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Scientia Pro Publica 32: Biology Overload

Posted by tigerhawkvok on June 07, 2010 03:01 in General , evolution , physics , biology , astronomy , news , anti-science , medicine , paleontology , sci-fi , public science , climate , scientia pro publica

Welcome to Scientia Pro Publica, 32th edition!

Scientia Pro Publica logo

Scientia Pro Publica logo (C) by Flickr user jmarcx via loryresearchgroup. (Hotlinked by my usual policy)

This round, it seems that the name of the game is biology. Submissions really ran the gamut in biology, including some delightfully from-left-field posts. Bryan Perkins having some fun with embryological development, and Amanda Morti shows us why we have actinomycete bacteria to thank for that fresh rain smell (and for throwing off Latinate intuition - anyone else read "actinomycete" and think muscley whale?). Speaking of whales, David "WhySharksMatter" Shiffman does a great bit of ResearchBlogging and reminds us why not all fish (fine, non-sarcopterygian gnathostome) stock are created equal - sandbar sharks (Carcharhinus plumbeus) are closer in population dymanics to bowhead whales and other balaenids than cod.

That wasn't the only bit of ResearchBlogging this time around (Hey! ResearchBlogging! Stop hating my feeds!). Kelsey has a great post about the intraspecific male competition among red-eyed treefrogs. Sure, they amplex for dear life, but what about before that? Turns out that ... they shake their butt (Does that mean that the frog Sir Mix-a-Lot is a lady?). Madhu R-Blogs over at Reconciliation Ecology takes the opportunity to do a great smackdown on a pet peeve of mine — evolution is not a "ladder" or any such silliness. It is blind and targetless. It was a statement from a Stanfurd professor, though, so what can you expect (Go Bears!)? But before we get ranty, Luigi diverts our attention from critterland and the rivalries of my alma mater to teach us about why Kibale's Wild Coffee Project didn't get off the ground, concluding that scientists, once again, just can't do "messaging".

Illustration: Peter Trusler for Wildlife of Gondwana/NOVA (PBS). From Grrlscientist's post.

Thonoir continues to take us down our diversion away from Critterland, showcasing two sets of endangered non-metazoans, and my total ignorance of plant/photosynthizing phylogenies. We don't stray from Critterland for long, though, as John at Kind of Curious details a very interesting ponderous borer. Emily talks about sensationalism, mountain lions, and that Fox, even as they get extirpated from areas densely populated by a certain primate. Which, as Amanda points out, is no good thing, and there are difficulties restoring predators to ecosystems that they have been extirpated from (trust me, a one sentence synposis does not do that entry justice). The great Grrlscientist brings us some aborignal rock art possibly depicting Genyornis newtoni (Dromornithidae, incomplete phylogeny link (Anseriformes)). This is both the oldest paintings in Australia at 40,000 years (predating the earliest European cave paintings) and is of something that can be loosely imagined as an ostrich-sized duck, which simply can't be awesome.

Now, we don't end here. Oh no. That was just organismal biology and evolution. How about a dose of medicine? Michelle Dawson is better than Mary Poppins, because her post about circadian rythyms certainly doesn't need any sugar for you to take it down (and introduces you to an interesting side effect of autism-spectrum disorder). Scientific Chick writes about cell phones improving mental performance in Alzheimered mice. Meanwhile, Wendy at Bioloser gives us the physiological background of shock, and a shocking description of shock in a man nearly severed in half.

The larger constructs of medicine were not neglected, either. Bradley Kreit discusses the fact that we need to accept our intellectual limits, while Luke examines the crazy in large groups, looking at HIV denialism and Ryan looks at child mortality.

Bisected men and child mortality? Lets get a bit more lighthearted. Jessica Drake at Soilduck ponders what makes a scientist a scientist, and Romeo Vitelli tells us how subliminal messaging was an advertising gimmick (how many levels of fake-out is that?). Adam Park redeems some sci-fi stories with various predictions made therein that have come true today. Of course, Asimov gets a mention for the mention of pocket calculators in Foundation, but Asimov also nailed our reliance on them as time went on in The Feeling of Power (psh, arithmetic).

