Thursday, January 27, 2011

A Dream for Discussing

This my have been a bad title, but I just woke up and dont feel like trying to create a better one.

ANYWAYS the purpose of this one is to recall a dream I had during the night that made me glad to be in evolutionary bio.

So it starts off at the beach along the, what I believe Mediterranean sea oddly enough (the name of the body was said at one point, but I cant remember it), and people from high school and middle school were all there. One guy from middle school became some fashion model (something along those lines) and so there was a photographer going around everywhere taking his picture. I specifically remember two girls from high school also being there and we were talking for a bit. There's the set up.
Beach looked more like this with a few bushes

A few minutes pass and the tide starts to move in, so everyone goes swimming. These waves got decent sized (compared to what I've seen) like 10 feet swells. It was very enjoyable, the water was not too cold surprisingly.

Then we notice a larger wave coming by, I'm guessing around 20 feet. So of course I go for it (note: I'm just swimming, no board). Just before I hit it, I turn and start swimming as fast as I can to keep up with it and start gliding on it. AND I DID! IT WAS FANTASTIC! Then it started slowing down as it was breaking under the water, and I started falling in mid air, but I wasn't really scared until I noticed something under the water as I'm falling towards it.

Anomalocaris
Under the water all I thought it was was just some rock, so naturally I'm afraid I'm going to hit it. When I splash down I don't feel any rock luckily. Thinking I just had a close call I walk back onto land, when I feel something on my leg and quickly shake it off (well it startled me). That's when I see something that I feel came out of the Cambrian time period.What I shake off is this scorpion looking thing, all black, body about the size of a lobster (20 cm long, maybe 10 cm wide, there about), stinging (I assume) tail that is maybe 30 cm long and is in beaded sections, long (40 cm) thin legs that were flattened came out from the side that go from black to red to white at the tips, and claws that are more circular, yet small at the end of maybe 10 cm long arms. (all these measurements are based of the rough size I can remember of it). It was like Anomalocaris crossed with scorpion.

So I had kicked it off my leg onto a pier pillar. It scurries around on the pillar and one of it's claws brushes up against some fisherman's leg, and he jumps up a bit. By this time the creature was on the sand, and this fisherman comes up to it and beats it with a plastic food tray killing it. The finishing blow broke the carapace and out shot a bit of blood that was black.

It is at this point when I sit there looking at it, and thinking of how it could have evolved.... This is why I'm an evolutionary biologist. Based on it's look, I would say descended from scorpions. Had the stinging tail and the claws to back up that conclusion. I don't recall seeing them, but it may have had some web-like structure between it's legs (?) to help it swim, but I don't think there was as the flattening would have provided decent locomotion. These legs looked a lot like the spines from a lion fish to give an idea of what the legs looked like, just fewer of them, I think it was eight. (At this point I wake up, but I'll continue anyways) As I had mentioned, the claws were smaller and more circular. The size could have been because it feed on small fish, larger claws would have been to hard to maneuver around smaller fish. As for the long tail, probably indicates ambush predator. My hypothesis is that it sits on rocks to blend in (recall dark body) and when a fish swims by over head, it would lift it's tail up slowly when the fish is in front and strike quickly down at spine paralyzing the fish. At this point it could swim up to it and start munching away. It was only the one specimen so I couldn't get much on mating or if there were sexual dimorphisms.

My thinking for how it became sea dwelling is that the ancestors were scorpions in the desert or some dried up ancient sea bed not too far from the ocean. Water levels then began to rise, forcing the creature to start living off dead washed up fish, or whatever it could find. Over time it developed a thicker shell to keep out the water and then began it's descent into the sea. Once in the water the tail (metasoma) grew longer to be able to attack fish better with the sting (telson), and the legs  got longer and flatter to help it swim better. I don't know this but having a beaded tail might be stealthier than a tail of consistent thickness. Based on the food source, the claws (chelea) then shrunk for a) better swimming and b) for less clumsy eating. And as previously mentioned, black coloration to blend in. Finally based on the size, I would guess this was an adult.

