Wednesday
Feb092011

High-Lights

When Results are not Results
“'Habituation is why you don’t notice the stuff that’s always there,' Schooler says. 'It’s an inevitable process of adjustment, a ratcheting down of excitement. I started joking that it was like the cosmos was habituating to my ideas. I took it very personally.'"

What if the scientific method were flawed? What if scientists' judgments were flawed? What if scientific reporting were flawed? What if the peer-review process were flawed? What if you found a result--a positive association between X and Y--and then when you repeated the experiment, the correlation between X and Y went down, and then when you repeated it again, the correlation went down even further, ad infinitum (or ad at least as many times as you or someone else replicated your experiment), until the significance was completely gone, the correlation no greater than chance? This happens! It's called "the decline effect," and it means that after a result is reported, future studies tend to find the result less and less pronounced, in an almost exponential way. Check out this article by RadioLab's Jonah Lehrer (PS thanks to RadioLab for giving me something to listen to while I walk my dog in the morning--holla back!) to learn  more. My question is, will the decline effect, now that it has been documented, be subject to the decline effect, and will that fix everyone's scientific problems?

"The Truth Wears off," The New Yorker.

Poor, Poor Astronomers of the Future
Within ∼ 10^11 yr after the Big Bang, all galaxies outside the Local Group
will exit from our event horizon...At that time, not only external galaxies but also the nearest extragalactic protons will be pushed out of our horizon and not be available for tracing the cosmic expansion. This realization has led to the naive expectation that an empirical reconstruction of the past cosmic history will become impossible.

Abraham Loeb of Harvard wants to know: How will the astronomers of the future know anything about the universe, when everything will be so far apart that observational confirmation of things like the age of the universe will be impossible? Actually, he wants to know, "Will it be impossible?" and, because he is a theorist and determines answers to questions most people consider only abstractly, he says, "No, man." Astronomers of the future will have hypervelocity stars, or stars whose velocity exceeds the escape velocity of their galaxy. Check out his article to see what the h-e-double-hockeysticks that means for the age of the universe.

2 Feb 2011, "On the Importance of Hypervelocity Stars for the Long-Term Future of Cosmology," http://arxiv.org/pdf/1102.0007v1.

Kiddos Find a Pulsar

"'Sometimes I just stop and think about the fact that I'm looking at data from space,'" Thompson said. "'It's really special to me.'"

So, full disclosure, I wrote this press release, and the news is from a program with which I'm associated. The Pulsar Search Collaboratory is designed to educate/train students in analysis and then set them loose on terabytes of data to find pulsars. Sometimes they do! Sometimes it's a 'recycled pulsar,' like this one.

2 Feb 2011, "Students Excited by Stellar Discovery," NRAO, http://www.nrao.edu/pr/2011/studentpulsar/.

Friday
Feb042011

Science Highlights this week:

Epidemiology to the rescue! Eradicate polio!

Exciting news this week in the story for the eradication of polio – Bill & Melinda Gates announced yesterday their goal & commitment to eradicate polio by 2012. They have increased their annual donation of $200 million to $350 million in support of polio eradication! Although 99% of poliovirus has been eradicated (data from CDC), there are still some cases in the conflict-ridden areas of Pakistan, Afghanistan, India & Nigeria. An important aspect to understand about polio is that although it causes paralysis in very limited cases, most people are silent carriers of the virus.

On a side note, I visited the CDC Museum and Vistor’s Center (open to the public Mon-Friday 9-5pm, Thursday 9-7pm) yesterday & they had an exciting array of documentaries on the fight for the eradication of polio. I highly suggest an outing if you’re in the Atlanta area.


Happy 10th Birthday Human Genome Sequence!

This month marks the 10th Anniversary of the two first papers (published in Science & Nature) to describe the nearly complete sequence of the human genome. J. Craig Venter, the man behind it all, sequenced his own genome, 3 million base pairs, in 9 months. This name may sound familiar because him and his hefty team are also responsible for sequencing the first complete genome sequence of a living species (Haemophilus influenzae) AND The Craig Venter Institute recently gained attention for their creation of an 100% artificial genome (the first self-replicating synthetic bacterial cell). Needless to say, this guy’s wikipedia is awesome. Though we have decades to go before we really understand the entire diploid human genome sequence and the implications of understanding these base pairs, this is a momentous occasion. What better to celebrate this Friday?