BP, the Gulf, and the utter dismaying farce of the spill have been in the news, and oil makes its showing in Scientia this time around. Scienceguy238 gives us a history leading up to the spill, and Grrlscientist looks at the ethics involved with oiled seabirds. Jeremy at The Voltage Gate writes about how the Saudi coast has recovered, 20 years later, from the 11-million-barrel (1.2 GL, or 1.2e6 m3) spill. A decade afterwards, 1 million cubic meters still persisted. Every spill is different, though, so hopefully ours won't be as bad.

You know you love it.

Finally, we round out with the physical sciences, which didn't get much love this time around. Lab Rat talks about bacteria and climate change, while Matt Wills talks about the more metaphorical breathing Earth, Charles Lyell, and mollusk damage in Greek columns. Finally, Sarah Kavassalis gives a great article on one of my favorite subjects: special relativity, astronomical distances, and the meaning of "now". After all, if a star (super)nova's in the distance, but you don't see (E&M) or feel (gravity) it, has it gone? She even does it without the inevitable jargoning I'd go into!

That does it for this round of Scientia Pro Publica! This was my first blog carnival, so I more than welcome suggestions. Hope you all enjoyed it!

If you want to learn more about this carnival, head over to the carnival's website. Be sure to check out the next round hosted by Andrew over at Southern Fried Science, on June 21st. And remember — this is a blog carnival! Submissions and hosts are wanted! If you're interested in hosting, check out the current schedule on the official schedule thread and drop Grrlscientist a line (or leave a note in the comments). If you find a cool article, submit it! Send a link via this submission form. Thanks again all!

Who needs facts when you can litigate?

Posted by tigerhawkvok on May 02, 2010 16:57 in politics , news , anti-science , climate

Well, hello blog. Long time no see.

So, I ran behind on TT's, decided to queue them, and as the queue got longer it got harder to catch up, so I'm going to call the missing weeks of Tetrapod posts a lost cause, and just try to restart (eg, don't expect a backlog).

Not to say that there hasn't been plenty to write *about*. Most of the notable interesting things have been political/legal in nature the past month rather than scientific, but that's not to say there hasn't been plenty of science knocking around.

Now, Virginia is happy to blur those lines, and just pull an insane political stunt involving science. The peice of work Ken Cuccinelli has decided that Virginia will probe Michael Mann, chief climate researcher at the University of Virginia, for fraud. Yep, disagree with climate change? Use taxpayer money to screw with a researcher! Now, Mann already was under an ethics investigation for the whole so-called climategate, and was exonerated (also brought up by AGW deniers). He also uses the CRU emails as a basis to bring suit to the EPA, saying "Faulty climate data must be corrected". Never mind two investigations in Britain also found the allegations were bunk (links for first investigation, second investigation).

Little things like facts or taxpayer money be damned, Ken Cuccinelli will litigate everything he doesn't like. Or otherwise work to change it. Like covering up a Roman goddess's breast in the Virginia state seal (seal on LA Times). Yeaaah.

It's official: WSJ and Guardian UK anti-science shills

Posted by tigerhawkvok on February 22, 2010 18:23 in General , anti-science , public science , internet

This is just a friendly public service announcement — ignore any science (which is usually actually "science") from the Wall Street Journal and the Guardian. They are both pretty uniform in being united against climate change (the broader issue, not even just anthropogenesis), with ocassional alt-med quackery and such. I'd nail them on evolution coverage but for now I'll give them the benefit of the doubt and assume they're just subject to the media's usual poor coverage of the subject.

If you'd like some pretty good, easily-accessible sources on climate change, check out:

  • "Tamino" is a researcher who works with the climate data, and frequently posts statistical breakdowns and debunkings of common claims. While the debunkings aren't instantly findable, they're quite thorough when you find them.
  • Skeptical Science has a list of frequently used arguments with knockdowns, citing peer-reviewed papers.
  • RealClimate is a site run by various climatologists.
  • "How to Talk to a Climate 'Skeptic'": A large number of articles sorted by class of argument and then by subargument.

So, yeah. WSJ? "Scientist says X" is meaningless unless it is peer-reviewed, and even more meaningless when they're not climatologists, and a "maverick" flying in the face of the consensus is not actually privvy to any special data. Also, stop saying "scientists" like it's a magical-catch-all phrase, or I'm going to have to start calling non-scientists "humanitists". A physical anthropologist or chemist has no special, extra-noteworthy climate position.

