Media Consumption 12/31/12-1/5/13

Back to rounding up weekly picks of some of the best/most interesting things I've read in the past week. I hope you'll enjoy them, and feel free to leave me links to your favorites!

Animation by Rose Eveleth for Nature Publishing Group. Found this great video on twitter this week (actually, found all of these links on twitter) about research papers and how a paper comes to be published in a journal like Nature.

Science Pick

Scientists Use Cells to Fold Origami – Joanne Manaster for PsiVid at Scientific American

Short but informative post about the latest in biotechnology for tissue engineering, which is something we’re all going to be hearing more and more about.

Cancer/Medicine Pick

Be Careful in Reporting on Composite Outcomes – Kevin Lomangino for HealthNewsReview.org

This post is the most recent in HealthNewReview’s Toolkit and Tips for Understanding Studies, which I think everyone might find helpful. This topic covers how to tell what conclusions should really be drawn from a study about a treatment’s effectiveness.

Writing Pick

Loyalty and obsession are intimates: Andrew Sullivan goes independent – Jay Rosen on Press Think

Popular blogger Andrew Sullivan announced this week that he is taking his blog independent (not only self published, but no advertisers) this post by Jay Rosen dissects the decision and the gamble that Sullivan is taking by asking his readers to actually pay for his writing.

Bonus Pick

Will Panda Blood Solve The Antibiotic Crisis? Unlikely. – Ed Yong for Not Exactly Rocket Science at National Geographic's new blogging network Phenomena

Mostly chosen because Ed Yong says he’ll eat a panda. Also chosen because it highlights National Geographic’s new blogging network (for which they scored several high profile bloggers, including Yong, from other places) and also tackles an interesting topic that shows the need for critical thinking and debunking in the way that some media outlets cover research.

Making Bone With An Ink Jet Printer. Well...Bone-ish.

Reading the headline, "Engineers Pioneer Use of 3D Printer To Create New Bones" from the BBC I can't help but imagine your standard ink jet spitting out layers of human bone until you come up with a whole femur. In case you aren't familiar with 3D cell printing, let me be the one to tell you that isn't the case. I think the BBC's headline leaves out a crucial piece of information: what the printer in question creates is a scaffold of bone-like material.

The research in the article was conducted at Washington State University, and I find their PR headline "3D Printer Used To Make Bone-like Material" more specific. I think 3D printing, tinkering with a printer so that it can make different kinds of biomaterials, is interesting in its own right. I'm okay with the fact that the material being made is only bone-ish and not really bone. Although and argument could be made for the BBC's headline... which I'll explain later.

Printing the bone scaffold via WSU

Here is the research rundown: led by Susmita Bose, professor of mechanical and materials engineering, WSU researchers used a 3D printer to to create a scaffold of calcium phosphate, silicon and zinc. When paired with actual bone, this scaffold provides a structure for new bone to grow on, to specifically manufacture the desired bone. The scaffold dissolves with no reported adverse effects, according to the researchers' in vitro tests in rats and rabbits.

Described in the journal Dental Materials, (according to the PR*) the printer works by having the inkjet spray a plastic binder over a layer of the calcium phosphate, silicon and zinc powder in very thin layers (about 20 microns, comparable to the width of a human hair). A computer directs the printer to create the scaffold in the desired shape and size. The researchers found that after a week in a medium containing immature human bone cells, the scaffold was able to support new bone cell growth. According to the researchers, the material is likely most suitable for low load bearing (so, not a femur) and could be available for human use in a few years time.

So back to the BBC's headline about the 3D printer creating new bone. Ultimately, that is what happens. New bone is grown around the scaffold, so the end product is real human bone. However, the printer is not itself printing bone. In my humble opinion, that doesn't make this research any less cool. While the BBC's headline wasn't itself inaccurate, I think it leaves a lot of wiggle room for assumptions (or at least imaginations like mine getting carried away with themselves) and accuracy is the end all and be all of science stories, isn't it? Something like "3D Printer Creates Scaffold For New Bone Growth" isn't as pretty as either headline used, but I think it would get to the heart of what this story is a little bit better.

