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  • December 6, 2010
  • 07:00 AM
  • 610 views

Is the Future Bisexual?

by Shaheen Lakhan in Brain Blogger

Last week, I heard a girl on the radio, who was talking about how she would have no problem doing a threesome with another girl, if her boyfriend desired it. The girl’s carefree attitude, revealing to hundreds of thousands of strangers that she was open to a bisexual experience reminded me of a certain 2005 study [...]... Read more »

  • December 6, 2010
  • 07:00 AM
  • 1,217 views

Sedentary Physiology Part 1 – Not Just The Lack of Physical Activity

by Travis Saunders, MSc, CEP in Obesity Panacea

Image by kaibara87
Welcome to our 5-part series delving into the fascinating research being performed in the emerging field of sedentary physiology.  Today, we’ll start with an introduction.
As regular readers will know, sedentary physiology is one of our favourite topics here at Obesity Panacea.  Later this week we will be examining the relationship between sedentary behaviour (aka behavior) and health, as well as the mechanisms that are thought to mediate this association.  But before we delve into those deeper topics, I’d like to give a bit of background.
What is sedentary behaviour?
Sedentary behaviours are those characterized by very low energy expenditure – typically those requiring 1.5 METs or less.  MET stands for metabolic equivalent, and is equal to 3.5 ml/kg/minute of oxygen consumption.  All you really need to know is that by convention, 1 MET is considered to be the resting metabolic rate while sitting quietly.   In contrast, moderate physical activity is defined as an intensity between 3-6 METs, while anything above 6 METs is considered vigorous exercise.  Given that sedentary behaviours are those with an energy expenditure of 1.5 METs or less, these are activities that are burning roughly the same number of calories as sitting quietly – e.g. not much at all.  With few exceptions, this means that any time you are sitting or lying down (watching TV, playing traditional videogames, using the computer, reading, driving in a car, etc), you are likely engaging in sedentary behaviour.  This does not mean that riding an exercise bike (which involves sitting) is sedentary, since it also involves an energy expenditure above 1.5 METs.  Ditto for certain energy-intensive activities in the prone position.  The figure below is from a recent paper published by several colleagues and myself, which illustrates the entire “activity continuum”, ranging from completely sedentary to highly active.  The figure also differentiates the focus of traditional exercise physiology research (e.g. moderate and vigorous physical activity), from the focus of the emerging field of sedentary physiology.
Being “sedentary” is NOT the same thing as being insufficiently physically activity.
Up until very recently, referring to someone as sedentary meant simply that they were not meeting current guidelines for physical activity.  In simple terms, if you were exercising for 60+ minutes/day, you were considered physically active.  If you were exercising 10 minutes/day, you were sedentary.  Case closed.  But as we will discuss later this week, accumulating evidence suggests that sedentary time is closely associated with health risk regardless of how much physical activity you perform on a daily basis. Further, it is entirely possible to meet current physical activity guidelines while still being incredibly sedentary.  Consider the following figure from the same paper as above:
As you can see, one individual (the white circles) performs a single bout of structured physical activity, but then remains completely sedentary throughout the rest of their waking hours.  In contrast, the individual represented by the black boxes accumulates a similar volume of structured physical activity, but dramatically less sedentary time.  And the evidence that I will present later this week suggests that the individual represented by the black boxes is likely to have significantly lower metabolic risk than the one represented by the white circles, even though they are both meeting physical activity guidelines.
All this to say that it is important that we recognize that sitting too much is not the same as exercising too little (a line which I am happy to borrow from Marc Hamilton, one of the leading researchers in this area).  As the above figure illustrates, an individual can be both highly active and highly sedentary at the same time, and it is thus important that we distinguish between the two whenever possible.
How much sedentary time do we accumulate on a daily basis?
The short answer?  A lot!
Several studies have aimed to quantify the amount of time that both adults and children spend sitting on a regular basis, and all have found it to be an incredibly large portion of the day.  For example, a recent nationally representative survey of more than 5700 Americans found that the average sedentary time was just over 8 hours per day.  That equates to roughly half of our waking hours.
The situation in children is, unfortunately, no different. There is evidence that children in both Canada and the USA accumulate more than 6 hours of screen-time (time spent in front of the TV, computer, or other screen-based device) on a daily basis.  Keep in mind that screen-time is almost exclusively sedentary (active video games excluded), and that all these hours of sedentary behaviour are in addition to the hours and hours (and hours) that kids spend sitting at school.  In fact, a recent study by our colleagues Lindsay Nettlefold and Ashlee McGuire reports that roughly 70% of class time, including physical education class, is completely sedentary (while slightly better than class time, children were also sedentary for the majority of lunch and recess).
Ok, so hopefully we are now on the same page with respect to what sedentary behaviour is, what it is not, and how it dominates most of our waking hours.  What is the health impact of this ubiquitous sedentary behaviour?  The short answer is that it’s certainly not good.  For the details, be sure to check back tomorrow for Part 2 in our series on sedentary physiology.
Travis
Tremblay, MS, Colley, RC, Saunders, TJ, Healy, G, & Owen, N (2010). Physiological and health implications of a sedentary lifestyle Applied Physiology, Nutrition and Metabolism
... Read more »