Ask yourself — what reasonable evidence do you need to demonstrate that climate change is happening? Will you honestly admit that you would be willing to change your position when you are confronted with that evidence? I have done some models of generic planetary temperatures, so I know many of the influences; I further, perhaps six years ago, as uncertain as to the anthropogenic nature of the argument. Soon after, I saw a long-term solar data analysis which removed the only reasonable alternative candidate from the equation. Further evidence keeps building to support anthropogenic climate change. You also have to look globally, and not just at the United States (which many of us in the US are prone to do). I don' think there is any evidence short of the catastrophic that will convince those of the Guardian or WSJ.

For various other topics, just ask and I'll put some links up when I get a request. Seems like the end of this post got slightly off-topic, huh?

Religion in the Classroom and the Slippery Slope

Posted by tigerhawkvok on February 14, 2010 15:33 in evolution , religion , anti-science , misc science , public science , creationists

Reading an article like the New York Times' recent one on textbooks and religion in the US has the magical ability to just make me so angry. The article itself is mostly neutral, but it brings up Don McLeroy, a dentist in Texas who has remarkable influence over science and history taught to children for the large majority of states. A history-denying activist moron er, "Young Earth Creationist" of the activist stripe, he has said

"Everything that had a beginning we can say had a cause," he tells his class of fourth-graders at Grace Bible Church. "And now science definitely says that the universe had a beginning. Therefore, the universe had to have a cause. And that cause is God."

Citation: Statesman.com

OK, normally, this would just be infuriating as he'd be a nutter on a school board that approves books for a state. But, seeing as Texas is the second largest textbook market in the US, and California is broke, it means this man essentially shapes the education of the rest of the country. To quote the Times,

And James Kracht, a professor at Texas A&M's college of education and a longtime player in the state's textbook process, told me flatly, "Texas governs 46 or 47 states."

As (admittedly) excessively vitriolic PZ Myers and other "strong" "New Atheists" can be, this is the sort of thing that makes me feel their position has merit. Evolution is not under controversy in any way in the scientific or educational community. Filth like McLeroy or David Barton are liars. The "Discovery Institute" are religious shills operating under an agenda to drive science out of the public arena and move to a religious educational system via the "Wedge Document".

Stories like this should inspire activism in freethinkers. Stories like this make it hard to reach a mutually agreeable arrangement in deference to the idea of non-overlapping magisteria (which, incidentally, I find highly problematic besides; a highly flawed concept with arguments similar to those Dawkins makes) — because if you give an inch, fools like Don McLeroy will try to take a mile.

Randall Munroe does it again

Posted by tigerhawkvok on December 13, 2009 23:08 in General , anti-science

Really says it all.

So-Called Climategate

Posted by tigerhawkvok on December 06, 2009 21:37 in anti-science , misc science , public science

Note: This references file version "d", which seems to be the one generally discussed. There is a later version, "e", that never made it into any used/published data sets.

Oh, "climategate". How you are poorly reported.

It recently came to my attention that, awesomely, much of this OMGZ CODE OF EVIL was written in IDL. Now, having done astronomy research in IDL, all my undergraduate data reduction in IDL, and my (horribly behind) sauropod research in IDL, I feel like I can competently comment on the code here.

So, this artificial decline hiding? Well, we can take a look at ./FOIA/documents/osborn-tree6/briffa_sep98_d.pro (aside: if you want to see the leaked data yourself, being aware that the data was illegally obtained, you can download it via BitTorrent and this magnet link: magnet link). They say a picture is worth a thousand words, so, let's start with a picture:

source in Emacs 23.1.1 buffer

Printscreen of emacs. The whole code, in all it's beauty. Click for a full-sized version.

 (More)

Wrongheaded Creationists 4: Hitler was an "Evolutionist" (Not)

Posted by tigerhawkvok on November 25, 2009 14:24 in evolution , religion , anti-science , creationists

This comes up so often, it needs a token response. Creationists (mostly) assert that Hitler was an atheist who used evolution to promote extermination of Jews. This is blatantly and verifiably incorrect.

