Tuesday, February 19, 2008

I'm Considering Changing the Name of this Blog

This frog from the late cretaceous has the greatest name ever: Beelzebufo ampinga.  But the really interesting part is what the frog has taught them about the geography of the continents during that time (ca. 65 million years ago).

This devilish amphibian seems to be related to several species of South American frogs, yet the discovery was made in Madagascar off the eastern coast of Africa.  This means that there must have been a path for animals to cross over the continents, and it was probably through Antarctica.

I'd leave the Americas for Madagascar too if given the chance.  All the cool animals live there

DS

Monday, February 18, 2008

The Colors of the Moon

Sweet.

http://www.wltx.com/FYI/story.aspx?storyid=58596

DS

Sunday, February 17, 2008

Alright, I Admit it

I was wrong yesterday.  There's nothing wrong with the things I was railing against.  I just wish the skeptic community was a little more diverse, but in the end it's a great movement.  One that I'm proud to call myself a part of.

Consider my tail between my legs

DS

Scienticians Says, I'm Sciencing as Fast as I Can!!!

I don't know why I found this so funny (well, actually I do.  It boils down to my mixed-Groening quote in the title).

"Columbus Given Exterior Science"????

Really?  Isn't there a good amount of science going on already on the exterior and interior of something so sophisticated as a space-station?

Turns out they meant that the Columbus part of the ISS is being fit with some new apparatus for performing experiments.  Was that so hard to say?  What's with the vagaries Brits?  Just kidding, I love you guys, and the BBC.

It's actually a cool set of experiments.  They are testing how the solar environment affects various biological samples.

DS

Abuses in Science

No, I'm not talking about scientists acting like catholic priests.  I'm talking about the well documented anti-science stance that has been taken up by this lame-duck administration.  I came across this webpage (actually I heard about it on Science Friday this week), which documents the laundry list of abuses of science perpetrated by this administration over the last 7 years.

It was put together by the Union of Concerned Scientists, a coalition of scientists who have been monitoring it all.  And the list is astonishing.  It's a fun way to go through these things (as fun as something so shocking can be, I guess), but more jaw-dropping than any individual claim is the unexplainable pattern of deceit and mistreatment of science.  I know, I know.  There is nothing new about this, we've been hearing about it for years.  But I think there are still people out there who would place this under the conspiracy theory fold and brush it off.  This is a nice resource to keep handy when trying to convey exactly how bad, and how much worse this administration has been than previous ones (including prior republican admins).  Basically, with all of the well referenced stories summed up here, it's hard to deny that they are simply a bunch of dicks.

DS

Saturday, February 16, 2008

A Lack of Skepticals

I got a chance to see Rebecca Watson, author of the blog Skepchick and co-host of the Skeptics Guide to the Universe Podcast, speak this afternoon at a lecture sponsored by the NYC Skeptics Society.  She was speaking about the lack of women in the skeptical community and showed some interesting figures on how critical thinking and scientific reason break down the gender lines.  Basically, it doesn't look good ladies.  More women than men believe in things like creationism, big-foot, psychics and all sorts of other stupid crap.  And less women can be found in the skeptical community in general.  Now, I find it highly unlikely that there is any fundamental reason causing women to be more prone to woo.  I think that social tendencies have forced women away from science at a young age, and pushed them towards fields that do not emphasize critical thinking.  Plus, I have to admit that the skeptical community is full of male nerds and dweebs.  I wouldn't go anywhere near it if I were a self-respecting woman.  The skeptical movement needs to do two things to bridge this divide:

1. Promote science education to girls at a very young age.  Get them thinking critically about science and everything they learn, get teachers to change their preconceived notions about boys being good at math and science and girls being good at humanities.  I see no reason to think that sex would have bearing on this at all.

2.  Skeptics, please stop talking about Star Wars, Star Trek, Dungeons & Dragons, World of Warcraft, and comic books (all science fiction and video games really).  It's lame, and it has nothing to do with the cause.  Think about it, if the skeptical community is full of people who look and act like the Comic Book Guy character from The Simpsons, why would anyone pay attention.  Let's stay keen to cultural interests, and try not to alienate people.

Sorry about that rant, but I was a little disappointed with the people who made up the bulk of the NYC Skeptics Society.  I mean, I am a total fucking nerd, but I try keep in tune with cultural trends, and not act with an air of superiority.  Not trying to pick on people, but it all ties together.  Skepticism will not have a major impact if it does not cater to the masses at least a little.  Still, the NYC Skeptics Society seems like a great organization trying to promote critical thinking and logic, so I guess I should not complain too much.

Man, I'm a jerk.
DS

Friday, February 8, 2008

4 Horsemen

I haven't had a chance to watch these yet, but it looks great.  Dawkins, Dennett, Hitchens, and Harris in one room.  Sounds intriguing, no?

