Monthly Archives: April 2014

Too bad crocodiles can't fly, oh God, that would be terrifying. Imagine them crashing through your window.

Why Turtle Science is Good Science

Recently, in my Herpetology class, my professor informed us about a recent revelation in turtle evolution.  The turtles’ closest living relatives are in fact, birds and crocodiles (collectively known as the archosaurs to which I’ll refer to this as the archosaur hypothesis).  This is quite different from what I learned while growing up mainly that turtles were a weird outgroup of reptiles (see the figure below).  This was even commonly accepted in the scientific community.  Intrigued that a major shift in the Tree of Life has happened, I listened intently.

Too bad crocodiles can't fly, oh God, that would be terrifying.  Imagine them crashing through your window.

Possible phylogenetic relationships in Turtles. Tree A represents the traditional tree with turtles as an outgroup of reptiles. Tree B represents a different take using morphology as an example. Tree C represents the new tree with turtles a sister group to the archosaurs (the “archosaur hypothesis”).  Image from Hedges (2012).

The first papers that questioned turtles’ relationship on the Tree of Life were few and far between; some of which were even inconclusive.  However, Kumazawa and Nishida (1999), Cao et al. (2000), and Iwabe et al. (2005), were among the first scientists to question if turtles were actually a sister group to the archosaurs.  They had found strong evidence that this was so.  But, all three of these were either led or helped by Dr. Kumazawa meaning only a few scientists supported this hypothesis.  This changed in 2011 when we got a deluge of papers dealing with turtle relationships.  Shen et al. (2011), Crawford et al. (2012), Chiari et al. (2012), Fong et al. (2012), and Lu et al. (2013) all concluded that turtles were actually a sister group to archosaurs (this partially excludes Fong et al. (2012) who thought that turtles were either a sister group to lizards or to the archosaurs).

Again and again and again, we see continual support for the archosaur hypothesis from various different research groups analyzing various different genetic components.  I thought this was cool, but my professor by the end of his lesson seemed more annoyed then gratified by all this research.  Yes, alright, we get it, turtles are a sister group to archosaurs, move on.

But I had an appreciation for these scientists and their experiments.  This is science at its best.  We have rigorous testing of a novel hypothesis that has shaken traditional knowledge.  And through this rigorous testing, again and again, the hypothesis stands strong.

  If the actual ref was here, the turtle ref would have been used in kart racing.

This may seem odd to praise repeated testing, but lately, science, particularly pharmaceutical science, has been faltering lately.  If you have the time, you should definitely read the article here which highlights how repeated testing has taken a backseat in modern science.  Why is that?  Well, as the article states, it could be that the scientists want to make a name for themselves by testing new things, or journals may have no interest in repeated testing, or it’s just too costly.  Any of these could be a factor.  This lack of critical, unbiased repeated testing harms science as certain information we could perceive to be correct could actually be false due to human error.

This was why I was pleased to hear these multiple experiments done on turtle phylogeny.  It showed me that scientists are still questioning not just science but each other.  What’s more, the turtle phylogeny question has still not been accepted by everyone.  Morphologists, who study the structure of organisms, disagree with the archosaur hypothesis based on turtle anatomy and the fossil record.  However, even they have seemed to accept this hypothesis as the amount of research papers refuting the archosaur hypothesis has gone down considerably since the mid-2000s.  What’s more, I even found a morphological paper, Bhart-Anjan et al. (2009), which supported the archosaur hypothesis.

As such, in the space of about two decades, we see a great example of how our perception of science can change from one standpoint to another.  First, we have a generally accepted hypothesis (turtles are an outgroup of reptiles).  This was then challenged by a few scientists (turtles are actually relatives of archosaurs).  Finally, it ballooned to many scientists coming forth and supporting this new hypothesis through repeated testing.  To me, I find this awesome.  And that is why, my friend, turtle science, is good science.

 

Bhart-Anjan S., and Bever G. S., 2009.  An Archosaur-like Laterosphenoid in Early Turtles (Reptilia: Pantestudines).  Breviora 518:1-11.

