Faculty of 1000

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Archive for the ‘f1000’ Category

Moving on

Posted by rpg on 27 April, 2010

Don’t panic!

The F1000 weblog has now been incorporated with Naturally Selected, at F1000 The Scientist.

Please update your bookmarks and use the new RSS feed. You can still find previous entries in our archive.

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Common people

Posted by rpg on 22 April, 2010

While trolling through the new, shiny beta F1000 site (shh! I’m not supposed to tell you about that yet) I noticed that a paper from way back in September last year is still up there on our top ten lists. This was a commentary in J Neurosci saying, among other things, that the

time has come for the scientific community to make a concerted effort in condemning animal-rights extremism and in reaching out to the public to explain our work, its importance, and our commitment to the strictest ethical guidelines of animal research.

Furthermore, say the authors,

A special effort should be made to emphasize the irreplaceable role for nonhuman primates in neuroscience research to the public.

(10.1523/JNEUROSCI.3738-09.2009)

It obviously touched a nerve because it garnered 17 evaluations (and Steve P blogged it), second only to a controversial paper from 2005 on non-Mendelian inheritance in Arabidopsis (that actually could be wrong—also see this report and editorial in The Scientist.) I get this—most people, I think, have a hard time accepting that animals should be used for scientific or medical research. Especially if they’re cute, fluffy or primates. But we can not maintain the standards of medical care we have come to expect without such testing, despite the protestations of PETA (who refuse to condemn terrorism, by the way) and the rest of them. Despite the problems with animal models (and there are many; the crucial thing is that we do know the limitations and can use other models in addition), animal-based research is the only way to increase quality of life for human beings.

Whether we should treat human beings preferentially in this way is of course another matter and one for philosophers to debate. (Natural selection of course falls over if a species decides not to do the best it can for itself, but let’s not go there.) But I have no time at all for those terrorists who by their actions rate animal life over human life:

we have seen our cars and homes firebombed or flooded, and we have received letters packed with poisoned razors and death threats via e-mail and voicemail. Our families and neighbors have been terrorized by angry mobs of masked protesters who throw rocks, break windows, and chant that “you should stop or be stopped” and that they “know where you sleep at night.” Some of the attacks have been cataloged as attempted murder. Adding insult to injury, misguided animal-rights militants openly incite others to violence on the Internet, brag about the resulting crimes, and go as far as to call plots for our assassination “morally justifiable.”

So I’m pleased to read that the Information Tribunal, that settles Freedom of Information disputes, has ruled in favour of the University of Oxford protecting its staff from potential terrorists: in this case a particularly mischievous request apparently from PETA concerning an individual at Oxford (you can see the decision here: PDF).

It makes interesting reading (from the Understanding Animal research website):

PETA was not satisfied with this decision and appealed again. The case therefore passed to the Tribunal service. In evidence to the Tribunal judge, the University acknowledged that being transparent was good for science and that ‘if there was no special extreme threat here, the exposition of this information would be for the good’.

The Tribunal Judge upheld the previous ruling by the Commissioner, and agreed that the exemption was correctly applied. They also agreed that the public interest in maintaining the exemption outweighed the public interest in disclosure.

[…]

We strongly support the rights of universities not to put individuals at risk.

Common sense prevails. At least in the UK: in the US, PETA tried to pull a similar stunt against the University of South Dakota. There, they also failed, thankfully: but only because they withdrew on a technicality. That’s not good enough—the law should be protecting researchers without question.

Unless you believe that animal ‘rights’ are worth more than those of humans, of course.

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Should I stay or should I go

Posted by rpg on 21 April, 2010

Epigenetic regulation is the new black, or at least charcoal. Modifying chromatin—acetylation or methylation of histone tails, or directly on DNA, in CpG islands for example—can change a number of things in addition to imprinting (turning gene expression on or off depending on parental origin). I’ve just finished one write-up of a F1000 Report discussing histone methylation in meiotic recombination hotspot specification and hybrid sterility, and another one of a paper showing that histone marks regulate alternative splicing patterns (look out for them in June’s The Scientist).

Viruses are getting in on the act too. When Epstein-Barr virus infects a cell it can either hide–latency–or replicate and continue the infection. It uses a single transcription factor to drive these states, depending on the epigenetic status of the host cell; in other words it uses the cellular machinery to wake up when conditions are right. Kind of like a molecular clock, actually. (And you’ve got to love an evaluation that quotes Mick Jones.) We’re also seeing strange but pretty strong effects in certain tumors: hypermethylation of two tumor suppressors in the parathyroid is associated with (and probably leads to) adenoma formation.

