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!

A Press Conference We Need

Posted by tigerhawkvok on July 25, 2009 21:03 in General , astronomy

I was thinking about the 40th anniversary of the moon landing, and I found myself wishing we were doing more to reach for the stars. So, here is a speech that I wish we would hear from President Obama — though I doubt very much we will.

My fellow Americans:

It has been forty years since humanity first set foot on another celestial body. It has been forty years since we left the fragile confines of our blue marble and looked down upon it from another world.

Those forty years have seen remarkable advances. Our pocket calculators, phones, and PDAs have more than the entire sum of processing power used to launch, land, and coordinate the Apollo missions. We escaped the Cold War, we built giant particle accelerators that attempt to glimpse the first moments of this universe.

And yet, for more than 35 years, we've all humbly retired to this planet of ours and been content to live our our lives here, not reaching out.

We've done great science on other planets. Kepler searches for Earths around other stars; Spirit and Opportunity and countless other missions to Mars map it out in increasing detail. New Horizons is pointed toward the rock we call Pluto, so far out our Sun is barely distinguishable from the rest of the stars in the sky. The great Jovian planets, and their moons, are photographed with wonderful instruments we send their way. But a human has not ventured out to another celestial body since the end of Apollo.

I cannot say it better than John F. Kennedy, so I won't try. The importance of reaching out beyond our globe is not for science, but for the human spirit. Its a deep motivation, and to give another generation the wonder of space, showing that another world is accessible to them. That they or their children might step foot on another world. It is time that humanity begins its process of slowly moving out of our fragile nest, and move in to new worlds.

To that end, I give our country, our species, a challenge. We shall land on the Moon once more by 2019, Mars by 2024 and have a permanent station on either by 2035. It will not be easy. It will not be cheap. And great advances will have to be made along the way. But I know we can do this. Each grand step into unknown territory has brought our species more knowledge, more technology, and further insights into our world, and even if we do not see it now, I have no doubt that we can do so again. Let it be said in 2109 that 2009 was the year that humanity truly looked up into the sky and decided that they had grown old enough, and wise enough, to become a species not of one world but of many.

Thank you, and goodnight.

Proving Inflation?

Posted by tigerhawkvok on May 04, 2009 19:48 in physics , astronomy , IYA

A quick little news snippet from Science: The ESA's new satelitte, Planck, is due to launch on 5/14/09 and will take up the mantle of COBE and WMAP. However, in addition to just improving measurements of the Cosmic Microwave Background, Planck will also possibly prove inflationary theory.

The nuts-and-bolts of inflation say that, in the early early universe, an inversion of the Higgs field resulted in spacetime expanding at superluminal velocities and rapidly slowed down. This explains the flatness of space, the lack of magnetic monopoles, and perhaps the most importantly the uniform temperature of space. This could mean that parts of space no longer causally connected once were, and thus had time to reach a thermal equilibrium before expanding apart.

As a side-effect of inflationary theory, though, we expect to see B-mode polarization of the CMB (that is, polarization of the magnetic field). To quote the article:

But the prize quarry for Planck researchers is the B modes. These features are swirls in the CMB polarization mapped across the sky, and spotting them would essentially clinch the case for the mind-bending theory of inflation.
Although inflation fits the facts so far, researchers do not yet have direct proof that it occurred. The B modes would provide that. Current theory predicts that inflation should have generated gravitational waves and that those waves should have left lingering swirls in the polarization of the CMB.

The polarization may not be strong enough for Planck to detect, but with luck, they will be — and 45 years after the discovery of the CMB, and 30 years after the proposal of inflation, we might finally have an answer.

DOI: 10.1126/science.324_584b

IYA Entry

Pulsars and Gravity

Posted by tigerhawkvok on March 14, 2009 02:56 in astronomy , news , IYA

Seeing as I mentioned gravity just a few days ago, while the Higgs boson is appropriate fodder, this "Perspectives" piece from Science magazine is a bit more topical.

In an effort to prove ever close to the ultimate answer, physicists and astronomers have been looking to probe gravity even deeper. The best results from orbiting pulsars agree with Einstein's theory of General Relativity to within 0.2%. Alternative models predict marginally, but measurably, different results with the most relativistic systems. The ultimate measure of relativistic gravity waves depend on orbital periods, eccentricity, and masses, so by seeking systems like these we can probe gravity even more deeply than we have already.

On the face of it, it may seem that 0.2% is good enough. 99.8% accurate will, in fact, get you to the Moon (in fact, that much error on your path amounts to a 1.74 km error in your landing site on a 384399 km trip). So why does it even matter? These alternative theories posit different fundamentals about the universe, including the necessity of dark matter and cosmic origin.

Pulsar schematic, via Wikipedia

Now, the most relativistic pulsar system we know of is PSR J0737-3039 — it has an orbital period of 2.4 hours, and an orbital decay of its semimajor axis of 7 mm/yr due to gravitational radiation in the form of gravity waves. Being a pulsar, it is an incredibly accurate clock, and enables measurements of such fine precision to be made, that we need to (and can!) measure the effects of its movement through the galaxy on its orbital decay. So, Deller et al. (DOI: 10.1126/science.1167969) show that using the VLBI and about a decade of observation can smash the possible GR error (or disprove GR at these precisions!) down to 0.01%.

Think about it. We're measuring something located ~600 parsecs away (1800 light-years [Lyr], give or take), measuring its orbital decay to millimeters to narrow constraints on one of the two most accurate theories in science to being "only" 99.99% accurate, up from 99.8%. Astronomy (and science in general) — bloody amazing.

By the way — I provide many links to scientific papers, in large part for rigor's sake, but if any readers (how many readers do I have? Do I have any?) are having difficulty, I'll see what I can do about finding free alternatives, such as arXiv.org preprints.

