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Kids' Microbiology Book Review: Germ Stories

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I was going through some kids' books today and found quite a few that I thought were wonderful and thought - well - I should post about some of them.  So that is what I am going to do.

The first I want to write about is Germ Stories by Arthur Kornberg with Illustrations by Adam Alaniz and Photos by Roberto Kolter.

 

I used to read it to my daughter all the time (she is two years older than my son) and then sometimes, when she was older, she would read it to my son.  A few things I like about this book:
  1. It is not all about pathogens - there are sections on yeast, penicillin, gut microbes and Myxococcus (although it is miswritten as Myxobacterium). 
  2. Everything is done as poetry / songs.  Some are cheesy, but my kids liked them.
  3. Each section on a different microbes has a little poem/song, a drawing, and a picture or two as well as a few mini facts (or I guess, micro facts). 
  4. The material is a bit scary / gross at times but not too over the top.
Anyway - I definitely recommend it if you want a microbiology book that will be good for reading to and reading by kids.

I added this book to a collection I am making via Amazon on "Microbiology Books for Kids".  I will write about some of the other ones at another time.




UPDATE - Wanted other suggestions for good kids' microbiology themed books ...

Harvard, hope and hype: the sad reason behind overselling diabetes stem cell work - raising money

Comment
Earlier in the week I got all fired up - not in a good way - about a press release and news stories relating to a new paper from Doug Melton on a insulin producing STEM cell study
With a little more discussion I just got more angry


I was angry both about the overselling of the implications of the paper and the fact that the paper was not published in an open manner. This was despite the stated goals of HHMI which funds some of the Melton Lab work.

I was especially upset that much of the press coverage was reporting on an imminent cure for type I diabetes when this was clearly not imminent. Although I note - some coverage was OK. Like these:

Another good piece of news - HHMI got Doug Melton to post a copy of the paper on a web site
Although this was kind of hidden

Another good thing - Paul Knoepfler, a colleague of mine at UC Davis wrote a blog post for his excellent STEM cell blog about the Harvard study and the hype.

But the hype was still spreading ...
So I felt like there was a continued need to say something about this
I even changed a talk I was giving on Sunday to include a discussion of this paper and the hype as, well, a bad thing
  


And I thought, and kind of hoped, that this might just go away. And then, many people forwarded me this email from Harvard sent out as part of a fundraising campaign. Most of the people who sent it to me sent it in happiness with the possibility of a cure for type 1 diabetes. Here is the email:



Of for $&*#*# sake.  Really.  So now Harvard was going to use this as a fundraising tool.  And they would oversell it even more:

"A giant breakthrough in making that possible" with "that" referring to "finding a cure".  And then they say "these cells can replace or augment daily insulin injections" without saying that this WAS NOT IN HUMANS.  THIS WAS IN MOUSE.  $*#($#) DECEPTIVE LYING SCHMUCKS.

And they end this email with "make a gift today."  How about this Harvard.  I will make donations to anyone but you until you stop marketing in hope and hype and start being responsible.

UPDATE 10/16/14 8 AM PST

Some of the overhyped statements relating to this story:

Harvard Press Story: “We are now just one preclinical step away from the finish line,” said Melton

Rawstory: Stem-cell cure for Type 1 diabetes ‘on par with discovery of antibiotics’

Telegraph: Cure for Type 1 diabetes iminent

Times of India: Type 1 diabetes cure within reach after breakthrough that could spell end of insulin injections for millions

BBC: Giant Leap to Type 1 Diabetes Cure







Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Comment
Sunday I gave a talk at the "12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference".  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:
The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.
It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things - diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:



Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:




UPDATE 10/16 -

I have scanned in my notes that I made in planning this talk.  Figured, why not post them.















Update: 12/10/2014 - just discovered a video of the talk was posted to Youtube 




All Nobel Prizes in 2014 Will be Microbially Themed: The Microbes Guarantee It

Comment
So - last year I secretly created a microbiome based spying system that can transmit the thoughts and emails of people who they colonize.  I introduced this community into all the people on the various Nobel Prize committees in order to get information in advance about their plans for the Nobel Prizes. After getting such information, and discovering that the Nobel's this year were NOT focused on microbes, I then created a microbiome-behavioral manipulation system and re-infected the Nobel committees with this community.  This community forces their host to think about microbes all the time.  All microbes.  All the time.  And thus I am nearly 100% certain that all the Nobel's this year will be about microbes in some way.

