Monthly Archives: May 2012

AMERCIA — spelling error or a campaign promise of increased surveillance?

Spelling error or campaign promise? Towards a surveillance society.

Mitt Romney’s “screwup” as reported in Slate. But perhaps it isn’t a misspelling??

Arrrrg or Rrrrg — choose your myth

Zombie or Pirate? Which lifestyle do you prefer? (image links to source)

A civilization’s nightmares encompass its darkest truths. The zombie myth has shown increasing traction in pop culture — witness the success of the Walking Dead series. And the zombie does somehow symbolize the fate of the many workers, sentenced to day after day of mind numbing drudgery. While you might have escaped this fate, you know of people who have not.

Nowhere is this better epitomized than in the classic Shaun of the Dead. The zombie apocolypes is not even noticed at first, and in the end Shaun and his (now zombified) friend still enjoy the simple pleasures of a video game in each other’s company. Society hasn’t changed.

Yet there is a second myth, more powerful than that of the zombie. A myth of walking out of society, of joining a band of independent and wild souls. This is the myth of the pirate.

Pirate or zombie, what’s it to be, matey? Arrr or rrrrg?

(of course some choose both)

Make lunch an academic subject (Michael Pollan on Deep Agriculture)

Michael Pollan

Michael Pollan (Omnivore’s Dilema) speaks at the long now

My notes:


Farmers are responding to the cultural mandate we gave them in the 1960s: get big or get out, give us cheap food. Prior to this humanity lived always in hunger or with the fear of hunger. Now we live in the age of cheap calories.

CDC reports that 3/4ths of health care budget goes to treat disease which is caused by bad diet & is thus preventable.

In 1970, it took 1 calorie of oil to produce 2 calories of food. In 2000, it takes 10 calories of oil to produce 1 calorie of food.

American agrigulture is highly centralized. GAO listed it as the most vulnerable to terrorist attack (the report was quickly buried). One lettuce facility produces 26 million salads/week. One hamburger plant feeds 50 million people/month. the US has 4 beef wholesalers and 3 grain traders.

Alternatives are there, but prevented by legislation & subsidies which encourage and only support large-scale industrial farming.

Farmers aren’t the problem; they are trapped by the regulatory system (i.e. illegal to produce & sell your own ham, so Hormel owns the ham industry). 881 billion on agriculture, farmer get 58 bil, packaging companies get 69 bil, and the rest goes to people who sell processed food.


education, transparency to drive legislative and cultural change. Our farmers will farm in the way we ask them to. Return to urban/mass agriculture.

Make lunch an academic subject. Teach kids how to grow, cook, and eat/appreciate/taste food.

Transparency. Show, on each package, how that food item was prepared (live video to feedlot etc), label how much fossel fuel it took, etc.

Home gardening. Note WWII victory gardens provided 40% of the produce for the country.

Ecology drives a global network of gene exchange connecting the human microbiome

Best paper I have read in a long time. Each paragraph reads like a full study, yet the overall conclusion is simple and stated in the title.


The authors identify horizontally transferred bacterial genes (HGT) by screening for blocks of nearly identical DNA (sequences of >500 nuks w/ >99% identity) in distantly related genomes (<97% similarity in the highly conserved 16S gene). 98% of such sequences correspond with predicted protein-coding genes, the majority of which (87% of unique sequences) are not known to be associated with mobility.

So: is is shared phylogeny, geography, or ecology? Phylogeny because selection would favor the persistence of genes from close relatives as these (presumably) are more compatible with the native genetic machinery. Geography because it may restrict dispersal. Ecology by selecting for the transfer and proliferation of adaptive traits, or because shared ecology increases physical interactions between inhabitants of the same zone.

Pairs of bacterial isolated from humans are 25-fold more likely to share transferred DNA than pairs from other environments, and two-fold higher again when taken from the same body site. This last corresponds to a recent HGT in > 40% of comparisons. Likewise, common (non-human) ecological niches have a 3-fold increase in pairs with HGT than pairs which cross (non-human) ecological niches.

Scary finding:

We found that bacteria from farm animals and human food were enriched in transfer of resistance with human-associated bacteria relative to other non-human-associated isolates (P = 1.7 × 10−11 and P = 0.01, respectively; Mann–Whitney U-test). In all, 42 unique antibiotic resistance genes were transferred between human and farm isolates. These transferred genes comprised nine families, all of which included both genes known to provide resistance to clinical antibiotics and genes known to confer resistance to agricultural drugs (see Supplementary Table 6). This suggests that livestock-associated bacteria can contribute to clinical resistance without directly infecting humans, because for these mobile traits, genes, not genomes, serve as the unit of evolution and proliferation. Moreover, we observed 43 unique antibiotic resistance genes crossing national borders, suggesting that because the human microbiome is globally connected, local contamination of the shared mobile gene pool can have significant transnational consequences.

