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John Baez
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Thank you!

The Azimuth Climate Data Backup Project is backing up 40 terabytes of US government climate data and copying it to a number of locations, to protect it from all possible threats:

http://math.ucr.edu/home/baez/azimuth_backup_project/

It's going well! Our Kickstarter campaign ended on January 31st and the money has recently reached us. Our original goal was $5000. We got $20,427 of donations, and after Kickstarter took its cut we received $18,590.96.

Soon I’ll tell you what our project has actually been doing — lots of good news. This time I just want to give a huge “thank you!” to all 627 people who contributed money on Kickstarter... many from here on Google+.

I recently sent out thank you notes to everyone, updating them on our progress and asking if they wanted their names listed. The blanks in the following list represent people who either didn’t reply, didn’t want their names listed, or backed out and decided not to give money. I’ll list people in chronological order: first contributors first.

Only 12 people backed out; the vast majority of blanks on this list are people who haven’t replied to my email. I noticed some interesting but obvious patterns. For example, people who contributed later are less likely to have answered my email. People who contributed more money were more likely to answer my email.

The magnitude of contributions ranged from $2000 to $1. A few of you offered to help in other ways. The response was international — this was really heartwarming! People from the US were more likely than others to ask not to be listed.

But instead of continuing to list statistical patterns, let me just thank everyone who contributed. Here's the list! (I’ll keep updating this list on the Azimuth blog, but not here.)

Daniel Estrada
Ahmed Amer
Saeed Masroor
Jodi Kaplan
John Wehrle
Bob Calder
Andrea Borgia
L Gardner

Uche Eke
Keith Warner
Dean Kalahan
James Benson
Dianne Hackborn

Walter Hahn
Thomas Savarino
Noah Friedman
Eric Willisson
Jeffrey Gilmore
John Bennett
Glenn McDavid

Brian Turner

Peter Bagaric

Martin Dahl Nielsen
Broc Stenman

Gabriel Scherer
Roice Nelson
Felipe Pait
Kenneth Hertz

Luis Bruno


Andrew Lottmann
Alex Morse

Mads Bach Villadsen
Noam Zeilberger

Buffy Lyon

Josh Wilcox

Danny Borg

Krishna Bhogaonker
Harald Tveit Alvestrand


Tarek A. Hijaz, MD
Jouni Pohjola
Chavdar Petkov
Markus Jöbstl
Bjørn Borud


Sarah G

William Straub

Frank Harper
Carsten Führmann
Rick Angel
Drew Armstrong

Jesimpson

Valeria de Paiva
Ron Prater
David Tanzer

Rafael Laguna
Miguel Esteves dos Santos
Sophie Dennison-Gibby




Randy Drexler
Peter Haggstrom


Jerzy Michał Pawlak
Santini Basra
Jenny Meyer


John Iskra

Bruce Jones
Māris Ozols
Everett Rubel



Mike D
Manik Uppal
Todd Trimble

Federer Fanatic

Forrest Samuel, Harmos Consulting








Annie Wynn
Norman and Marcia Dresner



Daniel Mattingly
James W. Crosby








Jennifer Booth
Greg Randolph





Dave and Karen Deeter

Sarah Truebe










Jeffrey Salfen
Birian Abelson

Logan McDonald

Brian Truebe
Jon Leland






Sarah Lim







James Turnbull




John Huerta
Katie Mandel Bruce
Bethany Summer






Anna Gladstone



Naom Hart
Aaron Riley

Giampiero Campa

Julie A. Sylvia


Pace Willisson









Bangskij










Peter Herschberg

Alaistair Farrugia


Conor Hennessy




Stephanie Mohr




Torinthiel


Lincoln Muri
Anet Ferwerda


Hanna





Michelle Lee Guiney

Ben Doherty
Trace Hagemann







Ryan Mannion


Penni and Terry O'Hearn



Brian Bassham
Caitlin Murphy
John Verran






Susan


Alexander Hawson
Fabrizio Mafessoni
Anita Phagan
Nicolas Acuña
Niklas Brunberg

Adam Luptak
V. Lazaro Zamora






Branford Werner
Niklas Starck Westerberg
Luca Zenti and Marta Veneziano


Ilja Preuß
Christopher Flint

George Read
Courtney Leigh

Katharina Spoerri


Daniel Risse



Hanna
Charles-Etienne Jamme
rhackman41



Jeff Leggett

RKBookman


Aaron Paul
Mike Metzler


Patrick Leiser

Melinda

Ryan Vaughn
Kent Crispin

Michael Teague

Ben



Fabian Bach
Steven Canning


Betsy McCall

John Rees

Mary Peters

Shane Claridge
Thomas Negovan
Tom Grace
Justin Jones


Jason Mitchell




Josh Weber
Rebecca Lynne Hanginger
Kirby


Dawn Conniff


Michael T. Astolfi



Kristeva

Erik
Keith Uber

Elaine Mazerolle
Matthieu Walraet

Linda Penfold




Lujia Liu



Keith



Samar Tareem


Henrik Almén
Michael Deakin


Erin Bassett
James Crook



Junior Eluhu
Dan Laufer
Carl
Robert Solovay






Silica Magazine







Leonard Saers
Alfredo Arroyo García



Larry Yu













John Behemonth


Eric Humphrey








Øystein Risan Borgersen
David Anderson Bell III











Ole-Morten Duesend







Adam North and Gabrielle Falquero

Robert Biegler


Qu Wenhao






Steffen Dittmar




Shanna Germain






Adam Blinkinsop







John WS Marvin (Dread Unicorn Games)


