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!

Scientia Pro Publica coming here!

Posted by tigerhawkvok on June 02, 2010 20:40 in General , public science

This coming Monday, this blog will be the host of Scientia Pro Publica, a blog carnival following in the footsteps of Tangled Bank. To quote Grrlscientist,

[...]That blog carnival was Tangled Bank, the "parent" of Scientia, which this blog carnival seeks to emulate by (1) communicating about science, medicine, the environment and nature to the public and (2) encouraging those who write about these topics by providing them with an audience who provides feedback and criticism on their writing.

Scientia Pro Publica logo

Scientia Pro Publica logo (C) by Flickr user jmarcx via loryresearchgroup. Hotlinked by my usual policy of hotlinking (rather than self-serving) copyrighted images

This is going to be my first blog carnival, and I hope I am a good host. This should be fun!

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.)

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.

NASA Temperature Data

Posted by tigerhawkvok on January 23, 2010 15:18 in misc science , public science

I got a comment on a tweet of mine from a friend of mine on Facebook:

Statistically? What does that mean? I mean, I think statistics like "1 in 5" or is that just NASA's way of saying '09 had an average temp equal to '98's average temp?

(Source: Facebook)

It's a pretty reasonable question, which kind of underlines the misperceptions on how temperature stuff is measured. John's second point is pretty close to the mark, but there are some subtleties that get lost along the way.

So, first consider the way these temperatures are measured. Obviously, there is inherent instrument error, but there are much larger sources of error. Consider what would happen if you had 100 sensors seperated by 1 m in Death Valley, one sensor in the middle of the Pacific, and one in Antarctica. Obviously, an arithmetic mean is grossly inadequate. So, the data has to be integrated in some weighted manner, which introduces statistical error. Then consider local effects. If you have a thermometer at location X, but if you move it one meter to the left a building drops a shadow over the thermometer. Which is "more true"? People and critters, etc, will experience both temperatures. Do you use both? What about locations that have such a situation, but only one sensor? You need a model to integrate the data.

Then consider what it means for the temps to be equal. Which is a higher temp: 30 +/ 0.3, or 29.8 + 0.5 / - 0.1 ? What about 30.1 +/- 0.7? There are good arguments on various sides, but the most honest thing to say is that they are statistically equivalent — that is, the temperatures all lie within the error bars of the other temperatures. However, the media would probably report the 29.8 temperature as the lowest and 30.1 temperature as the highest, though there is a compelling argument to be made for the reverse.

Here's a couple fairly extreme examples: is 32 +/- 0.1, or 30 +/- 5 larger? There is around a 30% chance that the second temperature is higher, and possibly as much as 3 degrees higher, which is significant. Statistically, you can't tell the difference between the two. A second case would be if you consider a stream of years with steadily improving detectors. If you had a five year span that the error bars kept shrinking, and each subsequent year was entirely within the error bars of the previous, can you say anything about trends in that data? Of course not.

Scientific data without error bars isn't scientific data, and it's a travesty the media almost never mentions error. There is a reason, though, that all the caveats are required and provided by people like NASA.

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.

Paralysis of Choice

Posted by tigerhawkvok on January 01, 2010 14:46 in General , misc science , public science

I've had some down time, but not posting, what gives?

Well, it's not to say I've not had work — but the fact of the matter is it's difficult to work without my primary sets of files an such. So, while I can work, it is almost certainly more efficient to wait until I end my visit with the family tomorrow and return to San Diego. But this merely adds reasons as to why I should be posting, but haven't.

I give you the paradox, or paralysis, of choice. I have so many ideas knocking around in my head that I can't decide which to commit to ... keyboard? So, instead, Twitter has been getting some degree of linkspam and random commentary. But, topical subjects wait for no man. As is virtually a requirement, therefore, I give you ten significant events of the past decade in science. Farewell, naughts! Into the 10's!

  1. Kitzmiller v. Dover smashes ID into a fine powder. Creationists continue to ignore it.
  2. China proves to be a veritable treasure trove of non-avian dinosaurs, providing many, many feathered theropods that changes the way dinosaurs are drawn.
  3. The Large Hadron Collider is finished, then breaks. Some physicists propose the Higgs boson is working backwards in time to keep it from working. It is fixed, and is currently ramping up in power.
  4. An Inconvenient Truth brings climate change into the mainstream conciousness. Cue debate from both sides here (but regardless of your position, it *was* significant).
  5. Stolen emails from HadCRU contribute to the derailing of the Copenhagen talks, despite demonstrations the mainstream interpretations were false.
  6. The chytrid fungus (Batrachochytrium dendrobatidis, or B.d) steps up its affects across amphibian populations.
  7. The Spirit and Opportunity rovers begin their 90 day missions. They are currently on day 2189 and 2168 of their missions, respectivley.
  8. Photons from SGR 1806-20, 50,000 lyr away, hit us and fried some sattelites.
  9. Persistant antivax movements lead to an outbreak of mumps in Brooklyn.
  10. NIF was completed, with ignition tests due to begin this year.
  11. Obviously this isn't a complete list. Any other interesting bits of science I missed?

    And Happy New Year, everyone!

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.


Zooseum Redux

Posted by tigerhawkvok on December 04, 2009 18:31 in General , biology , misc science , public science

I realized that the Zooseum has the flaw that on wet, cold, days, neither aspect of the zooseum would attract customers. However, this problem is easily rectified by having an underground portion of the zooseum.