Cao Y., Sorenson M. D., Kumazawa Y., Mindell D. P., Hasegawa M., 2000. Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes.  Genes 259:139-148.

Chiari Y., Cahais V., Galtier N., and Delsuc F. 2012. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC biology 10:65.

Crawford N. G., Faircloth B. C., McCormack J. E., Brumfield R. T., Winker K., Glenn T. C., 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs.  Biology Letters 8:783-786.

Fong J. J., Brown J. M., Fujita M. K., and Boussau B. 2012. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. PloS one 7:e48990.

Hedges S. B., 2012.  Amniote phylogeny and the position of turtles.  BMC Biology 10:64.

Iwabe N., Hara Y., Kumazawa Y., Shibamoto K., Saito Y., Miyata T., and Katoh K., 2005.  Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA–Coded Proteins.  Molecular Biology and Evolution 22:810-813.

Kumazawa Y., and Nishida M., 1999.   Complete Mitochondrial DNA Sequences of the Green Turtle and Blue-Tailed Mole Skink: Statistical Evidence for Archosaurian Affinity of Turtles.  Molecular Biology and Evolution 16:784-792.

Lu B., Yang W., Dai Q., and Fu J. 2013. Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles. PloS one 8:e79348.

Shen X. X., Liang D., Wen J. Z., and Zhang, P 2011. Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles. Molecular biology and evolution 28:3237-3252.

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The Last True Gaming Console

Back in February, Nintendo announced that it would disconnect the Wii and the DS’ internet service for games on May 20th, 2014 https://www.nintendo.com/whatsnew/detail/vyWpoM6CBIe6FjW8NIY7bvzOrgBURhzw.  When I heard this, I was both sad and not surprised.  I expected this to happen as Nintendo is not seeing any use for games that are no longer popular.  Ridding themselves of these internet services will cost them less money.

Even so, many of these games are now affected by their lack of internet connection.   Sure, games like Pokemon and Super Smash Brothers Brawl will not be totally impacted by this, but other games like the Professor Layton series would be.  In the Professor Layton games, you could download many puzzles which were otherwise not accessible in the games.  However, with the discontinuing of their internet connection, gamers, who might have picked up the games used, will not be able to enjoy these puzzles as we do now.

It’s here that we see the weakness of modern consoles and that is the internet.  The strong reliance of the internet makes modern day consoles handicapped to certain situations.  If you are in a place that has no internet connection then you can’t play online nor could you download patches or expansion packs.  As such, the enjoyment of certain games goes down considerably.  You can also get some games like SimCity 4 whose total dependency on the internet ended in complete disaster.  Eventually, most of these consoles will become obsolete as their games will eventually lose their internet service making them obsolete.

But I don’t see this happening for older, traditional consoles.  The beauty in them is that you can transport them wherever you go, connect them to the TV, and play some fun games without worrying about internet connection.  My N64 and Sega Genesis works just as well now as it did years ago.  These traditional consoles do not have to stress about being outdated as you can still get your full enjoyment from them (provided you have a TV you can connect them too).

As such, I believe the Nintendo Gamecube is the last of the traditional gaming consoles most of us grew up with.  Nowadays, modern consoles focus strongly on versatility by including features such as playing or streaming movies, social networking, surfing the web and so forth.  Video gaming itself almost takes a backseat to these consoles.

gamecube-console

The Nintendo Gamecube, however, strived to be an actual gaming console.  With its contemporaries already playing music with CDs or movies with DVDs, the Gamecube stuck to its guns with fun-to-play video games.  Also, the Gamecube didn’t have to worry much about internet services being terminated.  Yes, there were some Gamecube games that had internet capabilities (such as Phantasy Star Online) but that was it.  Some of these games, like Mario Kart: Double Dash, can still be played online using a LAN server.  Besides these exceptions, you did not need the internet in order to fully enjoy Gamecube games (besides, you had to buy the Gamecube Broadband Adapter which was sold separately from the console, again, supporting the fact that the Gamecube was not originally intended to be used for internet purposes).

