More Science Highlights

Scientists Lead a Second Life
Is what is missing about physical presence relevant at all to making scientific recommendations? In my experience, it is not.”
-Douglas Fisher, computer scientist, Vanderbilt University

Scientific organizations such as the NSF and the NIH bring thousands of people together every year to review grant proposals and to decide who should get barrels of money and who should cry themselves to sleep. But the cost of flights, hotels, deli sandwiches, coffee (lots of coffee), and honoraria for those people adds up to quickly, and the carbon footprint grows a few sizes larger every year. What if scientists instead met virtually? What if they hung out in the online world Second Life and discussed whether a proposal’s methods controlled for the correct variables? What if there were no dinners out after deciding to give some scientists $3,000,000?

No Money, Mo’ Problems (for the Higgs Boson, at least)
I think we presented a very good science case for continuing to run, but the fiscal realities just don't allow us to go forward.”
--Rob Roser, Fermilab

Fermilab, the Department of Energy’s high-energy particle physics lab, will be closing the doors on its beloved twenty-four-year-old atom-smasher, the Tevatron, in September. The Tevatron (or the people who run it) had hoped to discover the Higgs boson before the Europeans (CERN! LHC!) and become super-famous in textbooks and our hearts forever. However, upon asking the DoE for the money to keep up the search, the Tevatron was denied. Poor Tevatron.
God, particle, why won’t you just show up!(Get it?)

Scaling up
As an “educator” and “communicator,” I’m always looking for ways to relate huge numbers, huge sizes, and huge distances to people’s experiences and intuitions. This video does a great job of showing the scale of different celestial objects, starting with something whose size you can grasp and moving up to the biggest known star (which, I calculated, has a BMI of 1.4x10^10) and then making you feel very small and short and unimportant, like seventh grade.


Science Highlights this week:

Russia may be cooler than us: Raiders of the lost lake

“Arguably the most exciting — and certainly the most controversial — scientific endeavour in Antarctica's history is close to a breakthrough.”

(Original article: 17 January 2011, Nature 469, 275 2011)

Twenty years ago Russian researchers began a project to drill down 3,650 meters to get test samples of the largest subglacial lake on the planet, Lake Vostok in Antartica. They believe that in a matter of weeks they will hit this subglacial lake (methods found in original article). Samples from this lake will potentially provide us with an insight into life up to 35 million years ago. Imagine what could live under a 3,650 meters of ice, cut off from the atmosphere for millions of years (hint: bound to be cooler than arsenic bacteria)!

A new impact factor: How famous are you really?

“This is a new way to measure a scientist's influence. It captures fame on the grandest scale, weighing the cultural footprint of scientists across societies and throughout history.”

(Original article: 14 January 2011, Science 331 - 6014)

Adrian Veres and John Bohannon have created a database of the most noted scientists in the last 200 years ranked by their appearance of people’s names in books. Jean-Baptiste Michel and Erez Lieberman Aiden made this endeavor possible by creating an enormous data set based on trillions of words within Google Books (raw data, try it yourself).

Introducing the Science Hall of Fame (SHoF) (Don’t forget to look at their tips for being a famous scientist).

My science grandfather (Stanley Falkow) ranks at 4 milliDarwins, know anyone famous?

Visualizing the tiny: Malaria caught on tape

Watch the live video via New Scientist

(Original article: 20 January 2011, Cell Host & Microbe 9: 9-20)

David Rigler and David Richard, et al. have shown for the first time a live video of P. falciparum, a parasite from the genus Plasmodium, the causative agent of Malaria. They recorded the invasion of a human erythrocyte by P. falciparum. Not only is this just awesome to watch, this insight will help shed light on the complex mechanisms used by parasites to invade their host.


Kepler 10-b: the tiniest planet there ever was


As a child, did you lie in your bed at night unable to sleep for wondering how many planets like Earth existed? Does your curiosity still render you insomniac?


Well, have hope for your future REM prospects: NASA’s Kepler Mission, which boasts a dedicated planet-finding telescope, is taking a census of planets, from which we will be able to know, statistically, how common Earth-like planets are.



Artist's rendition of Kepler (JPL)
Recently, Kepler discovered the smallest planet ever. It, endearingly, is called Kepler 10-b and was discovered by Natalie Batalha, et al, “et al.” being fifty-one other people. Kepler 10-b has a radius 1.4 times the size of Earth’s and a mass 4.56 times the mass of Earth. The definition of “density” will tell you that it is more dense than our home planet, meaning that it cannot be a literal twin, but it is the closest we’ve come.