For more information about the technology check out this video from WSU's press page:

*I am typically loathe to post about a paper that I haven't at least looked at the abstract, but I cannot find this paper online anywhere. If someone has a link, that would be awesome. 

BioTechnology Patents: Kyoto Claims iPSCs

Can you patent a gene? What about a cell? When it comes to the components of life, and more importantly the ideas, processes, and procedures developed to manipulate these components, what belongs to who? This is a question that is certainly going to be fought out from the patent office to the courts as more and more biomedical discoveries are made.

iPS cell cluster. Source: NINDS.NIH.gov

One discovery that has recently (meaning August) been in the news for patent applications is Shinya Yamanaka's 2006 discovery of the combination of genes that can be used to reprogram adult cells to a pluripotent (capable of becoming any kind of cell) state. With these induced pluripotent stem cells (iPSCs) lies the hope of a suitable answer to the debate over the need for pluripotency, but the social and religious controversy over using human embryonic stem cells (which are naturally pluripotent).

While working at Kyoto University in Japan, Yamanaka found that the genes Oct3/4, SOX2, c-Myc, and Klf4 are key to pluripotency. This discovery led to the creation of the first iPSCs. Now, five years and millions of dollars in research later, Kyoto University has obtained patent rights for iPSC technology in six nations and two regions, including the United States. This development leads me back to the question I started with, can you patent a gene? What about the ideas or technology based on those genes? Apparently, you can because Kyoto University has. But, I'm still quite curious about how this will play out functionally.

The discovery of iPSCs was huge news. It prompted researchers around the world to start working with iPSCs, many of whom have subsequently made their own discoveries, published their own research in peer reviewed journals (just type pluripotent into PubMed you'll see what I mean), and expanded greatly on the existing body of knowledge about pluripotency. This includes the discovery of numerous variations of gene combinations that play a role in pluripotency. So if Kyoto University owns the original idea, do they own everyone elses' work too? According to university spokeswoman Akemi Nakamura, they do. Nakamura says the patent broadly covers variations of the technology developed since 2006 in laboratories around the world.

In a press release the University stated:

"The US patent covers combinations of nuclear reprogramming family factors comprising an Oct family gene, a Klf family gene, and Myc family gene; or an Oct family gene, a Klf family gene, and a cytokine. This means that if companies use a combination of the nuclear reprogramming genes and generate iPSCs, regardless of the kinds of vectors, they need to get the patent license."

So if Kyoto University owns the right to the genes, and the subsequent developments based on the genes what does that mean for iPSC researchers? Right now the university says it will not restrict research using iPSCs for non-profit purposes, so that would mean research whose end goal isn't the marketing of a specific product based on iPSC technology will be able to continue unhindered. Companies that want to work with iPSCs for profit may have to pay a licensing fee. Although, it is important to note that not all iPSC research is based on these genes - there are other combinations of genes that can induce pluripotency, and thus lines of inquiry in this field that don't belong to Kyoto University.

How important all of this will be, and when it will be important is a bit murky. iPSCs have their own problems (namely, teratomas) and haven't yet been developed for widespread, let alone commercial, use. Though, with all of the resources being poured into iPSC development, I think it is only a matter of time until the cells become more useable. This is a story to watch, it is hard to say exactly how it will work out but it is sure to be an issue that continues to come up.

As for me, I'm not really sure where I fall on this issue. I can see the need to protect intellectual achievements and make sure that the wrong people don't profit, but at the same time I wish it wasn't necessary and open inquiries could be pursued without people having to worry about others cashing in on their ideas. If only it could be that way.

A Pollution Solution, Brought To You By Lehigh University

The Lehigh Mountain Hawk in 2008
photo credit: Erin Podolak

If you've ever checked the About section of this blog, you'll know that my alma mater is Lehigh University. I loved my time at Lehigh (it's where I first learned about science writing) and thinking about the university evokes a lot of positive memories. But, as much as I love Lehigh, I have to admit it isn't exactly a premier research institution (despite what they might tell you in the pamphlets). Not that research doesn't go on at Lehigh, but it's no University of Wisconsin-Madison as far as a reputation for cutting edge research is concerned.

