Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Bad omics word of the day: waveomics

Let’s just cut to the chase.  The Bad Omics Word of the Day is Waveomics.  Suggested to me by SeaSaver.

On the one hand, I really like that people in biology related fields are putting out preprints in places like Nature Precedings.  On the other hand, this one is a bit painful from the omics terminology point of view: Waveomics: bringing experimental data to online collaboration : Nature Precedings
Well, the term is really just, well, awful.  Here is a key phrase about it:

A Robot is introduced here, waveomics, which provides the first example of allowing experimental data from multiple sources to be queried and shared in the Google Wave environment.

The concept is not so bad in principle – the author Neil Swainston (who has done some cool things – check out his blog and his slideshare presentations and his Academia.Edu page for some detail) was trying to design tools for streaming genomics data in Google Wave.  So this is not a critique of Neil or his work, just of the word waveomics.

Thankfully, in many ways, Google Wave is going extinct.  I guess we should wave good bye to waveomics too. 

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Twisted Tree of Life Award: NPR on the Evolution of Crying

Well, normally I really like NPR science stories. But this one dug into my anti adaptationism feelings. Adaptationism is, in essence, the practice of saying something must be adaptive (i.e., beneficial), simply because it is there in an organism. Such cases are also referred to as “just so stories” – a play on the old Kipling “Just So Stories“.  That is, in essence, people who claim something is adaptive just because it is there are in essence telling you something is this way because it is just so.   I am actually not sure of the whole history of using the just-so analogy to refer to adaptationist stories – I know Stephen Jay Gould discussed this a lot in his books and lectures, but not sure who first did it. 
Anyway – NPR has an adaptationistic doozy from Morning Edition: 

Teary-Eyed Evolution: Crying Serves A Purpose : NPR

Basically, it seems the gist of the argument here is the following line:

Scientists who study evolution say crying probably conferred some benefit and did something to advance our species — because it’s stayed with us.

Wow – that is like straight out of the adaptationist playbook.  The problem with this argument is that many things exist and persist in organisms even when they are not adaptive.  There are many reasons why this can happen from constraints (e.g., if bones were not adaptive in humans it would be pretty hard to get rid of them) to  invisibility to selection (e.g., some features that only show up after reproductive age may not really influence fitness) and so on.

In essence the NPR story is one of the worst examples of adaptationism in the good science press I have seen in a while.  Sure this shows up all over the place.  But rarely this bad at NPR.  The story ends with an even worse line than the rest

Maybe that’s another reason evolution kept humans weeping: Tears help reveal the truth. And that’s because along with the tears, we’ve evolved a very sophisticated ability to interpret them.

Yes that is right.  Crying has been maintained in humans because we also evolved another adaptive feature – the ability to interpret tears.  So the logic here is that crying is adaptive because it is needed for another adaptive trait for which there is no evidence it is adaptive.

So for their story on crying and for in essence inventing some just so stories to explain why they think it is adaptive, NPR is the recipient of my Twisted Tree of Life Award.  Previous recipients are

See also these things for some stuff on evolution of crying:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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More (you know you wanted it) on fecal transplants and the microbiome

ResearchBlogging.org

Image from
I Heart Guts blog

There is an interesting mini review in the Journal of Clinical Gastroenterology’s September issue that may be of interest to some out there. It is entitled “Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome” by Martin Floch and well, the title is indicative of the article.

Yes, the fecal transplant meme is here to stay. Sure, the cognoscenti already knew about fecal transplants. Perhaps they had read Tara Smith’s discussion of it in her Aetiology blog in 2007. Perhaps they had pondered it when they read the article from my lab on intestinal transplants. Perhaps they had seenthis discussion on MSNBC, or various other stories out there such asthis or this post from Angry by Choice. Or, maybe you just learned about it from Bora’s Carnival of Poop.

But the meme on fecal transplants really spread and many may have first heard about fecal transplants from Carl Zimmer’s New York Times article a month or so ago “How microbes defend and define us“

In the article Zimmer discussed how Dr. Alexander Khoruts used a fecal transplant to treat a woman with a persistent and severe Clostridium infection. And Zimmer discusses how, thought such transplants had been done before, this was the first time that the microbial community was carefully surveyed before and after. (Note, my favorite part of the article is this part, where my friend Janet Jansson describes her reaction:

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”

Anyway Zimmer’s article, as with many of his, garnered a lot of response and got many people discussing the poop on fecal transplants.

