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: connectome

Well, I have decided that I need to look beyond just new omic words to snark about here (I have been giving a “Worst New Omics Word Award” every once in a while”). So I am now going to post, as often as I can, a little ditty about any bad omics word that is out there. Yesterday’s winner was “phenogenomics” which I posted only to twitter.

Today’s winner is “connectome” (see for example NIH Launches the Human Connectome Project to Unravel the Brain’s Connections, July 15, 2009 News Release – National Institutes of Health (NIH)). I think it’s first major use was here but not sure. It even has a wikipedia entry which says:

A connectome is a detailed map of the full set of neurons and synapses within the nervous system of an organism. The production and study of such a map is known as connectomics.

Now I am not the first to be a bit annoyed by this word (e.g., see the Neurochannels blog post “Review of Seung’s talk at SFN”:

Incidentally, ‘connectomics’ is a cheesy mouthful of a word. Some words just weren’t meant to be biologized with the -omics suffix, and ‘connect’ is one of them. ‘Genomics,’ cool. ‘Proteomics,’ a little annoying and not very creative. ‘Connectomics,’ stop the bus I want to get off. At the very least let’s reserve the -omics for molecular biology. Thank goodness Bialek didn’t try to pull us into the world of ‘infomics.

Hat tip to Karl Broman for pointing this one out in comments here.

As with posts about other omes and omics words, I am not saying anything really at all about the science behind the word here. Just the word.

http://friendfeed.com/treeoflife/35376482/bad-omics-word-of-day-connectome?embed=1

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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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Wanted:Feedback on Importance of Finishing (Microbial) Genomes

To all

I am writing because I am working on a project to evaluate the importance of finishing microbial genomes. I know there has been lots of talk about this out there on the web and in papers, etc but I think a fresh discussion is useful. To get people up to speed below is a summary of the issue as I see it.

  1. Shotgun sequencing: Genome sequencing relies generally on the shotgun method at the beginning of a project where DNA fragments from an organism of interest are sequenced in a highly random manner.
  2. Assembly: After shotgun sequencing, the genome is assembled as best as possible into larger pieces (called contigs) and ordered sets of contigs (called scaffolds). All of this put together can be called an “assembly”
  3. Gaps: After the assembly phase, there are almost always gaps in the assembly. These generally come in two forms:
    • sequencing gaps (where we know two contigs go together in some orientation but where we do not know the sequence of the DNA in between the contigs)
    • physical gaps (where we have sets of scaffolds but do not know how the connect to each other).
  4. Quality: After the assembly phase, different components of the assembly can have different “qualities” where from example, some sections are somewhat ambiguous and others are highly reliable
  5. Finishing: Using any combination of laboratory, computational and other analyses one can both fill in gaps in the assembly and improve the quality of the assembly. This can generally be called “finishing“
  6. Quality of final product: Depending on the end quality of the assembly we could assign it to one of a few categories of “completeness” as outlined in a paper by Patrick Chain et al. In essence, you can consider the post to be a follow up to their paper and their work.
We plan to try to measure what one gains by the finishing steps. We need to know this because we would like to make intelligent decisions about how to allocate resources. If one gains a lot from finishing then it would make sense to allocate significant resources to it. I note, I and some colleagues wrote a paper about this issue “The value of complete microbial genome sequencing (You get what you pay for)” that was published in 2002. This is without a doubt not the only discussion of the topic but I just wanted to point out I have been involved in this debate before. Despite that, I think we simply do not know right now what the benefits might be in the new sequencing landscape.
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So the question I am asking here is:

What do people think are the potential benefits that could come from finishing?

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Here are some possible answers to get the discussion going:
  1. Gene discovery (e.g., there may be interesting/important genes in missing/low quality data)
  2. Esthetics of completeness (as in, it just feels better to have a finished genome)
  3. Improved analysis of genome organization (in particular from having contigs oriented correctly)
Also – I note there has been some discussion of this for animals, plants etc (e.g., see recent paper by Eric Green and others on vertebrates) Many of the issues are similar but they are different enough that I think a microbe focused discussion is useful.
Other links of interest:

ResearchBlogging.org

Blakesley, R., Hansen, N., Gupta, J., McDowell, J., Maskeri, B., Barnabas, B., Brooks, S., Coleman, H., Haghighi, P., Ho, S., Schandler, K., Stantripop, S., Vogt, J., Thomas, P., Comparative Sequencing Program, N., Bouffard, G., & Green, E. (2010). Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-21

Fraser, C., Eisen, J., Nelson, K., Paulsen, I., & Salzberg, S. (2002). The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) Journal of Bacteriology, 184 (23), 6403-6405 DOI: 10.1128/JB.184.23.6403-6405.2002

Chain, P., & et al. (2009). Genome Project Standards in a New Era of Sequencing Science, 326 (5950), 236-237 DOI: 10.1126/science.1180614