Science takes another back seat in the Republican spending cuts:

“The human race has reached a turning point. Man has opened the secrets of nature and mastered new powers. If he uses them wisely, he can reach new heights of civilization.” – Harry S. Truman

Today House of Representatives Republicans unveiled their plan to decrease funding for most civilian based research. Coming in at a devastating $74 billion lower than President Barack Obama’s 2011 request. To learn more about the budget cuts go here.

This new plan will be voted on by the House the week of February 14th.

Tuesday
Feb012011

The Murmur of the Hidden Monster: Supermassive Black Hole in Andromeda Goes Bonkers (in 2006)


What’s the problem with black holes? Well, for one, if you go within their Schwarschild Radius, you become spaghettified. And they mess up spacetime. To extend the oft-quoted bowling-ball-on-a-mattress analogy, if the mattress had sheets on it, the black hole-bowling ball would do a lot more than wrinkle them. Right? RIGHT?

Well, also, don’t forget that BHs don’t produce light. In fact, the point of them is that they trap light, stuffing it down their gullets and clamping their teeth shut.

However, we do see light associated with BHs. Light that is an effect of processes caused by their gravity. It’s not visible light, though—it’s X-rays, gamma rays, radio waves, spraying around Schwarschild radius, inside which is the part that gives “black hole” its first name. iMAGE: Jets of emission from BH at the center of a galaxy.
Marscher et al., Wolfgang Steffen, Cosmovision
NRAO/AUI/NSF

We infer the existence of black holes from this energetic activity, as well as from the orbital behavior of objects near suspected black holes (see video).


But all we can do is infer. And while we can make our inferences as scientifically robust as possible, we can’t know. So while we are all, “Duh, of course there are supermassive black holes at the centers of galaxies—they’re the only things with enough density to have the orbital effect of making a whole galaxy rotate around them yet not take up much space. Haven’t scientists accepted this idea for decades?” papers still contain mealymouthed phrases like “galaxies with a stellar bulge are thought to harbor,” which is how the paper I’m talking about today begins. The paper, whose title I heart, is called “The Murmur of the Hidden Monster: Chandra’s Decadal View of the Supermassive Black Hole in M31,” and is written by Li, Garcia, Forma, Jones, Kraft, Lal, Murray, and Wang.

The suspected, alleged, supposed supermassive black holes (SMBHs) in the local universe are radiatively quiescent. This is in contrast to far-away (a.k.a. “older”) galaxies that have “active galactic nuclei” (AGN), in which stuff is always a-fallin’ into their SMBHs.

Galactic nuclei like ours and our neighbors’ are sometimes called LLAGN, or low-luminosity AGN, because not enough stuff is a-fallin’ in. The most famous LLAGN is our own, SgrA*, but our hometown hero is actually a bit strange. Rather than having a fairly constant luminosity, SgrA* bursts periodically in its X-ray, infrared, and radio emission. Its X-rays are sometimes 100 times brighter than at quiescence. This behavior is unusual for LLAGN.

SgrA* was alone in its awkward outbursts till now, when Li, et al., showed that M31*, the SMBH at the center of the Andromeda (M31) Galaxy, also flares up.

But before we talk about that, let’s talk about this supposed “black” “hole.”

Fact the first: We infer the mass to be 1.4x10^8 solar masses.
Fact the second: The center of M31 has a double-nucleus, which astronomers interpret as a set of old stars orbiting the SMBH, which is at the center of one nucleus.

The Double Nucleus of M31  
Credit: T. R. Lauer (KPNO/NOAO) et al., HST


Fact the third: Telescopes have detected X-rays and radio waves that are believed to be caused by processes going on around the SMBH.

Subfact: We believe this because the suspected SMBH, the Xes, and the radios are positionally correlated.
Subquestion: Does it disturb you that coincidence (meaning co-incidence, not “isn’t it a coincidence that we have the same birthday?”) is how we infer causality?

I feel okay about it, but I thought I’d check in with you.

Li, et al. (2009) found that the baseline emission from M31* was 1.2 x 10^36 erg/s, which may look like a large number but is actually much smaller than it could be for a black hole of this mass.

Because these astronomers wanted to see if, perhaps, M31* acted like the center of the Milky Way—if its brightness varied drastically, they analyzed archived data from the X-ray telescope Chandra (located in SPACE), from 1999-2010.