Imagine my surprise as I was perusing Scientific American a few weeks ago when I stumbled upon Lehigh while reading an article (reprinted from ClimateWire) about a newly developed material that has the ability to pull carbon dioxide and methane pollution from other gases. The material was developed by Kai Landskron, Paritosh Mohanty and Lillian D. Kull of Lehigh's department of chemistry, and could potentially be used to help capture greenhouse gases.

Creating carbon-sucking materials has been a goal for scientists for years as a way to combat the effects of climate change caused by an excess of greenhouse gases in the atmosphere. However, existing systems tend to be expensive, use a tremendous amount of energy, or don't work well at high temperatures. The new material developed at Lehigh avoids these problems.

The new substance was created using chemicals called diaminobenzidine and hexachlorocyclotriphosphazene. These chemicals are cheaper than others used for carbon absorption, and can operate at heat as high as 400 degrees Celsius. In addition to avoiding the problems that have plagued early carbon capture systems the researchers also had to create something that could take carbon dioxide and methane out of a gas stream, but then release it at a later time for permanent storage underground once compressed.

Coal power plant Somerset NY
Credit: Matthew D. Wilson/Wikimedia Commons.

When they developed their "sponge" the researchers found that the material drew more carbon dioxide and methane from the air than other gases, like nitrogen. This makes the material idea for capturing harmful greenhouse gases out of mixed emissions. The researchers have suggested that the material could be placed inside a tower located adjacent to a coal burning power plant, the flue gas generated from the burning coal could then be transported via pipeline through the material to capture greenhouse gases from the emissions.

According to the researchers, the material has a 90% success rate capturing CO2 from a gas stream. However, some problems with the mass production of this material include the fact that real power plants would emit a more complex mixture of gases than was tested by the Lehigh research team, the material may be too dense for manufacture on a large enough scale, and production would create chemical byproducts that may become difficult to control.

The researchers are confident however, in the product they have created. Landskron told ClimateWire:
"There is no fundamental difference in doing this in the lab versus doing it at an industrial scale." This material hasn't been tested on a commercial scale and it remains unknown if it could actually be implemented practically, so we'll have to wait and see if the material can stand up to the high expectations its creators have set up for it.

Even though the chemicals used in the material are cheaper than others used for carbon capture, the cost of producing and implementing the technology is still a barrier to its use. The researchers hoped to test the material on an existing coal plant in the US earlier this year, but the effort stalled due to a lack of funds, even with a 50% investment by the Department of Energy.

On campus with friends before my graduation from
Lehigh in 2009.

So, while the research is promising and it demonstrates an interesting idea with a lot of potential for carbon capture it needs support and further research to make it something that could actually be used commercially. If you'd like to know more, the research was published in July in Nature Communications.

I was excited to see Lehigh in the news for scientific research. Research wasn't a big part of my life at Lehigh, in fact I rarely encountered it, but Lehigh is where my passion for science evolved into a career. It is where, with the support of the journalism department and the wonderful professors who gave me my first real introduction to writing, I realized that I could have a career dedicated to science without being a scientist, and that has shaped the course of my life. I'm proud of my school, and even prouder to know that Lehigh researchers are working to find solutions to our greenhouse gas problems. Now lets get some funding to make that research a reality!

The Robot That Walks On Water

I don't talk about religion on Science Decoded (with one exception) the way that I don't talk about politics (with one exception). So all Jesus walking on water references will be excluded from this post. Sorry if that disappoints. But, I am going to talk about a robot that walks on water, and that alone is pretty cool.

Credit: The American Chemical Society.

Researchers from the State Key Laboratory of Robotics and System, and the Harbin Institute of Technology in China, writing in the journal ACS Applied Materials & Interfaces, have developed a microbot that is able to walk across water's surface. The robot was designed to mimic the capabilities of water-striding insects like mosquitoes that can support themselves on water's delicate surface.

