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

CA Proposition 16: PG&E’s outrageous, offensive, misleading initiative

Just heard an ad on the radio from the Vote Yes on Proposition 16 campaign here in California.  And got a heads up from a friend about it too. Just to cut to the chase before getting into detail – this initiative is horrendous and deceptive.  Here are some details 


From Ballotpedia.Org:
“The proposed constitutional amendment would require a two-thirds majority vote of local voters before a local government could:



It is being pushed by promoters as the “Californians to Protect Our Right to Vote.” bill.  But really what this is a move by PG&E to help it make more money.  Some comments/questions


1. Why is the only major donor to the Vote Yes campaign PG&E?  See here for more detail on donors, where as of today the top donors are all PG&E. 


2. Every editorial I could find came out vigorously against it:

3. Not surprisingly, many other utilities have come out against this, as it clearly favors PG&E, aka the status quo.  I am not overly sympathetic to the opinions of these other utilities but it seems that the initiative is more about reducing competition than in favoring democracy.
4. One thing that really annoys me is the component of the proposition that a two-thirds majority vote will be required before local communities can change their energy plans.  To then say that this initiative is about protecting our right to vote is just absolutely offensive.  What this is a way to try and make change of any kind very very difficult.  In this day and age, with energy becoming more and more of an issue, we should have as much flexibility as possible.  What we do not need is an initiative that requires a 2/3 majority to make changes.
5. The most astonishing aspect of the proposal has been some of the words from the head of PG&E, as reported in the Mercury News

Asked why the company was sponsoring the initiative, Darbee referred to the 2006 battle in which it spent more than $11 million to prevent Davis, Woodland and West Sacramento from defecting to the Sacramento Municipal Utility District.

“So it was really a decision about could we greatly diminish this kind of activity for all going forward rather than spending $10 (million) to $15 million a year of your money to invest in this,” Darbee told the shareholders. “The answer was yes.”

So basically this is there way to limit the choices of cities by putting this on a statewide ballot.  In essence, whether liberal or conservative, Democrat or Republican, I can’t see why anyone would support this Proposition.  A conservative could easily see this as  PG&E trying to be the big hand of government to take away taxpayer choice.  A liberal could see this as a company using their money to buy votes and prevent choice in energy usage.  I really cannot see any potential upside in this for anyone but PG&E.  Lovely

Simple solution.  Vote No on Proposition 16.  More comprehensive solution would be to actually punish PG&E for the audacity and idiocy of this measure as well as the misleading nature of all of their ads and claims about it.  Not sure how to do that but boy do they deserve it.

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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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UC Regents 3/24 public/ustream discussion of recent "intolerance" issues

Just got this announcement:


“The UC Board of Regents, at its March 24 meeting, will hold an extended public comment period and discussion of recent incidents of campus intolerance and UC’s efforts to address them.

The Office of the President will provide live streaming video of the discussion, available to members of the public and the UC community at:
http://www.ustream.tv/regentsmeeting

The public comment period begins at 8:30 a.m., Wednesday March 24. Following that 40-minute period, President Mark Yudof, Regents Chairman Russell Gould, Interim Provost Lawrence Pitts, Senior Policy Advisor Christopher Edley and select chancellors will discuss the recent events and the actions they are taking to ensure that these types of incidents do not occur in the future.

For employees who are unable to watch the proceedings live, an archived tape will remain available at the same web address:
http://www.ustream.tv/regentsmeeting “

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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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Phyloseminar.Org 3/29 Streaming talk by Jens Lagergren on Gene Family evolution

Just got his email from the organizer of Phyloseminar.Org:

On March 29th, phyloseminar.org will present Jens Lagergren speaking

on “Probabilistic analysis of gene families with respect with gene

duplication, gene loss, and lateral gene transfer.” Abstract below.

NOTE: the seminar will begin at 10h PST, which is three hours earlier

than the previous seminars.

This is 13h Eastern Standard Time, 19h Central European Time, and 6h

in Christchurch and Auckland!

Here’s the abstract:

Incongruences between gene trees and corresponding species trees are

common. Gene duplication, gene loss, and lateral gene transfer are

three types of evolutionary events that can cause such incongruences.

I will first describe a probabilistic process that contains standard

models of nucleotide substitutions (i.e., such that underly

probabilistic methods for phylogenetic tree reconstruction) as well as

gene duplication and gene loss. This process takes place in a given

species tree and can be used to reconstruct a gene tree for a gene

family of interest and simultaneously reconcile the gene tree with the

species tree. I will describe the algorithms available for this model

and also describe how they perform on biological data compared to

competing methods. Finally, I will describe an extension of this model

that also contains lateral gene transfer and show how it performs on

synthetic data.