Friendfeed discussion of this post:

http://friendfeed.com/treeoflife/4999d16e/wanted-feedback-on-importance-of-finishing?embed=1

——–
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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Cool paper, & winner of "worst new omics word award": Predatosome

ResearchBlogging.org
And the bad new omics words keep streaming in. Today’s winner of the “Worst New Omics Word Award” is going to Carey Lambert, Chien-Yi Chang, Michael J. Capeness and R. Elizabeth Sockett from Nottingham for their use/ invention of “Predatosome”. They use this term in the title of their new PLoS One paper: The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio. Here is the very long sentence where the define it:

The gene products required for the initial invasive predatory processes have not been extensively studied but the genome sequencing of B. bacteriovorus HD100 [1] revealed a genome of 3.85Mb, including a core genome similar to that of non-predatory bacteria and some 40% of the genome comprising a potential predicted “predatosome” of genes, encoding both hydrolytic products that may be employed in prey degradation, and genes that may be required specifically for host predation and thus are not conserved across the Proteobacteria.

The paper is actually quite interesting. They use genomic approaches to characterize a fascinating organism – the bacterial species Bdellovibrio bacteriovorus. This bug is a predatory organism – eating other bacteria. Since it eats them from the inside out, some, including these authors, refer to this organism as a pathogen of other bacteria and their is some discussion here and elsewhere for its potential to serve as a “living antibiotic” in much the same way people are trying to use bacterial viruses (a.k.a. phage).

The paper overall is quite nice on first read. They used microarray studies to characterize gene expression patterns in different phases of the life cycle (see Figure above for the life cycle outline). They backed up this work by quantitative PCR studies and regular RT PCR. And based upon their analysis they found some genes that are “Up-Regulated in Predatory, but Not HI” phase (HI stands for host-independent). And here is where they really tell us what they mean by predatosome:

This category of 240 genes are very interesting as they potentially exclude those genes simply involved with release from attack-phase into growth, namely they should be part of the “predatosome” of predatorily specific genes.

It seems to me this terminology is completely unnecessary. All they need to do is say they are studying the genes related to the predatory phase. To assign these genes to the “predatosome” is a bit much. They continue in the paper to report some really interesting stuff. For example, they also examine another predatory bacterial species, and look at whether there are genes conserved in the process between species. They made some really nice figures by the way about the different phases of hte life cycle in this organism and which genes are expressed:

Anyway – the science in the paper is nice. However, the invention of yet another omics word is a bit much. And thus Lambert et al. are winners of the highly coveted “Worst New Omics Word Award” for their invention of “predatosome“. Details on the paper are below – and that is where the figures come from too. (Hat tip to Bora for letting me know about the paper, and the word).

Lambert, C., Chang, C., Capeness, M., & Sockett, R. (2010). The First Bite— Profiling the Predatosome in the Bacterial Pathogen Bdellovibrio PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008599

Friendfeed comments below:
http://friendfeed.com/treeoflife/9262afad/cool-paper-winner-of-worst-new-omics-word-award?embed=1

——–
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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ISI – late to index #PLoS One but now marketing that they do so

Well, just a mini post here. In case you did not know – PLoS One is now being indexed by ISI (see their announcement: PLoS ONE and see the PLOS blog post here
and see Erik Svensson’s blog post for an interesting take) and will get an impact factor and be in their Citation Index and all such things. Now mind you, I think “Impact Factor” is a silly thing overall in that we should evaluate papers not journals per se.

So why am I writing this – because I find it pretty funny that despite being slow to recognize PLoS One ISI is now promoting the fact that they are indexing PLoS One on their home page. See the screen capture above.

http://friendfeed.com/treeoflife/fa0c4b0b/isi-late-to-index-plos-one-but-now-marketing-that?embed=1

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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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GlaxoSmithKline opening up malaria data a wee bit, but more needed

Robert Langreth in an article at Forbes.Com on January 20 (GlaxoSmithkline’s Malaria Plan: Limit Profits, Open Labs) reports that Glaxo Smith Kline is becoming a bit more open with their data on malaria drug/vaccine development.  Apparently, they plan to open up their labs and some of their data to non profit collaborators such as Emory University.  Sounds like this could be a good first step.  But if they really want to advance malaria vaccine research, perhaps they should release their data to everyone? I get that they want/need to make a profit, but if they want to try and get credit for being open, I think they really should jump into the deep end and do something radical.  Just sharing bits and pieces of data with a few labs is not a particularly stunning move.

