Visualizing a complex connected network: lessons from E. Coli gene transfer

The Loom's "Festooning The Tree Of Life" tells how biologists have visually represented the history of E. Coli gene transfer. It's an example of "scientific visualization" and knowledge representation that belongs to any class or course on visualization and representation -- not to mention a future Tufte book.

Kafka's FBI Watch List over 1 million, grows 20,000 a month ...

Via FMH, the ACLU estimates the GOP/FBI "terrorist" Watch List (aka "the watchlist") has topped 1 million (ACLU estimate). It grows by 20,000 names a month, and it seemingly never shrinks. The ACLU provides a handy the counter and a form to complete if you've been harmed by the Watch List (typically extended inspection when flying).

The watch list is a corollary to the worthless no fly list. There used to be a TSA form to ask for removal from the no fly list, but the old link doesn't work any more. More recently the Traveler Redress Inquiry Program (TRIP) appeal program was recently reviewed by MSNBC (emphases mine):

... As of January 2008, some 24,000 people had used TRIP to appeal their inclusion on the lists. The TSA hasn’t revealed how many applicants have been officially cleared or whether clearance has actually resulted in no-hassle flying. Anecdotal reports from frequent fliers maintain that many travelers who were told they were cleared continue to be stopped in airports. 

The TSA press office in Washington, D.C. declined to take questions about TRIP from an Aviation.com writer, referring the writer to TSA spokesman Nico Melendez in Southern California. Melendez didn’t return the reporter’s telephone call or reply by e-mail for this story. 

In past years, TSA spokespeople suggested that aggrieved travelers contact the TSA ombudsman to set things right, but TRIP has largely superseded the earlier procedure. Perhaps that’s for the best, as the TSA ombudsman’s office has received scathingly bad reviews from TSA employees, as related by a report made public in late June by the Inspector General of the Department of Homeland Security. Complaining of poor training and tone-deaf management, some 20 percent of TSA screeners quit their jobs last year. 

As it stands, TRIP consists mainly of an online form. Travelers who want to tap into TRIP should go to the TSA’s Web site, look for the "Resource Center" section on the right-hand side of the page and follow the prompts...

Physicians would recognize the Watch List as one of those stupid lab tests that come out every few years claiming to find some nasty cancer, but ends up sending vast numbers of healthy people for misguided surgical procedures.

It's another Cheney/Bush legacy that Bush III (McCain) will institutionalize.

The ACLU's response is rational and similar to regulations for cleansing credit reports ...

• due process
• a right to access and challenge data upon which listing is based
• tight criteria for adding names to the lists
• rigorous procedures for updating and cleansing names from the lists.

Of course if the FBI actually followed those rules the list would be revealed as a worthless waste of money and a source of security-reducing noise.

The ACLU is doing good work. I should donate to them. Problem is, I've done that before. The ACLU has their own version of a "watch list" -- it's their "donor list". They use it to generate killer levels of paper spam (junk mail), and they sell it widely. I need a way to send plain unmarked bills to the ACLU so they can't spam me. Ideas?

See also:

• How worthless is the no fly list: 20,000:0 false to true positive (links to prior posts from 2004 to 2007)
• Link to a classic Morford rant
  

Update 7/21/08: Schneier has a review, with links to notabob's basic predictive value analysis:

... We match (50 + 6) / (444 + 50 + 6) = 11.2% of terrorists using this scheme. 

Of the people matched, (50 + 6) / (990,000 + 50 + 6) = 0.006% are terrorists. Put another way, 99.994% of all people matched are innocent...

In medicine, this is what's known as a "worse than useless test". Lousy sensitivity, impossibly miserable specificity.

This is why I want to stop teaching calculus in high school, and make basic probability a requirement for graduation. Heck, it will come in handy at the Casino at least.

If the FBI's matcher were a lab test, it would never be approved for use.

If McCain gets in this will never go away.

The core of Al Gore's energy proposal is a carbon tax

When even John McCain tries to sound like he's agreeing with Al Gore, you wonder if my favorite ex-politician isn't on to something.

In the middle of his energy speech is the key proposal:

The (Annotated) Gore Energy Speech - Dot Earth - Climate Change and Sustainability - New York Times Blog

...I have long supported a sharp reduction in payroll taxes with the difference made up in CO2 taxes. We should tax what we burn, not what we earn...