Given that, here are my predictions for the All-Microbial Nobel Prizes.

Medicine:
The Human Microbiome and Methods for Studying Microbial Communities.  Should go to Norm Pace and some other people.  Possibly Jeff Gordon.  Possibly Jo Handelsman.  Possibly others.  Depends on how much the microbes in the committees emphasize themselves versus all microbes.

Physics:
Vera Rubin for her work on "Dark Matter" since we all know that the key dark matter in the universe is "microbial dark matter".

Chemistry:
Discovery and characterizing of the mechanisms of CRISPRs.  No clue who will get this but it likely could include Jennifer Doudna and Emmanuelle Charpentier and others.

Peace:
Bill and Melinda Gates and their foundation for their work on global health, especially on protecting from infectious diseases.

Literature: Ursula K. Le Guin in particular for her Wrinkle in Time series and its emphasis is on mitochondria.

Economics:
Well, since microcredit has already won an Economics prize, I am not sure how this will play out but certainly it will involve some type of microeconomics.  Definitely NOT macroecnomics. I think the most likely winner here is Esther Duflo because of her work on both microeconomic topics and microcredit.


Me: Will survey results be published openly. Them: yes. Me: OK - will do survey. #opensurveys

Comment
Got this email:
Dear Jonathan, 
Your peers at the University of California, Riverside, Stanford University, and the Coachella Valley Association of Governments are seeking participation in a survey designed to explore the relevancy and perceptions of basic natural history knowledge and skills among professionals and graduate students in environmental science-related fields.
Professionals and Faculty (including post-doctoral researchers) may access the survey through the following link:https://stanforduniversity.qualtrics.com/SE/?SID=SV_9XmYW9WipZ0JGm1 
If you cannot complete the entire survey all at once, you can return to the survey within 30 days to complete it at your convenience. 
This survey will be distributed at universities, organizations and agencies state-wide, and we would greatly appreciate your participation! All responses will be kept completely confidential. The information collected will be used to provide summary statistics and form the basis of a peer-reviewed publication. 
Please feel free to forward this survey link to peers within California that may be interested in participating. Thank you for your assistance! 
****************************************************************************** 
Should you have questions about this study please contact us: natural.history.survey@gmail.com
Michelle Murphy-Mariscal, M.S. (Center for Conservation Biology, UC Riverside)Cameron W. Barrows, Ph.D. (Center for Conservation Biology, UC Riverside)Rebecca Hernandez, Ph.D. (Stanford University, Carnegie Institution for Science)Kathleen Fleming, M.S. (Coachella Valley Association of Governments)
-----------------------------------------
I wrote back
Thanks for the invite.

Can you tell me more about what will happen to the results from the survey? I only participate in surveys if the data and publications from the survey will be released in an open access manner.
Jonathan Eisen

And then got a very pleasing response:
Hi Jonathan, 
Yes, the results and data of the survey will definitely be published. Attached is a previous, survey-based study and we published the data set in Dryad (an online data repository that you are probably familiar with). The survey that my group and I are doing currently will follow the same format and strict adherence to open access. 
Thank you very much for your participation. 
Warmly,
Rebecca
And then I did the survey and sent this email:. 
Thanks so much for the response and I so pleased with your commitment to openness. I will now gladly participate and share w/ California colleagues.

Why I Tweet and Blog: Captured by Beryl Lieff Benderly

Comment
You know, many people ask me - why do I talk to science reporters so often.  They ask this and then claim that science reporters are just all kinds of evil because they always get quotes and facts and concepts wrong.  Well, that has really not been my experience.  Sure, I have my examples of problems.  But overall, I have been impressed and pleased more often than not.  And here is a great example. I was interviewed a while back by Beryl Lieff Benderly about my somewhat obsessive experimentation with social media for communicating science.  And then, of course, I forgot about it.  So I was exceptionally pleased when I saw the story come out today: To tweet or not to tweet? | Science Careers.  Beryl did a remarkably good job in capturing the essence of my thoughts about Tweeting, Blogging, social media, and science communication.

If you want to know what I think about how to not get overwhelmed with Twitter, how to not spend too much time on social media, and what I think abotu aboutb social media, you don't need to wait for me to try to write my thoughts on the topic down.  Read what Beryl wrote.




Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

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الأحد، 19 أكتوبر 2014

Kids' Microbiology Book Review: Germ Stories

I was going through some kids' books today and found quite a few that I thought were wonderful and thought - well - I should post about some of them.  So that is what I am going to do.