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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 from Yolo Basin

Here are some pictures from a recent trip to Yolo Basin

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

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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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Fun at the #UCDavis Raptor Center

Some pics from a family visit to the UC Davis Raptor Center open house

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

——–
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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Enough w/ the good: here are the top10 problems w/ the #scio10 meeting

Well, the blogosphere has been all atwitter with glowing feedback about the Science Online 2010 meeting (see Bora’s collection here). I even wrote some nice things (see “Top 11 things I learned at Science Online (#scio10) ” and “And the real mission of #scio10 is fulfilled: kids play with educational freebies“. Well I for one have had enough. Thus, even though this meeting was the most exciting meeting I have been to since Science Foo camp, I think we all need to put on our snarky hats and point out some general flaws with the whole #scio10 enterprise. And here are but a sampling of some of the unpleasant things about the meeting.
  1. There were many people at the meeting who, like some sort of celebrity, are known either by just one word or by their first name. Bora. Dr. Kiki. The Skloot. Dr. Isis., etc. (though I note, there was an actual Hollywood actress at the meeting). There were multiple people who went by “Goddess” in one way or another. There was a GarbageGirl a Spiderman, a Pharmboy and a DrugMonkey and yes, even a Pervwank. There was even someone who goes by the kind of shoes he wears and another by the color of her lab coat. And not only were there nerds galore, there were people who wanted to be called a nerd or just let it be known they were “curious“. There was even extensive discussion of scientists giving someone else a nickname to try to hide their identity. And so on. I mean, come on. We all know that the only way to keep track of scientists and people contributing to science is by formal full names right?
  2. There were not an even number of males and females. Sure it was just a difference of one (133 men, 134 women). But come on that is so biased.
  3. There were some sessions where some of the people attending the session were not live blogging or tweeting. I know, how could they? Well, it is possible their batteries ran out on their phones, but I mean, really, this is a meeting called “Science Online 2010”. If you are going to go to such a meeting you must bring the right tools.
  4. Someone bumped into the light switch during the keynote talk and shed light on it right when it was getting juicy. The atmosphere was crushed.
  5. There have not yet been any books published about the meeting. It’s true, in the sense that I did an Amazon search and did not find any (note to fact checkers – check that please).
  6. Though they indeed did provide free coffee and espresso drinks – but the bar at the hotel was unable to make mojitos. Bad hotel. Bad hotel.
  7. The hotel had sleep number beds but did not provide any Youtube videos for how to use them. How are we expected to figure out what to do?
  8. Nobody sequenced any genomes at the meeting. Yuck.
  9. Some people took notes on paper. How on earth are they going to tweet while writing stuff down?
  10. A new flu strain was created by all the recombining ideas and discussions of the sexual behaviors of ducks, cuttlefish and other organisms at the meeting. It is now known as scion flu, or H10N10. At least something form the meeting went viral.
  11. (Yes, this one goes to 11). The even allowed people under 18 to the meeting. Creepy and unacceptable.

Friendfeed discussion here:

http://friendfeed.com/treeoflife/fc823e6b/enough-w-good-here-are-top10-problems-scio10?embed=1

And thanks to many for comments / retweets on twitter including:



And here are some related blog posts:
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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.

——–

Confronting Intelligent Design arguments directly in the scientific literature

ResearchBlogging.org
A representative from Wiley publishing sent me a link to an interesting new paper. Entitled “Using Protistan Examples to Dispel the Myths of Intelligent Design” by Mark Farmer, from the University of Georgia and Andrea Habura, from the University at Albany, New York. It is from the Journal of Eukaryotic Microbiology and is based upon a presentation they gave at a workshop at a conference.

Basically, the article is a detailed discussion of how examples relating to microbial eukaryotes (I hate the term protist …) that are used by Intelligent Design advocates are, well, BS. And the article discusses the evidence that refutes the ID arguments.

One thing they discuss is the issue of the Cambrian Explosion. ID supporters, such as Stephen Meyer have made many arguments about they feel the diversification in the Cambrian is not explainable through evolutionary processes. Farmer and Habura refute this by pointing out that the diversity seen in microbial eukaryotes at the time of the Cambrian was immense and that what came out of the “explosion” was actually not that spectacular relative to what already existed in the microbial eukaryotes:

The extant diversity of the protists should therefore be seen as the “background radiation” of the eukaryotic Big Bang, with the Cambrian radiation of the metazoa being a subsequent event within a specific group.

They go on to discuss examples involving speciation, the fossil record, evolution of drug resistance in Plasmodium, and a few other things. In each case they discuss a claim by ID supporters and then discuss evidence for why this claim is not valid. Overall the paper is worth reading if you are involved in any discussions with ID supporters.


I note that when I finished the above writing, I went to look at Pubmed to find other examples of people taking on ID arguments in the literature with a focus on issues in microbes. Here are two other recent examples:

Some discussion of this has now popped up on the web:

FARMER, M., & HABURA, A. (2010). Using Protistan Examples to Dispel the Myths of Intelligent Design Journal of Eukaryotic Microbiology, 57 (1), 3-10 DOI: 10.1111/j.1550-7408.2009.00460.x

——–
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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And the real mission of #scio10 is fulfilled: kids play with educational freebies

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

——–
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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