Yep, that's the ticket.

It means gas prices don't go down though, and the price of electricity goes way up.

This is going to take a culture change comparable to what we need to reform America's lousy human development score.

If you have to tear off the top floor to add a new bathroom, you might as well add a new bedroom too. We need to do both changes together.

The MobileMe iPhone - Microsoft, I miss you!

So I'm looking at the entrails of MobileMess, and I'm thinking ... this is hopeless. No tasks. No notes. Weak synchronization. Broken stuff everywhere. No import or export in OS X iCal ...

In my heart I know Apple hates people like me. Dull people with complicated lives who need to get lots of dull stuff done.

Google doesn't like dull stuff either. They're all young; they hate old, complicated lives.

I understand, when I was young I could write my To Do list on a single piece of notepaper too. I remember when 35 items was a lot to do. Sometimes I miss those days.

I need a vendor who likes dull people with complicated lives. A vendor who'd create something like Outlook ... or Entourage ...

A vendor like Microsoft ...

Help and How-To for Microsoft for Mac Office Products | Mactopia

....By using Sync Services, you can synchronize your Entourage contacts and calendar events with an iPod, iPod touch, or iPhone.

Sync Services is a central database on your Macintosh computer that keeps track of programs and devices that share information. After synchronizing an Entourage address book and calendar with Sync Services, the information is also synchronized with your Macintosh Address Book and iCal. Then you can use iTunes to synchronize the information with your iPod or iPhone...

Sure, that's the ticket! Microsoft could create a Task and Notes app for the iPhone, and sync with Entourage and Outlook ...

Oh, wait. Microsoft isn't developing for the iPhone.

Hell has frozen over.

I miss Microsoft.

Jon Udell's Interviews with Innovators: Evernote as Memex

Among Jon Udell*'s Interviews with Innovators is this one with Evernote's Phil Lubin ...

... Phil Libin was the CEO of CoreStreet when he appeared as the first guest on Interviews with Innovators. Now he's back as CEO of EverNote, a company that aims to build the memex, or personal outboard memory, that Vannevar Bush famously imagined in his 1945 article "As We May Think."...

I criticized Evernote recently for a 'complete fail' on the first test I apply to anything that will manage my extended memory -- can I move the data ...

Gordon's Tech: Evernote fails the critical software as service import/export test

...So Evernote is not an option for my Palm to iPhone conversion, and I'd say it's not an option for anyone on any platform until they demonstrate Data Freedom...

Phil Libin responded in a comment:

Data Freedom is vital to our plans. We're serious about Evernote as an "external brain" and that means users have to have confidence that their memories will always be accessible. Part of that accessibility is making sure that users can import/export Evernote data in standard formats with no restrictions. Our current limitations on import/export capabilities are due to developer resource constraints, not any philosophical or business reasons; we can't afford to do import/export poorly because that could muck with your data and flood our support lines. Doing it well takes time.

We're currently testing a full set of Evernote APIs that will give people a lot of options for getting data in and out. We'll roll these out publicly later in the summer. We'll also be expanding the structured import/export capabilities on the local clients, though I don't have a specific date on that yet. We're doing this because data freedom is good for more than just peace of mind - it'll let us build lots of great functionality that we couldn't accomplish with a "walled garden" approach.

Now that I know Evernote is explicitly targeting the Memex/Xanadu vision, I'm even more interested in the product/service -- but I'm also even more demanding.

Even if I trust Mr. Libin completely after listening to the interview with Jon, it's too risky for me to adopt Evernote without a demonstrated, working, export capability. Heck, Evernote could be acquired tomorrow and Mr. Libin could retire the next day! The new owner might be more enchanted with customer lock-in than with changing the world.

Realistically, of course, almost nobody but me is really going to worry about this prior to signing up. Evernote would be silly to divert resources to accelerate import/export -- it's far more important for their market that they enhance the iPhone client.

I'm just sorry I won't get to play with them until they have an export tool. I'll be watching closely though ...

* I'm a longtime fan of Jon Udell's, and I recently had the pleasure of chatting with him. Oddly enough, he sounds exactly the way I'm imagined.

We suck. Lessons from the American Human Development Report

We rank 42nd for life expectancy, 12th for human development. More people in prison. Crummiest educational system. For example:

BBC NEWS | Americas | US slips down development index

...If the US infant mortality rate were equal to first-ranked Sweden, more than 20,000 babies would survive beyond their first year of life...