Well, this issue of the Journal of Clinical Gastroenterology may now be the biggest pile of information about fecal transplants around. That is because, in addition to this little review mentioned above, there are in fact three articles in this issue relating to fecal transplant. Alas, most of you out there will probably only be able to read the review since the other articles are behind a pay wall.

But the review is good. And I think this is not the last you will hear about this. (Though I note that, even though I think fecal transplants have some major potential, they seem to be being oversold a bit by many as some cure all — fodder for a future “Overselling the Microbiome Award” I am sure).

I will end with this line from the review which raises some other issues about fecal transplants:

Probably one of the major problems is to define how this therapy can become socially accepted. (Can you imagine the Food & Drug Administration discussion?)

Floch, M. (2010). Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome Journal of Clinical Gastroenterology, 44 (8), 529-530 DOI: 10.1097/MCG.0b013e3181e1d6e2

Grehan, M., Borody, T., Leis, S., Campbell, J., Mitchell, H., & Wettstein, A. (2010). Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora Journal of Clinical Gastroenterology, 44 (8), 551-561 DOI: 10.1097/MCG.0b013e3181e5d06b

Khoruts, A., Dicksved, J., Jansson, J., & Sadowsky, M. (2009). Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-associated Diarrhea Journal of Clinical Gastroenterology DOI: 10.1097/MCG.0b013e3181c87e02

Yoon, S., & Brandt, L. (2010). Treatment of Refractory/Recurrent C. difficile-associated Disease by Donated Stool Transplanted Via Colonoscopy Journal of Clinical Gastroenterology, 44 (8), 562-566 DOI: 10.1097/MCG.0b013e3181dac035

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Overselling the microbiome award: Stephen Barrie on pre and probiotics at the Huffington Post

Yes, I think the microbes that live in and on people are important, interesting, cool, and worthy of lots and lots of attention. However, I am getting sicker and sicker of the ways in which the effects of these microbes are, well oversold. So today I am starting a new series here on the Tree of Life – the “Overselling the Microbiome and Probiotics Award.”

And, we have a winner today. The winner is Stephen Barrie who has posted something at the paragon of high quality science – the Huffington Post (for more on the dubious science at Huffington Post, a good place to look is Bora’s Blog Around the Clock). Well, Barrie really takes the cake on this one

Stephen Barrie, ND: The Keys to Maintaining a Healthy Gut

He starts off OK – referring to the number of microbes in the human ecosystem and even quoting Jeroen Raes, who does some great work.

Then he mentions how

“These bacteria have a profound influence on human physiology, your immune system, your nutrition, and are crucial for human life.”

OK I can go with this — maybe an exaggeration but still within reasonable confines. Then the woppers begin

“The health of your body and mind is largely tied to the health of your gut”.

Wow- that is one serious jump – from these microbes have a profound influence to the gut driving health of body and MIND.

Then he goes back to some OK territory again, discussing some functions known for gut microbes, like vitamin production, preventing infection, etc. But just after this he switches to the woppers again claiming that out of balance microbes can cause allergies, inflammatory bowel disease, eczema, arthritis, irritable bowel disease, obesity, autism and personality changes including paranoia, hostility, aggression and so on. Completely ludicrous actually. What we know about these issues is that researchers have found that microbial populations may be altered in people with these maladies. But that does not mean the alteration in the microbes caused these maladies. It could be that other factors cause both the malady and the microbial alteration or the malady itself could lead to altered microbial populations.

But wait, it gets a bit better. Now that he has established that microbes cause all these problems, he tells us how to

“avoid one of the emerging causes of both obesity and food allergies? Lower your risk of inflammatory bowel disease, irritable bowel disease, eczema, colon cancer (15) strengthen your immune system? All this while reducing any levels of paranoia or hostility (and retaining your Jon Stewart sense of humor).”

