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Prof. A's Science Fix- Aug 17 2012 Edition

I would like to start my blog highlighting innovations.

FEATURED VIDEO: The invisible bicycle helmet


Video produced by WG Film with the support of The Swedish Film Institute - Film commissioner Andra Lasmanis. Swedish design students Anna and Terese took on a giant challenge as an exam project: they wanted to invent an invisible bicycle helmet. Why? Because, yes, as a cyclist I can tell you, helmets are annoying. But necessary, it’d be crazy to ride a bike in traffic without wearing a helmet. And bicycles are green, so anything that can be done to increase the number of people who commute by bike is a big plus for our planet. Do watch till the very end. You will not regret it. I loved the creativity! I wonder if it could be used for motorcycle riders, too.


And speaking about technological advances that can be good for humanity and our planet, here is another potential invention that can help humans, and animals, too. And hopefully would be not only more ethical, but also greener than the current methods of production.


Printing a lab-made 3-D edible burger or steak. Given that the demand for meat is likely to increase with increased human population, wouldn’t it be great to produce meat that did not involve killing animals and producing vast amounts of greenhouse gases? The Thiel Foundation (it was started by the founder of PayPal) has given a six-figure grant to Modern Meadow, a Missouri-based startup company that wants to print 3-D meat. We have discussed in this blog the possibility of printing blood vessels and maybe even organs for transplants, using bio-printing, which is a novel tissue engineering technology (A great, detailed explanation of what bio-printing is can be found here). Printing meat involves creating a template, that looks like a hamburger and a steak, and then the printer carefully prints several layers of cells, previously cultured in vitro in a bioreactor. If the layers, called bio-ink, are of different cell types (for example muscle and fat) and are mixed in a certain way, the texture and taste of meat could be reproduced. Their short term goal is to print an edible thin slice of meat, around two centimeters by one centimeter, and less than half a millimeter thick, which is edible. The company recognizes that marketing the lab-made meat will be challenging, but they are counting on daring culinary geniuses to promote it, and on the sector of the vegetarian community that rejects meat for ethical reasons. Interestingly, they seem to think there will be a kosher and halal market for the meat, since there is no need to regulate the method of slaughter. In theory, production could be cheap so the lab-made meat could be marketed as a more frugal alternative to the real thing. My question is: would you eat it?


A book is stored as DNA. Why would anyone bother to store a book as DNA? For once, it is cute and creative, and a technological challenge, therefore fun to undertake. But there is another reason: DNA is very stable (remember that we have managed to sequence Neanderthal DNA from fossil bones!) and the information could be stored for millennia and there would be no need to worry about compatible storage technology (remember floppy disks?).  Researchers have taken a book (53,000 words and 11 JPEGs), converted it into HTML (with a bit of JavaScript). The HTML took up 5.3 megabits, which were translated to a DNA sequence, one base per bit. They used A and G for one, C and T for zero.) They then split the sequence into chunks of 96 bases, and each chunk was linked to an address of 19 bases. The address was then flanked by extra bits of sequence that allowed the DNA to be amplified by PCR (polymerase chain reaction, a very common way to amplify DNA in the lab). The sequences were then printed on a DNA chip. And there’s your DNA book. So, how do you transform it back into the contents of the book?  Using deep-sequencing methods, that are getting increasingly cheaper, they sequenced each bit approximately 3,000 times (for error correction). Although there were some error-prone areas, they got their book back. They also think they have figured out a way to eliminate the errors.  For now the issue is cost, and the time it takes to retrieve the information. But if this invention were to be used for archival purposes only, these two drawbacks would not be very important.


And wouldn’t this next one be a great invention? One can never have too many safety procedures in place when it comes to avoiding unwanted pregnancies. Plus it would be very useful for guys who want to make super sure that they won’t become fathers by accident or by being tricked by a woman supposedly on the pill (I do know a couple of cases of the latter, unfortunately).


A male contraceptive pill in the horizon? A paper that just came out in today's issue of the prestigious journal Cell describes how a small molecule blocks the production of sperm (spermatogenesis) in a safe and reversible manner, in mice. The compound is called JQ1 and it was initially studied as a potential anti-cancer agent, because it binds to BRD4, a protein that regulates cell division. BRD4 has a "cousin" protein, BRDT, which is crucial to spermatogenesis because it controls the division of sperm cell precursors in the testis, and it was found to JQ1 was found to bind to BRDT as well. When given to mice, the compounds blocks spermatogenesis and within a month of taking the drug, the mice couldn't sire any offspring even though their mating behavior was normal. After a month or two off the drug, sperm counts return to normal and the mice could father healthy offspring again. Although the results are encouraging, further studies will be necessary to determine the safety of the drug before it can be tested in men. 


