Winner of the biggest & best overselling of the microbiome -@theallium on Salmonella Diet

OK.  Now this is some serious overselling of the microbiome: New Salmonella diet achieves “amazing” weight-loss for microbiologist | The Allium.  A must read for anyone interested in microbes and microbiomes.  My favorite part:

“For some time now, we have known that the microbes of the gut – what we term the “microbiome” – play a very important role in our daily lives. What we eat, how healthy we feel, etc. is all controlled by our microbiome. In fact, nothing else is important to our health, except the microbiome – it can defeat cancer, cure hunger, poverty, restore amputated limbs, everything”, said Dr. Nofit.

Although it might seem to be an exaggeration, I think this Dr. Nofit must be correct.  I will now never claim that anyone has oversold the microbiome, because, well, it does everything.

Top alternatives to quilt plots and heat maps

Quilt Plot from PLOS One

If you have missed the uproar over Quilt Plots and whether or not they are Heat Maps, well, you have then missed the uproar over Quilt Plots and whether or not they are Heat Maps.  It has been uproarious.  But you may not know that the literature pre-anticipated this uproar and many already developed alternatives, even if they did not know it.  And here are the top ones.

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Guilt plots

In "Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes" by Walker et al. they report the development of a method "we call Guilt-by-Association (GBA)."  Unfortunately, and amazingly, there are NO FIGURES IN THE PAPER.  Fortunately, lots of other people have done similar GBA methods.  A figure from one such study is below

A Guilt Plot

Alas even though some people now call these Eisengrams, they certainly should have been called Guilt Plots.  And that is what I am renaming them.

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Beet maps

Not much to say other than this is simply visionary:

Beet Map

A title and figures say it all: An In-Depth Analysis of a Piece of Shit (note - a bit gross)

I had heard about this paper a few weeks ago and was just reminded about it by a friend. To understand this paper all you really need are the title and Figure 1 and 2 which are below. Enjoy.

An In-Depth Analysis of a Piece of Shit: Distribution of Schistosoma mansoni and Hookworm Eggs in Human Stool.

#Microbe humor: Spacewalk 1986: Bacteria

"Who Cares About Bacteria?"

Comedy Central

Microbe humor of the week: Jon Stewart from 1999 on Giant Bacterium

Jon Stewart from 1999 on Giant Bacterium

The Daily Show with Jon Stewart	Mon - Thurs 11p / 10c
Other News - Baby's Got Bacteria
www.thedailyshow.com
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Science Humor of the Week: The Limits of Science from Mr. Show

This made my week: The Limits of Science from Mr. Show:
 

 Hat tip to Aaron Darling.

Evolution rap: 3.5* til infinity #music

Well, after a rough day I am in need of some lightness. And thanks to Eric Lowe, an undergrad. working in my lab, I got a giggle out of this:

If only scientists were as important as Rupert Murdoch

(CNN) -- A synthetic life scandal may have cost J. Craig Venter the nobel prize in medicine in 2011, but the maverick science mogul managed to end the year with a modest addition to his empire -- an account on Twitter.

Within 48 hours of debuting with tweets about family, work and his dogs, Venter had pulled in more than 5,000 followers and stirred internet debate over why the 60-year-old was now embracing a technology often used to attack him.

The tweets also raised doubts that the notorious technophobe was writing the messages himself. Science writer Carl Zimmer -- one of only eleven people being followed by Venter -- however insisted that the media mogul was writing "with his own voice, in his own way."

Venter appears to have made his Twitter debut some time ago but with the new year many are waiting anxiously for more posts with insight into his maverick lifestyle.

Top 10 Humorous Science Videos of the Year

I was starting to compile a Top 10 list of best humorous Science-related videos of the year.  And I got stuck on #1 because it is so so so good.  But I was able to find some others I liked (and listed them in no particular order)... so here goes.  If you know of other good ones please post/tweet ...

1. Bad Project video from the Zheng lab.  This is simply awesome.

2. Top 10 quirky science tricks for parties.  I found out about this from Twitter ... and it is very good.

Foundation: Nobel Prizes to be awarded via reality shows incl. Nobel Survivor, Sweden's Next Model (System) & The Amazing Particle Race

In a surprise last minute press release the Nobel Foundation has announced that this year's Nobel Prizes will be given out via reality show style competitions rather than by the traditional committee deliberations.

Marcus Snorch, Chairman of the Board of Directors of the Nobel Foundation said in at a press conference announcing the new system "We have noticed that in the last 5-10 years there has been a diminishing interest in the Nobel Prizes. This decrease appears linked to the steady increase in popularity of so-called reality show competitions. We felt like it was time for the Nobel Prize to try and attract a younger audience. Our reality Nobel series should be highly popular."