DS

Thursday, February 7, 2008

Update

Great shit has been going down at pharyngula since my last post. Basically, PZ's rabid and plentiful readers have torn apart the review article, which I discussed. On top of it being a terrible piece of crap, it turns out the bastards plagiarized parts of it! How big are their balls?! Seriously, you are going out on a limb to force your creationist viewpoints into a scientific journal, but your unwilling to take a few extra hours to word things in your own way? That's just laziness. We're fortunate that these people are, in fact, so lazy because it will help to stifle some of the claims which will inevitably be made by creationists.  I can hear them now: 'Extra! Extra! Creationist Research Published in Peer Reviewed Journal (it was plagiarized). Read All About It!(it's fraudulent)'

Anyway, I wrote a note to the Editor-in-Chief, Mike Dunn of Dublin, Ireland.  Basically, I said - in the nicest way possible - that I was extremely disappointed in the editorial board and its review process, and will find it extremely difficult to take articles that they publish seriously in the future because of this fiasco.  He replied quickly with a stock response, essentially saying that they are looking into the matter urgently and that "Clearly we hope to achieve an early and satisfactory resolution to this matter".  Fair enough.  But allow me to make a suggestion. When you decide to retract the publication of the paper - this is, without doubt, the only option based on the plagiarism alone no matter the reprehensible content - please explain to your readers how something like this managed to get happen.  Regardless of how embarrassing it is for your journal, please, please, please explain to us exactly how it went down.  It might just teach us something about the peer-review process, and its flaws in these matters.  If these two authors managed to take advantage of the system in order to inappropriately get their views published in a scientific journal, tell us how they managed to do it.  It just might help you save some face, but more importantly it may help other journals keep on the look-out for such rogues

DS

Wednesday, February 6, 2008

Mito-What???!!!???

Who the hell are these people? I came across this review article today (link to the abstract found here), and it grabbed my attention. Now, without giving too much info about myself - I like to remain mysterious - I work in a proteomics lab, and my thesis is rooted in this field, so I think it's not too forward of me to say that I know something about and think very highly of the field in general. I'm not an expert on mitochondrial biochemistry or anything, but as soon as I saw the title of this article, I nearly shit myself.

Mitochodria, The Missing Link Between Body and Soul: Proteomic Perspective Evidence??????

Seriously, how did this title stand up to peer response, let alone the article itself? (I'll say now that the article was a might difficult to read due to the fact that the authors were clearly not experts in the English language, but I don't think this was a matter of translation errors, for reasons that should become clear).

First, let me explain something about the type of article that this happens to be. A review article differs significantly from a research article. A review is meant to summarize all of the available literature within a particular field, sometimes that which has taken place over a specific period of time. Often the author(s) will go slightly out on a limb and hypothesize about what is the most likely explanation for a particular phenomena, and even propose experiments which would prove or disprove said hypothesis. What a review article should not do is overreach its grasp and try to predict something, when there is not a significant body of evidence to support it. This is exactly what has happened here.

The authors happen to call themselves the Mitochondrial Research Group (so you can imagine how high their pedestal for these admittedly important organelles is), at Inje University in Korea. I've never heard of this place, but that doesn't mean it's not a perfectly good institute. It does make you wonder how someone from a fairly unknown place can get away with stretching things so much, but I guess that's a little unfair, and besides the point.

In the abstract they say:

"These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative."

Wow. That's all I can say. Wow. The hypothesis that mitochondria arose from bacteria that took up residence within other cells is a long-standing one, that has withstood quite a bit of criticism to implant itself in the scientific mindset. Maybe they made that statement in the abstract just to grab our attention... oh, wait. They said it again:

"In accordance with this disciplined performance, the work looks at recent proteomics evidence that disproves previous
lines of thought on mitochondrial evolution in eukaryotic cells."

To be fair, the endosymbiotic theory is still a theory (as plainly stated in its name), but one with mounds of evidence to back it up. You better have some real good data to feel comfortable saying that you have disproved it. Let's see what they've got...

"A recent new interpretation in the proteomics front broadens our scope of understanding toward a better realization of the mitochondrial–cellular integration with the intimate relationship to other organelles. This relationship expands its coverage from the tiny peroxisomes [45] to the giant ER (Fig. 1). This shared relationship, however, is basically essential rather than complementary for cell survival."

OK, that sounds reasonable, so far. They are basically saying that cells cannot exist without mitochondria. Nothing outrageous there. The thought is that the symbiotic relationship between pre-mitochondrial bacteria and other cells is what allowed multi-cellular life to form. Not that mitochondria are a parasite. Anyway, what else have they got?

"Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life."

Damn children! That's a hell of a leap. I can't quote everything in the paper that lead up to this statement, but I can say that none of it was very convincing. Basically they tried to claim that there was zero evidence for an intermediate between a bacterial endosymbiont and a mitochondria, which is untrue. Then they say that a majority of the mitochodrial proteome is synthesized from nuclear DNA and transported into the mitochondria. Fair enough, but what does this prove? Nothing! The whole idea is that this happened so long ago that things will have changed drastically, and the host cell has adapted its processes to take advantage of the endosymbiont. It doesn't surprise me at all that the mitochodrion is contributing so little to the process, it's the host cell that is taking advantage of a specific mitochondrial function. And to say that it is more likely the fingerprint of a creator? I can say with 100% confidence that there is more evidence for the endosymbiotic theory than for the creator theory, so you have betrayed yourselves. You're a couple of creationists trying to shoe-horn your creation myth into science. Shame on you, and shame on the journal for publishing this.

Just, unbelievable.

DS

*Edit (5 minutes later)*
Son of a bitch!!! PZ Meyers totally scooped me. Why is reading Proteomics anyway? It's a middle-tier proteomics journal that I barely read, and I'm a proteomics guy!

Tuesday, February 5, 2008

Karma Chameleon!

Poor old chameleons. They've lost their most defining characteristic. Everyone knows that chameleons change colors in order to blend into their surroundings. I mean, that's what it means to be a chameleon, right? WRONG! Turns out their colors make them stand out. I guess we're going to have to come up with another descriptive for people who blend in. If we were being honest, we would call them octopi



Amazing!

DS