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.

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.

Beet maps

Not much to say other than this is simply visionary:

Beet Map

Wheat maps

Jorge Dubcovsky at UC Davis just won the Wolf Prize.  What did he win it for.  Wheat Maps of course.  Like this one from a Genetics paper in 1996.

Seat maps

If only someone had thought to make maps of seating arrangements in different facilities, like stadiums, or planes, they could have been famous.  Oh well.

Meat maps

I love meat maps.  They are just awesome.  And here are a few good ones.  And each should be trademarked in some way

Meat Map from Grist

An App of Course

The Meat Map of the World

Feet maps

OK.  I don’t really know what reflexology is but the “feet maps” here are cool to look at.

Tilt plots

See this one.

Tilt Plot

Wilt Plots

Many different kinds here.  This one is nice

A Wilt Plot

Of course there are so many more maps and plots that are on par with quilt plots that I could go on like forever.  I may post more – stay tuned.  This is just exciting stuff.

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.

Figure 1. Instruction form on how to collect whole-stool samples for the study

Figure 2. Processing of stool samples according to consistency including whole-stool homogenization.  Sausage-shaped-but-soft samples were processed like in (A) without taking samples from the center.

#Microbe humor: Spacewalk 1986: Bacteria

“Who Cares About Bacteria?”

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
Daily Show Full Episodes Political Humor & Satire Blog The Daily Show on Facebook

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.
His past 27 tweets include posts about celebrations of the birthday of the first synthetic cell, Osama bin Laden, President Obama, and biofuels. These have raised suspicions that Venter’s Twitter account was being used as a publicity tool to help improve his image after a damaging few years of people complaining he is trying to play God.
Trump is the Winklevoss of politics
Craig Venter via Twitter
Others claimed that the voice of the tweets, as well as their faltering grammar and punctuation, were unmistakably Venter. “You can tell by the tweets he’s doing it himself,” wrote Hamilton Smith, Nobel Laureate and colleague of Venter’s.
A spokesperson for the Venter Institute confirmed to CNN the account is genuine.
The account could offer new insight into a scientist whose life has been under intense scrutiny over the past few years after creating life, beating the public human genome project in the race for the genome, and using his boat as a decoy to study microbes that live in his body.
Twitter played a prominent role in many of the scandals around Venter when it was used to pressure funding agencies into limiting funding for Venter’s Institutes. Commentators said the loss of this revenue was a key factor in Venter’s decision to create life.
Venter’s subsequent appearance before a US Congressional inquiry into synthetic biology also caused a sensation on Twitter, particularly after his wife, Heather Kowalski, threatened to use one of their motorcycles to run over anyone who threatened Venter at the hearing
There were echoes of Venter’s congressional appearance — which he called the “most humble day day of my life” — in some of his tweets such as his comments about his visit to Syracuse University “Impressed with the student enthusiasm at Syracuse U.”
But there were also signs that the science mogul was still getting to grips with social media. Reports suggested he was forced to quickly delete one post — possibly after Kowalski leapt to his aid once again.
The Institute for Genome Sciences — a fierce rival of Venter’s — was among genome centers claiming that Venter was guilty of “tweeting-before-thinking” for suggesting that Francis Collins was evil.
The message was apparently removed, but not before someone tweeting as Heather Kowalski implored: “Venter – DELETE TWEET.” A further post on the unverified Kowalski account later added: “EVERY1: @jcventer was only having a joke pROMISE!!!” [sic].
Among other tweets by Venter, who also follows President Barack Obama, humorist Bill Maher, and MicrobeWorld, was an expression of support for President Obama’s vision for the future. 

With apologies (sort of) to CNN and their report on Rupert Murdoch’s use of twitter. Brought to you by FSN – Fake Science News.

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.

3. Cracked.Com has some funny spoofs, though usually not about science.  Here is one I found about science, sort of.

4. The Onion has some great science spoofs of course.  I found this one but there are many more.
Brooke Alvarez Has All The Answers, Even About Particle Physics 

5. Colbert has some brilliant Science spoofs.  This one however takes the cake in a way: Colbert nuclear explosion

6. Robotic Operation (which I found through

7. OK – so it’s very very long.  But there are some funny parts – the 2011 Ig Nobel Award Ceremony

8. Abby Harrison is very funny. … I first saw here microorganism stand up stuff but I think this one is better.

9. OK so this is not the funniest video with Brian Malow but it give some background on “The Science Comedian”

10. And perhaps my favorite – from the Daily Show — Science – What’s it up to?

Please suggest others …

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.