Tremblay, MS, Colley, RC, Saunders, TJ, Healy, G, & Owen, N. (2010) Physiological and health implications of a sedentary lifestyle. Applied Physiology, Nutrition and Metabolism. info:/

  • December 6, 2010
  • 07:00 AM
  • 538 views

December 6, 2010

by Erin Campbell in HighMag Blog

Pathogens use some pretty awesome tricks in order to replicate in and infect cells. Today’s image is of a bacterial pathogen that exploits the actin cytoskeleton in its host cell.... Read more »

Haglund CM, Choe JE, Skau CT, Kovar DR, & Welch MD. (2010) Rickettsia Sca2 is a bacterial formin-like mediator of actin-based motility. Nature cell biology, 12(11), 1057-63. PMID: 20972427  

  • December 6, 2010
  • 06:30 AM
  • 2,208 views

Amiodarone for Cardiac Arrest in the 2010 ACLS – Part III

by Rogue Medic in Rogue Medic

The research only demonstrates improved survival to admission, as if that does anything more than provide false hope and huge hospital bills. Why do we base the standard of care on such limited research?

Since there is no new amiodarone research, let's look at the old surrogate endpoint research that compares amiodarone with placebo. Keep in mind that this surrogate endpoint study is the basis for over a decade of still unproven treatment.... Read more »

Kudenchuk PJ, Cobb LA, Copass MK, Cummins RO, Doherty AM, Fahrenbruch CE, Hallstrom AP, Murray WA, Olsufka M, & Walsh T. (1999) Amiodarone for resuscitation after out-of-hospital cardiac arrest due to ventricular fibrillation. The New England journal of medicine, 341(12), 871-8. PMID: 10486418  

  • December 6, 2010
  • 06:00 AM
  • 1,337 views

Article review: Consensus methodologies in qualitative research

by Michelle Lin in Academic Life In Emergency Medicine

What types of methodologies are used to develop a consensus statement? I'm in the midst of helping to write a consensus statement manuscript in education and ran into this great review article. It's from the British Medical Journal in 1995. Basically, there are 2 general types of methodologies:Delphi ProcessNominal Group Technique Delphi ProcessAn example of a consensus topic might be: How will patient care be affected by the new ACGME Duty Hours rules? The Delphi process takes several rounds of discussions:Round 1: Opinions are expressed on a particular issue and categorized into headingsRound 2: Participants rank their agreement with each statement in the summarized opinions.Round 3: Participants view the Round #2 rankings and comments and re-rank their agreement with the opinions.The final results are analyzed for agreement. If there is no consensus, Round 3 is repeated. The Delphi Process allows a large number of experts to participate in a consensus statement because this entire process can be performed via email.Nominal Group TechniqueIn contrast to the Delphi Process, the nominal group technique involves fewer experts (usually 9-12).  Furthermore, this approach requires face-to-face discussion, which adds a more personal element to the methodology.Step 1: Each participant contributes one idea to the facilitator, who records it on a flip chart/projector screen.Step 2: The comments are grouped into different categories.Step 3: Each participant privately ranks each idea.Step 4: The results are tabulated and discussed in a large-group setting.Step 5: Each participant privately re-ranks each idea.Step 6: The results are tabulated to determine consensus.ReferenceJones J, Hunter D. Consensus methods for medical and health services research. BMJ. 1995, 311(7001), 376-80. Download the free PDF.... Read more »

