Your Very Special Bacterial Cloud

I mentioned this in a post a few months ago, but there is some seriously cool microbial community work coming out of Jessica Green’s lab at the University of Oregon.

And as luck would have it, Science Friday has done a cool segment all about our tendency to resemble Pigpen.

So listen up as Dr. Roxana Hickey and Dr. Jessica Green tell us about our own personal bacterial clouds.

 

Why we need money for basic science

The funding rates for science are not good (understatement…). Which has lead some in the popular science community to claiming that we don’t need government in research. We can do it on our own! We can make our own money! YOU’RE NOT THE BOSS OF ME!

This argument is dangerously and terribly wrong. Very wrong. What we need from governmental funding is the ability to be able to conduct basic scientific research. Not research focused on questions that have the potential to bring large profits. And governmental funding provides that.

Read about it over at Scientific American. 

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Reasons academia is NOT the worst

There are plenty of reasons to be frustrated by academia (anyone on the job hunt knows this all too well). I’ve spoken extensively about my hesitations about joining the academic workforce.

So it’s pleasant to find a post that does exactly the opposite, and lists the reasons being in academia is not only not so bad, but really pretty good.

Read about it over at the Guardian!introduction-h2

 

The CRISPR revolution: Where are the profits?

Usually when an industry gets a booming industry it is largely due to profitability, which garners interest from investors.

But in biotech there is a section of the industry that is gaining investors and various firms chasing a similar goal. However, how that is happening is a mystery. The companies are burning through millions, hasn’t started clinical work on a drug candidate and it will be years, “if ever” before it has something commercializable.

What industry am I referring to? CRISPR-Cas9 technology. We’ve talked on the blog before about the possibilities CRISPR has to offer human health, but over at The Economist here’s a post about whether or not it can be all we dream it to be.

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Have you heard of the Zika virus?

The Zika virus has been a rare tropical disease since it’s discovery in 1947. It’s a mosquito born virus that has been spreading at an alarming rate. It was previously confined to a few dozen cases ever (all in Africa) to millions of cases across South America.

The initial symptoms are quite mild. But there is evidence that it may in fact cause microcephaly, or babies born with small heads/brains. Which isn’t mild at all.

Consider Brazil. Over the past year ~ 1.5 million people have been infected. The virus is thought to have arrived with World Cup travelers in 2014, and spread rapidly. But what’s alarming, rather than simple flu like symptoms the rate of microcephaly in Brazil has increased 10 fold. (From several hundred to several thousand).

And what’s more, it has just been found in Puerto Rico, suggesting it could soon appear in the US.

Read about it over at Vox.

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Jose Wesley, a Brazilian baby shown here on Dec. 23, 2015, was born with microcephaly. His mother was diagnosed with the Zika virus that researchers think may cause the birth defect. (AP Photo)

 

 

 

Preventing Flies from Interbreeding

“Pour some cold cream into a cup of hot, black coffee, and you end up with a drink that’s midway between the two ingredients in color, temperature, and flavor. A similar kind of blending can occur if members of closely related species frequently mate with each other, but many species have mechanisms to prevent such mixing.” -HHMI News

My new favorite analogy about species inbreeding, and one that every academic can relate to.

But seriously, over at Howard Hughes Medical Institute Jay Shendure and Harmit Malik (a researcher I have long admired) has come up with a clever series of experiments to find the gene responsible for keeping two fly species separate.

Read about their new technique here!

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Citing retracted papers

Over the holidays I stumbled onto this blog post (from Retraction Watch), which has kindly calculated how many times retracted papers have been cited.

Both before retraction (forgivable, you didn’t know it was going to be retracted) and after retraction. How are these papers still being cited?

I’m taking a unkind view of this, and blaming everyone. I blame the authors for citing a paper that shouldn’t be citable. I blame reviewers of that paper for not realizing that their discussion or research is built on faulty evidence. I’m blaming publishers for not doing a better job conveying that something should not be common knowledge.

But I’m in my post holiday sugar slump. It’s possible I’m taking too harsh a view. Anyone else? Am I missing something?

 

Article Year of retraction Cites before retraction Cites after retraction Total cites
1. Visfatin: A protein secreted by visceral fat that mimics the effects of insulin. SCIENCE, JAN 21 2005Fukuhara A, Matsuda M, Nishizawa M, Segawa K, Tanaka M, Kishimoto K, Matsuki Y, Murakami M, Ichisaka T, Murakami H, Watanabe E, Takagi T, Akiyoshi M, Ohtsubo T, Kihara S, Yamashita S, Makishima M, Funahashi T, Yamanaka S, Hiramatsu R, Matsuzawa Y, Shimomura I.