The ancestor of the creature
Checking for a possible family, I find Scorpionidae (so clever), but also genus Heterometrus. These are forest dwelling scorpions, but humid dwelling. So while original hypothesis gets shot down, new one just places origins in the humid forests near the ocean, and they became more adapted to live in the sea. Just get better at handling humidity to the point where 100% is no issue. This genus is located in tropical and subtropical southeast Asia, (recall I guessed about where I was so this is still plausible) and contains some of the larger scorpion species. Finally not generally lethal to humans.

So what name to give it? That's my question to everyone who reads this. What is the species name? Personally I think that giving it a name based around the fact that it swims would be good, like maybe oceanus or aquarii.

Monday, January 24, 2011

Soft Tissues or Not?

When browsing for some fun recent science discovery, I came across an example of willful and slightly gleeful ignorance of the scientific process. The line was a common argument made by those who disregard scientific finds as poppycock. Paraphrasing it goes something like such: "Scientists have had to change their story so many times it's ridiculous! How can they still go along with this clearly made up story?" When this is encountered, you know that the person who said it just cannot be shown their ineptitude at logic. To answer this quickly, science changes with the data because science is striving to understand the world, when doing so they create hypotheses, which then get tested and a few go so far as to become theories. It is at this point scientists can then predict further findings in natural terms without the use o throwing up our hands and claiming magic was behind it.

The story I was reading about when I found this was about supposed soft tissues found in fossils over 65 MYA. This isn't really a new story, but I wanted to see if there was more about it, and as it turns out there is that was completely looked over by those exposing their ignorance.

It was long thought that soft tissues would become completely fossilized with in a few thousand years or so. Then in 2005 a paper by Mary Schweitzer found what appeared to be blood vessels with blood cells still in them. This was unprecedented, especially when considering the detail seen in the blood vessels (nuclei still present, showing probable relatedness to birds). This could have caused a paradigm shift in paleontology as DNA may actually be available for certain specimens in the fossil record giving us a better idea of what dinosaurs may have been really like. Questions like if they were warm-blooded or poikilothermic, or what color they were (although this can be determined now with analysis of pigments remaining is certain fossil finds). So yeah, kind of important find.

So the person claiming science as invalid used this as evidence for a young earth model of the universe (note: not an accepted model by scientists). This clearly shows that these fossils were buried much more recently than the scientific community claimed, they though. However science continued to give predictions as to how this could have occurred, and the paper I will discuss actually purports that these findings are results of bacterial biofilms found in the fossils.

This finding suggests that biofilms were actually the culprit for the seen results of blood, as they mimic osteocytes and blood vessels when bacteria are dissolved away. So this begs the question what is a biofilm? To get a rough idea, think if you put water into a glass and left it there for a while, algae would then grow in it yes?  Then remove the water and dissolve the glass without harming the algae, the film of algae would resemble the outline of the glass it was in. Well this is what the biofilm is acting like. Further, when testing the date of these biofilms, they found it dated back to the mid 1900's.... (I don't think even the young earther's could claim dinosaurs were around 50 years ago.) This would indicate that no, sadly the original findings were indeed not osteocytes or blood vessels. However this does not mean that soft tissue does not exist in fossils, it still may be out there.

Back to the original comment of scientific lacking, it makes me tristful that the commenter never thought to get the whole story. I do realize though, that if they had read it they would have(one would hope) understand a bit better the scientific process. When a paper gets published, it is torn to bits by colleagues to try and discredit the paper, because when torn apart, other studies will be warranted thus expanding our knowledge in the process. Also we can try to get closer to the truth of how our reality truly behaves. Taking a line from Matt Dillahunty, "I want to believe in as few falsities, and as many truths as I can."

When reading scientific studies remember to dive deeper and read critiques of the studies, or just make sure the study was conducted properly (unlike the recent arsenic paper from NASA).

Original papers -
Soft Tissues in Cretaceous Skeleton
Biofilms Responsible for Soft Tissue Findings

Sunday, January 23, 2011

Who Pulled the Fire Alarm?