The recipe for prevention is as follows:

  • Eat a low fat diet rich in vegetables, fruits and complex carbohydrates
  • Limit consumption of animal protein
  • Reduce sugar consumption
  • Increase pre-biotic and probiotic intake
  • Consume enough soluble and insoluble fiber to maintain a daily bowel movement. A slow bowel transit time leads to increased exposure of your body to toxic bowel contents.
  • Reduce dietary sulfate consumption.

Again, I am all for more research into the microbiome.  And I think microbes that live with us must have all sorts of positive and negative effects on our health.  And yes, I understand why “probiotics” and “prebiotics” are getting lots of hype.  But because Barrie has gone from what must be a gut feeling (sorry) to making medical claims without evidence and prescribing treatments to cure ailments that probably don’t exist, he is the recipient of my first “Overselling the microbiome award”.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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If a picture=1000 words, what is sound worth? #burrowingowls

Well, my brother Matt is visiting and he has in one fell swoop opened my ears to a whole new world.  We went for a walk on this trail near my house in Davis, CA where a massive number of burrowing owls live.  I have spent the last few months, on and off, trying to take some good pictures of these amazing owls.  Here is a slideshow of some of my favorites.

http://picasaweb.google.com/s/c/bin/slideshow.swf

Anyway, while going on this walk, Matt brought an extensive collection of giant strange looking sound equipment.

 You see, he is a sound engineer in his spare time and this is, well, what he does. And when we found some owls he told us to mosey on down the trail so he could record. And here are some of his recordings – completely changing my view of these owls.

http://player.soundcloud.com/player.swf?url=http%3A%2F%2Fsoundcloud.com%2Fmattrglenn%2Fburrowing-owls&secret_url=false Burrowing Owls by mattglenn

He has more detail about this on this blog.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bad omics word of the day: adversomics h/t @jennifergardy @mentalindigest

Well, I guess the bad omics blogger in me is back. The bad omics word of the day today is adversomics. First pointed out to me by Jim C at from MentalIndigestion and now reintroduced to me by Jennifer Gardy.
This one is so awful I had to write it up. The first I know of it is here in an article by Gregory Poland et al. entitled “Adversomics: The Emerging Field of Vaccine Adverse Event Immunogenetics”. And now in a new article by the same authors: Application of pharmacogenomics to vaccines where they say

Another area of importance is genetically determined vaccine-associated adverse events, which we have called ‘adversomics’

I note this is the same group that brought us a previous bad omics word of the day winner in “vaccinomics“. So they are double winners. Hooray for them.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Quick blog post: interesting piece on the evolution of ecology by Simon Levin

There is a very interesting piece in the Chronicle of Higher Education by Simon Levin on the “Evolution of Ecology.”

See The Evolution of Ecology – The Chronicle Review – The Chronicle of Higher Education

In it Simon, who I consider both a friend and colleague and who has been an inspiration to me for much of my work, discusses the history of the concept and the field of ecology. He repeats a key phrase he has used elsewhere:

Ecology, the unifying science in integrating knowledge of life on our planet, has become the essential science in learning how to preserve it.

I like this phrase and plan to use it a bit here and there, with attribution of course.
Levin also discusses how Darwin’s Voyage of the Beagle helped launch the field of ecology because it

defined a new and synthetic way of looking at nature—in which the patterns characteristic of particular regions found explanation in a unifying, dynamic framework

It was only after Voyage of the Beagle and Wallace’s work and others that the term “oekologie” came into being.
I particularly like the end where he connects ecology to study of other complex adaptive systems like economic ones and medical ones.
The article is really really really worth a read.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Lack of neutrality in bacteria and where pseudogenes go when they die

ResearchBlogging.org

Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland’s neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are not under negative selection) or helpful (i.e., they are not under positive selection).