Information about Kepler 10-b comes from the draft paper Kepler’s First Rocky Planet: Kepler-10b by Natalie Batalha, et al. [2010 Jan 10].

For a long time, people did not know a lot of things.
  1. That there was a such thing as a planet.
  2. That there were other planets in our solar system.
  3. That the Sun is a star, meaning that all the stars are like the Sun, but farther away.
Until recently, we could not contemplate the existence of planets outside the solar system. And without the technology to observe tiny, tiny hunks of rock and gas and dirt from light-years away, we could never go farther than contemplation.
Only in the past 18 years have we known for sure that exoplanets exist. The first confirmed planets were found in 1992, orbiting, of all things, a pulsar (Wolszczan & Frail, D. A., 1992). No planet around a pulsar would be habitable. It would be freezing and subject to the kind of General Relativistic effects that would make your face look like those kids in The Ring.



However, in 1995, Mayor & Queloz found an exoplanet orbiting a main-sequence (not big, not small, just right) star called, affectionately, 51 Pegasi. Newsflash: Other stars like ours could have planets. The existence of our solar system might not be remarkable, which is what astronomers like. Ever since those Earth-is-the-center-of-the-universe-no-wait-the-Sun-is-no-wait-the-galaxy-is-no-wait worldview shifts, they have been loathe to think that we are special.



Since 1995, we have found more than 500 planets, and astronomers are beginning to feel more comfortable. These 500ish planets (I say “ish” because more planets are discovered all the time, and if I were precise today, I’d be wrong tomorrow) have been found using indirect detection. Planets are usually 1/1000000 times as bright as the star they orbit, making it virtually impossible to directly “see” the planet. So how do we know the planets are there if we can’t see them?



The most common way is "transit timing." When a planet goes in front of a star during its orbit, the star’s light will dim slightly, periodically. Example below courtesy of NASA. [To see exoplanet methods discussed in detail, check out “The Detection and Characterization of Exoplanets” (Lunine, et al., 2009)].
This and other popular methods, however, are most sensitive to large planets in tiny orbits, a.k.a. “hot Jupiters” (Cumming, et al., 2008). We’ve had a hard time finding planets too much smaller than Jupiter, until recently. Until Kepler.



Kepler uses the transit method, but it is ultraefficient. Its mission goal is to find “Earth-sized planets around Sun-like stars.” No more of these “hot” “Jupiters.” Kepler, in space, will spend its entire life staring at the same piece of sky. Kepler simultaneously monitors the brightness of all ~100,000 stars that are in its field-of-view--24/7. It lies in wait for periodic variations until BAM it finds one, the astronomers get excited, and someone at a telescope on solid ground confirms the detection.



Most information about planets comes from information about their parent stars, things like asteroseismology, or how the star oscillates, and thus how big it is and what its interior is like, and thus what kinds of stars correspond to which kinds of planets.



Animation of stellar oscillations (NASA).

Stars and their planets formed in the same place out of the same stuff, so properties of a star are likely to be relevant to what’s inside the planet. For example, we know that stars with higher metallicity (and when astronomers use the word “metal,” they mean anything heavier than Helium) are more likely to have more massive planets (Marcy, et al., 2005).



So Kepler was staring at its spot, bored, and then it found something new: something not too big and not too small. Something called 10-b.



10-b’s host star is a main-sequence star that is 11.9 billion years old and 5627 Kelvin. It is 0.895 times the mass of the sun and 1.056 times the radius of the sun. In other words, pretty damn Sun-like.



10-b is 4.56 times more massive than the sun, but only 1.4 times as wide, giving it a density of 8.8 grams per centimeter-cubed (Earth’s is 5.52). That means that you won’t be moving to 10-b any time soon, as it's made mostly of rock. Astronomers create plots of what a planet made of, say, water-and-rock would look like on a mass-radius diagram, and then they compare that to exoplanet data. In this case, the planet looks more like something that has a ton of iron than a ton of irises.



But its uninhabitability does not make 10-b less interesting. Given the way exoplanet searches have exploded, and the number of earth-sized planets Kepler is likely to discover before it closes its eyes, we are well on our way to understanding how our solar system fits in.