The Chinese microbot is approximately six inches long and has 10 wire legs and 2 moveable oar-like legs. It is propelled by two small motors that help it to maneuver like a water striding insect. What makes the robot so much more impressive than what the insects do is that at 3.88 grams it weighs about as much as 390 water strider bugs. Despite its weight it is still able to walk, stand and turn on water's surface without sinking.

So what is the trick to walking on water? My favorite: Math. (Sarcasm intended). While I still might be a bit intimidated by math, I definitely appreciate the amazing ways that nature is really just math and vice versa. The microbot's legs are able to support it the way a water strider's legs can support it based on the radius and contact angle of the legs with the water's surface.

But the real question here is: aside from the fact that a robot that walks on water is just cool, why does it matter? According to the researchers this type of technology could be useful for developing tools for monitoring water pollution or water quality surveillance. Personally, I'm envisioning little robot spies stealthily sneaking across bodies of water, but that is something the researchers didn't speculate on.

It amazes me everyday the kind of advances we've made in robotics, as we automate the world around us I can't help but borrow the tagline from my friend Cassi's blog: We Live In The Future.

Prosthetic Devices: The Mystery of Human Design

In the course of an average day I go up and down the stairs in my apartment building, I walk to class, and I run errands – all on foot. Not having a car, or even a bike drives home just how much I rely on my legs to get me where I need to go. But what would I do, if simply getting up in the morning and walking to my destination wasn’t possible?

For millions of people in the world, it isn’t. When people say that we should appreciate our health, I think of viruses, cancer, heart disease, or mental illness – I rarely think of the fact that I have all of the parts of my body that I’m supposed to have. For those individuals who don’t have their legs either by a birth defect, traumatic accident or as a result of war, the loss of mobility changes everything about how you would go through your day.

via Wikimedia Commons

The leg, knee, ankle, and foot (the lower extremity) perform two biological functions – stability and mobility. The lower extremity is designed to hold the body’s weight. According to Dr. Mark Geil, Director of the biomechanics laboratory in the department of kinesiology and health at Georgia State University, the lower extremity is amazing in its ability to support the body given our height and the relatively small surface area provided by the foot. In addition to stability, the muscles in the leg are key to making us mobile at various speeds, and over a variety of terrains and conditions.

For people who don’t have or have lost their leg, replicating the stability and mobility of the natural leg is the challenge presented to the researchers who design prosthetic devices. Prosthetics are artificial legs made of metal and plastic that take the place of the lost limb. But what mechanical challenges does replicating the human body entail?

The process of creating an artificial limb that acts like a human leg is called biomimetic design. According to Dr. Geil, just the act of walking can be incredibly complex, so researchers study it to inform their designs. In some cases, the goal is not to get the artificial leg as anatomically similar to a real leg as possible – it is to get the functionality as similar as possible.

Dr. Geil gives the example of a foot, which uses controlled motion through eccentric action of a muscle, called the tibialis anterior, to absorb shock every time we take a step. A prosthetic foot/ankle unit has no muscles, so the function of shock absorption has to be replicated through materials built into the artificial foot that essentially has a solid, immobile ankle.

But are there elements of human design that cannot be replicated by the ingenuity, creativity, and dedication of researchers? The answer is quite simply, yes – muscles.

“Muscles are the only tissue that can actively produce force,” says Geil. “They are not just springs that can store energy and return it, they actively produce energy. There are a few powered prosthetic components available now, and they generate force, but they must do so via a heavy motor and batteries. Nothing comes close to the elegance and efficiency of muscle action.”

via US Army Flickr

According to Dr. Geil, replicating human anatomy and function is the “Holy Grail” for biomimetic design. But finding a way around the problem posed by muscles is only part of the problem. The human leg is designed to accomplish a vast array of activities – and this diversity has proved difficult to make possible with a single prosthetic leg.

