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.

LHC at 7 TeV!

Posted by tigerhawkvok on March 30, 2010 05:26 in physics , news , public science

So, I should be asleep. Or posting one of the FOUR Tuesday Tetrapods due today (Plans include Python molurus bivittatus, Pelecanus onocrotalus, Gypaetus barbatus, and Xenopus laevis. I've had them lined up for weeks, but haven't had a chance to complete them). But instead, I have to mention that the Large Hadron Collider just had its first collisions, minutes ago. The beams were at 7 TeV

7 TeV is an odd unit that needs perspective for the non-physicists in the crowd. So, consider, according to Wikipedia, that a flying mosquito has about .2 microjoules (µJ) in kinetic energy. A 7 TeV beam has protons that each have about .6 µJ (3.5 TeV in each direction).

That is to say, each proton has a kinetic energy similar to 3 flying mosquitos. If you were capable of feeling a single proton hitting you, that one lone proton would definitely be noticeable. For the record, a mosquito has about 1021 protons.

Physics is freaking awesome.

(Oh, by the way? World? Totally not destroyed.)

Repeat after me: HCR does NOT fund abortion

Posted by tigerhawkvok on March 15, 2010 19:53 in politics , religion , news , medicine

There is talk on the news (well, at least making headlines in Google News) about the bill funding abortion. Well, it doesn't. It is on page 2072 of the Senate bill. To quote PoliticsDaily,

But does the Senate reform bill finance abortion insurance coverage? The answer is no, and it is there in the bill, on page 2072: "If a qualified plan provides [abortion] coverage...the issuer of the plan shall not use any amount attributable to [health reform's government-funding mechanisms] for purposes of paying for such services." As Slate's Timothy Noah put it, "That seems pretty straightforward. No government funding for abortions."

But lets run with it for a moment. Assume it does fund abortion. So what? Objection to public funding for abortion runs along the lines of "I don't like it, I disagree, therefore I should not have to pay for it. It kills people". That's like saying "I object to Karl Rove. I disagree with him vehemently. He is responsible for the death of troops and civilians in the Middle East. Therefore, I refuse to pay taxes, since they fund services he uses." Neither argument really makes sense.

I don't really want to get into the abortion debate. All it does is lead to flame wars. I happen to feel that identical twins wreck about 90% of the arguments against abortion as a single argument, and being pro-choice detracts nothing from the other argument, merely leaves an option open to whoever wants it. Sigh.

Campaign Finance Reform

Posted by tigerhawkvok on January 22, 2010 11:21 in politics , news

So, the US Supreme Court (USSC, or Supreme Court of the United States, SCOTUS) yesterday overturned legislation dating back ~100, 60, and 15 years ago was overturned yesterday, allowing corporations and businesses to donate as much as they want to campaigns. Hello, Corporate America. First, I want to say this is not judicial activism, any more than Kitzmiller v. Dover was I want to say this is manifest judicial activism, as it overturns previous rulings by the USSC, as recently as 2003. However, given the current USSC makup, it is an inevitable decision. Now, since the Court overturned the legislative bits on the grounds that they were abridging the first amendment, we can figure out the crux of that past precedent by looking at what it says:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.

There are two ways to address this: either by defining terms, or by changing the reference point. I will consider the definition, first. Speech can be defined as using vocalisations to communicate. It is thus arguable that the entire first amendment applies to people, or persons. Since the campaign finance measures were struck down on unconstituationality, we need to look at amendments, an along this line here is a proposed amendment, based on the implicit and explicit use of people and persons as the objects to which the Constitution is referring:


People, and persons, under the law, are defined as organic beings, autonomous in their healthy state, with DNA differing no more than 5% per chromosome, with respect to a mean genomic profile of 100 reference individuals, selected randomly from the population every 100 years, consisting of equal parts genetic male and genetic female.

This explicitly excludes companies and corporations, requring rights to be enumerated to then rather than explicitly granted. Wording is chosen to prevent rare mutations (such as XXY) from disqualifying a person as a "person under the law", to smooth out individual genetic irregularities, and to accomodate population drift over time.

The difficulty in this method is, then, it requires ancillary legislation to grant groups basic rights. I don't think it's much of a problem, but in that case, we can look at a second class of amendments, ones affecting campaign finance only:

Amendment (v1; microdonations):

Campaign spending is limited to $100 donations per individual per campaign, adjusted for inflation to the 2009 USD, with an equal amount of public matching. A total limit to public matching may be declared by the states, but all individuals with at least 10,000 signatures are eligible for public matching.