First, so what? Even if he understood evolution and accepted it (he didn't), the fact he liked to drink beer doesn't make all beer-drinkers in favor of eugenics, anti-semetic, and dictatorial.

As to the point itself, here's a rebuttal, courtesy of Hitler himself, yanked from a comment over at Pharyngula:

In Mein Kampf, Hitler asserted the fixity of species, that god made man, that man existed "from the beginning" and did not descend from apes, that man was made in the image of god and was expelled from the garden of Eden, and that Jesus was his inspiration.
His words:

The fox remains always a fox, the goose remains a goose, and the tiger will retain the character of a tiger. - Adolf Hitler, Mein Kampf, vol. i, ch. xi

For it was by the Will of God that men were made of a certain bodily shape, were given their natures and their faculties. - Adolf Hitler, Mein Kampf, vol. ii, ch. x

From where do we get the right to believe, that from the very beginning Man was not what he is today? Looking at Nature tells us, that in the realm of plants and animals changes and developments happen. But nowhere inside a kind shows such a development as the breadth of the jump , as Man must supposedly have made, if he has developed from an ape-like state to what he is today. - Adolf Hitler, Hitler's Tabletalk

Whoever would dare to raise a profane hand against that highest image of God among His creatures would sin against the bountiful Creator of this marvel and would collaborate in the expulsion from Paradise. - Adolf Hitler, Mein Kampf, vol ii, ch. i

My feeling as a Christian points me to my Lord and Savior as a fighter. It points me to the man who once in loneliness, surrounded only by a few followers, recognized these Jews for what they were and summoned men to fight against them. - Adolf Hitler, speech, April 12 1922, published in My New Order

Hitler was a creo.

Yes, Hitler was a strong Christian and unabashed creationist. This does not equate creationists to Hitler, however. They're pretty foolhardy and willingly blinded all on their own accord, with no ties to Hitler's filth necessary.

Wrongheaded Creationists 3: Gaps, gaps, gaps

Posted by tigerhawkvok on October 13, 2009 23:56 in evolution , religion , anti-science , creationists

First, due diligence, as this entry in the series is brought to you by Bill O'Reilly:

Oh, Bill. Dare I count the ways you are flawed in your arguments?

  • A gap in scientific data should be explained as either "insufficient evidence" or a scientific conjecture. To quote Dawkins, "It's a most of extraordinary piece of warped logic to say because science can't fill in a particular gap you're going throw in your lot with Christianity." If it should be filled-in with myths, why not the Cthulhu mythos, Invisible Pink Unicorn, Greek Pantheon, Egyptian Pantheon, Norse Pantheon, or druidic theism instead of Christian mythos?
  • You fail Godwin's Law.
  • You realize you spoke more than your interviewee, right?
  • You realize Jesus probably looked more like a middle eastern guy, right?
  • Your theology fails the self-sacrificing pacifist test when you look at religious wars on the behalf of Christianity, and the opulence of the Vatican.
  • Saying there are more X than Y therefore what X believes is true is a fallacy.

I think when I return to SD I might create a powerpoint slideshow to showcase these "alternate viewpoints", and include a few (ie, soup, clay-assisted, RNA-world) scientific hypotheses thrown in for fun. Take it from universe creation to first autoreplicable form.

To drive the point home: gaps in scientific understanding, no matter your level of scientific understanding, should never be replaced with psuedoscience or mythology in its place

Here's a nice YouTube clip that's not quite related, but discusses the spread of misinformation by the Discovery Institute

Wrongheaded Creationists 2: Castrating Darwin?

Posted by tigerhawkvok on September 23, 2009 12:40 in evolution , religion , anti-science , creationists

From your local department of wingnuttery, you get to see the latest attempts of hardline theo-nuts to distort science and push their blindingly incorrect view of evolution on the populace. What do you do when a text is completely and freely available?

Well, you do the only thing you can do. You publish your own version, edited to roughly half-length by a ministry and with a 50-page prelude explaining how evolution is wrong and it's never been proven.

Hang on, didn't I already address this? Well, don't take my word for it, see for yourself:

The Facebook group and the richarddawkins.net page suggest amassing then donating, but the recent info that about half of the content has been killed off, I propose that yes, you amass all those wrteched copies — then go and purchase a cheap first edition and donate it to a library or school.