Bill Carter
Darth Chronis



Lawrence Stewart

Gareth Hodges

Colin Backhurst
Christopher Metzger

Rachel Gumper


Mariah Thompson

Falk Alexander Glade
Johnathan Salter




Maggie Unkefer
Shawna Maryanovich






Wilhelm Fitzpatrick
Dylan “ExoByte” Mayo
Lynda Lee




Scott Carpenter



Charles D, Payet
Vince Rostkowski


Tim Brown
Raven Daegmorgan
Zak Brueckner


Christian Page

Adi Shavit


Steven Greenberg
Chuck Lunney



Adriel Bustamente

Natasha Anicich



Bram De Bie
Edward L






Gray Detrick
Robert


Sarah Russell

Sam Leavin

Abilash Pulicken

Isabel Olondriz
James Pierce
James Morrison


April Daniels



José Tremblay Champagne


Chris Edmonds

Hans & Maria Cummings
Bart Gasiewiski


Andy Chamard



Andrew Jackson

Christopher Wright



ichimonji10


Alan Stern
Alison W


Dag Henrik Bråtane





Martin Nilsson


William Schrade
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The Crackpot Index for Media Content

It was bound to happen eventually: my "crackpot index" has been adapted for use in news reporting. I like it!

But in case you missed the original, here it is:

The Crackpot Index

A simple method for rating potentially revolutionary contributions to physics:

1. A -5 point starting credit.

2. 1 point for every statement that is widely agreed on to be false.

3. 2 points for every statement that is clearly vacuous.

4. 3 points for every statement that is logically inconsistent.

5. 5 points for each such statement that is adhered to despite careful correction.

6. 5 points for using a thought experiment that contradicts the results of a widely accepted real experiment.

7. 5 points for each word in all capital letters (except for those with defective keyboards).

8. 5 points for each mention of "Einstien", "Hawkins" or "Feynmann".

9. 10 points for each claim that quantum mechanics is fundamentally misguided (without good evidence).

10. 10 points for pointing out that you have gone to school, as if this were evidence of sanity.

11. 10 points for beginning the description of your theory by saying how long you have been working on it. (10 more for emphasizing that you worked on your own.)

12. 10 points for mailing your theory to someone you don't know personally and asking them not to tell anyone else about it, for fear that your ideas will be stolen.

13. 10 points for offering prize money to anyone who proves and/or finds any flaws in your theory.

14. 10 points for each new term you invent and use without properly defining it.

15. 10 points for each statement along the lines of "I'm not good at math, but my theory is conceptually right, so all I need is for someone to express it in terms of equations".

16. 10 points for arguing that a current well-established theory is "only a theory", as if this were somehow a point against it.

17. 10 points for arguing that while a current well-established theory predicts phenomena correctly, it doesn't explain "why" they occur, or fails to provide a "mechanism".

18. 10 points for each favorable comparison of yourself to Einstein, or claim that special or general relativity are fundamentally misguided (without good evidence).

19. 10 points for claiming that your work is on the cutting edge of a "paradigm shift".

20. 20 points for emailing me and complaining about the crackpot index. (E.g., saying that it "suppresses original thinkers" or saying that I misspelled "Einstein" in item 8.)

21. 20 points for suggesting that you deserve a Nobel prize.

22. 20 points for each favorable comparison of yourself to Newton or claim that classical mechanics is fundamentally misguided (without good evidence).

23. 20 points for every use of science fiction works or myths as if they were fact.

24. 20 points for defending yourself by bringing up (real or imagined) ridicule accorded to your past theories.

25. 20 points for naming something after yourself. (E.g., talking about the "The Evans Field Equation" when your name happens to be Evans.)

26. 20 points for talking about how great your theory is, but never actually explaining it.

27. 20 points for each use of the phrase "hidebound reactionary".

28. 20 points for each use of the phrase "self-appointed defender of the orthodoxy".

29. 30 points for suggesting that a famous figure secretly disbelieved in a theory which he or she publicly supported. (E.g., that Feynman was a closet opponent of special relativity, as deduced by reading between the lines in his freshman physics textbooks.)

30. 30 points for suggesting that Einstein, in his later years, was groping his way towards the ideas you now advocate.

31. 30 points for claiming that your theories were developed by an extraterrestrial civilization (without good evidence).

