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Forbidden fruit: apple pomace paper retracted for plagiarism

Retraction Watch

foodbioprodprocThe journal Food and Bioproducts Processinghas retracted a 2012 article on apple pomace — the remnants of a pressed fruit — by a group from India.

The reason? Turns out the paper “Utility of apple pomace as a substrate for various products: A review,” fell a little to close to the tree.

Here’s the retraction notice:

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Supreme Court: Natural DNA is not patentable (but cDNA is)

Supreme Court: Natural DNA is not patentable (but cDNA is)

The recent decision of the Supreme Court is a big relief for scientists like me, following the battle engaged between Myriad (the company behind the BRCA test and Angelina Jolie’s story). It clearly stipulates that natural DNA cannot be patented, but artificial (cDNA) can.
What are the differences and how it would impact us? Lets take the BRCA gene as an example.

Mutations in the BRCA genes (BRCA1 and BRCA2) are linked to increased risk in breast and ovarian cancer (thus explaining Angelina’s decision for the double mastectomy that I would argue against but this not the topic of this blog). Before the decision, Myriad had the exclusivity of the BRCA gene including the gene product (protein), thus making the development of detection kit and assays exclusive to Myriad (at least in the US). The problems of this test? Very expensive ($3000-6000 per screening) and not 100% reliable. On the other side of the Atalantic Sea, French have also a BRCA kit that is slightly cheaper than the US one but also more reliable. Thus, we can clearly understand that having the open access to the genome would help the development of new technologies and at the end decrease the cost of this kit, good for your health and your wallet.

The proof of my reasoning? Look at the cost of DNA sequencing. You even have a company called “23 and Me” that sequence your genome for $100 (but also opens another genie contained in the bottle).

In the other hand, artificial DNA is still under patent. What does it mean? For the general public not much but for scientist, that means now virtually everyone can patent any cDNA or recombinant DNA (for example someone that created a hybrid of the BRCA gene fused with a green-fluorescent protein contained in a plasmid could apply a patent on it). That can be a no-problem for scientists (as patents most of the time protect the intellectual property by the scientist that formulated that cDNA and you have to acknowledge them in your publications at minimum) but may become a hassle for all these companies like Affymetrix, Illumina or Agilent that heavily rely on cDNA for the DNA microarray analysis (the next BIG THING is personnalized medicine). So let’s how things are going in that direction….

 

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Glaxo asks Nature Medicine to retract paper by fired company scientist

Retraction Watch

natmedcoverIn what could be a significant blow to a major pharmaceutical company, Nature Medicine is reportedly set to retract a 2010 article by a group of researchers affiliated with a Chinese arm of the drug giant GlaxoSmithKline.

We’re not the first to report the news — you can read coverage of it on In the Pipeline and Pharmalot, for starters — which includes the revelation that Glaxo has fired Jingwu Zang, a co-author of the suspect paper and former senior vice president and head of research and development at the Shanghai facility: in other words, a big fish. (Big enough to have a profile in, well, Nature Reviews Drug Discovery.)

Pharmalot has quoted a Glaxo spokeswoman:

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Computer

Mac OS X 10.9…..Sea Lion?

Mac OS X 10.9.....Sea Lion?

As an Apple zealot, I always get into this fever in the wake of the annual WWDC, waiting for the next big thing from Apple in terms of hardware (iDevice, Mac) or software (MacOS, iOS). The two big things that are surely be talked on this WWDC (based on the hanging banners at the Moscone Center) are iOS (7) & the next MacOS (X). This very nice splash picture suggest that maybe we may face a new iteration of the MacOS X (After Lion, Mountain Lion, Sea Lion?). Curious to see how things will go but I would appreciate a major uplift of the system and hopefully the drop of the skeudomorphism adopted since Lion and iOS 5.

[Update] The WWDC was a remarkable comeback from Tim and was giving back this feel that we had with Steve. Mac OS X 10.9 aka “Mavericks” looks sleek and thanks for John Ive, byebye “skeudomorphism” introduced in the early iterations of Lion and Mountain Lion.

The next big thing was the sneak peek on the next gen MacPro, bringing back the sublime design concept introduced with the Cube but now filled up with promising specs.

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Sciences

Say hello to cousin Archie! (Archicebus achilles)

Say hello to cousin Archie! (Archicebus achilles)

This is one interesting article that got published in the Nature journal (for you that might be a profane, having a publication in Nature or Science is almost a golden ticket for a faculty position in any academic institution). It is all about a long lost grand cousin: Archicebus achilles.
He is old (55 millions years) but he is so far the closest individual of our evolutionary primate branch that gave the diversion from the prosimians (lemurians….) and the anthropoids (that subdivided in many other branches including those that gave chimpanzees, gorillas, baboons and of course us).