Utter, shameless propaganda by distributing altered copies of a text. If their argument was convincing, you'd imagine they could leave the text intact!

Wrongheaded Creationists 1: Transitional fossils

Posted by tigerhawkvok on September 03, 2009 22:53 in evolution , anti-science , creationists

Having blighted the internet and US politics with consistently bad arguments, I decided when I'm so inspired (which is frequently, given how often they make it into the media) I'll post a short blog entry, tackling misconceptions or outright lies by creationists. So, catalyzed by this:

[We will take PZ Myers] down with fine-tuning arguments and universally accepted facts of science like the absence of any transitional fossils in the fossil record. Pwnd.
Source: All-American Gun Show

Allow me to make this abundantly clear.

Pendanticism aside, there is an abundance of transitional fossils in the fossil record demonstrating branching behavior within major lineages, derivation of traits unique to lineages, and of the origination of multiple, major lineages. Denying this is a demonstration of an unwillingness to perform a Google search, deliberate ignorance, or baldfaced lies.

If you just want to read what I written, you can look at:

Crocoduck, as shown by Kent Hovind and Kirk Cameron. Via Freethoughtpedia. NOT a transitional form, despite both animals being archosaurs (crocodiles are crurotarsans rather than mesotarsans, and are no where near the ornithodiran node).

If you want to read some basic Wikipedia articles, you can look at:

A real transitional fossil. Via Wikipedia

If you want something a bit more solid, you can look at the 59983 results at Nature for the search term "Evolution", or the 31953 results from Science. Too hard? Look at the very specific 2008 paper in Nature on the evolution and development of snake fangs (doi:10.1038/nature07178). Finally, and critically, every thing that has ever lived upon this planet is a transitional form to the next generation. There is no, and never has been, a crocoduck. Such things confuse common ancestry with descent, which are markedly different.

Enough by way of transitional fossils and genomic tracking for you? Pwnd indeed.


How to get your High School T-Shirt in the News

Posted by tigerhawkvok on September 01, 2009 04:06 in evolution , religion , news , anti-science

It's 3AM, I should be going to bed, and I give my feeds one last look over ... and run into this travesty. In a nutshell? T-shirts are recalled from a high school in Sedalia, Missouri. Why?

Get ready for this. Because they had the stereotyped progression of man iconography.

The offending shirt

Well, it is a pretty wretched image. It goes well with the theme of the band concert (being a band shirt for a concert about the evolution of brass music from the 1960s to the modern day, and called "Brass Evolutions") as a well-recognized image, but that image is bad science. It implies that evolution is a linear process of improvement with no offshoots, and implying that our species is at some sort of pinnacle. I mean, it's a school, so maybe they want better science on their shirt?

Oh, wouldn't that be great. The real answer is, of course, that it offends fundamentalist Christian parents. To quote:

The band debuted the T-shirts when it marched in the Missouri State Fair parade. Summers said he was surprised when he received a direct complaint after the parade.

While the shirts don't directly violate the district's dress code, Assistant Superintendent Brad Pollitt said complaints by parents made him take action.

"I made the decision to have the band members turn the shirts in after several concerned parents brought the shirts to my attention," Pollitt said.

Pollitt said the district is required by law to remain neutral where religion is concerned.
From The SedaliaDemocrat.com.

You're not being religion neutral. You're favoring one particular brand of delusion by denying testable, prediction-generating, bloated in evidence FACT. You know, unless you're actually being consistent and following the brilliant parody of Steven Novella, and actually banning, say, shirts depicting the landing of Apollo 11 since it conflicts with the belief system of Krishnas. And banning iconography of music (goodby sheet music!) since some literalist interpretations of the Koran prohibit that.

Oh wait. You won't.

Sounds like Sedalia needs its own Bobby Henderson, and a good lawsuit.