32. 30 points for allusions to a delay in your work while you spent time in an asylum, or references to the psychiatrist who tried to talk you out of your theory.

33. 40 points for comparing those who argue against your ideas to Nazis, stormtroopers, or brownshirts.

34. 40 points for claiming that the "scientific establishment" is engaged in a "conspiracy" to prevent your work from gaining its well-deserved fame, or suchlike.

35. 40 points for comparing yourself to Galileo, suggesting that a modern-day Inquisition is hard at work on your case, and so on.

36. 40 points for claiming that when your theory is finally appreciated, present-day science will be seen for the sham it truly is. (30 more points for fantasizing about show trials in which scientists who mocked your theories will be forced to recant.)

37. 50 points for claiming you have a revolutionary theory but giving no concrete testable predictions.

http://math.ucr.edu/home/baez/crackpot.html

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Weird machines

At a workshop on cybersecurity at the Santa Fe Institute, I heard about the concept of weird machines. The description was poetic:

They hide in dark spaces — semantic gaps between levels of abstraction.

In short, they're not monsters like the Terminator here, but computer programs that do things you didn't think possible... because your way of thinking about a computer had gaps:

In computer security, the weird machine is a computational artifact where additional code execution can happen outside the original specification of the program. It is closely related to the concept of weird instructions, which are the building blocks of an exploit based on crafted input data. The functionality of the weird machine is invoked through unexpected inputs.

While expected, valid input activates the normal, intended functionality in a computer program, input that was unexpected by the program developer may activate unintended functionality. The weird machine consists of this unintended functionality that can be programmed with selected inputs in an exploit.

In a classical attack taking advantage of a stack buffer overflow, the input given to a vulnerable program is crafted and delivered so that it itself becomes executed as program code. However, if the data areas of the program memory have been protected so that they cannot be executed directly like this, the input may instead take the form of pointers into pieces of existing program code that then become executed in an unexpected order to generate the functionality of the exploit. These snippets of code that are used by the exploit are referred to as gadgets in the context of return-oriented programming.

Through interpretation of data as code, weird machine functionality that is by definition outside the original program specification can be reached also by Proof-Carrying Code, which has been formally proven to function in a certain specific way. This disparity is essentially caused by a disconnect between formal abstract modelling of a computer program and its real-world instance, which can be influenced by events that are not captured in the original abstraction, such as memory errors or power outages.

If you think about it, such things as viruses, prions and cancer also exploit gaps between a simplified abstract model of how organisms work, and the real world of chemistry with all its myriad possibilities.

For more, try this:

https://en.wikipedia.org/wiki/Weird_machine
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Trump gags the EPA

Trump has said he'll either get rid of the Environmental Protection Agency or leave "a little bit of it.” His nominee to run this agency, Scott Pruitt, is mainly famous for suing the EPA. More than 450 former EPA employees signed a letter to the Senate objecting to Pruitt.

But Pruitt seems sure to be confirmed tomorrow by Republicans in the Senate. In fact, the EPA is already being taken over by a "beachhead team" - that's a military term - set on destroying the agency:

The beachhead team is scaring agency employees into keeping quiet by holding closed-door meetings with small numbers of staff and giving them orders -- such as to begin removing climate-related information from the agency's website.

The team is reportedly not putting many orders in writing, so they cannot be sought later under the Freedom of Information Act, the source says. Also, the meetings are intentionally small so administration officials can identify staff if information is leaked.

Adding insult to injury, Trump is going to visit the EPA like a conquering warlord. Everyone at the EPA is wondering if they'll be forced to attend:

President Donald Trump's planned visit to EPA headquarters to sign executive orders scaling back the agency's climate change and other work is prompting questions about whether the president and Administrator-nominee Scott Pruitt might seek to require staff to attend, further deflating staffers' low morale.

One former EPA official asks, “Can Trump order EPA staff to be in the room?” The source says that career staff have been largely paralyzed by the Trump transition and beachhead teams, which imposed a communications freeze on headquarters officials, criticized agency scientists and hobbled work across program offices.

When Trump visited the CIA, he did not force anyone to attend his talk. Instead, he packed the first three rows of seats with people who cheered his remarks! They were not from the CIA.

Maybe he'll do this at the EPA, too.

Senate Democrats are trying to fight back with the limited tools at their disposal:

Senate Democrats are vowing strict oversight of Oklahoma Attorney General (AG) Scott Pruitt (R) after he wins confirmation as the next EPA administrator, warning his time as agency chief is not “going to end well” and drawing parallels with Reagan-era EPA Administrator Anne Gorsuch Buford, who was forced to resign in disgrace.

Gorsuch. Does that name sound familiar! Yes, her son is Trump's choice for the Supreme Court!

At a Feb. 16 press conference at the Capitol, several Democrats on the Senate Environment & Public Works Committee (EPW) vowed to drag out ongoing floor debate over Pruitt's nomination for as long as they could, up to 30 hours. Yet Pruitt is all but assured to win confirmation because no Republican except Sen. Susan Collins (ME) plans to vote against him, and the nominee also has the support of two moderate Democrats, Sens. Joe Manchin (WV) and Heidi Heitkamp (ND).

