Friday, September 07, 2018

Friday, May 18, 2018

Koalas, Chlamydia, Microbiomania, Katie Dahlhausen, John Oliver, Russell Crowe, and me.

I love Chlamydia.  Really I do.  It was in a paper analyzing two Chlamydial genomes that I first noticed a very strange pattern of genome evolution.

An external file that holds a picture, illustration, etc.
Object name is gkd25402b.jpg

This in turn led to our discovery that large genome inversions in bacteria and archaea are most common when they are symmetric around the origin of replication.

An external file that holds a picture, illustration, etc.
Object name is gb-2000-1-6-research0011-4.jpg

This may be my favorite paper from my entire career and I owe it all to Chlamydia.

Plus, there are all sorts of jokes one can make with the Giant Microbe Chlamydias like


Monday, April 30, 2018

No Microbiome Santa Claus we cannot magically convert correlative studies into causal ones. And scientists dishing out medical advice about vaping based on such bad science is ridiculous.

Aaarrrrrrrg.  That is how I feel right now.

Many microbiome studies involve examining the microbiome in various samples and asking and answering "Are there differences in the microbiome between my sample types?".  This is a standard correlative analysis used in all sorts of areas of science. and it can be quite useful in many cases.

However, in most cases it is not OK to take information from a correlative study and infer that the microbiome was "changed" due to some factor that differed between the samples.  Generally this would only be possible to do in some sort of controlled experimental manipulation experiment.  But so so so many people make such inferences and I am going to highlight an example that relates to a new study of vaping and the microbiome.

There is a new paper on this topic and an associated press release:
Basically the researchers compared microbiomes in three groups of people who had different behaviors (some non smokers, some smokers, some papers vapers).  Note - they did not study people before and after vaping or smoking.  They compared different people who differed in these behaviors but also differ in 100s to 1000s of other things like diet, gender, age, activity, housing, childhood, and more.

And when they did comparisons in relation to the main variables of non smoker, smoker, vaper, they found some differences in microbiomes and some similarities.  Small study.  But potentially interesting.

However, the PR significantly misrepresents what they did and found. Here are some examples of wording I have a problem with:

Press Release:
  • "Vapers and non-smokers have the same flourishing gut flora."
    • OK this has nothing to do with the point of my post but they do not in any way show "flourishing" flora.
  • "whilst smokers have significant changes to their microbiome".  
    • No.  They show differences.  Not changes
  • Significant changes were found in the gut bacteria of the smokers, with an increase in the Prevotella bacteria which is linked to an increased risk of colon cancer and colitis.
    • Again.  No.  They show differences.  They do not know if they are changes since they do not know what these people had before smoking. And thus they cannot show "increases" either.
  • There was also a decrease in the presence of Bacteroides in smokers, a beneficial bacteria or probiotic.
    • No - no decrease shown.  And for that matter - not all Bacteroides are beneficial or probiotic. 
  • More investigation is needed but to find that vaping is less-damaging than smoking on our gut bacteria adds to the incentive to change to e-cigarettes and for people to use them as a tool to quit smoking completely.
    • Jesus #(@(@.  No.  They did not show this. 
  • This revealed significant changes in the gut bacteria of the faecal samples.
    • Again, no. 

Monday, March 26, 2018

Monday, March 19, 2018

Science Magazine publishes "opinion" piece targeting a specific student w/ sexist "critique" and then won't publicly discuss what happened or what they will do about it

Well, I can't even begin to explain how disappointed I am in AAAS and Science Magazine over their actions recently. An "opinion" article was published last week in the "Working Life" section of Science which was stunningly inappropriate for Science Magazine. I first found out about this when I saw a Tweet from a colleague and friend Rebecca Calisi Rodriguez.
And when I started to dig into the story I was nauseated.

 To sum up - the article was by a student who was apparently trying to express some thoughts about #SciComm activities by others that she did not like. And in the piece she named and mocked the activities of another PhD student at her own institution who does SciComm in ways she does not feel comfortable with. Fortunately, when I started looking at social media responses to this, they were overwhelmingly in support of this targeted student - Samantha Yammine who does really quite phenomenal SciComm work. (See for example her Twitter feed and her Instagram feed.

 I am really thrilled and proud of the community that came out in support of her.

There have also been a few news stories related to or directly about the topic which are worth reading.
Also some of the Tweet streams about this are really worth reading. For example, this one from @christineliuart is a must read:

YAMMMM: Yet another mostly male microbiome meeting - Microbiome Therapeutics Europe Meeting

YAMMMM: Yet Another Mostly Male Microbiome Meeting:
Microbiome Therapeutics Europe Meeting

From their speakers page I estimated gender balance of speakers 

19:6 M:F 
or 75% male