The first I want to write about is Germ Stories by Arthur Kornberg with Illustrations by Adam Alaniz and Photos by Roberto Kolter.

 

I used to read it to my daughter all the time (she is two years older than my son) and then sometimes, when she was older, she would read it to my son.  A few things I like about this book:
  1. It is not all about pathogens - there are sections on yeast, penicillin, gut microbes and Myxococcus (although it is miswritten as Myxobacterium). 
  2. Everything is done as poetry / songs.  Some are cheesy, but my kids liked them.
  3. Each section on a different microbes has a little poem/song, a drawing, and a picture or two as well as a few mini facts (or I guess, micro facts). 
  4. The material is a bit scary / gross at times but not too over the top.
Anyway - I definitely recommend it if you want a microbiology book that will be good for reading to and reading by kids.

I added this book to a collection I am making via Amazon on "Microbiology Books for Kids".  I will write about some of the other ones at another time.




UPDATE - Wanted other suggestions for good kids' microbiology themed books ...
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الأربعاء، 15 أكتوبر 2014

Harvard, hope and hype: the sad reason behind overselling diabetes stem cell work - raising money

Earlier in the week I got all fired up - not in a good way - about a press release and news stories relating to a new paper from Doug Melton on a insulin producing STEM cell study
With a little more discussion I just got more angry


I was angry both about the overselling of the implications of the paper and the fact that the paper was not published in an open manner. This was despite the stated goals of HHMI which funds some of the Melton Lab work.

I was especially upset that much of the press coverage was reporting on an imminent cure for type I diabetes when this was clearly not imminent. Although I note - some coverage was OK. Like these:

Another good piece of news - HHMI got Doug Melton to post a copy of the paper on a web site
Although this was kind of hidden

Another good thing - Paul Knoepfler, a colleague of mine at UC Davis wrote a blog post for his excellent STEM cell blog about the Harvard study and the hype.

But the hype was still spreading ...
So I felt like there was a continued need to say something about this
I even changed a talk I was giving on Sunday to include a discussion of this paper and the hype as, well, a bad thing
  


And I thought, and kind of hoped, that this might just go away. And then, many people forwarded me this email from Harvard sent out as part of a fundraising campaign. Most of the people who sent it to me sent it in happiness with the possibility of a cure for type 1 diabetes. Here is the email:



Of for $&*#*# sake.  Really.  So now Harvard was going to use this as a fundraising tool.  And they would oversell it even more:

"A giant breakthrough in making that possible" with "that" referring to "finding a cure".  And then they say "these cells can replace or augment daily insulin injections" without saying that this WAS NOT IN HUMANS.  THIS WAS IN MOUSE.  $*#($#) DECEPTIVE LYING SCHMUCKS.

And they end this email with "make a gift today."  How about this Harvard.  I will make donations to anyone but you until you stop marketing in hope and hype and start being responsible.

UPDATE 10/16/14 8 AM PST

Some of the overhyped statements relating to this story:

Harvard Press Story: “We are now just one preclinical step away from the finish line,” said Melton

Rawstory: Stem-cell cure for Type 1 diabetes ‘on par with discovery of antibiotics’

Telegraph: Cure for Type 1 diabetes iminent

Times of India: Type 1 diabetes cure within reach after breakthrough that could spell end of insulin injections for millions

BBC: Giant Leap to Type 1 Diabetes Cure







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التسميات: , , , , , ,

الاثنين، 13 أكتوبر 2014

Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Sunday I gave a talk at the "12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference".  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:
The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.
It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things - diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:



Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:




UPDATE 10/16 -

I have scanned in my notes that I made in planning this talk.  Figured, why not post them.















Update: 12/10/2014 - just discovered a video of the talk was posted to Youtube 




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التسميات: , , , , , , , , , ,

الأحد، 5 أكتوبر 2014

All Nobel Prizes in 2014 Will be Microbially Themed: The Microbes Guarantee It

So - last year I secretly created a microbiome based spying system that can transmit the thoughts and emails of people who they colonize.  I introduced this community into all the people on the various Nobel Prize committees in order to get information in advance about their plans for the Nobel Prizes. After getting such information, and discovering that the Nobel's this year were NOT focused on microbes, I then created a microbiome-behavioral manipulation system and re-infected the Nobel committees with this community.  This community forces their host to think about microbes all the time.  All microbes.  All the time.  And thus I am nearly 100% certain that all the Nobel's this year will be about microbes in some way.