The Golden Ratio in the human womb. There is a new science journalist at The Guardian, Alex Bellos, and I really enjoyed his first article. A gynecologist in Belgium measured the ratio of height to width in the wombs of 5,000 using ultrasound, and he found that at the peak of a woman's fertility (ages 16 to 20), the ratio approaches 1.6, the Golden Ratio. This ratio is found all over in nature, from seashells to the seeds in flowers, and for some, it is the nature's "perfect number". In a Fibonacci series, where each number is the sum of the previous too, the ratio of any two numbers is or approaches 1.618. Interestingly, when girls are born, the ratio of uterine length to width is 2, it reaches the golden ration by peak fertility, and it decreases to an average of 1.46 in old age. The gynecologist who carried out the study was inspired by the observation that experienced gynecologists can tell if a woman will be fertile just by looking at the proportions of her uterus, so he decided to measure the ratio; we still don't know what it means, but it is a neat, intriguing little finding. The golden ratio is found elsewhere in the human body, for example the ratio of the 3rd to second phalanx (finger bones) approaches 1.618. The image is of fractals illustrating the Golden Ratio.


Sperm and womb…what do those words in association with each other make you think about? Babies, of course! Which brings me to the burning issue of Neanderthal-Homo sapiens babies.


Was there interbreeding between H. sapiens and Neanderthals? First it was assumed that no interbreeding had occurred between us and Neanderthals, based on mitochondrial DNA. Then came the genomic sequence of Neanderthals, and a comparison with the genomic sequences of Eurasian and Oceania peoples revealed that interbreeding had occurred, and 1-4% of the DNA of all humans, except sub-Saharan Africans came from the Neanderthals. This was 2-3 years ago already. Now a new study in PNAS suggests that the common DNA that we have with Neanderthals came from a common ancestor and not from interbreeding. These questions are hard to answer because they are answered statistically, and shared DNA between two species or subspecies can come from either interbreeding or a common ancestor. I do not know enough of the statistical methods used by geneticists to come to these conclusions but I was expecting this sort of development because this is the way science operates, especially around models, when we cannot directly experiment. The proponents of the Neanderthal hybridization/interbreeding hypothesis disagree with the results recently published in PNAS. So the jury is still out there on whether the ancestors of Eurasian populations had hot sex with Neanderthals.  It is possible that some of the sequences we share with Neanderthals come from a common ancestor, while others come from interbreeding. In other words, both hypotheses may end up being right to a certain degree.


After all this priming with stories about sperms, womb, and hot ancestor sex, it is possible that your mind is now in the gutter, so to speak. Better do some brain cleaning.


Scientists discover how brains keep clean. Getting rid of waste is one of our bodies extremely important physiologic duties. Every single cell and every organ produce waste and have mechanisms to get rid of waste products. The lymphatic system is in charge of getting rid of waste, so because the brain is the only organ without a lymphatic system, it was a mystery how the brain, an organ very sensitive to the accumulation of waste, cleared it up. A new study performed in mouse brains shows that waste is flushed out by being pumped alongside blood vessels.  New imagining techniques allowed the visualization of the process: cerebrospinal fluid runs right outside of blood vessels, through a “plumbing” system made out of protein structures. The fluid picks up the waste that accumulated between cells, and finally drained out through major veins. The new technique is called two-photon imaging, which can detect radioactive tracers hit with just two low-energy photons, and it can be used to peek inside the brain of a living animal, as opposed to previous imaging techniques such as those in the photo, which can be used only on dead tissue. This new insight could one day help treat Alzheimer’s disease, where amyloid protein builds up instead of being completely cleared up, as it happens in a healthy brain. The idea is to find a way to increase the rate of clearance of the brain’s “flushing” systemPhoto: the system of water channels is shown in purple, and the cells in green. The system is tightly wrapped around blood vessels.  Image: J. Iliff and M. Nedergaard


And now I would like to turn your attention to the other earthlings: non-human animals. And when we mix non-human animals with human intervention, strange stuff can happens, like zebras turning into polar bear killers.


Zebra herpes virus kills polar bears. There have been a number of polar bear deaths in zoos around the world, in Germany, and in San Diego, and the cause of death remained a puzzle until scientists dissected the brain of a female polar bear, Jerka, who died at the Wuppertal zoo. The veterinarians noticed that she had suffered from inflammation in the brain, and that is usually a sign of viral infection. They examined her tissues for signs of all kinds of virus, especially canine distemper or rabies, but they ended up finding only one virus: EHV1, or equine herpesvirus 1. This virus infects horses, donkeys and zebras in zoos, and it affects their lungs and brains. Jerka’s killer was actually a hybrid between EHV1 and another equine herpesvirus, EHV9. The zebra enclosure is over 200 feet away from the polar bear enclosure, so it is likely that zookeepers or other personnel acted as vehicles. EHVs have killed black bears, Thompson’s gazelles and guinea pigs, in other zoos.  At this point, we do not know how common infection with EHV1 or EHV9 is among zoo animals, or even how to control the spread. But we know one thing: equine herpesviruses are promiscuous and can jump from one species to others, relatively easily. Let us hope that zoos figure out a way to keep these potentially very dangerous viruses at bay.