Barbara Connon, chairman of the Nobel Foundation Board of Trustees concurred, "We all felt like a shake up was necessary. The Nobel Prize is so important for the world, yet nobody was paying attention anymore. Our new approach, where semifinalists are announced in advance and then a competition decides the winner, should bring new attention to the Prizes"

The announcement represents an agreement between the many institutions involved in awarding the Nobel Prizes including the Royal Swedish Academy of Sciences that presides over the prizes in Chemistry, Physics and Economics; the Nobel Assembly at the Karolinska which awards the Prize in Medicine, the Swedish Academy which awards the Literature prize and the Norwegian Nobel Committee that awards the Peace Prize.

At the press conference, the Nobel Foundation presented the new reality series, one for each Nobel Prize. The example they highlighted relates to this years prize in Physiology and Medicine which will be given out via "Nobel Survivor." This show will feature Nobel Semifinalists living on a remote tropical island and the competitions will feature major medical "events" that one member of each team will experience.  Each week the team that responds least well to the challenge will have to vote off one member.  The challenges will include infections by schistosomes and filarial nematodes, a series of autoimmune disorders, premature aging, erectile disfunction, and severe body odor.  The competitions will be presided over by Hugh Laurie.

"Many of the Physiology and Medicine prizes have been criticized for being too disconnected from actual Medicine.  So we figured what better way to pick the winner than to make them actually do some medicine, but without all the comforts of home," said Barbara Connon. This years semifinalists who will be participating include J. Craig Venter, Lee Hood, Joan Steitz, Alec Jeffreys, Carl Woese, Norm Pace, Mary Claire King, Douglas Coleman, Elaine Fuchs, and James Till.

Other shows for this and future year's prizes include:

Sweden's Next Model (System)
The 2011 Medicine and Physiology prize will feature a competition to determine what is the best model organism.

Real Literature Idol
The 2010 Nobel Prize in Literature will be given out via a literature reading and slam poetry series dubbed "Real Literature Idol"

The Amazing Particle Race
The 2010 Nobel Prize in Physics will be given out to the scientist who is best able to maneuver their particle through a month long journey around the globe.

Dancing Peacefully With the Stars
Enough with Peace Prizes being given to people who work on abstract global issues.  The 2010 Nobel Peace Prize will be given out through a dance competition.  All "stars" selected for the competition will be notorious for their difficulty in getting along with others and will include Mel Gibson, Alex Rodriguez, Lindsay Lohan, Barbara Streisand, Kanye West, Dick Cheney, Amy Winehouse, and Courtney Love.

The Swedish Chef
In order to make chemistry more "Real" for the public, the 2010 Nobel Prize in Chemistry will be awarded in a Swedish Cooking competition.

The Nobel Apprentice
The Prize in Economic Sciences (though not technically a formal Nobel Prize) will be awarded via a collaboration with an existing reality show "The Apprentice." Candidates for the prize will compete to be Donald Trumps economic advisor.

The Nobel Foundation is also soliciting feedback, right here on this blog, for ideas for other Nobel Prize related reality shows for future awards.  Please submit suggestions.

What's better than brain doping? Cello Scrotum is what.

OK I have a lot to learn. I was (and still am) pretty proud of the April 1 prank I pulled off this year with many other bloggers announcing a fake crackdown on brain doping. But my joke is not even close to this one. A letter in a recent issue of BMJ has announced that the malady known as Cello Scrotum was in fact made up. Why did they make this up? In response to a publication about guitar nipple (for more on this see CNN and the Times Online). And now they have confessed only 35 years later.

And I must say - God Bless Pubmed Central. Because here is the original very brief letter which I am posting below:

Palin announces opposition to research on Homo sapiens

Sarah Palin today has followed up her attack on fruit fly research by condemning much of the NIH Budget and a variety of other scientific earmarks.  At a town hall meeting yesterday while campaigning in Guam, Palin said

"We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not."

When asked by a teenage audience member to explain what was wrong with this research Palin said

"You probably are a homosapiens no? Or have many friends that are?  What we need to do is spend money on helping people change and not on studying these homosapiens"

The teen tried to respond but was escorted forcefully out of the hall by security while Palin continued on in her meeting.  At the end of the meeting Palin returned to the topic of science research and said "If elected, the McCain-Palin ticket will reallocate federal funds to eliminate waste on topics like homosapiens and fruit flies.  Enough is enough."