1970s 'Global Cooling' scare - except not

Posted by tigerhawkvok on July 29, 2009 20:27 in anti-science , public science

In a sideways way through Panda's Thumb, I ran across commentary about the purported "Global Cooling Scare" that went on in the 1970's. I'd always just chalked that one up to media alarmism that took scientific warnings to the extreme which discredits the current actual work on global climate, but I'd never done any research. Digging even just a little bit in, however, reveals this:

During the period we analyzed, climate science was very different from what you see today. There was far less integration among the various sub-disciplines that make up the enterprise. Remote sensing, integrated global data collection and modeling were all in their infancy. But our analysis nevertheless showed clear trends in the focus and conclusions the researchers were making. Between 1965 and 1979 we found (see table 1 for details):

  • 7 articles predicting cooling
  • 44 predicting warming
  • 20 that were neutral

Sources from realclimate.org and newscientist.com, with quotation from realclimate.

So, it's just a popular misconception, actually. The fact of the matter is there was no cooling scare — even in the 1970s, it was, charitably, neutral; in reality, the consensus was still overall warming (not to be confused with global monotonic warming).

There you have it. A little research goes a long way.

On Denialism

Posted by tigerhawkvok on June 15, 2009 14:48 in General , anti-science , misc science

Sometimes, I think we were too successful in doing our part to fix certain problems, such as the major elimination of DDT sources and reduction in CFC use. The rebound associated with these, such as the Bald Eagle from the brink of extinction, and reformation of the ozone layer from dangerous levels, really leads us to have the impression we can do whatever we want to the brink of disaster and rebound.

The global fish stocks are a symptom of this mentality. To a lesser extent, climate change is in there, too — though, I feel like the term "global warming" that isn't (i.e., some places will cool, which certainly makes it nonglobal and not warming) provides fodder for denialists.

This is my rebuttal to everyone who wants to look away, or wait: realize that the ecosystem is precisely that, a system. It is finely balanced, and virtually all changes take place on a century pace at the most breakneck. This means that the extirpation of wolves from Yellowstone increased erosion, shrink forests, and decrease water quality [ no wolves -> increased prey items, such as elk -> destroy young trees & feed more by the river, loosening dirt ]. It means that Bufo marinus causes snakes to shrink (DOI: 10.1073/pnas.0406440101) and an increase in Crocodylus porosus populations but a decrease in C. johnstoni populations (DOI: 10.1016/j.biocon.2008.04.031). Three degrees of climate change to the barrier reef could collapse bird and turtle populations.

These are things that affect us, too. We don't live in a vacuum. For example, sensitive phytoplankton provide about half the oxygen generation of the planet. You can argue about hippy-ness, tree-hugging, whatever you want ... but the fact of the matter is, if climate change proponents are wrong, you're just being a bit less wasteful and more efficient if you follow their advice, at the expense of a few dollars and a little time.

If denialists are wrong, and we follow their advice, we have environmental collapse, and in the worst-case scenario, mass extinctions a planet not quite so hospitible to humans. Life, even tetrapod life will do fine; it has adapted to dramatic changes in oxygen content before. We, however, would be in a much worse position.

Think of it this way: it's like Pascal's Wager, except, you know, real.

Daily Show and the LHC

Posted by tigerhawkvok on May 05, 2009 13:58 in physics , news , anti-science

The Daily Show has a brilliant segment on the LHC, and simply blasts the "OMGZ IT'LL DESTROY THE WORLD!" folk. Starts at about 8:57, but it should auto-play from there.


For my own take on this nonsense, see the post about the LHC.

Not dead!

Posted by tigerhawkvok on April 06, 2009 15:33 in General , evolution , anti-science

Yep, postless for a bit. Suffice it to say things have been hectic and suprisingly full. I have a list of things in my browser that auto open that I want to discuss, like stars in the Pleiades, sauropod neck position, still the Higgs post, and black holes.

However, until those get put up, I will just point you towards a researchblogging article by Grrlscientist (on Living the Scientific Life (Scientist, Interrupted)) about how birds read human eyes.

Also, via Badastronomy, I found out about the Florida Citizens for Science Stick Science competition. The idea is to make a stick-figure comic about a topic that is misunderstood in science (particularly evolution), and "correct the record". For my part, I've submitted the following:

comic

Alternate: large PNG. Disclaimer: Yes, I know that cladograms aren't right for development of an organism. Its a parody. Put the point is you can replace a real transition with the tree development steps here and get the same response.

I amused myself with that one. That's it for now, though. For more random blog entries, Rachael has a cool one up on a caterpillar entering its chrysalis.

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