Great news: the videos from the Stanford Microbiome Informatics Symposium talks are up! The symposium was held on May 27, and featured Rob Knight, Justin Sonnenburg, Ami Bhatt, David Relman,  and Susan Holmes.

You can see videos of the talks here (click on the tab “Videos”).

Thanks, Somalee Datta, Ami Bhatt, Roger Winkelman and team for making this possible.

Happy Independence Day!

I have mentioned this before, but this website not only contains blog posts, but pages with more static information as well. These pages include lists that I compiled of important papers on particular microbiome topics. I call this my Microbiome Paper Collection, and they are listed as pages (not posts) under the Microbiome Collection button in the grey bar under the picture at the top of this page.

Tonight, I’ve updated the collections on the following topics:

• Human Gut Microbiome
• Human Oral Microbiome
• Microbes in Space
• Microbiome of Death and Decay

Feel free to browse the Collection pages. The lists are not complete, but should be a good start for an overview of important papers. You can always let me know if I missed a paper by leaving a comment.

Today I found this new article in Wiley’s Environmental Microbiology:

Web Alert: Synthetic microbial communities: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

As is made clear in the title, this is not a regular review or research article, but a list of links to websites on this topic. Unfortunately, some of these links are more helpful than others: not all will take you to the paper itself, some lead to websites of research groups, and one was not written in English. But what is most disturbing to me is that Wiley put this article behind a paywall, so many people will have to pay $38 to have access to this list of links.

This is not the first Link-Fest article that this author wrote; there are now 5 of these published in Environmental Microbiology. I wrote about another one from the same author in April on MicroBE.net. All of these “Web Alert” articles are listed as regular publications in PubMed. It looks as if this author has found an easy way to expand his publication list, and as if Environmental Microbiology has found an easy way to fill their pages and earn more money

If you are interested in this particular topic but don’t have access to this paper, here is MicrobiomeDigest to the rescue. I have copied the list, improved all links to directly go to the publisher’s website, and updated the list with some missing relevant papers. This collection of papers on synthetic microbial consortia is freely available on a new page called Synthetic Microbial Communities.

This might also be a  good moment to point out that I have made several of these lists of papers on a particular topic, and that you can find all of them here on my page called Microbiome Collection. You will find many topics here that might be of interest, or a good start to a literature search on a particular subject.  And all of them are free! Also note that these are Pages, not Posts. Enjoy!

Update Monday, June 20th at 8 AM: ASM has removed the video from YouTube. Scroll to the end of this post to see ASM’s responses on Twitter.

Update Monday, June 20th at 11 AM: ASM has edited the video to make it solely about explaining your science to a lay person in 30 seconds. See new version here. 

I’m a bit upset tonight because of a video by the American Society for Microbiology (ASM). It was brought to my attention by a tweet by @Yersinia / Jane EB Smith:

So I checked out the link, and it leads to a video that ASM has uploaded to YouTube called “Can you explain your science in 30 seconds to your mom?” (UPDATE: link no longer works; video has been removed). The video was created by two ASM staff members (a video producer and a media specialist) during last week’s ASM Microbe 2016 meeting in Boston. It starts with a cartoon of a young male scientist and a voice over with the challenge to “explain your science in 30 seconds”, followed by a dramatic pause, followed by: “TO YOUR MOM?”

The two ASM staff members then enter the Boston conference building and challenge 8 young scientists to do an elevator pitch. Most of them fail the test. But one scientist does really well, and she wins the contest.

But back to the title of the video. The question apparently assumes that moms are, well, not that smart. And that moms will look completely puzzled when you tell them your science. And that moms wear purple flowery dresses.

Since the ASM conference was during the Father’s Day weekend, why didn’t the video makers use the title “Can you explain your science in 30 seconds to your dad?” Did they think that that challenge would sound easier?

Anyway, it’s just a little annoyance. Just one of those many tiny disappointments women in science feel almost daily. By itself, it’s not even worth mentioning. But all these tiny sad moments do add up, especially when we see that biology labs and conference halls are filled with at least 50% women, but when the speaker podiums and panel tables only filled up with less than 30% women.

Dear American Society for Microbiology, I really love you for all you have done for women in science, but this video sets you back at least 20 years, and is a disappointment for the many women who are a member of the ASM.

Next morning update: ASM has removed the video. They don’t offer any apologies to moms, but they will try to do better in the future. Here are their replies on Twitter.

And here is their official reply on the Youtube comments: 

Detlef Weigel (@PlantEvolution) attended me on Twitter to a nice #LabStockPhotoFail in the New York Times – who should know better than to blindly use stock photos with incorrect labels. His tweet included a screenshot of the New York Times article, in which an image of a protein gel is used to portray a DNA sequence.

The source of the stock photo was listed as Science Source, which describes themselves as “The best in stock photography, specializing in Science, Medical and Nature images and video”. Not a site where you would expect to see this:

Note: the “DNA gel” photo has been quickly replaced as of today in both the New York Times article as well as on the Science Source website.

Here is a link to the New York Times article as it appeared yesterday, as archived by the WayBack Machine on Archive.org.

Two beautiful examples of the intersection of microbes and art:A Synthetic Biologist’s Beautiful Palette of Bacteria Art – Noémie Jennifer – The Creators Project

Tal Danino grows various strains of bacteria into detailed, microscopic patterns that pull you in close. During a recent residency at Eyebeam in New York City, he researched how bacteria could be used as inks in various printing processes, like silkscreening or stamping. The resulting series of works, Microuniverses, is a marriage of nature and engineering—in the artist’s words, “you can control these patterns, but then they evolve on their own.” The concept of “controlling universes” is part of Danino’s day job. As the director of the Synthetic Biological Systems Laboratory at Columbia University, Danino is figuring out how to program bacteria so it can detect and treat diseases in our bodies.

It’s The Zika Virus In Action, Drawn By A Scientist-Artist – Maggie Zackowitz – NPR

A watercolor by scientist-artist David S. Goodsell just might make the Zika virus easier to visualize. The painting, which depicts an area about 110 nanometers wide (a nanometer is a billionth of a meter), shows the virus in the process of infecting a cell. (…) Of course the comic book-bright structures shown in the painting aren’t so simple and colorful in real, microscopic life. “These things are actually smaller than the wavelength of light, so they don’t really have a color,” Goodsell says. He chose his own color palette to highlight the function of each component — and to make them look beautiful.