Jones J, & Hunter D. (1995) Consensus methods for medical and health services research. BMJ (Clinical research ed.), 311(7001), 376-80. PMID: 7640549  

  • December 6, 2010
  • 05:24 AM
  • 1,368 views

How marsupial embryos develop (a short story)

by Captain Skellett in A Schooner of Science

Marsupials are just plain weird when it comes to procreating. I’m not talking about bifurcated penises (where the penis has two heads) although that’s pretty freaking weird. I’m talking about the embryos. When a baby marsupial is born after a 4-5 week gestation, it’s a tiny pink speck of nothing much. About the same size [...]... Read more »

  • December 6, 2010
  • 04:09 AM
  • 805 views

Unquestioning dogma: the gatekeepers of science

by Björn Brembs in bjoern.brembs.blog

This morning my friend Ramy reminded us of the recent spats over PLoS One publications (Darwinius, Red Sea) and how they were used to question the 'reputation' of PLoS One as a journal. Of course, it is about as meaningful to talk about the reputation of a journal as it is to talk about the reputation of the cover of a book. Journals are containers which say very little about their content. But on to the really relevant point:Specifically, Ramy pointed out how the current spat about a publication in the journal Science on a purportedly arsenic-based lifeform (see, e.g., Pharyngula and especially Rosie Redfield) didn't reflect on Science at all, despite the basically identical story-line of media hype before publication followed by more sober commentary from the scientific community after publication. Why is PLoS One criticized in the first two cases, but nobody questions Science in this (or the numerous other) cases? Clearly, the two GlamMagz Nature and Science both have their share of in some cases pretty embarrassing blunders. My personal favorite is a paper in Nature about fly thermosensation, easily the worst conducted study in this field in quite a few years. Yet, nobody questions the 'reputation' of Nature. Also in this case, none of the critical commenters questions the legitimacy of the gatekeeper function that the GlamMagz are so happy to tout.Let's be honest about it: there's no journal without fault. Everyone makes mistakes. Journals are no more gatekeepers than the persons working there. Any perceived hierarchy among journals is merely that: perceived. A perception caused by visibility, historical baggage, group-think and circular reasoning.It doesn't matter where something is published - what matters is what is being published. Given the obscene subscription rates some of these journals charge, if anything, they should be held to a higher standard and their 'reputation' (i.e., their justification for charging these outrageous subscription fees!) being constantly questioned, rather than this unquestioning dogma that anything published there must be relevant, because it was published there. If anything, every single contested paper should be used to question the level of subscription fees raised by these journals.In fact, every retraction should lead to an immediate reduction in subscription fees for the journal in which the retracted paper was published, because the journals failed to serve its gatekeeper purpose. If the journals justify, as they do, their obscene subscription extortion with their outstanding peer-review process, their price needs to drop every time it fails. Given the hyper-inflation of retractions, we should see a precipitous drop in subscription charges immediately, should such a policy be enforced.Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P., Anbar, A., & Oremland, R. (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science DOI: 10.1126/science.1197258... Read more »

Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. DOI: 10.1126/science.1197258  

  • December 6, 2010
  • 04:00 AM
  • 773 views

How To Cuddle Your Lady Right, by Smoove A

by Miriam in Deep Sea News

You are probably aware that Smoove A* is an authority on crustaceous love. Some have gone so far as to describe Smoove A as the authority on all multi-legged ladies. I am an amphipod (Gammara pulex), a microscopic crustacean that inhabits lakes and streams, and I cannot confirm or deny this report, I can only say . . . → Read More: How To Cuddle Your Lady Right, by Smoove A... Read more »

  • December 6, 2010
  • 03:19 AM
  • 711 views

Blog: Qubits and Crypto

by Torah Kachur, Rheanna Sand and Brit Trogen in Science in Seconds


Secrets and lies define the government and military, that and being led by bumbling fools.  There is no doubt that some military information should be kept secret like technological advances, battle locations and strategies and George W. Bush's IQ.  For secrets to be kept away from Wikileaks, cryptography is essential.  The new type of cryptography that is being tested by the US military research division, DARPA, is quantum cryptography.  Because if codes like DaVinci's Last Supper weren't complicated enough, might as well throw in the most complicated scientific issue in the world today - quantum theory. 