Hope to see you there!

——–
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: Bibliome

(Note – this was supposed to be published tomorrow but clicked the wrong button – so we will have two today – yay)

And here is a doozy.  The bad omics word of the day is … Bibliome. See for example, the source of all knowledge (Wikipedia): Bibliome – Wikipedia, the free encyclopedia Which also refers to some other related omics words the literaturome and the textome.  Now, every one at once, 1,2, 3, groan.

Back to the bibliome which is described in Wikipedia as follows:

“The bibliome is the totality of biological text corpus. This term was coined around 2000 in EBI (European Bioinformatics Institute) to denote the importance of biological text information. 

The first uses seem to be in and around 2001. See this article from Nature Reviews Genetics in 2001 Mining the bibliome.  And another one with a very similar title in EMBO in 2002: Mining the Bibliome (with some other words in the title).  And another one in Pharmacogenomics entitled Mining the bibliome. 

And though I would have thought and hoped that it would not get used much it has shown up here and there for a while (see for example Ten thousand views of bioinformatics: a bibliome perspective.). 

So here is a question – what exactly is “the totality of biological text corpus”?  And does this thing, whatever it is, need an omics word?

Hat tip to @rdmpage and others for pointing this one out.

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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: epitehliome epitheliome

The Bad Omics Word of the Day: Epitheliome. Not really much to say. See for example:

The epitheliome: agent-based modelling of the social behaviour of cells. [Biosystems. 2004 Aug-Oct] – PubMed result

Hat tip to Steve Koch on Friendfeed for this.
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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: nutriome

And the winner is …
From the abstract “strategies to determine dietary reference values of single micronutrients and micronutrient combinations (nutriomes)”

As with my last Bad Omics word, I have no real clue what that means. But it seems this author has been using the term for a while.

Some other papers have defined it more concisely such as “Nutriomic analysis is a postgenomic-based study of nutritious components (nutriome).”

Yuck yuck and double yuck is what I say.


Hat tip to @nutrigenomics and @larry_parnell and @eurogene for pointing this one out. 
——–
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: transactome

Hat tip again to Rami Aziz for pointing this out on twitter
From the abstract: “The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined “transactome”).”

I have no real clue what that means.

I confess, going to skip this paper.  So I will not figure out if there is some clearer meaning. But here’s a guess – the word is unnecessary.

——–
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.

——–

Bad omics word of the day: N-terminome

Yes indeed. Someone has used N-terminome.

Nature Protocols: System-Wide Proteomic Identification of Protease Cleavage Products by Terminal Amine Isotopic Labeling of Substrates

From the introduction:
“The sequence and nature of all the protein amino-termini (N-termini) within the proteome (the N-terminome) provides valuable functional annotation, since translation start sites, N-terminal isoforms, modifications and truncations determine the cellular localization, activity and fate of most proteins”
Prediction: will not get widespread use.
But they will get an award today: the Bad Omics Word of the Day.

Hat tip to @mglo for this one.
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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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Good words on bad omics words: "A crisis in postgenomic nomenclature" from 2002

Just got pointed to a fun paper from 2002 “A Crisis in Postgenomic Nomenclature by Stanley Fields and Mark Johnston” by Mark Johnston himself. Their paper, in Science, is available for free on Stanley Fields website here. It is actually a hilarious tongue in cheek read where they proceed from arguing for more specificity in omics names (e.g., they go so far as to propose a EC# like system with things such as the “4.7.5.3.8ome” and also that conditions should be specified like the “37°-7.4-G1-Golgi-N-but-not- 63 O-linked glycosylome”.  And they end with a proposal to replace the term “the cell” with either the someone or the omesome.  It is definitely 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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Bad omics word of the day: miRNAome

Hat tip to Rami K. Aziz on Twitter for this.

The winner of today’s Bad Omics Word of the Day is a paper in PLoS One: PLoS ONE: Characterization of the Melanoma miRNAome by Deep Sequencing

They even slipped the word into the title. I do not think the word was coined by them as I found some older references going back at least to 2005: MicroRNA Gene Expression Deregulation in Human Breast Cancer in Cancer Research.

Given that there were only 847 google hits as of today, the word clearly has not taken off, which is good.  But alas it is still being used, even in titles.  As far as I can tell, what they mean by the term is “All the miRNAs in a particular cancer class” — unclear to me why that needs an ome.

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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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