Even with one foot lingering in the past, the Gamecube was still a product of its time.  Some of its characteristics we still see in modern consoles today.  There was the use of discs instead of cartridges which prompted the use of memory cards as well.  As said before there was (some) internet connectivity.  The Wavebird Controller was wireless and freed the gamer from the restriction of cords.  This was also the era of videogames when old games were being redone in higher graphics (e.g., Metal Gear Solid: the Twin Snakes, Resident Evil 1 and 2, and etc.).  All of this indicates that the Nintendo Gamecube represents a bridge between the then and the now.

Regardless, a focus on games and a freedom from the internet means that the Gamecube is the last of the true, gaming consoles.  Which means I can take my funky lunchbox console wherever I go and have a blast with it.  Arceus bless you Gamecube, you silly, dorky, fun-as-hell console.

The Darkness Series by Harry Turtledove

Long before I knew about Game of Thrones, there was another fantasy series that I was heavily invested in during the course of its publications.  It was known as the Darkness Series, written by Harry Turtledove (also known as “the Master of Alternate History”).  The Darkness Series is, in a sense, very similar to the Song of Ice and Fire series.  Mainly, many viewpoint characters that are from different nations whose individual stories weave a larger, more epic story.  These characters are from a fantastical world in the grip of war and who, even if they are a viewpoint character, can still die.

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There is also another similarity the two have.  If A Song of Ice and Fire is inspired by the War of Roses, then the Darkness Series is not only inspired by, but directly paralleled with, the events of World War 2.  Each country in the Darkness Series, which takes place in the fiction continent of Derlavai, is usually based on one (sometimes a few) country(s) in our world.  For instance, Algarve represents Nazi Germany while Unkerlant represents Soviet Russia.  The similarities don’t stop there as these fictional nations have the same languages, city names, customs, and so forth as our world does.

These similarities though are highly jumbled.  The Algarvian people speak Italian, have red hair, and wear kilts.  Unkerlantians, meanwhile, speak German, wear tunics, and have a darker complexion.  For those of you who are curious, the Jews are a race of people called Kaunians who are fair skinned, tall, have blonde hair, and speak a Slavic-like language.

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But here, the similarities to our world end.  Great rhinos are tanks, dragons are airplanes, fierce leviathans are submarines, rifles and pistols are wands that shoot energy beams, and magical crystals serve as communicating devices similar to our radios and telephones.  Also, like Game of Thrones, the world’s countries are mainly monarchial.  These fantastical elements are amazing and give a great twist to a world at war.

I never had such joy in reading and appreciating a series such as this before.  Figuring out what historical events are happening and guessing how the characters will survive was a real treat.  And though we know that dear Algarve will eventually lose the war, what we don’t know is if our characters will survive the war or not.  Some of my favorite characters did eventually past away and that was a great shame.

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Turtledove has a greater appreciation for characters than George R.R. Martin does.  Though characters may die, their deaths do not seem premature or forced.  We have grown to love and respect the viewpoint character as Turtledove takes time to flesh them out.  We are also not bogged down with tons of characters who may show up for a few chapters and then go away without any further notice on what exactly happened to them.

Some of the best moments in the book are when viewpoint characters meet each other for a brief moment.  They may fight each other in the battlefield, walk by one another in a busy town, or develop an actual relationship of some kind with the other viewpoint character.  I even developed an intricate diagram years ago dedicated to how all of the characters were connected to each other and it was amazing (too bad I can’t find it now).

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Well before I knew about Game of Thrones, I imagined what it would be like for this series to hit the small screen.  At the time, I thought it would never happen but now with Game of Thrones being quite popular nowadays, that idea isn’t too far off.  However, because of their similar concepts, people might think it was just a shameless rip-off which is too bad.  Regardless, seeing the Darkness Series in live action would be amazing.

In short, if you are fan of Game of Thrones, epic fantasies, or World War 2, this is a great series of novels that is fun to read.  I highly recommend it if you have the time.