So what did the researchers find, in terms of variation, between the 90s and today? Did the SMBH finally stop wearing its Nirvana t-shirt?

  1. 1999-2006: Quiescence, constancy.
  2. 2006: Outburst! AH! 250 times as bright as quiescent state.
  3. 2006-2010: A more active state, with frequent, smaller-scale brightness variations and a baseline 23 times brighter than quiescence.

This SMBH is so like being in a relationship, am I right?

While outbursts (AH!) in most LLAGN are attributed to tidal disruption (i.e. a star coming close to the SMBH) (Rees, 1988), M31*’s outburst does not have the same qualities as those others. Mostly, it is 10^34 times less bright, proportionally. It does, however, look similar to the outbursts from SgrA*.

Inference: The M31* and SgrA* outbursts share the same physical cause because they have the same physical characteristics. Tada.

While you may not find the results of this study fascinating, what fascinates me is our inability to access the objects we’re studying. In almost every other field, you can smell or scan or spin or dissect or otherwise manipulate your material. Any number of investigative methods are at your disposal, and you can control situations and variables yourself.

In astronomy, however, the variables come to you, and you’re just lucky enough that space is big enough that chances are that something out there will suit your purposes. But you have to find it. And then all you can do is catch photons it lost a long time ago.

We can’t take a spaceship and measure the gravity around a black hole ourselves; we have to measure the effects of the gravity in order to find out what the gravity is. We can’t go make sure that spatial co-incidence is actually causal connectivity. We can’t send one person to M31* and one person to SgrA*, make them watch for millions of years, and then have them meet up to discuss the similarities of their observations.

No, we must wait. And use phrases like “it is reasonable to speculate that.”And it is, I do believe, reasonable to speculate that.

REFERENCES
ResearchBlogging.orgZhiyuan Li, Michael R. Garcia, William R. Forman, Christine Jones, Ralph P. Kraft, Dharam V. Lal, Stephen S. Murray, & Q. Daniel Wang (2011). The Murmur of the Hidden Monster: Chandra's Decadal View of the Supermassive Black Hole in M31 The Astrophysical Journal Letters, 728 (L10), 1-6 : 10.1088/2041-8205/728/1/L10

Li, Z; Wang, Q.D.; Wakker, B.P. 2009, MNRAS, 397, 148.
Rees, M.J. 1988, Nature, 333, 523.

Friday
Jan282011

Science Highlights this week:

Red blood cells can tell time?

“We hope that our findings may shed light on a number of apparent paradoxes concerning circadian clocks, such as how they continue to keep time accurately…”

O’Neill JS & Reddy AB. Nature January 27 2011 469, 498

This week John S. O’Neill & Akhilesh B. Reddy published their data indicating red blood cells have a circadian clock. From bacteria to human, circadian rhythms or biological clocks are a fundamental property of living cells. Circadian rhythms are a physiological & behavioral phenomenon that persists within ~24 hours. Briefly, it has been thought these clocks are determined by transcription-translation feedback (mRNA & protein production), but human red blood cells do not have DNA, therefore no transcription or translation. So how does it run? Without skipping too much, peroxiredoxins, highly conserved antioxidant proteins, undergo ~24-hour redox cycles, which they have shown to persist for many days under constant conditions. In addition they can be tuned using environmental stimuli!

TLDR: Scientists are never right when they make assumptions.

ResearchBlogging.org
O'Neill JS, & Reddy AB (2011). Circadian clocks in human red blood cells. Nature, 469 (7331), 498-503 PMID: 21270888

Programming mosquitos to fight the diseases they spread

6000 “genetically sterile” male mosquitos were released in Malaysia on December 21, 2010. These mosquitos were produced to combat dengue virus. Martin Enserink reported, “when females mate with these transgenic males, there are no viable offspring; the hope is that, as a result, the mosquito populations will collapse”. Though the study is not conclusive yet, there was a previous release of 3 million sterile mosquitos in Grand Cayman last summer and the paper describing the results reports an 80% decrease in mosquito numbers (unpublished, submitted to Science).

(original article by Martin Enserink, Science News, 27 January 2011)

Look out this week for: The Panic Virus: A True Story of Medicine, Science, and Fear by Seth Mnookin

“Vaccine opponents point out that science can never be absolutely certain, especially about a negative. But it is close to certain that vaccines do not cause autism and that non-vaccination leads to epidemics.” – Melvin Konner, Nature (2011)

This is a picture I wanted to share, any thoughts?

