theoretical background of the evolution of multicellularity is a little mind numbing and by nature non-empirical, there are existing organisms that can give us clues about how it might have occurred. For example: the weird ooze pictured about is a cellular slime mold that begins its life as a group of unicellular organisms, but eventually matures into an enormous multicellular (and gooey) individual! Weird!

6. Primordial Ooze to Unicellular Life - ???

What am I, a biochemist?

Here at Jacks of Science, we recognize that not all scientists (or science blogs) are perfect. That said, there is always room for improvement. So, in the spirit of the new(ish) year, we've come up with some new year's resolutions to make Jacks of Science the best science blog it can be. Prepare for a seriously good year at Jacks of Science!
More regular posting - Kieran
What can we say? We've been slacking off lately. We're going to dust off the cobwebs this year and bring you the ZANIEST and MOST THOUGHT PROVOKING blog posts you've ever seen! Think we're lying? Just look at our post archive! The zaniness quotient of each post has been increasing exponentially (or maybe logistically, I guess!)!
Science blog community involvement - Chris
90% of blogs are about Paris Hilton gossip and recycled tech news from Slashdot and Digg. In the same vein, 90% of blog readers probably don't give a hoot about science. That's exactly why it's so important to nurture the tiny blogosphere we have and participate in the community. Engaging people in science is a goal of ours which extends much farther than the grasp of our lowly blog. Not to mention it's a great way to steal readers from other sites.
Sustain and increase comedy/drama levels - Chris
Comedy levels have been pretty erratic on the site and drama levels are at an all time low. Come to think of it, I haven't cried after reading a blog post since Bumblebees in a Plastic Box when Kieran told me he had to rip off their wings to study them! So what we're really striving for in 2008 is a nice dramedy.
More posts about peer-reviewed research - Kieran
While comedy certainly has its place, one of the great things a science blog can do is bring science out of the ivory tower and into the salivating brain-mouthes of people around the world. Since we read many cutting edge research papers anyway, we fully intend to distill out the boring and bring on the sexy in the new year.

Understanding the relationships between species is hard. Usually, its just not clear who evolved from who and when. On top of this, we're not even exactly sure what a "species" is!

Luckly, the information age has made inferring phylogenies easier than ever. Many software packages now exist to help weakling biologists figure out their complex datasets. Unfortunately, many of these otherwise great packages are Windows only! Since I have to do phylogenetic analyses on DNA sequence data all the time, and all I have is a paltry MacBook, I've had to find some alternatives. Here they are:

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