Yes, it is a music video about missing bad germs after being sick (I’m cured by Aimee Mann)

Do you miss your bad germs after you were sick? If you do, this is for you …

 Nice outfit too.  Found out about this from Laist.

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.

Science music video of the week: Some budding yeast I used to grow

Hat tip to Gian Baucom and Susan Perkins

Bad words: Nebraska declares many words and names to be off limits when spelled/written

For immediate release
From the Nebraska State Government Headquarters

In response to criticisms of our handling of the sign language based signing of a child’s name we have decided that it would only be rationale to also apply the same standard to written and spoken words.  Therefore, be it declared that any words or names that are one letter substitution away from anything bad should be banned.

For example, due to the danger associated with the word G-U-N (which we note – we are just spelling here but not actually writing the word) the following names have been banned: GUS, GUY and the following words are not allowed either GUM, GUY, BUN, RUN, SUN, FUN, GIN, PUN, GUT

For similar reasons it has been deemed that the following names and words to be banned:

  • Names: Ash, Bart, Buck, Butch, Cam, Coco, Dick, Dirk, Fitch, Huck, Luck, Mitch, Nick, Santorum, Tito
  • Words: abs, ads, ash, ask, asp, batch, bits, buck, bum, bunt, butch, can’t, cart, cent, chit, cub, cud, cup, cut, dart, deck, dice, dink, disk, diss, ditch, dock, dock, duck, fare, farm, fits, fort, funk, hiss, hitch, hits, hum, hunt, itch, jock, kick, kiss, kits, lick, lock, luck, miss, mock, muck, mum, nits, part, pick, pitch, pits, puck, punt, rock, rum, runt, santorum, shin, ship, shot, sick, sits, skit, slit, snit, sock, spit, such, sum, tart, tats, tick, tins, tips, tots, tuck, wart, witch, wits, yuck, yum

To help everyone out we have organized the names into clusters based on the banned word (which we would rather not spell out here).

Group 1:

  • Names: Butch, Fitch, Mitch
  • Words: batch, butch, witch, ditch, hitch, pitch, itch

Group 2:

  • Names: Coco
  • Words: dock, jock, lock, mock, rock, sock

Group 3:

  • Names: Tito
  • Words: tots, tats, bits, fits, hits, kits, nits, pits, sits, wits, tins, tips,

Group 4:

  • Names: Ash
  • Words: ash, abs, ads, ask, asp,

Group 5:

  • Names: Bart
  • Words: farm, fare, fort, cart, dart, part, tart, wart

Group 6:

  • Names: Santorum
  • Words: santorum

Group 7:

  • Names:
  • Words: spit, slit, skit, snit, chit, shot, shin, ship

Group 8:

  • Names: Huck, Luck, Buck
  • Words: funk, buck, duck, luck, muck, puck, tuck, yuck, such

Group 9:

  • Names:
  • Words: can’t, cent, bunt, hunt, punt, runt

Group 11:

  • Names: 
  • Words:  miss, diss, hiss, kiss, 

Group 12:

  • Names: Nick, Dirk,
  • Words: kick, lick, pick, sick, tick, deck, dock, disk, dink, dice

Group 13:

  • Names: Cam
  • Words: gum, bum, rum, hum, mum, sum, yum, cut, cud, cub, cup, cut

More groups / banned words coming

Trying to track down source of cartoon about coining "ome" words #badomics

I have this cartoon of direct relevance to my crusade to end the use of badomics words.  I have been trying to track where it came from for – like – ever.  And though I did not want to post it without getting permission I have decided to do so to try and track it’s source.  Here it is

I note – I tried using Google Image search (see a discussion of how to do this here) and it finds some other versions of this cartoon online but none of them have a source for it either.  

So – does anyone out there know where this came from?

Mars Curiosity discussion on Colbert

The Colbert Report Mon – Thurs 11:30pm / 10:30c
John Grunsfeld
Colbert Report Full Episodes Political Humor & Satire Blog Video Archive

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

Best. Microbiology. Video. Ever.

Well, I could say so so much about this.  But it speaks for itself.  Funny.  Gross.  Cute.  And more.  Just watched it – like – seven times in a row.  Best. Microbiology. Video. Ever.

From Jennifer Gardy.