Amendment (v2; gross transparency):

At the end of all video advertisements for a campaign or issue, a screen not shorter than 3 seconds and occupying at least 50% of the video frame used must list the name, dollar amount, fractional ad amount, and affiliation of the top five donors to that advertisement. Subsequent text must be listed revealing the location of a publicly accessible list with the full list of donors with the same information.

For nonvideo visual media, this notification must occupy at least 25% of available space. This information must be read out for audio media.

Amendment (v3; explicit opt-in):

Groups, corporations, and other agglomorations may not spend money on campaigns unless the money used are fully obtained by group members opting in to such spending with federal form XXX-NNNN. If a member or employee does not opt in, all money and profits derived from them is not allowed to be spent in this fashion. If the profits associated with this individual are part of a composite product, their fractional work in completing said product is the fraction of profit derived from such product banned from spending.

So, each of these has their ups and downs. The first just largely scales back campaigns, and puts every person an a thoroughly equal footing. Then, corporate rights are not abridged in that campaign financing has special rules that limit donations to people, an furthermore, no person has more buying power in an election than any other. Public matching is there to help the campaigners, and low signature count allows more viable, third-party candidates.

The second is pretty obvious. By being grossly transparent, buying out an ad is much less effective if the ad has the top five donors all from AIG.

The third would be the hardest to impelement, but keeps people honest. No double spending, and no working to influence a campaign in a direction you don't like. Corporations are free to spend as much as they like, but not on the back of employees who disagree with the policies they promote. Otherwise, in the status quo, it's possible for a corporationto directly oppose something you support, and for your donation to be meaningful, you need to donate X to override what your employer spent on your behalf, then pay Y, your own donation.

In any case, I think all of these would address the issue at hand, and all in a more-or-less fair way. Of course, another funny way to look at it would be to say since corporations are persons, bankruptcy is killing a company, which is thus murder. Which is a kind of amusing idea, and just as ludicrous as giving corporations full first amendment rights.


Edit: Reflecting, on the first proposed amendment, it would also have to state that legislation granting non-person entities person-rights have a delay of at least two years. This would allow people to elect-out representatives that allot too much power to corporations again, and not have such rulings take instant effect and nullify the point of the amendment. There are also AI concerns, but then the only way to include them from here is an intelligence threshold, which excludes certain people from the legal definition of person.

International Year of Biodiversity

Posted by tigerhawkvok on January 01, 2010 15:34 in General , biology , news , misc science , public science

2010 is the International Year of Biodiversity according to the UN — the IUCN will highlight a different endangered animal each day of the year, apparently. Today's animal is apparently the polar bear (remember last week's Tuesday Tetrapod? Ursus maritimus), but I can't find the list yet. I'll update this post when I do, but it looks like events and press releases and such will kick off on the 11th of January.

Google Wave and (no) Internet Explorer

Posted by tigerhawkvok on September 30, 2009 16:21 in news , websites , internet

To follow up on my anti-IE6 post, looks like Google's Wave project won't support IE. To quote Ars:

The developers behind the Wave project struggled to make Wave work properly in Microsoft's browsers, but eventually determined that the effort was futile. Internet Explorer's mediocre JavaScript engine and lack of support for emerging standards simply made the browser impossible to accommodate. In order to use Wave, Internet Explorer users will need to install Chrome Frame.

This isn't even just IE6 — this is all versions of Internet Explorer. Hilarious!

Sean Hannity vs. Endangered Fish

Posted by tigerhawkvok on September 30, 2009 14:20 in news , misc science

Apparently, Sean Hannity has it out for Hypomesus transpacificus, or the (endangered) Delta Smelt.

H. transpacificus is an otocephaline teleost, a member of the family Osmeridae. It is actually euryhalinical, and tolerant of a wide range of salinities — so if Stewart is correct on the motivation (salinity), then it is bad news indeed, and the protection needed to be done anyway. The height of the water column is also important to these fish, being pelagic (ie, residing in the middle-area of the water column, away from the surface and from the bottom). However, more importantly, the fish is indeed fairly basic to the food chain, and feeds bass and salmon.

I didn't realize yesterday was Tuesday, so a late Tuesday Tetrapod will be up this afternoon.

Glenn Beck Vs. Amphibians

Posted by tigerhawkvok on September 24, 2009 22:43 in General , politics , news

Ok — ignoring everything else, if I had had any respect for the train wreck that is Glenn Beck, I'd have lost it after this:

Apparently, throwing frogs into boiling water to make your point is OK. It's possible he didn't actually keep holding onto one ... in which case he's just shamming boiling frogs? Which is also really screwed up. Yeaaaah ....

UPDATE: Nate Silver gives an analysis of Glenn Beck, and what he represents.

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.