GUESS HOW I WOKE UP TODAY! I'm glad I can wake up at a moments notice, or at least I can when there's a blaring alarm going at over 100 dB. I suppose that's all that really matters from this exercise though, waking up and getting out of the, almost hopefully, burning building. Honestly though, when a fire alarm get's pulled you kind of hope that the building is fucking on fire or else you got rudely awakened for nothing.

So it all began during a grand dreaming state, ah those were the good times. Then things went for a turn! All of a sudden it's like fucking WWII! Every moment from waking up to getting out the door, you expect bullets to be whizzing by your head, and few people to be taken out as they go for the door. Everyone swearing at those damn sleep Nazi's for waking them from slumber. I ripped my fingers away from my ears to try and hear others around me, but to no avail. All that went through my ears was the piercing screech of the alarm warning that fucking bombs may soon be falling.

After getting through the blaring noise in the hallways and stairways, we finally make it outside. First thing we hear is from people accusing each other, as if they informed the Nazi's of where we all were; some jokingly, some... well didn't sound as joking. Jay's only words during this whole experience were, "I'm going to kill Frankie", Jay is now on a 24 hour watch to make sure he doesn't do anything rash.

I was very impressed by the fire department, the US in this analogy (except they actually had a good reaction time and didn't get their asses in gear only when they were attacked), they came in completely nonchalant ready to take out this dream invading scum. At this point we were all standing outside like French people's being conquered, and I'm a little worried because I know there are some people not out there with us (turns out they went out the other exit).

So the fire department takes out the evil in seriously under 2 minutes, and we all return to our native lands freed of the fascist regime tormenting us with sound. And here I sit now on my computer telling this story.

(Disclaimer: No we were not in Nazi Europe, this was simple an analogy to give a better idea of what those few minutes were like. Any likeness to individual people, places, or events it entirely coincidental and should not be seen as deformational. The events taking place within this story were hyperbolized, but the main story concerning us waking up to a fire alarm is completely true, and took place in the span of only 5 minutes. This post too longer to write than the actual events.)

Friday, January 21, 2011

The Happenings

So I've been silent for a while... So much so that it was deafening. How has my life been so far, well let me tell you:

Starting with apartments, because we have finally started on that. So far there is a group of 5 of us (with a possible 6th) and we are now looking in to South and West Davis or apts. Personally I like the South Davis area better; closer to downtown, Safeway, Rite Aid, Kaiser, all that good stuffs. However West Davis is far prettier, and most anywhere will be next to a lake. The real worry right now is the group. One is Charlie, good guy he's no problem (we already have ideas for pets, perhaps a bit early). The others though were recently participants in an unexpected evening. Let's just say it didn't leave a good impression, but they have been told to never again do such stupidity.

Now on to classes, starting with math. The TA is starting to bug me. Last week he asked us to prove that every subsequence of a sequence has an infinite number of values, or something like that, THAT'S NOT THE POINT. The point is that when he asks for proof, I'm thinking mathematical proof, like induction or such, but nooooo, he draws a circle, and then cuts it in half, then cuts one o those in half etc. YOU HAVE TO BE BULL$^(%ING ME. THAT IS NOT A PROOF. This is one of those times where he waves his hand, calls it math and moves on... Today he did it again, only this time did it knowingly and practically mocked us for it. I shit you not, he told us, "Well you don't want me show the actual proof for you."... THEN WHY BRING IT UP? Seriously! There was no point to it other than to show off... I will say though, he is better than the last TA who liked to discuss her personal life other than teach. But there are more classes to get to.

Computers has gotten, I feel, really fun. Like the programming is actually interesting to me because it requires different ways of thinking. I did realize what makes it more difficult though, I'm learning two languages at once. One is C programming, and at the same time Linux. And to complicate things further, I'm working off of a Windows machine so I have to write the program on my computer in C language, test it on Windows, then send it to Linux to test on there, to then finally turn it in with Linux. And for the big kicker, I just found that all our problems have come from the book with the equations already in hand, AFTER I had already derived the equations based off the inputs and outputs of the program... I is full of da smarts making.

And Drew just fell asleep while on the phone... fascinating. So time to shoot him with the Nerf gun... He was apparently... he was thinking about a leprechaun???