 

Quantum cryptography is based on using electromagnetic waves like light to carry information.  Photons carry information as qubits (not Q-bert...unfortunately) and light can be polarized by only allowing a particular magnitude and phase of light through a specialized filter.  This polarization gives light a specific binary (0 or 1) property depending on how it is polarized.   You can polarize light at different angles and wavelengths thus the photons carry information.   If two parties that send and receive the polarized light have detectors to receive and interpret the phase of photons, then a code is born. 

 

            

 

The major advantage of using quantum bits for encryption is the Heisenberg Uncertainty Principle which says that if you try to intercept a quantum-coded message, the act of trying to measure one property of a quantum state will disturb another.  In other words, if you touch this message (01001100) it will self-destruct in T-minus 1 second.

 

To add to the complexity, encryption can come in the form of quantum entanglement.  Entanglement is the phenomenom that says that two or more separate but similar objects can be linked and respond to changes in eachother, even over a distance.  So if a photon is split into two lesser energy photons (like UV into infrared) then those two photons are linked over a theoretically infinite distance.  If point A (commonly called Alice) and point B (Bob) are separated but carry entangled photons then they can communicate by changing the properties of one photon and expecting its twin to respond similarly.

 

Most of this encryption isn't sending long-winded messages about military targets or whether or not Bill inhaled, instead the information sent and received is usually the key to decode encrypted messages sent over regular communication channels.   So far, scientists have been able to send 1Mbit/s of information along an optical fiber 20kms in length.  The hope is that transmission distances can be extended to even communicate through space to the International Space Station.  

 

 The newest rage in quantum encryption is using photons to encode more than just 0's and 1's.  Now, in a recent paper published in Science, researchers have been able to measure more than just the phase of the photon but also the angle, which means that the possibilities are infinite for encryption.  All of a sudden, entangled photons can communicate both the 0's and 1's and also an entire alphabet of angular information.

 

 

 

What will this mean to Bond, Langdon and Gagdet?  Faster and more secure encryption for the military which means more secrets.  It isn't clear if these secrets will include the "Don't Ask. Don't Tell" policy.

 

Leach J, Jack B, Romero J, Jha AK, Yao AM, Franke-Arnold S, Ireland DG, Boyd RW, Barnett SM, & Padgett MJ (2010). Quantum correlations in optical angle-orbital angular momentum variables. Science (New York, N.Y.), 329 (5992), 662-5 PMID: 20689014
... Read more »

Leach J, Jack B, Romero J, Jha AK, Yao AM, Franke-Arnold S, Ireland DG, Boyd RW, Barnett SM, & Padgett MJ. (2010) Quantum correlations in optical angle-orbital angular momentum variables. Science (New York, N.Y.), 329(5992), 662-5. PMID: 20689014  

  • December 6, 2010
  • 01:45 AM
  • 1,856 views

Violent Games increase Prosocial Behavior

by Dr Shock in Dr Shock MD PhD


Dr Shock is utterly biased when it comes to gaming. Especially when Call of Duty is used for research into the topic of possible negative or positive influences of exposure to violent games. This recent research with the action game “Call of Duty” did not support any negative influence of gaming on prosocial behavior or [...]


Related posts:Violent Video Game Playing Does Not Lead to Aggressive Behavior
Computer Games Increase Cognitive Ability
Video Games Affect The Brain, Good or Bad?
... Read more »

  • December 6, 2010
  • 01:04 AM
  • 588 views

The Flying Snake Portion of your Dissertation Work…

by Scicurious in Neurotic Physiology

Sci usually blogs about things related to health, being a biomedical scientist as she is. But this, this is AWESOME. COMPLETELY AWESOME. It’s people. Tossing snakes. From towers. And it made me think so forcibly of the Snake Fight Portion of One’s Thesis Defense (which is brilliant and should be required reading for every grad [...]... Read more »

  • December 5, 2010
  • 10:15 PM
  • 518 views

Warming is Shortening the Tibetan Plateau Growing Season

by Michael Long in Phased

The onset of the growing season on the Tibetan Plateau is occurring later in the year, and dormancy is occurring earlier, due to global warming.... Read more »

  • December 5, 2010
  • 08:25 PM
  • 1,228 views

Always a Bigger Fish Part 1 – Dogfish as Predators

by Chuck in Ya Like Dags?