Given that, here are my predictions for the All-Microbial Nobel Prizes.

Medicine:
The Human Microbiome and Methods for Studying Microbial Communities.  Should go to Norm Pace and some other people.  Possibly Jeff Gordon.  Possibly Jo Handelsman.  Possibly others.  Depends on how much the microbes in the committees emphasize themselves versus all microbes.

Physics:
Vera Rubin for her work on "Dark Matter" since we all know that the key dark matter in the universe is "microbial dark matter".

Chemistry:
Discovery and characterizing of the mechanisms of CRISPRs.  No clue who will get this but it likely could include Jennifer Doudna and Emmanuelle Charpentier and others.

Peace:
Bill and Melinda Gates and their foundation for their work on global health, especially on protecting from infectious diseases.

Literature: Ursula K. Le Guin in particular for her Wrinkle in Time series and its emphasis is on mitochondria.

Economics:
Well, since microcredit has already won an Economics prize, I am not sure how this will play out but certainly it will involve some type of microeconomics.  Definitely NOT macroecnomics. I think the most likely winner here is Esther Duflo because of her work on both microeconomic topics and microcredit.


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الجمعة، 3 أكتوبر 2014

Me: Will survey results be published openly. Them: yes. Me: OK - will do survey. #opensurveys

Got this email:
Dear Jonathan, 
Your peers at the University of California, Riverside, Stanford University, and the Coachella Valley Association of Governments are seeking participation in a survey designed to explore the relevancy and perceptions of basic natural history knowledge and skills among professionals and graduate students in environmental science-related fields.
Professionals and Faculty (including post-doctoral researchers) may access the survey through the following link:https://stanforduniversity.qualtrics.com/SE/?SID=SV_9XmYW9WipZ0JGm1 
If you cannot complete the entire survey all at once, you can return to the survey within 30 days to complete it at your convenience. 
This survey will be distributed at universities, organizations and agencies state-wide, and we would greatly appreciate your participation! All responses will be kept completely confidential. The information collected will be used to provide summary statistics and form the basis of a peer-reviewed publication. 
Please feel free to forward this survey link to peers within California that may be interested in participating. Thank you for your assistance! 
****************************************************************************** 
Should you have questions about this study please contact us: natural.history.survey@gmail.com
Michelle Murphy-Mariscal, M.S. (Center for Conservation Biology, UC Riverside)Cameron W. Barrows, Ph.D. (Center for Conservation Biology, UC Riverside)Rebecca Hernandez, Ph.D. (Stanford University, Carnegie Institution for Science)Kathleen Fleming, M.S. (Coachella Valley Association of Governments)
-----------------------------------------
I wrote back
Thanks for the invite.

Can you tell me more about what will happen to the results from the survey? I only participate in surveys if the data and publications from the survey will be released in an open access manner.
Jonathan Eisen

And then got a very pleasing response:
Hi Jonathan, 
Yes, the results and data of the survey will definitely be published. Attached is a previous, survey-based study and we published the data set in Dryad (an online data repository that you are probably familiar with). The survey that my group and I are doing currently will follow the same format and strict adherence to open access. 
Thank you very much for your participation. 
Warmly,
Rebecca
And then I did the survey and sent this email:. 
Thanks so much for the response and I so pleased with your commitment to openness. I will now gladly participate and share w/ California colleagues.
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Why I Tweet and Blog: Captured by Beryl Lieff Benderly

You know, many people ask me - why do I talk to science reporters so often.  They ask this and then claim that science reporters are just all kinds of evil because they always get quotes and facts and concepts wrong.  Well, that has really not been my experience.  Sure, I have my examples of problems.  But overall, I have been impressed and pleased more often than not.  And here is a great example. I was interviewed a while back by Beryl Lieff Benderly about my somewhat obsessive experimentation with social media for communicating science.  And then, of course, I forgot about it.  So I was exceptionally pleased when I saw the story come out today: To tweet or not to tweet? | Science Careers.  Beryl did a remarkably good job in capturing the essence of my thoughts about Tweeting, Blogging, social media, and science communication.

If you want to know what I think about how to not get overwhelmed with Twitter, how to not spend too much time on social media, and what I think abotu aboutb social media, you don't need to wait for me to try to write my thoughts on the topic down.  Read what Beryl wrote.




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الأربعاء، 1 أكتوبر 2014

Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

Crossposting from microBEnet:

Some new papers that may be of interest to people:

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