Fat’s back in town. Lab rats are obese—morbidly so. But the problem is if you don’t let them feed at will then they get stressed, apparently, which is bad if you’re trying to do experiments on a normal, healthy ‘control’ animal model. Lots to think about there. I’m not going to repeat a comment a colleague made about them being a normal model for certain nationalities, but maybe we could look at knocking out hedgehog, which seems to suppress the generation of white but not brown fat.

Finally (sorry, no room for cytoskeletal porn this week), Faculty of 1000 published its 90,000th evaluation yesterday! David McManus at Weill Cornell Medical College wrote about a paper in the Journal of Clinical Oncology that looked at combination therapy in the treatment of advanced clear cell renal carcinoma.

We’re looking forward to 100k.

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Think you knew librarians?

Posted by Callum Anderson on 15 April, 2010

Librarians can sometimes suffer unfairly from stereotypes. But footage like that below suggests there could be much more to your average librarian than might initially meet the eye.

I certainly wouldn’t like to be on the receiving end of a late fine from any of these warrior librarians!

See how long you can stifle your giggles. And rest assured in the knowledge that the book-cart-drill-team contest will be held again this year at the ALA annual conference.

Posted in Conferences, f1000, Random | Tagged: , , , | 2 Comments »

Everybody’s Talkin’

Posted by rpg on 15 April, 2010

It’s been a while since I’ve said anything about the F1000 website. You might remember that’s what I was working on when I first arrived at SNG (much to my surprise, it has to be said); since about February I’ve been increasingly full time on The Scientist. I still maintain a professional interest in what’s going on across the office, though, especially when it comes to a couple of my pet projects.

One of those projects is user comments.

We’ve been having a bit of a discussion about comments on evaluation pages. My original plan was to have a separate forum so that people could talk about articles evaluated by Faculty Members. But for various reasons that morphed into comments directly on the evaluation itself, which I think is probably a better way of doing things. This does cause a few headaches, though: we don’t want to ‘dilute’ the impact of what our FMs say, we’re a serious site—by professionals, for professionals—and need to honour the trust our users place in us (so can we allow comments from just anybody, and how are you, as a reader, to judge the worth of those comments?), we want to avoid trivial and inappropriate content but at the same time commenting for the bona fides should be as easy and straightforward as possible.

I’m encouraged that Nature are now allowing commenting across the site, and will be watching what happens with interest. In the meantime, Neil Saunders has some useful advice for publishers who want to encourage comments.

My question to you is, what else would you like?

I should point out that we’ve already decided that only registered users who are in a ‘subscription zone’ can comment (only subscribers can read the content anyway; except for the articles we make free), and that all comments will go live immediately, and there’ll be the ability to flag comments as inappropriate. That’s on the advice of our lawyer, so is unlikely to change! But have at it: what really annoys you/stops you from commenting on other sites?

Posted in f1000, Website | Comments Off on Everybody’s Talkin’

Flattery to deceive

Posted by Callum Anderson on 14 April, 2010

Is orange juice a new superfood? Perhaps in some situations it can benefit the body. But the term ‘superfood’ often belies negligible effects in vivo.

A paper by Husam Ghanim, Chang Ling Sia, Mannish Upadhyay, Kelly Korzeniewski, Prabhakar Viswanathan, Sanaa Abuaysheh, Priya Mohanty and Paresh Dandona at the State University of New York at Buffalo (evaluated by our wonderful Faculty of course), suggests that consuming orange juice alongside a fatty, high-carbohydrate meal could limit the adverse effects of all that junk food.

On a slightly related note – while writing this post I was directed by RPG towards a list of The 40 Deadliest Fast Food Meals – and I wonder how much orange juice we might have to drink to alleviate the effects of the top entry? The article clogging, 1300 calorie, 38 grammes-of-saturated-fat-Baconator Triple from Wendy’s!

Right – back to more serious pontification now.

The paper hinges around a comparison of orange juice, water and glucose drink alongside a fatty, high carbohydrate meal and the subsequent production of reactive oxygen species by polymorphonuclear cells, measures of cytokine and endotoxin activation in mononuclear cells, and plasma levels of endotoxin and matrix metalloproteinase.