[...]

As a result, once Pruitt is confirmed, Democratic senators are planning multiple unspecified steps regarding litigation, ethics disclosure, and press inquiries that can “open things up quite a lot” to lawmakers' scrutiny, according to EPW member Sen. Sheldon Whitehouse (D-RI). He said Pruitt's record challenging EPA regulations is a massive conflict of interest for an administrator, adding his tenure leading the agency would not “end well.”

It will certainly not end well. The question is just who will suffer more: him, or us.

The quotes here are from Inside EPA. You can get a free month-long subscription here:

https://insideepa.com/

Get a front-row seat to the rape of our Earth by henchmen of the fossil fuel industry! At the Azimuth Climate Data Backup Project we are at least helping save the scientific data acquired by the EPA and other federal agencies. Impeaching Trump would help more.

The painting is by Steve Breen of the San Diego Union Tribune.

#climateaction
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The Trump Resistance Movement

Last Saturday hundreds of protesters showed up at a town hall meeting hosted by Tom McClintock. He's a Republican in the House of Representatives who ran for the California governorship in 2003 and lost, and ran for lieutenant governor in 2006 and lost again. He's too right-wing for most Californians. He did well in his district, a rural area near Nevada. But on Saturday so many protesters showed up that when the meeting ended, he left with a police escort.

Holding signs reading, "Resist," "No Muslim Ban, No War in Iran," "Protect Social Security," and "Do Your Job! Represent Us All!", the demonstrators turned up early at the event in Roseville, a conservative suburb north of Sacramento.

"I think we're on the wrong side of history right now," said Janine Allwright, who lives in McClintock's district. She came to the meeting with her 9-year-old daughter and said she's passionate about protecting refugees. "We're making decisions that will effect us for decades to come and I think it's wrong."

People upset over the election of Trump have repeatedly taken to the streets over issues like his immigration ban and flooded the U.S. Capitol with phone calls. With this protest at a Congressional town hall meeting, voters appear to be saying they won't limit their demonstrations to targeting leaders at the highest level of government.

The mood in the town hall was tense throughout the hour-long session. McClintock, who won re-election with 63 percent of the vote, was inundated with questions ranging his from support for a border wall to how he would help impeach the new president (54 percent of the district voted for Trump).

"I understand you do not like Donald Trump," McClintock said. "I sympathize with you. There have been elections where our side has lost."

His comment was met with jeers from the crowd, which wanted to talk about issues like Obamacare.

One of the town hall attendees, David Emerson, said his wife has a heart condition and they couldn't afford her medication without the Affordable Care Act.

"If you vote to cancel the ACA and you see her name in an obituary, shame on you," he told McClintock. The lawmaker responded that ACA must be replaced with something better for the majority of users.

This is just one of many protests that are making the news. For example, Trump's new Secretary of Education Betsy Devos knows nothing about public schools - she got the position by donating $200 million to Republicans. When she tried to visit a public school in DC yesterday, she was blocked by protesters:

http://www.cnn.com/2017/02/10/politics/devos-protest-at-washington-school/

I'm not in favor of physically blocking Trump employees from doing their jobs (she eventually snuck in another way), but I think it's excellent to let them know what we think at every possible opportunity!

On Thursday Jason Chaffetz got a taste of this. He's a Republican from Utah, and he's the head of the "House oversight committee", so he overlooks egregious conflicts of interest. He was booed by a rowdy crowd at his town hall meeting when he said the president was not subject to such laws:

http://talkingpointsmemo.com/livewire/hundreds-chaffetz-town-hall

Rep. Jason Chaffetz (R-UT) was confronted with hundreds of people at a town hall outside of Salt Lake City, Utah, on Thursday night, where the crowd jeered at the congressman and grilled him on investigating President Donald Trump.

The audience filled almost all of the 1,000 seats in the Brighton High School auditorium, and a crowd of about 1,500 people stood outside the event, according to the Salt Lake Tribune.

At one point during the town hall, members of the audience stood up and began to chant, "Do your job!"

Later Chaffetz claimed that the protestors had been paid. I doubt it. But it's not a coincidence that all those people showed up. We are organizing to attend town hall meetings, and I think that's a good thing. If you're interested, check out the Town Hall Project:

https://www.facebook.com/TownHallProject/

You don't have to join the dreaded Facebook to see this - click on "Not Now". And their actual list of upcoming town hall meetings is here:

http://bit.ly/2lfywFH

There are a bunch today and tomorrow!

This is just one of hundreds of ways people are resisting the craziness of the Trump administration. We need to keep it up - because pro-Trump commenters are still hoping the resistance will fade after a while.

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Gag reflex

The Trump gang is trying to gag scientists - make us shut up. But they're also making us gag, as shown below. So we're fighting back.