Too True

Posted by tigerhawkvok on August 31, 2009 15:03 in General , news , paleontology , misc science

Click on the picture to see the whole thing.

Click for whole comic. Via Saturday Morning Breakfast Cereal.

Alas, too true. Also, read today's comic. Also, far too true. That and "feature creep" on papers.

To make this a bit more substantial, how's this for some interesting news: scientists have found microstructures on a fossil feather (40 MY old) that indicate it was iridescent. Nifty!

Cable News and Valley Girls

Posted by tigerhawkvok on August 19, 2009 12:47 in General , news

What the ...

Cable news networks have gone retarted. Just sayin'.

Apparently, R&D is a myth.

Posted by tigerhawkvok on June 26, 2009 15:35 in General , news

So I was reading an article on the WSJ, and, well, I feel it fundamentally misses the point of a cap and trade system. The key mistake in the bill lives here:

[...] As the cap is tightened and companies are stripped of initial opportunities to "offset" their emissions, the price of permits will skyrocket beyond the CBO estimate of $28 per ton of carbon. The corporate costs of buying these expensive permits will be passed to consumers. [...]

This takes place in the context of post-2020 restrictions on CO2 emissions in the proposed Waxman-Markey bill. However, this has the fundamental assumption that overall CO2 emissions will not markedly decrease, and thus there will be fees passed onto the consumer. This is incorrect. The purpose of a cap and trade system is to allow corporations to optomize at their own rates, and those that cannot reduce CO2 emissions in a timely manner can "buy" emissions from other companies that have. However, the fact remains that companies will reduce their overall CO2 emissions. A cap and trade system must have caps that eventually impose exorbitant fees in order to make the R&D of finding more efficient processes the financially responsible one. These R&D fees will briefly be passed onto the consumer only at the end of the cap and trade cycle. Those that invest early in R&D will be able to pay their R&D fees by selling their own CO2 quotas.

I'm not sure how the WSJ missed this point and instead claims:

The hit to GDP is the real threat in this bill. The whole point of cap and trade is to hike the price of electricity and gas so that Americans will use less. These higher prices will show up not just in electricity bills or at the gas station but in every manufactured good, from food to cars. Consumers will cut back on spending, which in turn will cut back on production, which results in fewer jobs created or higher unemployment. [...]

No no no. And then it took its analysis from the Heritage Foundation, a self-identified "conservative think tank"? They too missed the whole point that the only losers in this game are the laggards that fail to innovate, and thus, should fail in a free-market system anyway. Those who innovate too slowly are left holding the bill, while those that did so earlier are already selling products to customers. In any reasonable sense of competition, this also means that if in a given niche one company innovates before the other, the innovator is able to offer its product at lower rates if the competitor takes too long to develop their own methods of reducing CO2.

Sigh. A cap and trade is probably the most economically neutral kick-in-the-pants possible, but some people just don't want it for strict party-line reasons, it seems. I've really not heard a credible response that doesn't put blinders on and ignore R&D / the scientific community.

At a Ren Faire this weekend in Fair Oaks, then work at LHS begins on Monday. Good times.

Warp Drive in the Headlines

Posted by tigerhawkvok on June 15, 2009 15:05 in physics , news , sci-fi

Alcubierre metric

Alcubierre metric. (CC-BY-SA) Allen McC.

Slashdot brings up another resurgence of Warp Drive in the media. While it'd be amazing, it's still at the theoretically interesting stage. Though the theory is good, it requires a lot of energy. While before it required energies similar to that of the universe, now it seems like it will need only about 1045 J. This is in the ballpark of about 5.9 jovian masses. So, better, but still pretty impractical.

The figure at the right pretty cleanly describes the effect. In essense, spacetime is compressed and expanded around the ship so it can "surf" on a wave of expanding spacetime, which itself "moves" faster than c=299792458 m·s-1, but the spaceship itself remains stationary and thus violates no physics. It is, in a fairly literal sense, a warp drive. It is perfectly valid for space to have superluminal expansion rates; distant objects in our Hubble Volume recede from us at apparently faster than light, and the hyperinflationary epoch was defined by an incredible, superluminal spacetime expansion.

The whole thing is based on the Alcubierre metric, described by

Alcubierre metric

Alcubierre metric. Variable definitions as used by Alcubierre available at Wikipedia

In a very technical sense, this is not a solution to the Einstein Field Equations, but rather has ADM forms that can be adapted to various observers that are actually not physically distinguished from each other. However, as a Hamiltonian formulation, the solution is not exactly one to the EFEs, but is much easier to work with and is often used in practical and theoretical studies.

This was probably one of my "denser" posts, so for those of you that understood it, I give you an icon to use:

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.

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