As more research on animal behavior is carried out, we increasingly realize that even though we are extraordinary animals when it comes to our intellectual abilities, the difference is more one of a degree rather than of kind. Do go to the discussion and check the comments, to read about a touching reunion of brothers


African grey parrots capable of inferential reasoning. One of the hallmarks of human intelligence is that we are capable of making logical inferences. We are not the only ones, because great apes can do that too. The classical example is that apes can infer when a treat is hidden in a container by the noise the container makes when shaken by a tester. If the container makes no noise, the clever apes will immediately infer that it is empty and disregard it.  However, monkeys and domestic dogs fail that test. They cannot use acoustic references (sound) to infer whether a container has treats or is empty. But a new paper just published in the Proceedings of the Royal Society Biological Sciences claims that African grey parrots can instantly infer that a container is full when they hear the noise produced by the shaking of a container with a treat (nut).  They tested six African grey parrots, ages 10 to 35, from a parrot rescue in Vienna (Austria). Just like great apes, the grey parrots spontaneously used the presence and the absence of a rattling noise to deduce in which container the treat was hidden. When the parrots were played a recorded noise, but the container was not shaken, they did not choose it. So it appears that they understand the link between the shaking and noise, and that the treat is causing it.  They solved the task with the same success rate as human 3 year-olds. Strangely, they can make the inference if the container is shaken side to side, but if it was shaken vertically, they made mistakes. The authors speculate that the vertical shaking looks like the vertical head bobbing so typical of parrots and that it interferes with their ability to make the correct reasoning, by distracting the birds. The birds responded to the vertical shaking with head bobbing of their own. Animal behavior experts have previously observed that if the anticipated response interferes with a component of the species’ behavioral repertoire, conditioning training was not possible, so this striking fact could be related to that observation. Nevertheless, it is remarkable that untrained parrots spontaneously solved this task from the first try, while trained capuchin monkeys consistently fail.


I’m a sucker for new species, and I want to share with you this interesting new specimen from the depths of the ocean.


Strange New Fish Found Deep off New Zealand. This strange looking creature is an unknown species of flabby whalefish (who came up with that name?), found 1.7 miles down in the ocean east of New Zealand. This strange has tiny eyes and they completely lack ribs (hence, “flabby”, I assume). The 12.5-inch-long (32-centimeter-long) New Zealand's National Institute of Water and Atmospheric Research (NIWA) reports other odd-looking species as well found trawling at that depth.  Below 1.3 miles deep, there are very few other species, so the flabby whalefish is rather lonely at those depths.


Meanwhile, on another galaxy:


Record-breaking star formation in huge galaxy cluster. Michel reports in The Daily Cosmos: galaxy clusters typically have the following properties. They contain 50 to 1,000 galaxies, hot X-ray emitting gas and large amounts of dark matter. The distribution of these three components is approximately the same in the cluster. They have total masses of 1014 to 1015 solar masses. They typically have a diameter from 2 to 10 megaparsecs (see 1023 m for distance comparisons). The spread of velocities for the individual galaxies is about 800–1000 km/s. It is already amazing that from the bottom of our gravity well we can conceive of these things, let alone have factual knowledge about them. Hot gas flows to the center of these huge clusters, cooling in the process, a perfect breeding ground for new stars. But astronomers are puzzled because this does not seem to be the case, in general. Now the found this new cluster, the Phoenix galaxy cluster, is one of the biggest in the universe, and it is 5.7 billion light-years away from Earth. The Phoenix cluster is booming with star formation events; astronomers speculate that this is because the cooling of gas is not being neutralized by emission of hot jets from a central black hole. The finding is significant because it is the first example of a galaxy cluster where a substantial fraction of the cold gas is giving rise to stars. It’s possible that the Phoenix cluster is at a temporary stage in in the evolution of clusters, just before the central massive black hole starts counteracting the cooling of gas at its center.