Some examples:

1) Scientists are keeping track of how Trump gang is changing the EPA website, with before-and-after photos, and analysis:

https://www.nrdc.org/onearth/behold-tweaks-trump-has-made-epa-website-far

There's more about "adaptation" to climate change, and less about how it's caused by carbon emissions.

2) The Trump gang is taking animal-welfare data offline. The US Department of Agriculture will no longer make lab inspection results and violations publicly available, citing privacy concerns:

http://www.nature.com/news/us-government-takes-animal-welfare-data-offline-1.21428

3) The Environmental Data and Governance Initiative is working to archive public environmental data. Go to a data rescue event:

Feb. 4th, NYC
Feb 10th-11th, Austin
Feb. 11th, San Francisco Bay
Feb. 18th, MIT
Feb. 18th, Haverford
Feb. 18-19th, Washington DC
Feb 26th, Twin Cities, Minnesota

or work with them to organize one of your own! They're developing online tools to help:

https://envirodatagov.org/

4) Less relevant, but too fun to ignore, is Operation "Kiss Our Asses, Release Your Taxes". Hundreds of people are planning to gather at 3:30 p.m. on Sunday, Feb. 12th and moon Trump Tower in Chicago - that is, aim their naked butts at it. The goal is to get Trump to release his tax returns.

I think people should do this each time he emits an offensive tweet.

5) A new bill would prevent the US government from providing access to geospatial data if it helps people understand housing discrimination. It goes like this:

Notwithstanding any other provision of law, no Federal funds may be used to design, build, maintain, utilize, or provide access to a Federal database of geospatial information on community racial disparities or disparities in access to affordable housing.

For the important ways this data has been used, see:

http://www.philly.com/philly/blogs/public_health/Where-will-data-take-the-Trump-administration-on-housing.html

6) The pushback is so big it's hard to list it all! For now I'll just quote some of Tabitha Powledge's article "The gag reflex: Trump info shutdowns at US science agencies, especially EPA".

THE PUSHBACK FROM SCIENCE HAS BEGUN

Predictably, counter-tweets claiming to come from rebellious employees at the EPA, the Forest Service, the USDA, and NASA sprang up immediately. At The Verge, Rich McCormick says there’s reason to believe these claims may be genuine, although none has yet been verified. A lovely head on this post: “On the internet, nobody knows if you’re a National Park.”

http://www.theverge.com/2017/1/26/14395642/twitter-accounts-rebelling-trump-federal-agencies-national-park

At Hit&Run, Ronald Bailey provides handles for several of these alt tweet streams, which he calls “the revolt of the permanent government.” (That’s a compliment.)

http://reason.com/blog/2017/01/26/trump-twitter-and-the-revolt-of-the-per2

Bailey argues, “with exception perhaps of some minor amount of national security intelligence, there is no good reason that any information, data, studies, and reports that federal agencies produce should be kept from the public and press. In any case, I will be following the Alt_Bureaucracy feeds for a while.”

NeuroDojo Zen Faulkes posted on how to demand that scientific societies show some backbone. “Ask yourself: “Have my professional societies done anything more political than say, ‘Please don’t cut funding?’” Will they fight?,” he asked.

http://neurodojo.blogspot.com/2017/01/asking-scientific-societies-to-show.html

Scientists associated with the group 500 Women Scientists donned lab coats and marched in DC as part of the Women’s March on Washington the day after Trump’s Inauguration, Robinson Meyer reported at the Atlantic. A wildlife ecologist from North Carolina told Meyer, “I just can’t believe we’re having to yell, ‘Science is real.’”

Taking a cue from how the Women’s March did its social media organizing, other scientists who want to set up a Washington march of their own have put together a closed Facebook group that claims more than 600,000 members, Kate Sheridan writes at STAT.

https://www.statnews.com/2017/01/25/science-march-washington/

The #ScienceMarch Twitter feed says a date for the march will be posted in a few days. The group also plans to release tools to help people interested in local marches coordinate their efforts and avoid duplication.

https://twitter.com/ScienceMarchDC

At The Atlantic, Ed Yong describes the political action committee 314Action. (314=the first three digits of pi.)

https://www.theatlantic.com/science/archive/2017/01/thanks-to-trump-scientists-are-planning-to-run-for-office/514229/

Among other political activities, it is holding a webinar on Pi Day – March 14 – to explain to scientists how to run for office. Yong calls 314Action the science version of Emily’s List, which helps pro-choice candidates run for office. 314Action says it is ready to connect potential candidate scientists with mentors–and donors.

http://www.314action.org/want-to-run/

Other groups may be willing to step in when government agencies wimp out. A few days before the Inauguration, the Centers for Disease Control and Prevention abruptly and with no explanation cancelled a 3-day meeting on the health effects of climate change scheduled for February. Scientists told Ars Technica’s Beth Mole that CDC has a history of running away from politicized issues.

https://arstechnica.com/science/2017/01/self-censoring-fears-swirl-as-cdc-abruptly-nixes-climate-and-health-summit/

One of the conference organizers from the American Public Health Association was quoted as saying nobody told the organizers to cancel.