“We think nothing of ascending and descending stairs, walking slowly or quickly and sometimes running, stopping, turning, sitting and standing. We walk on varied surfaces and up and down ramps. We climb ladders or kneel,” says Geil. “I believe that something we’re still missing, and something that might be designed into future prosthetics, is the adaptability required for different conditions and tasks.”

While the technology needed to give people who have lost a limb a prosthetic that can do all the things that a natural leg would be able to do isn’t available yet, there is progress being made to understand the way the human body works. The more researchers know about the body – the better they will be at making machines the act like the human body.

For all of human history we have been studying ourselves, trying to figure out how these bodies work – and there is still so much to know. The next time I take the stairs in my apartment building, and walk the few blocks to campus, I know I’ll have a new appreciation for the legs that are getting me there. Not just because I have them, when so many others don’t, but because I appreciate how beautifully, and still mysteriously, they are designed.

Defining & Finding the Higgs Boson Particle

I know that I love on the BBC quite a bit, I make no bones about it being my preferred source for daily science news coverage. However, the article "LHC has two years to find Higgs" is an unfortunate departure from the BBC's typically stellar science coverage.

The article caught my attention because I'm already familiar with the Large Hadron Collider (LHC) a particle collider operating underground along the France/Switzerland border. A particle collider takes protons (a small part of an atom), runs them around at speeds close to the speed of light, and crashes the particles into each other. Hence the name, particle (the protons) collider (the smashing them together part.)

The other part of the BBC article's title that caught my eye was "Higgs" which refers to the Higgs Boson Particle. The Higgs is a theoretical particle - meaning that it is a particle that physicists THINK exists, but they don't actually know for sure, it might not exist at all. In trying to understand the universe and what gives all matter mass, physicists have come up with several theories.

One of these theories is the Standard Model - which is based on the existence of the Higgs. If it exists the Higgs would explain how particles get mass. The LHC is looking for the Higgs by analyzing the teraelectronvolts (TeV - a measurement of energy) that would be emitted by the process through which particles get mass. The LHC should be able to detect the TeV of the Higgs - if it exists.

Part of one LHC tunnel. Source: Wikimedia Commons

I realize that the BBC's article is clearly an update piece about ongoing research, but it just glosses over some very important explanations about the LHC and the Higgs. If I didn't know that LHC was a particle collider or that the Higgs is a theoretical particle I would have no idea what this article is about from the title. Even as you go through the body of the article, there is no background information. To say that particle physics is complicated is an understatement. All the more reason why this article needs background information to make it understandable. As it is, this article is not appropriate for lay audiences.

The timely component of this article, or the reason why an update on the LHC is needed, is that researchers have announced that if the Higgs isn't detected by the end of 2012 they will conclude that the particle does not exist. If the Higgs doesn't exist then the Standard Model is not the way by which the universe is organized, meaning researchers would have to re-define their understanding of sub-atomic physics.

This is a news worthy update, however I feel like the reporter didn't do the story justice. Even the quotes do nothing to explain what LHC is, what the Higgs is, or what the significance of its existence or non-existence would be. I have a particular problem with the paragraph:
"According to Professor Tom LeCompte of the Argonne National Laboratory, US, who works at the LHC: "The most likely place for the Higgs to be is in a very good place for us to discover it in the next two years."

I have no idea what this quote means. "The most likely place for the Higgs to be is in a very good place..." What? My best guess is that the scientist is trying to say that research at LHC has progressed to the point that if the Higgs isn't detected in two more years, it doesn't exist. But obviously, that is NOT what he actually said.

This is a prime example of a quote that shouldn't have been used. Rather than just using the confusing quote the reporter could have asked the source to clarify or say what they meant in a different way. The reporter could also have paraphrased what the researcher was trying to say. Just because an intelligent and successful scientist makes a statement, doesn't mean that statement is gold. As a writer you have to decide what quotes add to the story, and what quotes are just confusing. You shouldn't put in quotes just to have quotes.

I realize that this is just a short article and it isn't trying to do an in depth analysis of the LHC, the Higgs, or particle physics, but that doesn't mean that background information and good quotes should go out the window. This topic is particularly complex and nuanced, and I've struggled to provide a decent explanation here - but just because something is hard doesn't mean you don't have to even TRY to explain it clearly.