And from this assumption we have supposedly learned about mutation rates and patterns (because if they are neutral then the changes in pseudogenes should be reflective of mutational processes, not selection) as well as all sorts of other features of genome evolution.
Over the years, some have challenged the assumption of neutrality of pseudogenes (e.g., see here) like many have questioned whether Switzerland is really neutral. But overall, the feeling that pseudogenes were mostly neutral seems to have stuck. However, that may change a bit with a new paper from Chih-Horng Chu and Howard Ochman in PLoS Genetics (PLoS Genetics: The Extinction Dynamics of Bacterial Pseudogenes).
In their paper they report: (this is their authors summary)

Pseudogenes have traditionally been viewed as evolving in a strictly neutral manner. In bacteria, however, pseudogenes are deleted rapidly from genomes, suggesting that their presence is somehow deleterious. The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of these apparently functionless regions is attributable to their deleterious effects in cell fitness, suggesting that a sizeable fraction of pseudogenes are under selection.

Basically, what they did was the following
1. Compare Salmonella genomes. Identify putative pseudogenes and trace their evolution onto a phylogeny of the species.
Figure 1. Distribution of pseudogenes among Salmonellagenomes.
The phylogenetic tree was inferred from 2,898 single-copy genes shared by all fiveS. enterica subsp. enterica strains and the outgroup S. enterica subsp. arizonae.

doi:10.1371/journal.pgen.1001050.g001


2. Carry out a variety of analyses of the pseudogenes such as
  • looking at ratios of Ka/Ks (this is in essence a ratio of amino acid changes – aka non synonymous substitutions to “silent” synonymous changes which occur when the DNA sequence changes but the same amino acid is encoded).
  • examining the types and frequencies of gene inactivating mutations
3. Then they looked at the “ages” of pseudogenes – with age being estimated by the position in the tree in which the pseudogenes appear to have arise.
4. Finally the examined the age class distribution of pseudogenes as well as whether there were other differences between pseudogenes of different ages. And what they found was inconsistent with a neutral model. Instead, what they conclude is that something is making it advantageous to delete pseudogenes more rapidly than one might expect.
What explains this? After testing multiple possibilities the authors conclude that their is some negative selection against pseudogenes (or I guess positive selection for deletion of pseudogenes).
They conclude by suggesting this is likely to be pervasive across all bacteria and even in archaea. And furthermore make a connection to possible selection on intron size in eukaryotes. Anyway – the paper seems quite interesting and worth a read. Still pondering what it all means, so I would welcome comments.

Kuo, C., & Ochman, H. (2010). The Extinction Dynamics of Bacterial Pseudogenes PLoS Genetics, 6 (8) DOI: 10.1371/journal.pgen.1001050

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Starting to like Academia.Edu, except for annoying emails re: who is searching for me

Well, I am continuing to play around with Academia.Edu. I created a profile there for myself and am also building one for my father Howard Eisen as part of my campaign to “Free my father’s publications.” Academia.Edu has some nice features. I think I still like Mendeley more, but am reserving judgement.

That being said, the default setting at Academia.Edu for email updates is really annoying — I keep getting messages like

Hi Jonathan,

Someone just searched for you on Google, and found your page on Academia.edu.

To see the search query they used, what rank you are on Google for this query, and what country the search came from, follow the link below

Link removed by me

Thanks,

The Academia.edu team

Tip:

To ensure that your Academia.edu page appears high up on Google, link to it from the website of your department, college, university or blog. 88% of people on Academia.edu who link to their page like this appear #1 on Google for searches for their name + university, e.g. ‘Richard Price Oxford’.

First of all, getting emails like this should be Opt In not Opt Out. Second, I find this to be a bit too earnest an attempt to manipulate google rankings to help out Academia.Edu. (I note, while creating this post, I did a search for myself and Academia.Edu and got the links above and then I got an email again, telling me someone searched for me. I know. It was me. I mean, I guess link trading is a real thing, but telling me to add a link do that my Academia.Edu profile might move up in searches is I guess annoying to me.

Anyway – still playing with Academia.Edu. Still liking much of it. But if you search for me on the web and go to Academia.Edu I am sorry but I will not know as I will be disabling email messages from them.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Ooh – Science Quiz Show for the Explorit Museum in #DavisCA #ScienceIsFun

Quick link here — for those in the Davis area interested in science in any way you might want to check out the upcoming Explorit quiz / game show/ challenge. October 7 2010 at Freeborn Hall.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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