I believe it. Just one more example of the chilling effect on global warming. In politics, once the Dear Leader’s wishes are known, some hirelings will rush to gratify them without being asked.

The APHA guy said they simply wanted to head off a potential last-minute cancellation. Yeah, I guess an anticipatory pre-cancellation would do that.

But then – Al Gore to the rescue! He is joining with a number of health groups–including the American Public Health Association–to hold a one-day meeting on the topic Feb 16 at the Carter Center in Atlanta, CDC’s home base. Vox’s Julia Belluz reports that it is not clear whether CDC officials will be part of the Gore rescue event.

http://www.vox.com/2017/1/26/14402234/cdc-climate-change-conference-al-gore-trump

For Tabitha Powledge's whole article go here:

http://blogs.plos.org/onscienceblogs/2017/01/27/the-gag-reflex-trump-info-shutdowns-at-us-science-agencies-especially-epa/

#climateaction

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Synthetic biology

I met some cool people this week, and here's one: Kate Adamala. She's a postdoc at the University of Minnesota. She creates artificial cells in the lab.

These aren't full-fledged cells that can reproduce and metabolize on their own. They're much simpler - but they're made from scratch, not from existing cells. She calls them protocells.

A typical protocell has some RNA inside a little membrane made of fatty acids. She can get the RNA to copy itself, and she can get different protocells to fuse, building more complicated systems from smaller parts.

My own career as a postdoc was much more boring! Kids these days are amazing. :-)

Here's a paper of hers:

• Kate Adamala and J.W. Szostak, Non-enzymatic template-directed RNA synthesis inside model protocells, Science 342 (2013) 1098-1100. Available at http://www.protobiology.org/reprints/Adamala_Szostak_Science_2013.pdf

Abstract. Efforts to recreate a prebiotically plausible protocell, in which RNA replication occurs within a fatty acid vesicle, have been stalled by the destabilizing effect of Mg2+ [magnesium ions] on fatty acid membranes. Here we report that the presence of citrate protects fatty acid membranes from the disruptive effects of high Mg2+ ion concentrations while allowing RNA copying to proceed, while also protecting single-stranded RNA from Mg2+-catalyzed degradation. This combination of properties has allowed us to demonstrate the chemical copying of RNA templates inside fatty acid vesicles,
which in turn allows for an increase in copying efficiency by bathing the vesicles in a continuously refreshed solution of activated nucleotides.

Though it's one of the most recent on her website, this paper is not so new; she's doing even cooler stuff these days. Check out her work here:

http://www.protobiology.org/index.php

and in her talk.


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Biology as information dynamics

I'm at the Beyond Center in Phoenix Arizona - a center devoted to understanding the origin of life. They're having a workshop on whether biological complexity can be measured in a quantitative way.

Why? One reason is that NASA plans an $800-million mission to Enceladus, to see if there's life lurking in the underground oceans of this moon of Saturn. How can they actually detect life if they see it? That's a hard question. I just heard a talk about this by Chris McKay. They're going to look at stuff like the abundances of amino acids, which are very different on Earth than on meteorites. But there's not enough theory about how this should work for life on another planet!

There's also something else, even more exciting to me: developing a mathematical theory of living systems. Some other talks will touch on that, including mine here:

• Biology as information dynamics, https://johncarlosbaez.wordpress.com/2017/01/31/biology-as-information-dynamics/

The idea is if biology is the study of self-replicating entities, and if information is important in biology, we should look at how information theory is connected to the replicator equation — a very simple model of population dynamics for self-replicating entities. In this model, the population of each kind of self-replicating entity grows at a rate equal to its population times its fitness. But its fitness can be any function of the populations of each kind of entity.

There are some nice results connecting the replicator equation to information theory. The relevant concept of information turns out to be the information of one probability distribution relative to another. This is called relative information, or often the Kullback–Leibler divergence - a term I hate, because it's completely undescriptive, and it hides the importance of the actual idea.

What's the idea? It's this: when you learn something, how much information you get some depends on what you believed before!

Using relative information we can get a new outlook on free energy, see evolution as a learning process, and give a clean general formulation of Fisher’s fundamental theorem of natural selection.

I had a lot of trouble understanding Fisher's fundamental theorem until I reformulated it. In rough terms, his theorem says:

“The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time."

or a bit more precisely:

“The rate of increase in the mean fitness of any organism at any time ascribable to natural selection acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time."

But there are a lot of assumptions required to prove this result, and there are lots of situations where those assumptions don't hold. My version, which is more general and incredibly easy to prove, says exactly this:

" If a population evolves according to the replicator equation, the square of the rate at which the population learns information equals the variance of its fitness."

You can see an explanation on my blog:

• Information geometry (part 16), https://johncarlosbaez.wordpress.com/2017/02/01/information-geometry-part-16/

The idea of "the rate of learning information" is made precise using the Fisher information metric - a way to measure distances between probability distributions, closely related to relative information. I explain this concept in my talk, and in more detail in my blog article.