(for those who are curious the series goes Into the Darkness, Darkness Descending, Through the Darkness, Rulers of the Darkness, Jaws of Darkness, and Out of Darkness)

Possible New Super Smash Bros Characters

With the new Nintendo Direct approaching soon, I thought I would offer my thought on possible characters that Nintendo might be introducing in the new Super Smash Bros games.  I’m already happy that one of my favorite characters, Little Mac, got in.  However, there are still other characters who I would like to see as well.  Who would be added to the roster as well?

Masahiro Sakurai, creator of SSB, has said when concerning characters “When we’re looking at candidates for new characters, we get a list of characters that people are interested in and we go through those with a fine tooth comb. The biggest feature we look at in Smash Bros is, what does this character bring to Smash Bros that other characters don’t?” (http://www.nowgamer.com/features/2034386/super_smash_bros_sakurai_speaks.html).  As such, here is my list of characters I think are very likely to be picked in the upcoming games based on SSB history and on what they would bring to the overall roster.  It’s entirely possible that NONE of these characters will be chosen, but I’m hoping at least one of them does.  I go from most likely to least likely, enjoy.

Mii

Mii:  The Mii character is perhaps the most likely character to be included in the new SSB game.  With the Mii available for both Wii U and 3DS, personalizing your fights has never been so easy.  Also, the Mii has already been used in the Mario Kart games so it shouldn’t be too much of a stretch to include him in SSB as well.  His attacks could include tennis racket, golf club, baseball, and other wii sports and 3ds mini games that he has done.

Why it wouldn’t happen: the Villager is already the “everyman” type of character, do we really need a second similar character as well?

New Challenger Approaching?  Very Likely

Chrom_(FE13_Artwork)

Chrom:  Chrom is an obvious choice as well for the next SSB game.  Since Melee, we have had a Fire Emblem character that was featured in a recently made Fire Emblem game.  With Marth making a return as usual, it stands to reason that this time, the unique Fire Emblem character will be Chrom.

Why it wouldn’t happen: Another sword fighter will bring down the uniqueness of Chrom.  Chrom’s character needs to have a different approach to fighting with his sword if he wants to stay in.

New Challenger Approaching? Very likely

Tails

Tails: Tails is definitely a character that the new SSB game will benefit from.  Tails can be a combination of Sonic and Diddy Kong; light and fast, with use of gadgets to help him in a fight.  The Deathbattle Youtube series definitely highlights Tails’ fighting diversity, check it out.

Why it wouldn’t happen: Sega already has Sonic which more than covers the Sega franchise.  Why need another character?

New Challenger Approaching? Likely

Simon-belmont-captain-n

Simon Belmont: Whip it!  WHIP IT GOOD!  With Mega Man and Little Mac joining SSB, Simon Belmont would round off the classic NES characters and create one Hell of a nostalgiafilled roster.  A variety of attacks would make him a unique and interesting fighter who could kick balls and take names.  Also, Snake was from Konami, so we know that Konami isn’t a stranger in allowing Nintendo to use their characters.  Do it Nintendo, do it for the fans!

Why it wouldn’t happen: It’s just too good to be true.

New Challenger Approaching?  Likely

bomberman

Bomberman: Bomberman has been a recurring character in Nintendo history ever since the NES days and has appeared in almost every major Nintendo console since.  He is also very different at what he does which is BOMB THE HELL OUT OF EVERYTHING.  He can kick bombs, throw bombs, make bombs bigger, throw even more bombs, and…ride kangaroos??  Regardless, Bomberman is awesome; he’s a unique fighter who would be a welcome addition to the roster.

Why it wouldn’t happen: At this point, he’s been snubbed so many times that it just makes you wonder why Bomberman has not been recognized at this point.  Plus, if Konami had to go for one character, they probably would choose Simon over Bomberman.