IYA Entry

Late Kepler Post

Posted by tigerhawkvok on March 10, 2009 20:16 in kepler , astronomy , news , research , IYA

So, I composed most of a post on the Kepler launch, then, well, forgot to post it. Belatedly, here we are:

So, Kepler. I mentioned it a little while ago, what was I talking about? Well, I was talking about the Kepler mission (kepler.gov) being sent up by NASA, set to launch on 3/6/09 (This is one of those "Whoops, posted late" parts).

Kepler is a sattelite that will observer one portion of the sky for its entire mission, looking for transit events. To understand a transit event, consider a lightbulb. When something passes in front of it, it obscures part of the surface from your view, and thus reduces the amount of light you observe. So, by observing the same starfield for its mission duration, Kepler can detect any minute changes in stellar flux, thus detecting a planet. The amount of flux change then gives you the planetary size (since color/spectral profile -> temperature -> size -> flux ).

However, there is a caveat here. Sunspots can often be regular, long lasting, or otherwise look like planets. So, my own impact on the Kepler project came with my research work with Gibor Basri, in which we wrote routines in IDL to analyze our own star for the influence of magnetograms on stellar luminosity profiles (IE, where are sunspots? How big? etc).

Various identification methods picking out
umbrae and penumbrae

A particularly good example can be seen in the figure to the left, where various versions of the algorithms pick out different features in a sunspot group. It is important to note that the differences are exaggerated -- the sun is very bright, so the "dark" spots are valued about 0.85 on an absolute scale. you can also see on the right an early version of the algorithm picking out by far most of the major solar features, including the harder-to-discern faculae, or unsually bright areas (which are, of course, very hard to observe in photos such as these).

Early feature identification

The detection and automation algorithms we developed were actually fairly robust and accurate, though CPU intensive (running through about 100 photos took about 3-4 hours on my now-deceased laptop Liz), though our funding ran out over here before I could complete an algorithm to reverse-construct a star from its magnetic profile. Thus, by also observing the long-range magnetic profile of the stars (particularly Sun-like stars) we can rule out some categories of false positives. Looking at some more "final" algorithm photos, you can see why this could be relevant:

light contrast

Solar feature identification with
later versions of the algorithm

If a dark spot such as that passed along the star, it is enough of a brightness dip that it could register as a false positive — that is to say, it could look very much like a planet. While prolonged observation is one way to get around this, feature identification is another way. And I had a part in it! Nifty!


Updated: 3/13/09

IYA Entry

Possible 22 year old confirmation of gravity waves

Posted by tigerhawkvok on March 04, 2009 17:18 in astronomy , news , IYA

Via Slashdot and the arXiv blog, it turns out that we may have actually detected gravity waves in 1987 associated with SN1987A.

OK, that was a bit of a rush. Let's unpack that a bit. Astrophysicists have been searching for gravity waves for a while now, which are linearized plane wave solutions to the Einstein Field Equations with two polarizations (the other fourteen dropping out). The key bit to this solution is that the coordinate positions of the particles remain constant for all τ, but the fractional change in distance between points A and B changes in an oscillatory manner (as 0.5a sin[ωt+δ] ). Since all but two polarizations drop out, this means that for a plane wave oriented in the z direction, wave effects are restricted to the orthogonal x,y plane.


Modern interferometers use long arms with a laser cavity to measure very very small fractional changes in distance via destructive & constructive interference. However, before this, large aluminum cylinders with piezoelectric crystals arranged about it were constructed in an attempt to measure these gravity waves. When SN 1987A went off (Supernova 1987 A, as the first one in 1987), John Weber reported that he detected gravitational waves from the SN detonation. However, calculations of first-order effects (almost always the largest) showed that his detector was insufficiently sensitive to have found any gravitational waves.

However, a new paper (preprint) shows that asymmetries in the 1987 explosion could lead to an enhancement by a factor of 104 in SN1987A, putting these waves right in Weber's detectable range.

So, it seems in retrospect that Weber got the short end of the stick, all things considered. But it's definitely worth re-examining his data to see if he did, in fact, confirm gravity waves 22 years ago.

IYA Entry

Goal and Astronomy

Posted by tigerhawkvok on March 02, 2009 15:43 in General , astronomy , IYA

So, I will announce a goal for this month: I intend to post an average of 3 times per week on this blog. There. Maybe posting this will keep me to it.

Sadly, I missed the timetable to post something interesting about Comet Lulin, which is incredibly low magnitude by now, and would be a shade tricky to spot even with a telescope (at least a 12" would really be needed at this point). However, if you're out stargazing this month, things are fairly boring quiet. You will be able to see Venus set around 8:30 PM (getting earlier as the month progresses), and Saturn transit (move across the meridian) around midnight. These are pre-DST time, so after March 8th they will advance an hour (IE, transit at 1 AM).

On the docket: Mus musculus, and perhaps a bit about evolution.

IYA Entry

Black holes and revelations

Posted by tigerhawkvok on February 21, 2009 15:50 in physics , astronomy , IYA

Last night, I gave a talk to the Tri-Valley Stargazers about black holes. It actually went rather well, and as usual, I enjoyed lecturing.

For those who are curious, here is the PowerPoint presentation (Office 2007) and the PDF.

IYA Entry

Happy New Year, and Welcome to IYA!

Posted by tigerhawkvok on January 02, 2009 00:06 in General , astronomy , IYA

Happy New Year everyone, and welcome to the International Year of Astronomy! It has been 400 years since Galileo turned a telescope to the sky, and first looked into the heavens. In addition to what posting I do (I'll try to keep it up at a higher rate), I'll try to post more about astronomy-related topics. See the link in my sidebar about this. Let's whet some appetites:

APOD 20090102
IYA Entry