I’ve found myself with some breathing room between grading my students and studying for my own exams, so it’s time to write up a post I’ve been thinking about for a while.  I’ve been wanting to do a quick summary … Continue reading →... Read more »

  • December 5, 2010
  • 05:19 PM
  • 982 views

Psycasm - Half Full, or Half Empty? Well, That Depends on the Shape of the Glass.

by Rift in Psycasm


[Wherein our hero investigates why our eyes are frequently bigger than our bellies]To welcome the new blogger to the LabSpaces line-up (JaySeeDub, here), I have themed my post accordingly. To Food.My girlfriend has this rediculous (and infuriating) habit. When I pour her a glass of water it needs to be filled to within millimeters of the brim. It doesn't matter the size of the glass, just tha; (read more)

Source: Rift - Discipline: Psychology... Read more »

  • December 5, 2010
  • 03:03 PM
  • 980 views

Science and Hype – Arsenic Life?

by Paul Vallett in Electron Cafe

One of the things that inspired me to write a blog about science is that I believe science does not have to be “dumbed down” for everyone to think that it is interesting. Researchers shouldn’t be afraid to use clear and understandable language to explain what is interesting about their results. Sometimes scientists (and science [...]... Read more »

Wolfe-Simon, F., Blum, J., Kulp, T., Gordon, G., Hoeft, S., Pett-Ridge, J., Stolz, J., Webb, S., Weber, P., Davies, P.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. DOI: 10.1126/science.1197258  

  • December 5, 2010
  • 02:58 PM
  • 808 views

[guest post: Alex Bradley, PhD] Arsenate-based DNA: a big idea with big holes

by Kevin Bonham in Food Matters

In the wake of the NASA excitement over the new arsenic study, and my promise to give a detailed review of the paper itself, I have recruited a colleague with strong opinons about the work, a solid chemistry and microbiology background, and "Dr." in front of his name to share his analysis. I will be posting my personal and less-technical take on the whole thing soon, so stay tuned.

Dr. Alex Bradley uses modern geochemistry and microbiology tools to study the evolution of life and Earth. He has the following to say about the paper.




There's been a lot of hype around the news of GFAJ-1, the microbe claimed to substitute arsenate for phosphate in its DNA. In the midst of all the excitement, one thing has been overlooked:

The claim is almost certainly wrong.

The study published in Science has a number of flaws. In particular, one subtle but critical piece of evidence has been overlooked, and it demonstrates that the DNA in question actually has a phosphate - not an arsenate -backbone.

To understand why, we need to back up a bit. One thing that everyone agrees on is that all things being equal, DNA with an arsenate backbone will hydrolyze quickly in water, while DNA with a phosphate backbone will not. Steve Benner has pointed out that the half-life of the hydrolysis reaction is about 10 minutes.

Wolfe-Simon et al. recognize this, but claim that the bacterium GFAJ-1 must have some unknown biological mechanism to compensate, and this prevents the DNA from falling apart in the cells. Let's assume for now that they are correct. It might be plausible - biology has all kinds of strange tricks and this idea can't be quickly dismissed, even if it seems radical.

But chemistry is much more predictable. Once DNA is out of the cell, pure chemical processes take over, and experiments have demonstrated that hydrolysis of arsenate links is fast. So you could do a simple experiment to test whether DNA had a phosphate or arsenate backbone: just remove DNA from the cell and put it in water for a few minutes. Then examine whether it hydrolyzes or not.

In an accidental way, Wolfe-Simon et al. performed precisely this experiment. The result indicates that the DNA of GFAJ-1 has a phosphate backbone.

The details are this: to isolate DNA, Wolfe-Simon et al. performed a phenol-chloroform extraction. In this technique, after cellular disruption, DNA and other cellular material were dissolved in water, and then the non-DNA material (such as lipids and proteins) were cleaned out of the mixture using phenol and chloroform. This is a pretty common laboratory procedure, and typically would take an hour or two. But here is the key point:

During this whole procedure, the DNA was in water.

Remember, proteins were removed from this mixture. Any cellular machinery that stabilized arsenate-DNA was removed. In the absence of biochemistry, pure chemistry takes over: any arsenate-DNA would have been quickly hydrolyzed in the water, breaking down into fragments of small size. Alternatively, phosphate-DNA would not hydrolyze quickly, and large-sized fragments might be recoverable.