New Challenger Approaching? Likely

Paper Mario

Paper Mario: If Dr. Mario was in SSBM, why not Paper Mario?  However, unlike the good Doctor, Paper Mario has skills and equipment that regular Mario doesn’t have.  Hammers, stickers, badges, partners, the list goes on.  His main draw though would be his paper powers like paper airplane, paper tube, and other papery gimmicks.

Why it wouldn’t happen: Mario is already in the house so Paper Mario’s chance is kind of low.  However, if Toon Link is making a return, why not Paper Mario as well?

New Challenger Approaching?  Likely

250px-150Mewtwo

Mewtwo: I know I’m not the only one shouting this Legendary Pokemon’s name, many people want him back.  His chances of coming back would be really low if it wasn’t for Pokemon X and Y.  The return of Mewtwo in the recent movie and in the game has brought a popularity surge for him.  Also, his Final Smash attack would obviously be his Mega form, either X or Y.  If there was a chance for him to return, it’s now, or never.

Why it wouldn’t happen: Freaking Lucario.  With Lucario returning, Mewtwo’s chance has plummeted.  Nintendo can’t have too many characters from one franchise and they have to pick carefully who they want to fight.  Perhaps if they got rid of Pokemon Trainer?

New Challenger Approaching? Somewhat likely.

225px-Ryu-tatsunoko

Ryu: HADOKEN!  Street Fighter may not be popular with Nintendo as it once was, but that shouldn’t stop Ryu from joining up with SSB.  One of the best fighters in the Street Fighter universe going toe-to-toe with Mario and co. would be fantastic.  And since CAPCOM already has Mega Man, why not Ryu as well?

Why it wouldn’t happen: CAPCOM may decide to stick to just Mega Man.  Also, Ryu may be too similar to Mario or Little Mac.  But Mario’s fighting style has been changing these last few games so Ryu might stand out more as such.  Aw well, there’s always Blanka.

New Challenger Approaching? Somewhat likely.

KingKRoolDKJC

King K. Rool: More enemies!  We need more enemies!  GET KING K. ROOL!  The different outfits for him would be hilarious.  His attacks would be just as diverse as well; crown attack, blunderbuss, boxing gloves, body slam, and so forth.  They can definitely play around with him since he’s not very restricted at what he does and how he does it.  Many people have been calling for Ridley but I don’t see it happening, I’m putting my money on the King.

Why it wouldn’t happen: There’s already a lizard King on the battlefield.  Plus, King K. Rool may be a little out there.  I don’t know, he just doesn’t strike me as someone Nintendo will be like, yeah, let’s choose him on our roster!  Fingers crossed though!

New Challenger Approaching?  Somewhat likely.

Phoenix Wright and Professor Layton

Phoenix Wright and Professor Layton:  These two sleuths go hand in hand.  Both of them are featured prominently in Nintendo’s handheld consoles by consistently chugging out great hit after great hit.  Their crossover game also showed that their parent companies aren’t afraid to lend their characters elsewhere.  They don’t traditionally fight in their games though Layton isn’t afraid to swing a sword and Phoenix has gotten his hands dirty in a recent Capcom vs. Marvel game.  Nintendo may have to think a bit on how they fight but if the Villager can get in, why not PW and PL?

Why it wouldn’t happen: Unfortunately, as stated before, they aren’t really fighting characters so that’s a barrier they may have to overcome.  Also, both of them may even be the other’s worst enemy as their brains over brawn manner may eliminate the other character’s chances.

New Challenger Approaching?  Somewhat likely.

banjo_kazooie

Banjo-Kazooie: Holy crap, yes.  They starred in two of the (arguably) best platformers in the N64 era.  Their fighting would be similar to Ice Climbers but probably with the two characters more closely tied to each other and less independent.  Unfortunately, I haven’t played any of their games yet but from what I have seen, not only would they bring their own unique style to SSB, but they would fit in extremely well with the rest of the crazy cast.

Why it wouldn’t happen: Microsoft currently owns Rare, as such, any chances of getting B-K are extremely low.  Aint gonna happen.

New Challenger Approaching?  Highly unlikely.