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Sciences

Let Them Eat Wood! (If It’s Turned Into Starch)

Let Them Eat Wood! (If It’s Turned Into Starch)

Wood! Wood! Wood…This is maybe one of the most material that humankind may have learn to craft, and few materials showed such versability than wood. What do we do with wood? We use it first to keep us safe from weather inclements, we used it for a long time to heat ourselves and our food (and accessory to keep predators at large…), we use it for our furnitures and even for writing our thoughts and spread the information.
Wood is such a magic material and the study of wood is also a science by itself. Peter, one of my teaching fellow had built a very nice lecture on wood anatomy and taxonomy and was able to bring it to life.
One thing we were discussing is that the lignin that give the robustness to wood is also a very stable polymer that is very hard to breakdown chemically, making the use of wood as biofuel very limited.

But this article based on a recent publication in PNAS show how synthetic biology may be an helping hand in degrading another polymer present in plants: cellulose.

Cellulose and starch are very similar chemicals, a brick of glucose repeats. One thing that everyone knows is that glucose is a main fuel for our body and also a very good storage form (glycogen or fat). We can eat starch but why cannot we eat grass? It is all about a chemical bond, the the glycoside bond. Starch have an alpha conformation bond, cellulose has a beta conformation bond. One way that certain mammals (cows, sheeps…) dealt with evolution was to host some symbionts that would degrade these beta bonds and thus make the cellulose.

If we can have this process operated by biological engineering, that would be a good source not only for food as mentioned in the article but also as a possible ethanol production to complement our car fuel, thus redirecting back some of our crops from fuel production to food production.

We can also think about complementing the protein-rich diet obtained from insects and get a sort of a healthy “soylent green” that may have the source of two essential nutrients: protein and carbohydrates.

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Sciences

Rethinking the human evolution cliche

Human evolution as seen as today

 

Wait a minute, I am not arguing against the idea that apes and humans share common ancestor. But I believe this picture is wrong the way it is represented and just keep nurturing the misconception that “humans comes from monkey”.
Here is why. Lets take Pan troglodytes (or the chimpanzee)  and Homo sapiens (the human being in its current iteration). There is no doubt that we share most of our DNA with a very high fidelity, but we are still different.
Lets take the family approach that one of my exceptional colleague (Adrian G.) used to explain the phylogenic tree to our students. If we take this approach, let’s make this common ancestor as our great-great-great…-great grandfather (or grandmother). This parent had some offspring that took different paths. These offsprings have a biological bond (of course they are siblings) but one did not generated the other. Now let’s get back to now to our chimp and us. We are very distant cousins, we share traits but we did not generated each other, thus void the picture depicted over.

Add to it some variants among our history (that good ol’ Neanderthal and the still mysterious Desinovian) and that makes it even more interesting if we consider that such species may have bred together (I would definitively recommend you to watch National Geographic “Sex in the Stone Age”).

If you want to know more about human evolution, I would recommend you to follow John Hawkes (a wonderful anthropologist from UW-Madison).

 

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Videogames

Geeky Archeology: is the E.T. dump be the first videogame archeological site?

‘Atari Dump’ Will Be Excavated, After Nearly 30 Years (NPR)

Is the current trend of retrogaming and the recent sell of the Apple I brought back some old daemons? This article from NPR brings back the famous “ET dump” of New Mexico and sounds like the first time ever of geeky archeology.

Lets get back to the story: It is end of the year 1982. Atari and other companies are in full sail with their 8-bit consoles. Atari bet high on two franchises: E.T. (the movie from Steven Spielberg) and Pac-Man (that set a milestone back then in arcade games). Back then, sounded easy money. However, bad programming  and awful gaming adaptations was the spark to induce the crash of the videogame industry, that was certainly as powerful as the extinction of the dinosaurs.

Long story short, Atari ended with a lot of surplus ET cartridges and dumped them into a dumpyard somewhere in New Mexico, rapidly known as the “E.T. dump”. Among the mystery that shroud around it, some people claims that also defective hardware and more interestingly prototypes may be buried in it.
This maybe the first time ever of documenty geek archeology ongoing and I would be very curious how after 30 years some trash may become treasure. We may certainly  transform a bogus game into an instant hit but it will be a great archeologic moments for anyone that ever sweared by their 2600.

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My first blog

Hello world!

This is my first message of my blog. I will fill up this blog with anything that has to do with science but also some funny stuff about old-school gaming, movies or music that I got particularly interested.

Stay tuned for some more news!