Saturday, November 03, 2018

Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center.  And people from my lab have done some excellent pumpkins in the past.

See for example some details on their 2014 pumpkin:

And I have on and off carved pumpkins on sciency themes every once in a while.

So this year, when the Genome Center admins sent around an email saying they had bought pumpkins for people to use, I decided it would be fun to do something this year.  But then 10/30 came and we had still not done anything.

So I came up with a crazy idea.  Cut up pumpkins in different ways as an example of genome sequencing strategies.  And, with the help of a few people in my lab and some of the people in neighboring labs, this is what we did.

So - first - we took three pumpkins.

And we decided to make one of them a representation of long read sequencing and another a representative of short read sequencing.  So - using a saw provided by people in Justin Siegel's lab, I cut one pumpkin into horizontal slices and remove the innards and made that the "long read sequencing" example.  And then I took pumpkin #2 and again cut into horizontal slices but this time I  then cut those slices up into chunks.  And we then stored the pumpkin pieces overnight and Katie Dahlhausen in my lab made some nice signs to add to the display. In addition, the decorated pumpkin #3 with some "Shotgun sequencing" motifs.  And voila, we had our pumpkins ready for the contest for 10/31.

So I headed in to work early, and set up our display.

And I posted about it to Twitter.

But something seemed lacking.  So I went and got another pumpkin

And now it felt complete.

And then, after the symposium I decided - hey - we should try to reassemble these.  I took some pics of this and made them into videos / gifs.
Long piece assembly. 

Assembling the long piece pumpkin shotgun was easy.

Linking assembly.

Assembling from the linking pieces was harder.  And in the end we did not quite get it back together.

We did not even try to assemble the small pieces. But the next day I did ponder recovering them and the other pieces and doing a meta pumpkin assembly.

Anyway - this ended up being pretty fun.  Lots of ideas about how to do it better (e.g., we should have barcoded / labelled the pieces so that we could guide the assembly if we failed to do it without guidance).   And thanks to all the discussions with people out there and to the people in my lab who helped put this all together.

Also I made a Wakelet of some of the Twitter discussion

Wednesday, October 31, 2018

And today in #microbiomania (aka overselling the microbiome) - ridiculous claim from Raphael Kellman's book marketing group

Just got this email below.  It is from a marketing person promoting Raphael Kellman's new book.  And it has an absolutely dangerous, ridiculous claim in it.  They claim that if you have memory loss, or mood problems, these are not in your head at all - this is caused my problems in your microbiome. What absolutely bullshit.  Sure, the microbiome can impact the brain and mood.  But to go from that to claiming that all memory loss and mood issues are due to problems with the microbiome.  Dangerous.  Deceptive.  Scary.  Snake oil.

But yes, I would be happy to write about your book.  Right here.  Right now.

Here is the email


We are excited to announce the publication of The Microbiome Breakthrough: Harness the Power of Your Gut Bacteria to Boost Your Mood and Heal Your Body by Raphael Kellman, M.D. This revolutionary guide by the author of The Microbiome Diet offers a medication-free, scientifically-based approach to healing depression, anxiety, and brain fog by focusing on your “whole brain” – the brain, the gut, the microbiome, and the thyroid. 

If you are one of the millions of people who feel that you have memory loss or an inability to maintain a balanced, happy mood, the problem is not “in your head,” it is in your microbiome (the trillions of health-promoting bacteria in your body) and your gut. In The Microbiome Breakthrough, you’ll learn about the latest cutting-edge science and discover the Whole Brain Protocol, a powerful four-week plan that advises you on what to eat and which supplements and probiotics to take, so that your brain functions at its best level. Along with delicious, health-supporting recipes, meal plans, and other tips and strategies, The Microbiome Breakthrough will help make your brain work better, enabling you to feel calm, energized, and clear headed without prescription medications.

We would love to partner with you to spread the word about this groundbreaking book from a pioneer in holistic and functional medicine. If you would like to review it on your blog or website, promote it on your social media or email newsletter, or host a giveaway, we would be more than happy to send you a copy.

I look forward to hearing from you!

Thank you,

Marketing Department
Da Capo Press | Lifelong Books | Seal Press
An Imprint of Perseus Books | A Hachette Book Group Company
53 State St., 9th Fl. | Boston, MA 02109

Saturday, October 27, 2018

A 22 step guide to how to write a story to stir up germophobia.

Another day.  Another excessively germophobic news story. Today it is:

What's the dirtiest surface on an airplane? The result may surprise you | CBC News

In reading this article I realized, as others have before me, that these tend to follow a simple script.  Swab. Report on how dirty things are.  But I decided to dig in a little more.  And I have come up with  a foolproof way to write such stories. Just follow these 13 steps. These do not have to be done in the order below.
  1. Swab something
  2. Send swabs off for testing with a microbiologist or testing company to make it seem like there is some serious science going on. 
  3. Bonus points for showing microscopes or bacterial plates or other science things.
  4. Don't report the full methods or data. Just make it seem like you know what you are doing.  Be vague some of the time.  And use really big #s other times.
  5. Report on the results that make things seem way dirtier than people might have expected.  Say things like "Dirtier than a toilet seat". 
  6. Mention feces.  Or fecal matter.  Pretend or just flat out lie about how the testing you did shows that feces was in the samples.
  7. Mention something else that is gross. Condoms.  Bodily fluids.  Vomit.  Disease.  Vermin.
  8. Repeatedly use synonyms of "dirty" or "gross". 
  9. Mention human illness.  Often. 
  10. Bonus points for telling people they "could" or better yet - "likely will" - get specific diseases from touching these sites even when there is likely absolutely no evidence regarding likelihood of transmission.  
  11. Bonus points for mentioning nasty symptoms of human illness like diarrhea or vomiting or things involving bleeding.
  12. Mention specific microbes but only ones that make people sick and don't mention all the other microbes in samples.
  13. Definitely do not mention that some microbes you are calling dangerous also frequently come in non dangerous forms.
  14. Get a known fear mongering germophobe to comment about the results. 
  15. Bonus points if the person you get to comment has a nickname involving microbiology.
  16. Bonus points if the person you get to comment runs a company involved in infection prevention.
  17. Tell people to use hand sanitizer.
  18. Discuss how nobody cleans the surfaces swabbed in the story as often as you would have thought.  
  19. Bonus points for misleadingly saying that you can say something about how often or how well people clean the sites being studies from a limited amount of indirect swab data.
  20. Link to other germaphobic stories or videos.
  21. Ask the people responsible for the sites that were swabbed to comment without really providing them with enough details to be able to know what exactly was done or whether it means anything.
  22. Ask employees or other personnel to comment about other gross things they have seen associated with the sites being sampled.
And today's article has most / all of these.  I will leave it to you, dear readers, to figure out how to map these 22 things onto this and other stories.

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.

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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.

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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.