So what size are the fragments of DNA extracted from GFAJ-1? They are large. Figure 1 shows a single strong band. This pattern is a bit unusual for a genomic DNA extract, but the important thing is that the fragments in this band have around 10,000 nucleotides between breaks in the DNA. These long chains of nucleotides did not hydrolyze in water. Yet it is precisely this DNA band that is claimed to have an arsenate backbone.

How can this be?

The answer is: it can't be. If this DNA did not hydrolyze in water during the long extraction process, then it doesn't have an arsenate backbone. It has a phosphate backbone. It is normal DNA.

So what accounts for the claim of arsenic in this DNA? Wolfe-Simon et al. used a technique called nanoSIMS to analyze elemental concentrations of the agarose gel at the location of the DNA band. They determined that the part of the gel containing DNA also contained both arsenic and phosphorus. But what did they really analyze?

The answer is that the nanoSIMS determined the concentration of arsenic in the gel - not specifically in the DNA. Arsenic was present in the gel at the location of the DNA band. But these data do not require that arsenic is part of the DNA, only that it is somehow associated with the DNA. So here is a more plausible explanation: arsenate sticks to stuff. When you grow bacteria in media containing lots of arsenate, cellular material gets covered in arsenate. If you analyze this material chemically, you see a high arsenic background. The arsenic background will remain even after you separate the cellular material into its constituent parts - DNA, lipids, and proteins - because the chemical separation is imperfect. You could imagine a parallel experiment: if you grew bacteria in seawater, a band of DNA extracted from these bacteria might show a high background of sodium and chloride. This would not be very surprising - and it certainly wouldn't imply that the DNA had a chloride backbone.

Wolfe-Simon and her colleagues might quibble with this, and claim that arsenate is not that 'sticky'. This should have been resolved by running a negative control. Grow some bacteria with phosphate-backboned DNA in media containing high concentrations of arsenate. Then extract the DNA, run a gel, and just demonstrate that the gel does not have a high arsenic concentration associated with the DNA band. That would be evidence that my explanation is wrong. But this simple control was not performed in study published in Science.

One objection to my claim might be: if the GFAJ-1 DNA contains phosphate, where did the phosphate come from? The researchers claim that there wasn't much phosphate in their growth media. In fact, they did a very good job of quantifying the background phosphate concentration: it was about 3 micromolar, which was certainly much lower than the arsenate concentrations (by a factor of about 10,000).

But here's the relevant question: Is 3 micromolar phosphate a lot? Or a little? One point of comparison is the Sargasso Sea, where plenty of microbes survive and make normal DNA. Here, the phosphate concentrations are less than 10 nanomolar - or 300 times less phosphate than the "phosphate-free" media in the GFAJ-1 experiment. At such low phosphate concentrations, some bacteria compensate by removing phosphorus from their lipids - but not from their DNA.

So the Sargasso Sea tells us that some bacteria are capable of making DNA at very low phosphate concentrations. The most plausible explanation is that the bacterium GFAJ-1 can make normal DNA at micromolar phosphate concentrations, and that it also has the ability to tolerate very high arsenate concentrations.

There are numerous other aspects of this study that don't make sense. Why would bacteria from Mono Lake need the ability to substitute arsenate for phosphate in their DNA? Yes, arsenic concentrations are high in Mono Lake. But so are phosphate concentrations, which approach 1 millimolar - or 100,000 times higher than in the Sargasso Sea. Mono Lake has more phosphate available than nearly any other environment on Earth. There is no selective pressure for the evolution of what would surely be a massively complex switch in nucleic acid chemistry from phosphate to arsenate. I can only begin to imagine the structural problems that would be imposed on DNA by this switch, which would change bond lengths between nucleotides, and cause secondary problems with transcription, etc. Then there is the radical suggestion that nucleotide chemistry is stable because might occur in a 'non-aqueous' environment. It's not clear how that could work.

Finally, there's a simple experiment that could resolve this debate: analyze the nucleotides directly. Show a mass spectrum of DNA sequences demonstrating that nucleotides contain arsenate instead of phosphate. This is a very simple experiment, and would be quite convincing - but it has not been performed.

This study lacks any real evidence for arsenate-based DNA; unfortunately these exciting claims are very very shaky.