Tuesday
Jan252011

To get a flu shot or to not get a flu shot, that is the question.

When people ask me about my dissertation research I skip to the good stuff (the stuff we say to the NIH to get grants): researching vaccines for a bioweapon. If the conversation doesn’t completely stop there the next part of the conversation generally leads to questions about vaccines & autism or the flu vaccine – but my favorite question is always, “should I get the flu shot this year?

Short answer:
Yes, if you want a lowered chance of throw-up inducing inconsolable pain for 2 weeks. Plus you get a bonus in the 2010-2011 flu vaccine - they have added not only the 2 main flu strains but the very cross-reactive (protects against multiple flu viruses) H1N1 vaccine.

Long Answer:
Not necessarily, if you’re like me, or some of the professors I know that study flu – you’re sufficiently scared of the phenomenon known as the Original Antigenic Sin (OAS).

Briefly, influenza has afflicted humanity for hundreds of years, and despite vaccination efforts 5-20% of the population gets infected with influenza viruses each year (Smith, 2006). The influenza virus is constantly undergoing evolutionary change; therefore, despite the fact vaccination with a single influenza strain provides life-long immunity to that strain, we are still very susceptible to newly forming influenza viruses. This is referred to as antigenic drift and the variation (mainly) occurs in two surface sugars of the virus, hemagglutinin (HA) and neuraminidase (NA). Now does it make sense that the swine flu variant is called “H1N1” and the avian flu variant is “H5N1”?

Switching to immunology - when the body comes into contact with an antigen, a foreign substance or molecule (ex: bacteria or viruses), the immune system (specifically B cells) produce antibodies to kill or neutralize that antigen now recognized as a harmful invader. This immune response has been utilized to vaccinate humans for centuries. Edward Jenner started the first officially documented case of mass vaccination in 1796 using live cowpox virus (vaccinia virus – coincidence that “vaccin” is in “vaccinia”? I think not) to protect hundreds of people from contracting smallpox. Most immune responses follow this general idea.

For flu vaccines (both live vaccines & killed-vaccines) we utilize our immune response by producing antibodies that can neutralize the viral particle. The antibodies bind to the virus particle and literally neutralize any effect it has biologically and subsequently destroys the virus. When our bodies produce these life-long antibodies against specific flu strains the viruses adapt and evolve to escape neutralization and destruction. The outcome of viral evolution is the production of viruses that share similar proteins, including surface proteins HA & NA (ex: H1N1 and H5N1 both share similar neuraminidase glycoproteins), therefore you have variant viruses that consist of shared proteins and novel proteins. Ideally when your body comes into contact with a new variant virus there would be activation of the immune system that would produce 1) antibodies that recognize the “shared” proteins, the viral proteins that the body has seen before in another virus & 2) antibodies that recognize the newly evolved viral proteins.

This is where the Original Antigenic Sin comes into play: So if you imagine you are continually exposed to influenza proteins (every year when you get your vaccine) you will have built up an army of antibodies specific for each influenza strain. What if you’re exposed to a new variant (EPIDEMIC!!!) and instead of producing both 1) and 2) antibodies, your body is now trained to just produce 1) antibodies. Therefore, you have been priming your body to fight specific flu variants - so you will no longer produce new antibodies that recognize the new epidemic influenza virus. If you do not produce antibodies to the new influenza virus you cannot neutralize it = sick for days, or death for some.

This is bad. But is it true?

There has been back and forth in the research community – with support for both sides. Recently, Jin Hyang Kim, et al. (2009) found that immunization with inactivated influenza viruses (the vaccine most of us receive as adults) led to minimal original antigenic sin when challenged with a new variant influenza virus. However, the live influenza viruses (the vaccine children take – think nose swabs) led to severe original antigenic sin responses. The antibody response to the live virus strain was almost exclusively against the original antigen “severely limited responses against novel epitopes in the drifted [new variant = epidemic] strain”.

So, will you still get the flu vaccine??

References
Smith, NM, et al. Mobid. Mortal Wkly Rep Recomm Rep, 55, 1 (2006).

Kim, J., Skountzou, I., Compans, R., & Jacob, J. (2009). Original Antigenic Sin Responses to Influenza Viruses The Journal of Immunology, 183 (5), 3294-3301 DOI: 10.4049/jimmunol.0900398
ResearchBlogging.org