Bruce Bistrian of the Beth Israel Deaconess Medical Center says in his evaluation

Orange juice reduced the oxidative stress and prevented the formation of pro-inflammatory components, including the increase in plasma endotoxin, compared to either water or glucose. Somewhat surprisingly, there was no increase in plasma glucose with orange juice as found with the meal plus water or the meal plus glucose, despite the substantial carbohydrate and caloric load.

And he added

it is likely that the authors’ suggestion that the mechanism for the antiinflammatory actions was due to the flavonoids naringenin and hesperidin present in orange juice is correct.

So the flavonoids in orange juice may be preventing inflammation after an unhealthy meal, in short limiting the damage.

However, I would not go as far as to suggest that orange juice is particularly brilliant in this respect, especially as the highest concentrations of hesperidin are found in the white parts and peel of oranges, which do not provide a particularly appetising juice. Furthermore, this article suggests that grapefruit provides a significantly higher concentration of naringenin than orange.

But criticism aside; the mention of flavonoids in this paper got me thinking more generally about these so called superfoods. And then more specifically about a press release I saw doing the rounds recently concerning rhubarb. Scientists are inherently aware that test tube or laboratory work does not always transfer into the real world. And the rhubarb press release is a good example of why.

Rhubarb was christened as a new superfruit by some sections of the media due to its high concentration of polyphenols. And the point of these chemicals is that in test tube study, they scavenge free radicals and show other benefits when used in high concentration. But they also have currently undefined mechanisms by which they may reduce the risk of cancer or heart disease. I would be very surprised however if these benefits effectively make the transfer from vitro to vivo. Basically, the concentration levels of ingested polyphenols are usually extremely low, and may be too low in many cases to make any real difference.

A recently published paper by Balz Frei entitled Controversy: What are the True Biological Functions of Superfruit Antioxidants? highlights further problems when flavonoids in particlular find their way into the body. He says

Flavonoids are poorly absorbed into blood and rapidly eliminated from the body; thus, flavonoids have low eventual biological availability.

So really, despite having high levels of helpful chemicals; once ingested, concentration of many of these so called ‘super’ chemicals still lags way behind more common cellular antioxidants.

So eating rhubarb is not going to affect chemical levels for particularly long, because the unique chemicals simply don’t hang around for very long in the body. And this is why I really like the paper by Ghanim et al. Ghanim and his team acknowledge the short bioavaliability of flavonoids and test them in a situation where their effect is clearly measurable against the high calorie meal.

Perhaps I am being too harsh here? In the rhubarb press release, Dr Nikki Jordan-Mahy does admit that the real application of her research lies away from ‘Superfoods’. She says

But if we can extract the polyphenols they may be useful in helping to fight cancer along with chemotherapy.

And this point hits the nail on the head, we need to be thinking how to extract and concentrate these chemicals to make them worthwhile, and in the meantime, the mainstream media needs to understand that positive laboratory tests do not always signify benefits in vivo.

Posted in f1000, Journalism, Medicine, Press Releases | Tagged: , , , , , , | Comments Off on Flattery to deceive

At the movies

Posted by rpg on 7 April, 2010

Busman’s Holiday

Faculty of 1000 published 1472 evaluations last month. This is a world record! And it should help you predict when we’re going to hit 90,000. Remember, we’re running a competition: simply twitter the date and time you think we’ll make 90,000 evaluations with the hashtag #F90K for a chance to win some F1000 goodies.

Easter Hollidays

Image: Richard Wheeler, Wikimedia Commons

Faculty member Fyodor Urnov wants to know if you remember the lecture on homologous recombination (HR) from your genetics class in college. I certainly remember tutorials, and seeing micrographs of Holliday Junctions for the first time. I was fascinated and not a little excited at actually seeing a physical representation of an incredibly important biological process.

Fyodor answers his own question,

For many people, sadly, the answer is “no, and not regretting it.” This is a shame — not only are we the products of HR that took place during gametogenesis in our parents but the repair of double-strand breaks (e.g. after a dental X-ray) keeps our genomes intact.

and recommends you read a recent paper in Nature showing that double Holliday junctions are indeed involved in repair of double-strand DNA breaks. He goes on to bang the drum for traditional biochemistry:

single-locus analysis continues to offer remarkable insight into biology, despite the ubiquity of massively parallel omics. A proper Southern blot — of which this paper has many — is a very, very powerful tool.

