More on gene editing rules, CRISPR in humans and dogs, bioethics & breakthroughs

THE HUMAN GENE EDITING SUMMIT, CONT’D Citizens seeking to understand what was decided at last week’s Human Gene Editing Summit might be understandably confused by the contradictions in these headlines: Scientific community approves human gene

Storify of Discussions About Shameless Behavior by #AAAS Relating to #Ebola Papers

Are you a Twitter Science Superstar?

by Brainleaf Communications

In the beginning, there was Neil Hall’s tone deaf “Kardashian Index”. Then there was Science Magazine’s list of 50 Twitter science superstars. Combined they painted a pretty clear picture that being active on social media was only considered a desirable characteristic in a thin slice of the population – you know, white dudes.

Hall did so by mocking young scientists who are active and effective on social media. Science Magazine did so by featuring very few women or people of color in their list.

PZ Myers, who did make Science Magazine’s list, takes them, particularly the editors, to task:

Isn’t it weird how invisible people suddenly become apparent if you just look for them?

In doing so, PZ reminded me of a Blues Brothers themed piece I wrote a few years ago for Nature’s Soapbox Science about finding audiences where they are on social media. Rather than fighting over the niche audience of science fans, we need to be convincing people to be science fans – much like Jake and Elwood convinced people to like the Blues.

The methodology used by Science Magazine involved looking at the accounts being followed by obvious science superstars, like Neil deGrasse Tyson. A problem with this method is that Tyson, for example, followed less than 50 accounts at the time, and those accounts were not particularly diverse.What the methodology of the list demonstrated above all else is that our most famous science advocates need to follow a more diverse set of people.

Not only are such lists biased against women and minorities, they are biased against anyone who is not inheriting a following from other media, such as television, books, or magazines.

The phenomena are related.

Having been excluded from traditional methods of building an audience, women and minorities have taken to newer media and social media. While their audiences may not be as large, those audiences are hard earned. They are based on the quality of content produced. They are engaged – and they are fiercely loyal, as Science Magazine has discovered.

In the spirit of lemonade, one upshot of this mess is that it has brought attention to several excellent lists of female and minority advocates for science*:

Laura Keeney – “Women Tweet Science Too”

Paige Brown Jurreau – “Awesome Women Scientist Tweeters”

Erika Check Hayden – “Women Scientists” on Twitter

Victoria Herridge – “Women in Science” on Twitter

PZ Myers – “Women and Science on YouTube”

Katie Mack – “Women in Astro/Phys/etc”

Stephani Page – “BLACKandSTEM”

Joanne Manaster – “10 Women Scientists You Should Follow on Twitter”

*This list cannot possible be exhaustive. Feel free to add ones I’ve missed in the comments.

Filed under: Follies of the Human Condition Tagged: blues brothers, Erika Check Hayden, Feminism, Joanne Manaster, Kathryn Clancy, Katie Mack, Laura Keeney, nature, Neil deGrasse Tyson, Paige Brown Jurreau, PZ Myers, race, science magazine, soapbox science, social media, Stephani Page, Twitter, Victoria Herridge, women, women in science

The Representative Disapproves

Representative Jackie Speier (CA, 14th District) has taken Science Magazine to task (PDF of full letter here) for their controversial cover and controversial response to criticism of that cover.

The July ll issue of Science Magazine featured a lurid cover photograph of transgender women in tight dresses and high heels with their heads cropped out of the frame.

She rightfully questions not only the choice, which dehumanizes transgender individuals and works against making science a welcoming environment for diverse individuals, but the perspectives of the senior editorial staff of Science Magazine, who failed to exercise reasonable judgment on this cover choice.

I appreciate the apology from Science ’s editor-in-chíef, but question how such a sexist, racist, and transphobic cover was selected in the first place.

The fact that the poobahs at Science Magazine seemed surprised by the response implies quite a few unpleasant things about the decision-making process. She also extends responsibility to Science Magazine‘s parent organization, the American Association for the Advancement of Science.

Importantly, Representative Speier has not simply registered a complaint. She has demanded a substantive response, which I suspect Science Magazine will be more likely to act on than any letters I send.

As one of the nation’s preeminent science organizations, I expect you will take action to eradicate harassment and inequality in the scientific community. Please reply with the specific steps you will take to become part of the solution, instead of a contributor to the problem.

It also has footnotes.

Filed under: Follies of the Human Condition Tagged: house of representatives, Jackie Speier, Linkonomicon, science, science magazine, transgender

Please make it stop – overselling the microbiome award for rugby, exercise, microbiome stories

Well, I think today's lesson is, many people, including many scientists and science reporters, just do not get that there is a difference between correlation and causation.  I know - this is like beating a dead horse since many write about this issue.  But it just needs to be called out every time until it stops.  And today's fun comes from stories and the original research articles about how exercise supposedly alters the gut microbiome.