So anyways.. I think I'm gaining fat. I've been noticing my stomach flab has been increasing these past few weeks I MUST STAVE OFF THE FAT!! That's it going to the ARC at least twice a week now, or maybe just work out in the room. But I feel so out of shape. and my 'f' key might be dying on me, I've just had to retype 'f' like 4 times. After CrossFit I was so proud of myself for the workout. -I think I'm getting sick.- 
like I really felt strong when doing it. Next year may try to start that next year with the roommates.

Time for the sleeping though, even if my first class is at 10

Tuesday, January 4, 2011

JOB! ME? In Yosemite? Why yes I will try for that!

Recently got an email from a club I'm in that is promoting some job positions in Yosemite National Park. Amazing, is it not? But even better one of the openings is for amphibian and reptile surveying! HOLY CRAP!!! As soon as I saw that I immediately started getting everything together that I could. Resume is now all up to date, cover letter has been written, and references found (mostly). The last few things to do is get a transcript and get the last reference (reminds me I need to call her again). 

But I'm not the only one to see this opportunity. No, no, no Charlie has also found it and applying to the same position. Hopefully we both get one of the 6 available spots. Some good news about this is that we are part of the salamander research project here in Davis so we have direct experience with amphibians and surveying techniques! We have excellent chances.

From the email:
We anticipate hiring six individuals for the PARK WIDE SURVEYS for amphibians and reptiles. Duties include: surveying for amphibians and reptiles; using GPS and other handheld devices to collect data; maintaining proper quality control/quality assurance practices; andassisting in photo documentation of sites. Positions may begin as early as late-May and may continue into late-August, depending on weather conditions including snowpack.
This would be fantastic to get in to. My only worry is that because this was sent to everyone in the club, I have strong competition. I've met a few of them and they seem to KNOW their reptile shit. I think what will get me in is my current position as a field assistant (exactly what they're looking for), along with my past experience with data collecting and managing. I like the quality control/ quality assurance part especially due to the Arcade Creek Project. One of the biggest saying in that project was "Quality Assured, Quality Control" or QAQC. Every time we entered data we always QAQC'd the data.

I would FINALLY have a productive summer, after so many years of boredom. And I'll get paid for it as well, a bonus to an already amazing position!








Not a Tiger Salamander, what the hell Google ->

Winter Quarter Doth Begun

I walk into the room and first thing I find out is that Sean will most likely be gone this quarter. MOST DEPRESSING!!! Then I read his Facebook status where he claims no Davis for the rest of the year... BEYOND DEPRESSING!!! Long story short, his scholarship didn't come through in time so Davis was like, No, and then we were like What? and Davis was still like No. So that's the big thing so far.

Now to the classes.
The easy course the quarter will be the Dinosaurs course. Using Dinosaurs as a case study we will study evolutionary theory and the process of SCIENCE!! The teacher so far seems very interested in the subject and fun. So this is good. Even better though! I share the class with both Drew and Charlie, let the competition begin. These two are the biggest dinosaur nerds I know of, so it will be fun to see who knows more. They both seem to research this stuff for fun, so its a fairly even playing field, but Charlie definitely beats both of us in scientific names and taxonomy. However with Drew's passion for history he may know more background of this study. So far though the score is Charlie-1 and Drew-1/2. The reason is Charlie got to answer what dinosaur was up (an Iguanadon), but Drew had his hand up. I recognized it but couldn't think of it in time. I expect to lose this competition.

Another anthropology course, this time Intro to Archaeology. So far it hasn't been too interesting, but first day. We just talked about what archaeologists do and what they look for. We did watch the classic section from Indiana Jones with the golden idol, this was to show what archaeologists don't do. Professor doesn't seem to be bad, he's interested, but he isn't as engaging. again this could just be because it's the first day. Discussions in that class are 40% of the grade though, INTENSE! And it's classically graded, meaning 90%+ is A, 80-90 is B, 70-80 is C etc. May be harder than hoped for.