Most powerful army though, so we could always conquer Sweden and improve our numbers. Heck, last time I looked my Canadian homeland could probably be taken by the National Guard.

Thank heavens for Russia, we're probably ahead of them.

This is a deep hole. We have a cultural problem here that will take generations to fix.

A part of the fix will be to develop a political system with two respectable alternatives. That means getting the GOP out of power completely so it can reform itself or be replaced by another, healthier, party.

Please stop using videos for documentation. Please.

Explore Google Maps is supposed to let me learn about how to edit location descriptions, add content, etc.

It's all video.

The video for adding a location is very short. It consists entirely of "We're sorry, this video is no longer available".

What's with all the #$!$ video? I admit, a brief screencast can work very well, but these take way too long to load and view. A few words would be much less trouble to prepare and update, more reliable (see above), and it would be much faster and easier to process. Not to mention that words can be indexed (hint for Google - I thought you did search?).

There's a mania now for video display. I haven't seen this noted anywhere, nor have I seen any explanation of why video has taken over. (Yeah, sure, we all think it's the fault of those dang-gummed video games.)

I'm hoping it's a silly fad, and that we'll eventually settle down to a more appropriate mixture of text and screencasts.

The view from 2000 - really, we can stop now

The K Chronicles looks forward from 2000. When you put it all together like that, it's no wonder we're tired. (PS. K did get married and he and his wife have one son.)

Even the jihadi are getting tired.

I can't imagine getting away from the Bush regime. In my bones I feel the US will elect Bush III (aka McCain). If, by a miracle, Obama does win ... well, it will be like awakening from a long nightmare.

Full text search and digital prostheses: new email, new mind

I'm preparing to do an internal corporate presentation on email management in the world of full text search (Windows Search 4.0, specifically).

It's a fun topic. I'll get to revise my Beating Email and GTD with full text search posts for one. More importantly, I get to think about how the purpose of my email has changed.

It used to be I sent email to the person on the To: line, and maybe to a small, carefully selected, group on the CC line.

That's still true, but there's a new recipient for every email -- my future self. The message is an encapsulated bit of knowledge about people, time, subject, body and, sometimes, tags. The subject line describes the message and tasks for my recipients, but it also supports future retrieval and interpretation.

I've been doing this for years now, and I'm getting better at writing for the current and future audiences. I put in a small amount of extra context -- maybe not necessary for the moment, but invaluable for far future interpretation. Every subject line is considered in terms of future selection. "Tomorrow" becomes a specific date, keywords are worked into the description, I clean up mail threads to make them more useful on retrieval, I make subject lines unique. Every month I add a new tweak of one kind or another.

So now my email is still a message, but it's also a post into multi-GB knowledge base. It's becoming a core part of my memory.

That's where the curious bit happens. I said I've been doing this for a while.

It's changing the way my mind works. A lot of what used to reside in my head now lives only in the repository. My head is full of pointers, references, retrieval strategies, tags and fragments, but it's not so solid as it was. When I have the repository I have a far better memory than I've ever had, but when I don't have it I feel partly disabled.

Maybe I'm more susceptible to this than most -- I've always had an associative graph memory rather than a structured hierarchy. I suspect I'm not alone in my increasing reliance on digital prostheses however.

New abilities, but also new dependencies.

Interesting.

PS. Thanks to Jon U for stimulating my thoughts on this topic.

A critique of Congress - and a defense

On the one hand, I thought the 9% approval rating for Congress was absurd. The Democratic Senate has blocked a lot of harm, and started the multi-decade cleanup that may continue if Obama is elected. Since the Dems need some GOP support to get by filibusters and a Bush veto, the scope for action is necessarily limited.

On the other hand, this critique is interesting ...

Congressional Do's and Don't Do's | Britannica Blog

A recent poll of Americans turned up the fact that just nine percent approve of the job the present Congress has been doing...

I consulted the online calendar of the House of Representatives for the day I write this, Friday, July 11, and found that the House was in recess. They’ll be back to work on Monday, they promise, though not until 12:30 in the afternoon. The day before, it seems that the bulk of the day was spent discussing the creation of a new historic trail commemorating something from the Revolutionary War. A bit of time was given over to congratulating NASA for some anniversary, and some more time to something to do with flood insurance. Heady and very patriotic stuff, to be sure.