Back to the talks! Now Kate Adamala is talking about her attempts to synthesize chemical systems that act a bit like life... but simpler. Her talk is called "Alive but not life".

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Cracks in the rule of law

+Yonatan Zunger put his finger on what's really disturbing about today's news: the breakdown of the rule of law as the Department of Homeland Security flagrantly violates the orders of Federal judges... and somewhat hidden by the chaos, the elevation of Steve Bannon to the Principals Committee of the National Security Council. Yes, Bannon - the guy who said this:

“Lenin wanted to destroy the state, and that’s my goal too. I want to bring everything crashing down, and destroy all of today’s establishment.”

You should always try to look behind the crazy new stories that Trump creates, to see what's going on more quietly. Trump is not dumb. He may seem dumb, but he would not be bossing all of us around if he were dumb. When we make fun of him we may temporarily feel we're winning... but so far, we're losing.

We need to get serious. If we let him get away with violating the orders of Federal judges, there's no telling what he'll do. Phone your senators and representatives - it's more of a pain than sending emails or playing around on social media, but that's exactly why it works. This website makes it easy:

https://www.5calls.org/

Next I'll quote Yonatan - if you didn't read his whole post, please read this!

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Some updates on the political situation. Everything is very preliminary right now, because it's (apparently deliberately) unclear.

Several Federal judges have issued stays against the "Muslim ban" order. However, there are confirmed reports from multiple sources that Customs & Border Patrol (CBP, part of the DHS) is willfully disregarding those stays, denying access to counsel, moving the people they're holding to undisclosed locations so that nobody can get habeas corpus, and deporting people. This is very certainly not a local commander's decision; it goes up to the Sec'y of HS at least, and directly to Trump at most.

But – and here's the kicker – it's incredibly unclear what the scope of this refusal is. There's no clear news coming out, and we're getting more useful reports from the Twitter feeds of top attorneys in the field (both from groups like the ACLU, who have done heroic work tonight, and from attorneys at top firms, who have been joining this pro bono) than we are from anywhere else.

If this is a refusal of unambiguous Federal court orders, then this is serious, serious beyond the scale of anything we've seen in our lifetimes: it's DHS saying that if Trump tells them to do one thing and the courts another, they will do what Trump says and best of luck to the courts trying to enforce that. Which is to say, they're establishing a precedent that DHS actions are not subject to any sort of court review, or to anything other than the personal fiat of Trump – including their right to detain people, deport them, or hold them incommunicado.

Alternatively, this might be something else, a decision by CBP counsel that certain court orders don't apply to certain cases; this is serious too, since they're trying to create "facts on the ground" faster than the courts can react, but it doesn't mean a wholesale rejection of the system of law. I simply don't have enough information yet, and hope to update as we know more.

Separately, there was another story today: Trump reorganized the National Security Counsel. The two most prominent changes are this: Steve Bannon now has a seat on it, and the Director of National Intelligence and the Chairman of the Joint Chiefs of Staff were both demoted: they only attend meetings of the Principals Committee which "[pertain] to their responsibilities and expertise."

(The other full members of the PC, incidentally, are the secretaries of State (Tillerson), Treasury (Szubin), Defense (Mattis), and Homeland Security (Kelly), the AG (Sessions), the President's Chief of Staff (Priebus), the National Security Advisor (Flynn), and the Homeland Security Advisor (Bossert). You can read the full order here: https://www.whitehouse.gov/the-press-office/2017/01/28/presidential-memorandum-organization-national-security-council-and)

The demotion of the DNI and CJCS is surprising and I don't yet know what it means. There currently is no DNI – Coats' nomination is yet to be confirmed. It's hard to imagine what meetings wouldn't pertain to their "responsibilities and expertise," especially given that secretaries with much more specific responsibilities (like Treasury) weren't demoted. Bannon's promotion, however, is more significant: Trump is known for not attending many meetings, and delegating those, and Bannon is likely to be his principal representative in the NSC.

My gut read is that this is something which will prove very important in the long run. Trump's rift with the existing military and intelligence establishments is well-known, and he's made numerous statements, directly and through surrogates, about his interest in constructing alternative establishments reporting directly to him. Bannon would be a logical person to manage that subchain, as his "Chief Strategist" role doesn't come with a large org to manage already, or with Congressionally mandated restrictions. That would be the skeleton of a new internal security system, with the DHS and FBI (both very loyal to Trump) in the loop, together with a new private "security force" rolling up to Keith Schiller that takes over a lot of Secret Service roles, and a hypothetical new intelligence force, with Bannon being either de facto or de jure in charge of all the new organizations, and little to no legal supervision over them.

It's not clear, again, that this is where it's going, but it's definitely the configuration I would keep my eyes open for. It would promote Bannon from a Goebbels to a Himmler, which I suspect he would be just fine with.