Located centrally under the zooseum, you can locate the food court and a few stores (with, of course, others by the entrance/exit). Throw in some paths with moving walkways to connect exhibit to exhibit, and arial enclosed connections for nearby exhibits (think Birge-LeConte, or parking structure-airport in L4D's "Dead Air").

This provides an all-weather aspect to the attraction, and means that unlike most zoos, the hours of operation don't need to be strictly confined to animal activity. With hidden paths, lighting does not need to account for disturbance to the animals, as the interconnects can be well-lit, but being underground, should provide little to no animal irritation. Though animal activity will drop off, all that becomes needed are suggestions or notices that there will be reduced animal activity after a certain time can be made, and with longer operating hours, the zooseum should see a higher profit than a standard zoo *or* museum.


Posted by tigerhawkvok on December 03, 2009 00:05 in General , biology , misc science , public science

Zoos are awesome, and so are museums. So, I wonder, why has no one taken the obvious step and combined natural history museums and zoos?

I think the way you do this is that the physical layout of the "zooseum" echos a phylogenetic tree. Different branches are linked up by aerial cable cars, giving a nice set of sightlines while preserving the message of evolution and interrelatedness of animals. Along these branching paths, there are interspersed buildings with fossil representations and extinct members of lineages.


Sample layout. Red lines represent potential arial paths.

In addition to this being a largely natural layout for the animals and fossils on display, this also helps instill a proper phylogenetic way of thinking for visitors. Thus, aviaries would be most closely placed to crocodile and alligator enclosures, and between the two would be exhibits on non-avian dinosaurs and pterosaurs. Additionally, finally, Dimetrodon would be placed in fossil exhibits on the ways to the mammal section of the "zoo", and any oceangoing mammals (ie, dolphins or porpoises, with whales being obviously unfeasible) would be most adjacent to hippos, pigs, and cervids, and bovids.

Despite the "unusual" layouts mentioned in the last paragraph, much of the layouts are quite natural. The cats are together, birds of prey are together, snakes are together (and closest to varanids), etcetera. This also provides the unique opportunity to provide an insect/arthropod exhibit that presents relations of these generally underdescribed (both in the literature and in the public) animals.

This "zooseum", then, is effectively a one-stop shop for the natural world. The unique display mechanism and unique content could also provide a draw for personnel, and good merchandising opportunities. The purpose of the museum portions would be more education than research, with (therefore) few real fossils and mostly casts, emphasizing comparative biology and morphologies. The aerial paths connecting various groups could be centered around the amniote split, acting like a hub.

Perhaps this entry was kind of rambly, but I felt like this is a nifty idea, and I wanted to post it — any thoughts?

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.

Are hybrid-electric cars really the solution?

Posted by tigerhawkvok on July 29, 2009 14:17 in public science , energy

For those of you who haven't heard the "Long Tailpipe" argument against electric / hybrid cars, I thought I'd mirror a post that Kit put up on it:

It really bothers me when people opposed to electric cars use the "long tailpipe" argument, which calls attention to the fact that switching to electric vehicles won't solve the energy requirement problem, since our power plants (most of which run on fossil fuels) will have to generate the excess energy for cars as well. In effect, this just shifts the source of pollution from the streets to the power plants; the amount would be roughly the same.

There are two problems with this assessment. Number one, shifting the source is the whole point. If there were some miracle new power supply that did not run on fossil fuel, or if we could make nuclear engines for every car, then of course they would run on electric motors utilizing this new energy anyway. As it is, most of our energy DOES come from fossil fuels, so that if our main concern is carbon production and other atmospheric problems (waste heat, particulate matter, etc), why not have the problem occur in a centralized, easier to maintain environment? It boils down to: which is worse, a million cars spewing a ton of CO2 into the air from a million tailpipes all over the place, or one big smokestack spewing a million tons from one location? Clearly, it is easier to put expensive filters, catalytic converters, etc on one exhaust pipe than a million, it is easier to clean the air/water/soil near one source of pollution than a million, utility companies can afford to be safer/more environmentally conscious/cleaner than a poor single person with a car, and the government can better regulate them. In all, I'd rather have to clean a quart of shit in my toilet than a quart thinly spread all over my house.

The second problem is that the amount of emissions is actually lower with a localized source. There are many ancillary carbon expenditures to maintain a fossil-fueled fleet of cars, such as the cost of fuel transportation to hundreds of gas stations instead of one power plant, and the fact that the land occupied by gas stations could be used for parks or homes or whatever else. It is arguably safer, too. Consider a coastal power plant (as many are): if it's near a refinery, the fuel can just be immediately pumped into the plants storage tanks. Even if not, an oil tanker could distribute it from a refinery to a pumping station and achieve the same goal. No tanker trucks, gas cans/tanks, or rail tanks needed.

So, even if it isn't THE solution to the problem, it makes it more manageable, and I think it's worth it. Crank out those electric vehicles!

For some reason, I just find the the mental imagery with "quart of shit spread thinly over the house" grossly amusing.

There might be an argument to make about the energy / carbon / etc costs associated with making the batteries with hybrid and electric cars, but those fall through so long as the marginal returns on energy production / localized CO2 emissions / etc can do better than break even over the lifetime of the battery per car. I'd be interested to see the costs associated with producing the batteries and the marginal returns — I'm curious how short the timeframe is.