... Read more »

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC.... (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.). PMID: 21127214  

  • December 5, 2010
  • 02:00 PM
  • 1,131 views

Acupuncture, some dodgy maths and a cracking review paper

by Lorimer Moseley in BodyInMind

I have a challenge for you. Imagine you’re in ancient China and you’ve had this idea that health and disease hang on the flow of energy through invisible energy pathways called meridians that can be manipulated by applying needles in certain specific points. How do you go about systematically validating this theory? How do you [...]... Read more »

Donald M. Marcus. (2010) Is Acupuncture for Pain a Placebo Treatment? An examination of the evidence. The Rheumatologist. info:/

  • December 5, 2010
  • 12:57 PM
  • 593 views

How do you spell "success" after bariatric surgery?

by Maureen McCormick in GourMind

The sweet smell of "success" . . . it's so intangible, so personal, so dependent on the point of view. Here's a sampling of what I have heard from patients:"I can buy clothes in a regular department store!"Often after years of buying shapeless clothes in specialty stores, many people - women and men! - enjoy trying on clothes in a department store, feeling stylish and reveling in colors other than black."I don't need a seat belt extender on airplanes anymore! And I actually fit into the seat properly."Many post-bariatric-surgery patients start flying again after many years of staying at home because of shame at the ordeal of negotiating the seat constraints. Attending far-away family events suddenly becomes possible and taking vacations just for the fun of it becomes part of the normal routine."I don't have to wear my CPAP mask anymore!"CPAP stands for Continuous Positive Airway Pressure and the mask is attached to a machine that pumps air into and out of the nose throughout the night. It is the work-around of choice for a condition known as sleep apnea. Wearing a CPAP mask is nobody's idea of a good time, but waking up refreshed and having energy throughout the day makes the ordeal worthwhile for many people. Obesity is a significant risk factor for sleep apnea, and it often clears up after weight loss. Sleeping without the mask and the machine represents a dramatic improvement in quality of life for many people."I'm off all my medications!"Other conditions that often clear up after weight loss or simply after gastric bypass (see previous posts) include Type 2 diabetes, hypertension, high cholesterol, and psoriasis. Fewer medications means saving money, time and trouble. And individuals may feel a sense of greater autonomy over their own health.Which brings us to the question of point of view . . . how do researchers define success after bariatric surgery? After all, the outcomes measured for a research study must be quantifiable. And, while there are questionnaires that assess a person's quality of life, today we are going to examine a study that looks at weight loss only.Specifically, a way of measuring weight loss not in pounds, but expressed as a percentage of the weight an individual needs to lose. For example, if an individual weighs 300 pounds, and the ideal weight is 200 pounds, then 100 pounds is the excess body weight (EBW). If the person has now lost 40 pounds, then the percentage of excess weight that has been lost is 40%.Snyder, B., Nguyen, A., Scarbourough, T., Yu, S., & Wilson, E. (2009). Comparison of those who succeed in losing significant excessive weight after bariatric surgery and those who fail. Surgical Endoscopy, 23 (10), 2302-2306. DOI: 10.1007/s00464-008-0322-1In this study, "good weight loss" was defined as >= 50% EBW, and "poor weight loss" as <= 30% EBW within the first year after surgery. They included patients who had had gastric bypass and gastric banding procedures.There are problems right off the bat. First, these are not generally accepted definitions, and the authors provided no justification for their choices. And, in general, I am always wary of analyses that throw out data. Why not include all the data in a linear analysis rather than creating 2 extreme groups? This question was not addressed.Second, weight loss in and of itself is not necessarily the best definition of success. Ultimately, it is lifestyle change that allows patients to maintain weight loss.Third, the most obese patients likely did not have enough time to lose 50% EBW. In other words, we might predict that the "good weight loss" group is going to be disproportionately made up of people who started out with a lower BMI. And this is exactly what was reported in the study for both gastric bypass and banding groups.And fourth, the timelines for weight loss differ based on the procedure performed, that is, gastric bypass patients generally experience a drastic weight loss in year 1, tapering off to their maximum at the end of 3 years, and gastric banding patients see a more steady curve over those first 3 years. Often the results at the end of 3 years are similar, but that first year looks very different based on the procedure.... Read more »

  • December 5, 2010
  • 12:02 PM
  • 1,546 views

Bilingual Brains: Reading in Hebrew and in English

by Jason Goldman in The Thoughtful Animal



I've got an article that appeared in this week's Jewish Journal of Greater Los Angeles about recent research from Hadassah University on the neurobiology of bilingual (English-Hebrew) reading.