 

   2007 247 776 1023
2. Purification and ex vivo expansion of postnatal human marrow mesodermal progenitor cells. BLOOD,  NOV 1 2001Reyes M, Lund T, Lenvik T, Aguiar D, Koodie L, Verfaillie CM.

 

2009 655 214 869
3. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. LANCET, FEB 28 1998Wakefield AJ, Murch SH, Anthony A, Linnell J, Casson DM, Malik M, Berelowitz M, Dhillon AP, Thomson MA, Harvey P, Valentine A, Davies SE, Walker-Smith JA.

 

2010 675 308 983
4. An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. PLANT JOURNAL, MAR 2003Voinnet O, Rivas S, Mestre P, Baulcombe D.

 

2015 897 N/A 897
5. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO JOURNAL, NOV 16 1998Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC.

 

2015 792 N/A 792
6. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC EVOLUTIONARY BIOLOGY, JUN 28 2004Jobb G, von Haeseler A, Strimmer K.

 

2015 748 N/A 748
7. Spontaneous human adult stem cell transformation. CANCER RESEARCH, APR 15 2005Rubio D, Garcia-Castro J, Martín MC, de la Fuente R, Cigudosa JC, Lloyd AC, Bernad A.

 

2010 371 269 640
8. Combination treatment of angiotensin-II receptor blocker and angiotensin-converting-enzyme inhibitor in non-diabetic renal disease (COOPERATE): a randomised controlled trial. LANCET, JAN 11 2003Nakao N, Yoshimura A, Morita H, Takada M, Kayano T, Ideura T.

 

2009 572 101 673
9. A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. CELL, JUN 12 2009Valastyan S, Reinhardt F, Benaich N, Calogrias D, Szász AM, Wang ZC, Brock JE, Richardson AL, Weinberg RA.

 

2015 530 N/A 530
10. Regression of human metastatic renal cell carcinoma after vaccination with tumor cell-dendritic cell hybrids. NATURE MEDICINE, MAR 2000Kugler A, Stuhler G, Walden P, Zöller G, Zobywalski A, Brossart P, Trefzer U, Ullrich S, Müller CA, Becker V, Gross AJ, Hemmerlein B, Kanz L, Müller GA, Ringert RH.

 

2003 348 166 514

Academic publishing companies make how much?!

Academic publishing is a 25.2 billion dollar a year industry. I’m not kidding.

Long ago in a land far far away, Forbes predicted that the academic publisher Elsevier’s relevance and lifespan in the digital age was going to be short. “Cost-cutting librarians and computer-literate professors are bypassing academic journals- bad news for Elsevier” the article proclaimed.

But here’s the thing. Elsevier hasn’t been run out of town. In fact, it’s thriving. So are Springer, Taylor & Francis, and Wiley. In fact, Elsevier in 2013 had a higher profit margin than Apple Inc.

Why is this? Brian Nosek, a professor at the University of Virginia and director of the Center for Open Science, has an idea:

“Academic publishing is the perfect business model to make a lot of money. You have the producer and consumer as the same person: the researcher. And the researcher has no idea how much anything costs. I, as the researcher, produce the scholarship and I want it to have the biggest impact possible and so what I care about is the prestige of the journal and how many people read it. Once it is finally accepted, since it is so hard to get acceptances, I am so delighted that I will sign anything — send me a form and I will sign it. I have no idea I have signed over my copyright or what implications that has — nor do I care, because it has no impact on me. The reward is the publication.”

Read more about it over at SAS Confidential.

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Beware of Sea Tomatoes

Arctic lakes are not known for their cute and cuddly organisms. But to be fair, they must endure crazy extremes. During the summer they are blasted with 24 hours a day of ultraviolet radiation, and during the winter they endure months of icy blackness, and low levels of life-sustaining nutrients all around.

And yet, some life seems to thrive in this environment. Take for example, the sea tomato. Sea tomatoes are round, plumn and look adorable. However, they are actually colonies of toxin-producing cyanobacteria. And they are piling up on the bottom of Greenland’s lakes. Although sea tomatoes are not uncommon in general, the sheer size and abundance of these particular pile ups are unusual.

Read about it over at Eos. So strange…

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