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Comment was by Neal on August 20, 2012 at 12:49pm
That is way cool. =)
Comment was by Adriana on August 20, 2012 at 11:10am

More on the book made out of DNA:

No Longer Science Fiction: Data Encoded In DNA

Game-changing research just published in Science.. Geneticists at Harvard have encoded an entire book into DNA:

Biology’s databank, DNA has long tantalized researchers with its potential as a storage medium: fantastically dense, stable, energy efficient and proven to work over a timespan of some 3.5 billion years…Church’s team married next-generation sequencing technology with a novel strategy to encode 1,000 times the largest amount of data previously stored in DNA. (via Science Daily)

The result? 5.5 petabits, or 1 million gigabits, per cubic millimeter! Further, ~4 grams of DNA could theoretically store all of the digital data humankind creates in one year. The prospect? As geneticist George Church explains in WSJ:

“A device the size of your thumb could store as much information as the whole Internet.”

Emerging technologies in science are exciting. When the research is conducted by a friend, they’re even more so… Congratulations to Sri Kosuri and his team at the Wyss Institute.

Using next-generation sequencing technology and a novel strategy to encode 1,000 times the largest data size previously achieved in DNA, a Harvard geneticist encodes his book in life's language. (Credit: Image courtesy of Harvard Medical School)

Comment was by Doone on August 18, 2012 at 1:08pm

Don't Cry, Your Weekly MultiPass to Science is Here!

22 Amazing Movie Cinemagraphs

22 Amazing Movie Cinemagraphs

The Fifth Element

Comment was by Michel on August 18, 2012 at 11:33am

... and physics and cosmology. Photons are our best friends =)

Comment was by Adriana on August 18, 2012 at 11:18am

That aphid article will be featured on my next Fix, I think, too interesting!! I read it yesterday evening but had no chance to incorporate it here.

And yes, Michel, the advances in imaging are truly spectacular and very helpful in understanding cell biology and physiology.

Comment was by Doone on August 18, 2012 at 11:15am


Kathryn Lougheed in Nature:

ScreenHunter_33 Aug. 18 14.11The biology of aphids is bizarre: they can be born pregnant and males sometimes lack mouths, causing them to die not long after mating. In an addition to their list of anomalies, work published this week indicates that they may also capture sunlight and use the energy for metabolic purposes.

Aphids are unique among animals in their ability to synthesize pigments called carotenoids. Many creatures rely on these pigments for a variety of functions, such as maintaining a healthy immune system and making certain vitamins, but all other animals must obtain them through their diet. Entomologist Alain Robichon at the SophiaAgrobiotech Institute in Sophia Antipolis, France,and his colleagues suggest that, in aphids, these pigments can absorb energy from the Sun and transfer it to the cellular machinery involved in energy production1.

Although unprecedented in animals, this capability is common in other kingdoms. Plants and algae, as well as certain fungi and bacteria, also synthesize carotenoids, and in all of these organisms the pigments form part of the photosynthetic machinery.

More here.

Posted by Abbas Raza at 08:12 AM | Permalink

Comment was by Michel on August 18, 2012 at 10:40am

Yes, great post!

Two photons imaging is really cool!

Two-photon excitation microscopy is a fluorescence imaging technique that allows imaging of living tissue up to a very high depth, that is up to about one millimeter. Being a special variant of the multiphoton fluorescence microscope, it uses red-shifted excitation light which can also excite fluorescent dyes. However for each excitation, two photons of the infrared light are absorbed. Using infrared light minimizes scattering in the tissue. Due to the multiphoton absorption the background signal is strongly suppressed. Both effects lead to an increased penetration depth for these microscopes. However, the resolution remains diffraction-limited. Two-photon excitation can be a superior alternative to confocal microscopy due to its deeper tissue penetration, efficient light detection and reduced phototoxicity.[1]

It makes amazing pictures:

Two-photon excitation microscopy of mouse intestine. Red: actin. Green: cell nuclei. Blue: mucus of goblet cells. Obtained at 780 nm using a Ti-sapphire laser.

A lot of what happens in science is about quality of measurement.

Comment was by Adriana on August 18, 2012 at 8:39am

Thanks, Neal. I will not be eating printed meat either, and not because of the gross factor. I feel fine not eating meat at all. actually, I feel better. But also, growing animal cells in vitro requires growth factors and those for the time being, come from bovine serum, it may be more environmentally friendly but still not vegetarian. It will be possible to grow it with growth factors made in bacteria by genetic engineering, but i don't think it's what they are doing now. But I think it's a good step forward: let me put it this way, it cannot be any worse than the current situation, with so many people eating so much meat.

Comment was by Neal on August 18, 2012 at 8:01am

Excellent as always. I will not be eating printed meat, though I can see the need for it in so many ways. Limiting the inhumane treatment of animals, reducing greenhouse gasses and other environmental pollution; win win I guess if that's what you like.


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