I think the BBC article could have been a lot better if more effort was put into trying to at least define the LHC and the Higgs for the reader. After all, the reader isn't going to care that some particle might not exist if you don't explain what that particle is and why it matters.

If you want to learn more about the LHC, I can't help but recommend the following video. I still get a kick out of watching physicists try to rap and dance. You will find the explanation of the Higgs in the video far more complex than mine. Physics is out of my realm of comfortable understanding - but I gave it a shot and tried to keep it as basic as possible.

Humans Contaminate DNA Databases

Interesting research has been published in the online journal PLoS One, describing a problem with contamination in non-human DNA databases. DNA databases are libraries of genetic information about specific species. When a species has its genome sequenced, its genetic data goes into a database so that other research can be conducted based on that known genetic information.

When a DNA database becomes contaminated it means that there is other information that has corrupted the data stored in the database. In the new PLoS One paper the researchers (from the University of Connecticut) evaluated human contamination of databases that were supposed to contain other species - like the zebrafish. So contamination occurs when human DNA gets incorporated into the database for another species. When researchers go to work with the data about the zebrafish for example, they are actually working with human data without knowing it.

The University of Connecticut researchers looked for human contamination in NCBI genome databases, the University of California Santa Cruz (UCSC) databases, and the Joint Genome Institute databases. They found human DNA where it shouldn't have been in a total of 492 of 2,749 evaluated databases.

This contamination issue is extremely problematic because research conducted based on contaminated information can not be trusted to be accurate. It can also be very difficult to track down which databases are contaminated unless the resources (time, money, etc) are spent to evaluate databases for clarity - as was done in this new research.

Database contamination is a relatively new issue brought to light be the massive influx of new genetic information made possible by improved genome sequencing technology. A similar issue that has existed for decades is cell line contamination which occurs when cells that are suspended in culture (alive outside of the body) are contaminated with cells that aren't supposed to be there.

No regulatory body has stepped up and put a stop to cell line contamination in the last thirty years. I just hope that database contamination doesn't follow suit.

To learn more, read the paper about Database contamination, or read an article I wrote for BioTechniques about cell line contamination. As taxpayers we spend a lot of money to fund scientific research, so it is important to know what problems (like contamination) exist in the research community.

Sequencing Genomes to Save Species

For this post I’m trying something a little different. I mentioned a few weeks ago that I’m using Science Decoded for class, and as a part of that we were assigned to write a post in the form of a list.

*****

All living organisms are made of DNA, a series of nucleotide bases (Adenine, Guanine, Cytosine, and Thymine) contained in chromosomes. Genome sequencing is an analysis of DNA, conducted by “reading” the different patterns of nucleotides A-G-C-T for differences between species, and abnormalities within a species. Researchers around the world are working to sequence the genomes of a variety of organisms, including those on the endangered species list.

1. Orangutan (Pongo abelii) – In January 2011 the National Institutes of Health (NIH) announced the publication of the orangutan genome sequence. Funded by the NIH, researchers from Washington University School of Medicine in St. Louis, MO and Baylor College of Medicine in Houston, TX sequenced the genome of a female Sumatran orangutan, five additional Sumatran orangutans, and five Bornean orangutans (Pongo pygmaeus.) The research shows that orangutans share 97% of their DNA with humans, but compared to humans and chimpanzees, orangutans have evolved much slower leading to fewer mutations (variations in the code between individuals of a species). (Read more) 

2. Tasmanian Devil (Sarcophilus harrisii) – Fifteen years ago a facial cancer was identified in tasmanian devil populations. The cancer has ravaged the species, resulting in an 80% decline that has forced the species to the brink of extinction. This cancer is transmissible, which means that biting the face of an infected animal passes it between individuals. In September 2010 researcher from the Wellcome Trust Sanger Institute and the genome sequencing company Illumina announced that they sequenced the tasmanian devil genome in an attempt to learn more about the cancer and how to stop it from wiping out the species. (Read more)