Starting my computer science career with programming and problem solving. Surprise, I'm taking it with David. So far we talked about a bit of history of programming, but the next lecture promises to be good. "The mechanics of shoot-em-up games." I'm a bit curious when we will start learning C programming, but that may just be from the text book with the daily homework. This should definitely be an interesting course and have already met some nice people in there and the professor is very entertaining.

More Math, horrah. Well this time it's sequences and series, one of the last topics we covered in IB so this should be more review for me. The problem is that this is in the engineering course so its more competitive. The professor is VERY ASIAN, with a thick accent. He seems really nice, but it can get hard to understand him when he changes l's to r's. May sound racist but it's true.

Finally I'm to chemistry. This one will prove to be the most frustrating in the beginning. I'm on the wait list, unfortunately I wasn't able to get into the lab today, and if you miss a lab then you drop the class. I have only  3 chances to make this lab, if not then I drop the class. This would be unfortunate as I made a new friend in the discussion, but at the same time it would be nice as I would then do chemistry with Charlie and get Enderle as a professor again. So for now, I'll try but it doesn't look good.
One oddity about this is that the girl I met texted me saying that the TA called me, but I wasn't allowed into the lab as a wait-listed student, so I'm not sure what this entails.

If chemistry gets knocked off then I shall try to find some other class to get a few more units out of, possibly psychology or something in that vein. We'll see.

Saturday, January 1, 2011

Classic Gaming

Needed to do a blog on this. GAMING! Some may think of me as a gamer, but really I'm much more of a classic gamer. Newer games I find, well... less interesting or less entertaining. I don't know. May just be because I grew up with an N64 and NES both at home and at school. Really though I find that my favorite console is the N64.

Quickly, some specs for it, because I feel nerdy right now. To the iPhone!!!
 Reason it was called N64, well N for Nintendo (I would hope you all know that), 64 because it is a 64 -bit machine. It competed with the Sega Saturn and the Sony PlayStation. It was the only contender that continued to use cartridges. This was a slight limitation. But it was the tech that made it more advanced. The graphics were all thanks due to Silicon Graphics. Because of the advanced graphics, the machine was thought to rival supercomputers of the time. It was also the first console to have force feedback technology (Nintendo is really good at innovating, perhaps something on that some other time). So those are some fun things, but to get to the other stuff.

Games: The best part.
MARIO 64, honestly who doesn't like this game? One of the two launch titles!
Blast Corps., basically go around and destroy buildings so that the truck with nuclear bomb or something doesn't crash. It's something like that, t crashes it goes boom, what more is there to say?
Mario Kart, classic.
Tetrisphere, fun, but hard game. Yes tetris, kind of, but the idea is there are creatures stuck under the planet created by tetris blocks. Very hard.
Bomberman 64, unlike any other Bomberman game really, difficulty curve grows exponentially making it frustrating at a certain point.
Starfox 64, really a remake of the original Starfox for the SNES, made mostly to show of the capablility of the machine to do 3-D effects unlike the Genesis. The 64 version is a lot of fun, and very nostalgic for me. Always asked to beat the final boss for kids at daycare.. ah good times.
Smash Bros. Heck Yes! The original one. They didn't think it would do very well really because it was just another fighting game, but it became a proof of concept and then came Melee, personally the best of the series. If you find the original in a store you are very lucky, it came at the end of the consoles life so relatively few were ever made.
Banjo-Kazooie, I have mentioned before, but oh the times. This one really is the most nostalgic of the games because it takes me back to like 4th grade with Tyler. One of my best friends back then and all we did was compare notes for this game, The memories.
007 Goldeneye. This game just about single handedly created the first person shooter genre. Still having to go back and get better at it, freaking Natalie must hate life. She just stands in the middle of the room and gets shot at expecting you to defend her. Finally got through that though, now I have to defeat Jaws... oye vey.

So those are the main games I have so far, but those are some of my favorite games for the machine. Among other classic gaming machines I've got are the NES and Genesis. These really make me feel like these classic games were more difficult than newer games and much more creative. Nowadays I feel like they are focusing more on the graphics than creativity. That's really part of why I don't play many of the newer games, also price, I'm cheap. Now to go out and find pictures.