Astronomers estimate that about 40% of stars have planets. Given the 100 billion stars in the Milky Way, there are 40 billion stars with planets. Given the 100 billion other galaxies in the universe, there are 4,000,000,000,000,000,000,000 stars with planets in the universe. Our solar system probably represents only 0.000000000000000000025% of all solar systems.



If that doesn’t put you in your place, I don’t know what will.


Andrew Cumming, R. Paul Butler, Geoffrey W. Marcy, et al. (2008). "The Keck Planet Search: Detectability and the Minimum Mass and Orbital Period Distribution of Extrasolar Planets". Publications of the Astronomical Society of the Pacific 120: 531–554.
Lunine, J;
Macintosh, B; Peale, S. (2009). "The Detection and Characterization of Exoplanets". Physics Today 62 (46): 47-51.




How does the body use DNA as an antimicrobial agent?

Generally when I think of antibiotics I imagine taking a pill that delivers tiny death packages to individual bacteria that have invaded my body. These micro-molecules float through my blood stream to be delivered to my organs, obliterating any foreign cells they can find, taking no prisoners.

In addition to these pilled, bottled and administered antibiotics, there are inherent antimicrobial activities your cells have evolved to combat pathogens & escape infection. One specific cell type has been shown to have potent antimicrobial activity for over 100 years, feared by all microbes large and small: the neutrophil (Metchnikoff, 1901).

Aside from being notorious for forming pus at the site of infected wounds, neutrophils are known for their immediate response to infection by migrating via the circulatory system to the site of inflammation (for an excellent review on neutrophils: Nature Immuno Reviews, Nathan, 2006). Once at the site of infection, neutrophils engage in full-contact battle by engulfing the pathogen in a membrane-bound vesicle called the phagosome. This phagosome will mature into the phagolysosome where microbes are exposed to antimicrobial peptides and reactive oxygen species. After maturation of the phagosome, most neutrophils undergo apoptosis, controlled and anti-inflammatory cell death. Recently scientists found that, in addition to apoptosis, neutrophils also have a very distinct and interesting cell death pathway that results in formation of neutrophil extracellular traps (NETs) (Brinkmann et al., 2004) (Fig 1).

What are NETs?

Brinkmann, et al. (2004) first described NETs as “extracellular fibers… composed of granule and nuclear constituents that disarm and kill bacteria extracellularly.” NETs get their fibrous structure from DNA, the major structural component. DNA is naturally negatively charged and binds to positively charged proteins and cationic antimicrobial peptides (CAMPs). Other enzymes such as neutrophil elastase (NE), an enzyme that degrades virulence factors of bacteria, also bind to NETs (Weinrauch, 2002). Bacteria secrete virulence factors to evade host antimicrobial mechanisms, & their degradation weakens the defense of the invading bacteria. In addition, like in the nucleus, DNA binds to histones (Fig 2), naturally bactericidal proteins (Hirsh, 1958).

But is the production of NETs an early pre-determined cellular fate, or is this pathway a late reaction to infection? Recently Papayannopoulos, et al. (2010), found that NE and myeloperoxidase (MPO) (Fig 2), two antimicrobial peptides that bind to DNA in NETs, regulate chromatin density during the formation of NETs. Chromatin decondensation is necessary for the relaxation and release of DNA, required for NET formation. This is excellent data, but we need to collect additional data to identify the beginning steps of NET formation in order to determine how and when neutrophil NET fate is determined.

Why I find this interesting?

I love the idea that our body has evolved countless mechanisms to fight bacteria – including a mechanism that involves cellular suicide and antimicrobial agents binding to a giant extracellular DNA net. Generally we think of DNA in the nucleus wound up around histones, occasionally being read by polymerases – but this new antimicrobial mechanism shows that there is versatility and that endless eukaryotic cellular components have dual functions. NETs showcase how beautifully we have evolved.

Hirsch JG, J Exp Med 108(6), 925 (1958)
Weinrach Y, et al. Nature 417, 91 (2002)
Metchnikoff E, Limmunité Dans Les Maladies Infectieuses (1901)
Papayannopoulos V, J Cell Bio, 191(3), 677 (2010)

Brinkmann, V. (2004). Neutrophil Extracellular Traps Kill Bacteria Science, 303 (5663), 1532-1535 DOI: 10.1126/science.1092385

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