3. Giant Panda (Ailuropoda melanoleuca) – Arguably one of the cutest endangered species, the giant panda is a prominent symbol of China, where it lives in a restricted mountain area. According to the Beijing Genomics Institute (BGI) the number of giant pandas left in the wild is estimated between 1600-3000. In December 2009, BGI published the complete sequence of the giant panda genome. With the information obtained by the genetic analysis researchers hope to learn more about the genetic and biological factors that shape this species behavior to assist in disease control and conservation efforts. (Read more)

4. Tibetan Antelope (Pantholops hodgsoni) – Listed by the United Nations as an endangered species since 1979, the Tibetan antelope could hold the key to understanding the pathogenesis of chronic plateau sickness. The species calls China’s Qinghai-Tibet Plateau home, making them ideal for studying the evolution of species that thrive in environments characterized by extreme cold and low oxygen levels. The genome sequence of the Tibetan antelope was announced in December 2009 by researchers from BGI and Qinghai University. (Read more)

5. Coral Reefs (Acropora millepora) – Coral reefs are among the world’s most diverse ecosystems, yet according to the Genome Center at Washington University it has been predicted that in the next 50 years between 40%-60% of the world’s coral reefs will die. In 2005 the NIH funded the sequencing of the coral A. millepora (which is not an endangered species, though coral reefs as a whole are endangered ecosystems) to serve as a “lab rat” for studies of the environmental factors (light, sediment load, or acidity) that can cause coral death. (Read more)

Not quite endangered & not fully sequenced:

6. Polar Bear (Ursus maritimus) – Recently removed from the list of endangered species recognized by the United States, researchers at BGI are still working to sequence the polar bear genome. The polar bear sequence is a part of a three-pronged project to sequence the Tibetan antelope (completed in 2009) and emperor penguin genomes.

7. Emperor Penguin (Aptenodytes fosteri) – One of the most recognizable penguin species, the Emperor Penguin is found in Antarctica. The emperor penguin is currently under consideration for inclusion under the Endangered Species Act, due to the effects of climate change. The genome sequencing project is being conducted by researchers from BGI in conjunction with sequencing the polar bear, and Tibetan antelope genomes. (Read more)

8. Snow Leopard (Uncia uncia) - In October 2009 researchers from Oregon State University, the Western University of Health Sciences, and the Miller Park Zoo (IL) announced plans to sequence the genome of the snow leopard (which is on the Endangered Species list). According to Oregon State, the snow leopard is prone to diseases that do not plague other big cats including pneumonia, enteritis, hip dysplasia, and papillomaviruses. Sequencing the genome could help researchers identify what makes the snow leopard susceptible to these disorders. (Read more)

Genome sequencing technology continues to develop, making it easier and cheaper to sequence the genomes of various organisms. While an endangered species has yet to be saved due to the information obtained by sequencing its genome, what researchers learn will help them gain a better understanding of endangered species, which is a step in the right direction towards improving conservation efforts. 

Technology Takes A Look At A Pliosaur Skull

Source: Flickr

The article "Colossal pliosaur fossil secrets revealed by CT scanner," caught my attention because it describes an interesting new use for existing technology. Researchers took the skull of a pliosaur, a creature that lived in the oceans during the Jurassic period, and scanned it to learn more about the fossil remains - which may belong to the largest pliosaur yet to be discovered.

The creature is estimated between 10-16m, based on the skull which is 2.4m long. By comparison, a killer whale is 5-8m and a human is only 1.5m. Needless to say, these things were big. According to the BBC article, a pliosaur would have had the jaw strength to bite a car in half.

The CT scanner used for the research belongs to the University of Southampton in the UK. The machine is one of the largest of its kind, which was necessary to beam through the dense fossil to form a 3D image of what the inside of it looks like. The findings may be able to help researchers establish if their fossil is a different species, or just an abnormally big example of a pliosaur. 