So yes, feeding antibiotics to livestock is a really, really bad idea.



GNR papers

Fig. 6. General properties showing the relationships between structure of regulatory networks and the maximum diversity of steady states. The derivation is shown in Appendix B: (a) A cascade structure in a regulatory network generates one steady state at maximum. (b) A loop structures in a network generates two steady states at maximum. M separated loops generate 2M steady states at maximum. (c) Multiple loops sharing the same genes generate two steady states at maximum. The shaded genes are example of the ROPs. From (Mochizuki, 2008)

Looking at network dynamics, fell into “gene regulatory networks” and found

Mochizuki A. Structure of regulatory networks and diversity of gene expression
patterns. J Theor Biol. 2008 Jan 21;250(2):307-21. PubMed PMID:17988691.

Paraphrase of the abstract:

The basic premise: the activity of a gene should be a function of the controlling genes. Thus, a gene should always show unique expression activity if the activities of the controlling genes are unique. Based on this, the maximum possible diversity of steady states is determined using only information regarding regulatory linkages. Two properties:

  • multiple loop structures in regulatory networks are necessary for increasing the diversity of gene activity.
  • connected multiple loops sharing the same genes do not increase the diversity.

Also the following two, both very influential and both focused on the biology, not the network structure:
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic
determination of genetic network architecture. Nat Genet. 1999 Jul;22(3):281-5.
PubMed PMID: 10391217.
uses clustering of mRNA levels to identify putative networks, and track their dynamics. They found that most clusters have non-periodic temporal profiles.

Friedman N, Linial M, Nachman I, Pe’er D. Using Bayesian networks to analyze
expression data. J Comput Biol. 2000;7(3-4):601-20. PubMed PMID: 11108481.

uses Bayesian networks to discover/recover interactions between genes

Bike of Dreams

Bike of Dreams

One of the best ideas I have seen in a long time.

Will mobile computing kill ad-revenue driven web services?

The world is going mobile. Result:
<li>reduced display space
<li>limited bandwidth
What does this mean for web services whose revenue model depends on ads?

Google search on my android. Fewer results, zero display ads.

What is YouTube going to say to users who complain that mobile video ads eat up all the bandwith in their monthly plan?

Of course if everything is an app, the app can perhaps toss in the ads (think Economist swipe ads). But I don’t WANT an ap for everything I might want to do on the internet. Then I have to search through thousands of aps.

Hmmm, maybe an app browser…

more extreme idiology correlated with simpler language in Republicans

Grade level of Congressional Record speeches declines among Republicans as the voting record becomes more conservative. Among Republicans, the drop from the most moderate to most conservative averages three grade levels, from 13th to 10th grade.

Graphic and the following from the Sunlight Foundation

Background reading/speech levels:

  • 8-9th Average US citizen
  • 9.4 MLK “I Have a Dream”
  • 10.6 Today’s US congress
  • 11.2 Gettysburg Address
  • 11.5 US Congress in 2005
  • 11-14 Major US newspapers
  • 17.1 Federalist Papers
  • 17.8 US Constitution

based on the Flesch-Kincaid test, which scores based on word and sentence length. (Flesch wrote Why Johnny Can’t Read)

I find this historical trend most interesting:

Between 1996 and 2005, Republicans overall spoke at consistently 2/10ths of a grade level higher than Democrats … [following 2005 Republicans declined] from an 11.6 grade level to a 10.3 grade level. For Democrats, it was a decline from 11.4 to 10.6.

20,000 (police??) march at Frankfurt Occupy protest rally?

From the Seattle PI, one of the best photo/headline mashups of the year

If only more protest marchers wore this uniform…

This is how it appeared on the PI homepage

Photo credit is Michael Probst / AP. I don’t know who paired it with this headline.

If you suggest a better caption, I will post it and give you credit.

An idea worth at least 40 nanoKardashians of your attention RT

Ethan Zuckerman proposes a new unit to measure attention on the internet, the Kardashian.

Kim Kardashian

The Kardashian is the amount of global attention Kim Kardashian commands across all media over the space of a day. In an ideal, frictionless universe, we’d determine a Kardashian by measuring the percentage of all broadcast media, conversations and thoughts dedicated to Kim Kardashian. In practical terms, we can approximate a Kardashian by using a tool like Google Insights for Search – compare a given search term to Kim Kardashian and you can discover how small a fraction of a Kardashian any given issue or cause merits.

(I choose the Kardashian as a unit both because I like the mitteleuropean feel of the term – like the Ohm or the Roentgen – and because Kardashian is an exemplar of attention disconnected from merit, talent or reason. The Kardashian mentions how much attention is paid, not how much attention is deserved, so naming the unit after someone who is famous for being famous seems appropriate. Should the unit be adopted, I would hope that future scholars will calculate Kardashians using whatever public figure is appropriate at the time for being inappropriately famous.)