Roman Holiday

You probably saw that Nature Reviews suffered its first retraction across its stable recently. In an interesting case of intellectual plagiarism, Mariam Sticklen was accused of writing a paragraph that was “paraphrased without attribution”. This becomes interesting in that the principle of anonymous peer review has been challenged: Sticklen reviewed a paper and allegedly lifted the offending ‘thought’ directly from it. The editor of Plant Science, Jonathan Gressel, said
“When you have done something that’s way beyond the pale, you forfeit your anonymity as a reviewer,” and “I think Nature Reviews Genetics was nice to her in allowing her to say ‘paraphrase’.”

The full story by Bob Grant is available at The Scientist. I only mention it here, really, for the comment thread, in which we see both editors getting involved, as well as Sticklen herself and her ex-husband, who gives her a glowing character reference. If there’s any film makers out there who want to make a blockbuster about science, this has all the ingredients.

And finally

Trees are good for you. At least, if you’re an arboreal—i.e. tree-dwelling—mammal. But not a primate or marsupial. If you’re one of those (what are you doing reading this?), you

should have longer lifespan than terrestrial species of similar body mass, the rationale being that arboreality reduces the risk of predation by terrestrial predators.

As Douglas Adams once said, coming down from the trees was a bad idea.

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Faculty of a Million?

Posted by rpg on 1 April, 2010

Apparently, the two self-proclaimed ‘top’ scientific journals, Nature and Science, have ended their hundreds of years-old feud and teamed up to launch a new journal, to be called either Scientific Nature or Natural Science, depending on the result of a text-message vote by the scientific community.

Sounds good? Well, not really. We’re a bit upset that they’re also creating a social networking site called ‘Faculty of a Million’, funded by a grant from Facebook, where scientists can vote papers for acceptance by pressing a “Like” thumbs-up button or reject the paper by pressing a “Dislike” button. Our company lawyer has just had an apoplectic fit.

And this seems to be a direct invasion of privacy:

readers will have the option of Skyping authors directly to share their thoughts and feelings about a paper simply by clicking that author’s name. As an added incentive, the first 100 new subscribers will get free genome scans.

It’s a nice cover though:
Easter bunny

Posted in f1000, Friday afternoon, Literature, The Scientist | Comments Off on Faculty of a Million?

We will rock you

Posted by rpg on 31 March, 2010

Three’s a crowd

Who would have thought that plants could teach us about deafness? Or single-celled yeast about blood vessel development? Orthologous genes in different species can have totally different effects, and a statistical data-mining technique has thrown up not a few surprising models for human disease. The paper is free at PNAS and reviewed at Faculty of 1000. You can read more at The Scientist and Nature.

In another bizarre turn of events, it turns out that dilute biochemistry is all it’s cracked up to be. People have, over the years, ragged on biochemistry for dealing with dilute proteins and ignoring the ‘crowding’ effects of the cytoplasm (despite biochemical predictions often being borne out by in vivo work, but anyway). An outstanding computational paper looks at models of crowding in the bacterial cytoplasm, successfully simulating the relative thermodynamic stabilities of individual proteins:

But the overall take-home message seems to be that the effect of crowding by steric exclusion is largely cancelled by hydrophobic interactions with the crowders. Protein biochemistry in dilute solution has gained new respect.

The full paper, Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm, is available from PLoS Computational Biology.

Got rhythm?

Another strange one, lurking in PNAS (Social Sciences/Psychological and Cognitive Sciences), suggests that humans are born to rock and roll:

One of the most curious effects of music is that it compels us to move in synchrony with its beat. This behavior, also referred to as entrainment, includes spontaneous or deliberate finger and foot tapping, head nodding, and body swaying.

Children under the age of two (and pre-verbal) spontaneously to music, but not speech.As Katrin Schulze, down the road at UCL says,

This suggests a predisposition in humans towards engaging rhythmically to a musical beat.

Yeah.

And finally

It’s competition time!

Faculty of 1000 is approaching the publication of 90,000 evaluations. This morning we had 89210 on the two sites, Biology and Medicine. We’ll be running a little internal compo for the people in the office, but we’d like to throw this open to all our Twitter followers and readers too. Use the hashtag #F90K to tell us the day you think we’ll make the 90 thousand. For a tie-breaker, feel free to put in the time, too (best use UTC. And here’s a clue: our editors work London office hours). Visit http://f1000biology.com/ and http://f1000medicine.com/ to help you with your guesswork.

As usual, a bag of F1000 swag for the winner. Good luck!

Posted in Competition, Weekly roundup | 1 Comment »