Help Me Obi Wan Kenobi

My experience with holograms doesn't extend much farther than Princess Leia's secret message to Obi Wan Kenobi, entrusted to R2D2 in the first Star Wars movie released (but really the fourth story in the series) A New Hope. Yeah, Nerd Alert, I'm OK with it. Anyway, Star Wars has shown us that holograms are something used in a galaxy far far away, certainly not here on Earth, and certainly not in present day. But alas, Star Wars has led me wrong.

Source: Wikimedia Commons.

New research from the University of Arizona is close to making holograms a reality. So far, the group is able to film a video image and beam it to a new location where it updates in "near" real-time. The research team has been working to improve the speed at which the images are conveyed, and has gotten them as fast as every two seconds. Video with a continuous flow of images, like Princess Leia's famous message, is just around the corner.

The BBC article by Jonathan Amos, "Hologram messaging coming of age," breaks down the process like this:
1. A series of cameras arranged in a semi-circle take multiple images of a person or object from lots of different angles.
2. The images are fed into a computer, where they are processed and then sent to another computer at a different location
3. A specially designed 3D printing system receives the images and based on the information contained in them, controls a laser that "writes" the images onto a screen made of a special plastic.
4. The special plastic screen can update every two seconds, but a light source is needed to be able to see the changing holograms.

The researchers say that holograms will be useful for manufacturing, to update plans or blueprints as workers are designing new models. I think it has value simply for being cool and for proving to Star Wars geeks that IT COULD ACTUALLY HAPPEN, well at least the hologram part.

Commercialized Space Flight

NASA Space Shuttle Atlantis. Source: Wikimedia Commons

People have been taking about commercializing space flight for years, but according to the BBC article "Runway opens at worlds first spaceport" Sir Richard Branson (the Virgin group) is going to make it a reality within the next few weeks.

Of course you don't get to spend any real time in space, they are marketing a three hour journey where you get launched into space and then come back. If you have the money though it would be pretty cool to be able to say that you've been to space. At least 300 people at $200,000 each think so, and have already signed up for the flight.

Rare Variants

My article from the October issue of BioTechniques is out! I reported this one back in August right as I was moving to Madison. It is exciting to finally be able to see it in print. It is also available online, which means you should be reading it right now.

Diamonds in the Rough: Rare Variants Scratch the Surface

Many thanks to the scientists who spent so much time talking to me about rare variants, and to the editorial staff at BioTechniques for editing, and editing, and editing some more. 

Posing with the October issue!

Before you dive into the article, I'm sure you are asking yourself what is a rare variant, and why do I care? Well - rare variants are specific mutations in the genome that only happen in a few individuals, in some cases even just a single person. These variants are important because any time that something is amiss in your genome, it has an effect on you. At times these effects include causing disease. So, studying rare variants can tell doctors important things about disease and possibly help come up with new treatments. But, studying these rare variants is extremely difficult. To learn why, read the article!

The Latest in Protein Folding: Video Games?

I wanted to highlight this BioTechniques article (yes, finally showing off something from BTN that I didn't write lol) by Ariel Elghanayan about an new online video game for protein folding.

The online video game is called Foldit, and was developed by a group from the University of Washington. Recently debuted in a paper in Nature, the game challenges players to compete to manipulate the structure of proteins to create the most stable model. I thought it was an interesting way to make science more fun and approachable, but also to help people understand how proteins fold and re-fold, which is a topic that can be difficult to explain to someone who doesn't have a science background.

Hard At Work

I spent all day today working on a new article for BioTechniques. The editor in chief of the journal offered me a freelance job, which is awesome, but the stipulation was that I had to get it done in two weeks. We're now at the one week mark, and I've now got a working draft, so I'm happy with that progress.

I got to interview David Goldstein from Duke University today for the article, which was pretty cool... even if he only gave me 15 minutes. The article is about the hunt for rare variants and how genome wide association studies were never intended to find rare variants, only common ones. Its slated to run in BioTechniques print edition in October. It still needs a few more sources, and some editing so hopefully in between moving (tomorrow!) and settling in Wisconsin I'll have the time to do more interviews... I better find the time.