So: Many signs out there, but nothing clear yet. These could range from incredibly serious to passing things, depending on how the next week or so plays out.

Update (00:51 PST): The DHS has put out an official statement, and I'll be damned if I can figure out what it means. It starts out by saying that they will continue to enforce all of Trump's orders, and that the orders remain in place, but it does offer a nod (later on) to complying with judicial orders.

Text here: https://www.dhs.gov/news/2017/01/29/department-homeland-security-response-recent-litigation

Update (02:06 PST): The Washington Post's story pulls together a range of official statements, which make it clear that this is deliberate and central policy, ordered personally by Trump. The exact meaning of the DHS statement remains unclear, but most people are reading it as an intent to continue to do whatever they want; it may involve a suggestion that if they don't want to grant a waiver to someone with a green card, they may do it by simply revoking the green card on the spot.

https://www.washingtonpost.com/local/social-issues/refugees-detained-at-us-airports-challenge-trumps-executive-order/2017/01/28/e69501a2-e562-11e6-a547-5fb9411d332c_story.html?hpid=hp_hp-top-table-main_airports-1046am%3Ahomepage%2Fstory&utm_term=.560b5a336b45

Update (07:55 PST): Sources confirming that DHS lawyers had flagged the banning of legal permanent residents as illegal ahead of time, but were specifically overruled by Bannon. Note the implications both for the deliberacy of the act and for the extent of Bannon's power. Also, Priebus confirmed on "Meet the Press" that the omission of Jews from the Holocaust Remembrance Day statement was deliberate and is not regretted.

http://www.rawstory.com/2017/01/steve-bannon-personally-overruled-dhs-decision-not-to-include-green-card-holders-in-travel-ban-cnn/


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Check out +Greg Egan's posts on G+!

I haven't been in the mood for posting fun articles on math and science - the situation in the US is so disastrous that it feels like "fiddling while Rome burns". I actually feel better working on the Azimuth Backup Project, trying to save climate data. It may not be much, but at least I feel I'm doing something, and I'm meeting lots of great people who are eager to donate their time and money for this cause.

Anyway, if you like articles on math and science, I urge you to add +Greg Egan to your circles. And if you haven't yet, read some of his fiction! 
Honeycomb mist

I recently started converting a number of the Java applets on my web site to JavaScript, in part because the ever-more-dire security warnings that both web browsers and Java itself throws at the user make it seem like a dangerous thing to enable, even though I've signed all my applets and made sure that they run in a sandboxed mode where they can't actually do anything mischievous (unless Java, or the browser, is broken ... but then, if there are bugs in the browser they're just as likely to be exploited by malicious JavaScript as by malicious Java).

Anyway, the point of this post is not to moan about the War Against Java, but to point out a nice method I stumbled on for generating an endless fractal texture, which could be used for such things as the elevation in a procedurally-generated landscape.

In the particular applet I was converting to JavaScript, I wanted an endlessly rising "curtain" of mist. The old method I was using generated this by means of a large number of linear "fault lines" that criss-crossed the view: as you crossed each fault line, the density of the mist would either rise or fall, and with a sufficient number the density takes on a fractal texture.

But it's hard to ensure that the eye won't pick up some lingering linear edges in the final density, and the problem actually becomes more acute the more individual shades of grey you render. So, I went looking for another way of doing this.

The method I ended up using was devised by Benoit Mandelbrot, no less, and I read about it in Appendix A of The Science of Fractal Images, edited by Peitgen and Saupe. The idea is to start with a tiling of the plane by hexagons of some maximum size, and then to repeatedly subdivide them, with each step replacing every hexagon with three smaller ones, as in the image. To get a fractal density from this, you first assign random densities to all the vertices of the largest hexagons, and then the extra vertices added at each subdivision are assigned averages of the surrounding points, plus a random offset.

You can do something similar with a process that subdivides a square grid, but that suffers from exactly the kind of linear artifacts that I was trying to avoid. By using a hexagonal subdivision, the artifacts themselves become fractals, like the boundaries of the multiply-subdivided hexagon, and so they look much more like a natural part of the texture.

Of course, when it comes to actually programming this, you don't want to construct any hexagons as such, but to work with lattices of points in which the geometrical relationships can be expressed as arithmetic relationships between the lattice coordinates. Because the density in the points you want to render can ultimately depend on values at hexagon vertices that lie far off-screen, rather than constructing a uniform lattice for the entire territory that needs to be covered in some way, it's more memory-efficient to work with a separate lattice for each level, so the coarsest lattices can span a lot of ground, geometrically, with just a few points, and the finer ones come close to just spanning the rendered region.

If the lattice points are stored according to their coordinates in a suitable basis, the whole thing can be "scrolled" quite efficiently, to allow for an endlessly rising curtain: when you move past the end of the lattice data used for the initial image, you just wrap to the beginning of the same array and overwrite the old values that are no longer needed.

The JavaScript applet that uses this method can be seen here:

http://www.gregegan.net/HORROR/Horror.html

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