Quotes from the science blogosphere

"As Nature's experiment in open peer review showed, and as can be seen from the lack of commenting on papers in Nature and other journals that encourage it, researchers see little to be gained from open discourse before or after publication. Not only are they busy, as the above quotes attest, but there's no credit to be gained, and some risk if one makes an erroneous or critical statement in public"

From a recent editorial at Nature (again, not exactly from the blogosphere)

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Quotes from the science blogosphere

"By setting up strict reference limits, the journals instead tend to devalue the reference system by leading one to believe that referencing a paper is nothing but a mere courtesy, as opposed to an obligation"

-Editorial at Lab Times (not exactly a quote from the blogosphere, but still).

I agree. Limiting reference number and failing to rightfully acknowledge the correct and original source of a claim, idea or result, due to "space constrains", is frankly, irresponsible.

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A clever genetic strategy for the study of circadian output pathways

Circadian clocks control a large number of daily processes in most organisms. These endogenous cellular timekeepers regulate rhythms in gene expression, physiology and behaviour and enable organisms to anticipate predictable environmental variations.

Circadian clocks are composed of a central oscillator and two signaling pathways: input pathways convey external signals to the oscillator, so that it can be synchronized with the environment and output pathways allow the oscillator to temporally regulate diverse cellular processes.

The ascomycete Neurospora crassa, instrumental to the history of molecular biology (See The Almighty Fungi: The Revolutionary Neurospora crassa), has one of the best-understood circadian systems, in which a molecular negative feedback loop involving FREQUENCY and the WHITE COLLAR (WCC) complex lies at its core. Briefly, the WCC directly activates transcription of frq, and levels of FRQ protein start then to build up. FRQ inhibits its own expression by modulating the activity of the WCC, which results in the daily oscillation of both the frq mRNA and protein levels, and ultimately, in the rhythmic expression of a variety of clock-controlled genes (ccgs).

Despite the extensive knowledge accumulated on the molecular basis of some eukaryotic oscillators, including Neurospora’s, and the identification of a number of ccgs, little is known about the mechanisms that allow central oscillators to temporally control gene expression and the activity of different clock targets.

In this post, I will discuss a fascinating article from the Bell-Pedersen lab aiming at characterizing circadian output pathways in Neurospora.

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Quotes from the science blogosphere

"PC at work, Mac at home- it's like a computer mullet- business in the front, party in the back..."

-Alan Marnett (BenchFly founder, who twitted this at me)

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The 2009 Journal Citation Report is in!

The 2009 Journal Citation Report has just been published!

Just as last year [See The 2008 Journal Citation Report is in! ], there are not many surprises on the top (considering ALL journals), with some medical (CA-CANCER J CLIN, NEW ENGL J MED) and review journals holding on to most of the top 10 positions (including biology related review journals like NAT REV MOL CELL BIO -with an amazing 42.198, which ranks it 4th overall- and NAT REV IMMUNOL).

Also in the top 10, we find Nature (34.480, compared to its 2008 IF of 31.434) and Nature Genetics (34.284, compared to its 2008 IF of 30.259).

Cell, which last year was among the top 10, is now ranked 12th, with 31.152, compared to its 2008 IF of 31.253.

Science, the other glam journal, is now at the 15th position overall, with 29.747, compared to its 2008 IF of 28.103.

Note that, just as I said last year...

you know how I feel about the IF [for example see here] and I've talked about the special care one has to have with it before, so I don't want you to get the impression that just because I'm posting the news I think we should all live our lives around the IF (which of course, I don't... don't be silly). The list, however, is a highlight so we are bringing some details right to your RSS reader (if you follow us through one of those).

Now let's get down to business: who made the Top-20 in the Biochemistry & Molecular Biology category?

In descending order: CELL, ANNU REV BIOCHEM¹, NAT MED, ANNU REV BIOPH BIOM¹, NAT CHEM BIOL, MOL PSYCHIATR, MOL CELL, PLOS BIOL, NAT STRUCT MOL BIOL, MOL SYST BIOL, BBA-REV CANCER¹, TRENDS BIOCHEM SCI¹, GENOME RES, TRENDS MOL MED¹, CURR BIOL, CRIT REV BIOCHEM MOL, MOL BIOL EVOL, CURR OPIN STRUC BIOL¹, PLANT CELL, NAT PROD REP.

¹ Review journals

Here's the 2008 top-20 list in the field, for comparison:

CELL, ANNU REV BIOCHEM¹, NAT MED, ANNU REV BIOPH BIOM¹, NAT CHEM BIOL,TRENDS BIOCHEM SCI¹, MOL CELL, PLOS BIOL, MOL PSYCHIATR, MOL SYST BIOL, PROG LIPID RES, NAT STRUCT MOL BIOL, CURR BIOL, BBA-REV CANCER¹, GENOME RES, TRENDS MOL MED¹, PLANT CELL, CURR OPIN STRUC BIOL¹, CRIT REV BIOCHEM MOL¹, EMBO J

Just as last year, let's take a look at how some of the PLoS journals are doing (why? because we love PLoS and what it represents, see here and here)

First, the heavily criticized PLoS ONE shows that their novel strategy is working, with a great 4.351!.

PLoS Medicine now leads the way for the PLoS journals with 13.050 (last year PLoS Biology held the top position)

Also, PLoS Biology 12.916 (close second!), PLoS Pathogens 8.978, PLoS Genetics 9.532, PLoS Computational Biology 5.759, PLoS Neglected Tropical Diseases 4.693.

That's it for the moment.
I have to get back to my bacterial transformations and to watch some World Cup games ;-)


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Around the Journals: your source of new and exciting molbio articles

Remember to add "Around the Journals" to your RSS Aggregator to stay on top of current developments in the fascinating field of molecular biology.

Go there now! -> Around the Journals

Do you feel your field in underrepresented in our Picks? Send me an email with your weekly picks and we'll post them here!

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Science Rock Band Names in Twitter

In between experiments, I went into Twitter (you can follow me here)only to find out that a very funny (and yes, geeky) meme was started by @Albertagael and @hyphaltip . The idea? To give a science-related name to a hypothetical rock band.

Tweets are being grouped under the hashtag #sciencerockbandnames. Check it out!! There are some very funny contributions.

Here are some of mine (in bold are my personal favorites):

X-Linked

Open Access

Heatblock

The Non Specific Band

The Probes

Free Radicals
Statistically Significant

Impact Factor

The 3rd Reviewer
The Et al's

The Knockouts
FISH and ChIP

The BLAST

The Spliceosomes

Loading Control
Circadian Rhythm

These are some of my favorite from other Sciencetweets:

@modernscientist: Gibbs & The Delta Gs
@nocx "Massive a Taq"
@matthewherper "heavy metal": Black Staphist, Pantothera, Microbatallica, AC/GT


I will be updating this list with more funny names.





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