I was pointed to this just a few minutes ago on Twitter:

In this Tweet Bernat Olle points to a "news" story in Medpage Today: Exercise Boosts Gut Microbiome Diversity by Kristina Fiore.   Well, so of course I started digging around.  And, not surprisingly, the study that this is based on shows absolutely no causal connection between exercise and the gut microbiome.  The study is in the journal "Gut": Exercise and associated dietary extremes impact on gut microbial diversity.  And here is what they did:
  • They selected subjects - 40 "elite" rugby players.
  • They identified healthy male "controls" with similar age and size and from similar place. 
  • Then they collected faecal and blood samples from participants and did surveys about their nutrition and clinical data.
  • Among many measurements, they did 16S sequencing from the fecal samples
  • Then they did some bioinformatics and found differences between the rugby players and the controls in many features including microbiomes.
And amazingly, from this they report, in their abstract
The results provide evidence for a beneficial impact of exercise on gut microbiota diversity but also indicate that the relationship is complex and is related to accompanying dietary extremes.

The key part of this to me is 
The results provide evidence for a beneficial impact of exercise on gut microbiota diversity
For which they have no support.  They do not in any way show that exercise has ANY affect on the microbiota.  They show it is correlated to the microbiota.

And sadly there is a commentary on the article in the same issue of Gut that makes the same mistake.  Georgina Hold in The gut microbiota, dietary extremes and exercise writes:
The article is the first report that exercise increases gut microbiota richness/diversity and highlights that exercise is another important factor in the complex relationship among the host, host immunity and the microbiota.

No.  They did not show exercise increased gut microbiota diversity.  How can the difference between correlation and causation be missed in these articles?  Are these not even reviewed?  Sure - this is consistent with exercise affecting microbiomes but it is also consistent with rugby players having different diets and other behaviors.  There is a big difference between showing cause and effect and showing correlation.  For not distinguishing between correlation and causation regarding the rugby player microbiomes I am giving all involved here an "Overselling the Microbiome Award".

Here is a microbiome theory I will leave you with.  I hypothesize that these papers, and all the other ones that oversell the microbiome, themselves cause major changes in the microbiome of many people.  Evidence for this?  Well, none yet.  But I have a correlation.  The correlation is, after reading these papers,  I feel sick to my stomach.  That must be proof right?

UPDATE 6/11/14

Author of the Medscape Medpage today article Kristina Fiore says she will update the article to more accurately reflect the science. See some of the thread below

UPDATE 2: 6/11/14.

The press release from Gut associated with this paper contains many inaccurate statements.

Examples include:
  • Title: Exercise boosts diversity of gut bacteria
  • Text: Exercise boosts the diversity of the bacteria found in the gut, indicates the first study of its kind published online in the journal Gut.
Somewhat surprised that such mistakes would come from the journal itself.

UPDATE 3: 6/12/14.

Kritina Fiore has fixed the Medpage article.  Nice.

UPDATE 4: 6/12/14.

Science Magazine gets the causation vs. correlation issue wrong in their little news piece about this.  Yuck.

UPDATE 5: 6/12.

Alexandra Sifferlin has a good article about this at Time


More accurate coverage by Claire O'Connell in the Irish Times Generally a good article here: Rugby players show good guts


Popular Science messes it up too


Keeping track of some of the Tweets about this on Storfy.

UPDATE 9 6/13/14.

NPR News Falls for the Hype

UPDATE 10: 6/13/14.

Just found another inaccurate claim in the original paper

UPDATE 11: 6/13/14

Oh FFS. Now I have found some articles reporting not only that exercise affects gut microbial diversity but that this is why exercise reduces obesity. See Exercise lowers obesity risk by stimulating diverse gut bacteria in the NVO News, for example.

Quote from the story:
A latest research suggests that exercise actually lowers obesity risk by stimulating diverse gut bacteria

UPDATE 12: 6/13/14

Fox News did better with the science (at least in their headline) than many other News Agencies (and much better than NPR).  They report "Exercise may lead to healthier gut bacteria".

Just that word "May" makes me happy.  I know.  Low bar.  But I will take what I can get.

UPDATE 13: 6/13/14

Genome Web also is reporting on the story and on the "overselling" that was done.

UPDATE 13: 6/18/14

And now the New York Times joins the fray: Exercise and the ‘Good’ Bugs in Our Gut where Gretchen Reynolds writes:
The findings suggest that, in addition to its other health benefits, frequent exercise may influence our weight and overall health by altering the kinds of organisms that live inside of us.
No - the findings do not suggest that.  The findings are consistent with that theory but they are consistent with many many many other theories.  FFS this is maddening.  And the article ends with a quote from one of the authors:
But even in advance of those findings, he said, it seems likely that any amount of exercise should make your gut more welcoming to the bacteria that you want residing there.
I note - I found out about this article via Twitter