Is the English-reading brain somehow different from the Hebrew-reading brain? You might not expect any major differences; after all, both languages are alphabetic and are read more or less phonetically by breaking words into their constituent sounds. Compare English and Hebrew to a logographic language like Chinese or Japanese, and the similarity between the alphabetic languages becomes obvious. But new research by Hadassah University researchers Atira Bick and colleagues, published online in October in the Journal of Cognitive Neuroscience, found that despite their similarities, there are some key differences in the way the brain processes English and Hebrew words.

I'm particularly excited about this as its my first in-print article, but also because this is part of my ongoing effort to get science into publications where you wouldn't otherwise expect it (i.e. "push journalism"). It's a particularly tough (but fun) challenge to entice readers into reading an article about science if they're not already seeking it out.

Bick AS, Goelman G, & Frost R (2010). Hebrew Brain vs. English Brain: Language Modulates the Way It Is Processed. Journal of cognitive neuroscience PMID: 20961169 Read the comments on this post...... Read more »

  • December 5, 2010
  • 08:56 AM
  • 677 views

Are we ‘illiterate listeners’?

by Henkjan Honing in Music Matters

'French babies cry differently as compared to German babies. This was the conclusion from a study that was published a year ago in Current Biology (see earlier entry). Three day old German babies cry in a downward fashion, their French contemporaries showed an increasing swelling of the cry and stop abruptly. It was a surprising observation, especially in the light of the general belief that in crying the pitch should always drop as a physiological consequence of the respiratory cycle. Apparently, babies of just a few days old can control both the dynamics and the intonation contour of their crying. Why would they do this?The researchers interpreted it as the first steps in the development of language. In spoken French the mean intonation contour is rising (dropping at the very end of an utterance), in German the mean intonation typically exhibits a falling contour. This combined with the fact that the human auditory system is already functional in the last trimester of pregnancy made the researchers conclude that these babies picked up the intonation contours of their native language in these last months and consequently imitated them in their crying.This observation is also surprising since the literature suggests that children only get interested in their native language roughly between six and eighteen months, when they start to imitate it in their babbling. Is it indeed the case, as stressed by these researchers (and the recent literature citing it; e.g. Elk & Hunnius, 2010), that this is unique evidence for a much earlier sensitivity to language than commonly thought? Or is there another interpretation possible?Although the empirical results are clear, this interpretation is a typical example of what one could call a ‘language bias’: an understandable enthusiasm of linguists to interpret a range of phenomena in the real world as ‘linguistic’. One can, however, easily make the argument that this early sensitivity to intonation contour is a not a linguistic skill but a musical one.Most linguists see the use of rhythm, dynamics, and intonation as an aid for making infants familiar with the words and sentence structures of the language of the culture in which they will be raised. Words and word divisions are emphasized through exaggerated intonation contours and varied rhythmic intervals, thereby facilitating the process of learning a specific language. These aspects are referred to as prosody, but they are actually the basic building blocks of music. Only much later in the development of a child will this ‘musical prosody’ be used, for instance in the marking, and consequently the recognition of word boundaries. But these early signs of musical skill are — and I like to stress this – not of a linguistic nature. It is the preverbal and preliterate stage of our musical listening in development.' (Opening from inaugural lecture De ongeletterde luisteraar; Honing, 2010)Honing, H. (2010). De ongeletterde luisteraar. Over muziekcognitie, muzikaliteit en methodologie. Amsterdam: Royal Netherlands Academy of Arts and Sciences (KNAW).Mampe, B., Friederici, A., Christophe, A., & Wermke, K. (2009). Newborns' Cry Melody Is Shaped by Their Native Language Current Biology DOI: 10.1016/j.cub.2009.09.064Elk, M. van & Hunnius, S. (2010) Het babybrein, over de ontwikkeling van de hersenen bij baby's. Amsterdam: Bert Bakker.... Read more »

Mampe, B., Friederici, A., Christophe, A., & Wermke, K. (2009) Newborns' Cry Melody Is Shaped by Their Native Language. Current Biology. DOI: 10.1016/j.cub.2009.09.064  

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