Over in the Senate, David Vitter – he whose phone number somehow got into the hands of the so-called “D.C. Madame” – and Larry Craig – he of the unfortunate “wide stance” in men’s rooms – are cosponsoring a “Marriage Protection Amendment” to the Constitution. Mere ridicule fails before such gall. I doubt that even that master of political shiv work, Mort Sahl, could have adequately satirized these two buffoons...

... Now, it’s unfair, I know, to criticize on the basis of one day’s record of floor proceedings in the House. There are committee hearings – on major league baseball, for example – and staff work and constituent assistance and such things going on in the background. And fund-raising, Lord knows. My local newspaper carries a report on the recent activities of our congresspersons which can be summarized thus: No sweat.

So let’s go to the tape:

• Health care: Nothing
• Social Security: Nada
• Energy policy: Zip
• Immigration: Bupkes
• Earmarks: You kidding?

It could be argued that we the citizenry are actually better off for congressional inaction. This might well be true but for the fact that inaction now simply leaves in place the bad policies already on the books. Having mandated that gasoline contain a certain proportion of ethanol, for example, certainly counts as a stab at an energy policy, while forbidding the import of cheap sugar-based ethanol in favor of the domestic kind, which drives up the price of corn and myriad other corn-based food and non-food products, counts as reelection-inspired stupid policy.

Know what Congress is really good at? Creating federal crimes...

It's an interesting list of inactive topics. Here's my take at why nothing can happen, and as usual the fault is not Congress. In fact, it's not even all the GOP's fault. The fault lies in us:

• Health care: Dems can't override a Bush veto. So nothing can happen here. Real reform will either increase taxes or redistribute costs among health care consumers, so it can only be done at the start of year one of a 2nd Obama term. (Seriously, real reform is at least that far away. America is not ready for how much this will hurt. The fault is ours.)
  
• Social Security: Social security needs important tweaks, not an overhaul. Health care is the problem. The author has bought into Bush propaganda. Invest in dementia prevention research.
  
• Energy policy: The Bush problem, again. This could improve in year one of a first Obama term.
  
• Immigration: Too close to an election, and we need much more national discussion. This will get addressed after the election, no matter who wins.
• Earmarks: Voters love them. We're the problem, not Congress.
  

Schneier: The Chinese Hacker Explained

[via James Fallows]

One of the disadvantages of time spent with very good science fiction writers is a persistent sense of deja-vu. I feel I read this story in Gibson's Neuromancer 24 years ago [1]:

My Take : Discovery Channel - Bruce Schneier

... These hacker groups seem not to be working for the Chinese government. They don't seem to be coordinated by the Chinese military. They're basically young, male, patriotic Chinese citizens, trying to demonstrate that they're just as good as everyone else. As well as the American networks the media likes to talk about, their targets also include pro-Tibet, pro-Taiwan, Falun Gong and pro-Uyghur sites.

The hackers are in this for two reasons: fame and glory, and an attempt to make a living. The fame and glory comes from their nationalistic goals. Some of these hackers are heroes in China. They're upholding the country's honor against both anti-Chinese forces like the pro-Tibet movement and larger forces like the United States.

And the money comes from several sources. The groups sell owned computers, malware services, and data they steal on the black market. They sell hacker tools and videos to others wanting to play. They even sell T-shirts, hats and other merchandise on their Web sites.

This is not to say that the Chinese military ignores the hacker groups within their country. Certainly the Chinese government knows the leaders of the hacker movement and chooses to look the other way. They probably buy stolen intelligence from these hackers. They probably recruit for their own organizations from this self-selecting pool of experienced hacking experts. They certainly learn from the hackers...

Essential reading. Schneier is a fellow Minnesotan, btw.

Mercifully, these young men don't have Macs.

[1] BTW, as Gibson points out, there are no cell phones in Neuromancer -- or Idoru for that matter. It's very hard to write predictive near future science fiction. Of course in Heinlein's "Citizen of the Galaxy", which was really science fantasy/space opera, computer output is on paper strips ...

Google's development handicap: worldwide support

I get frustrated because of things like Google's broken Outlook synchronization, or their non-existent task/calendar integration, or a dozen other things I'd like to see them do with gCal and, even more, with Google Apps.

What do they do with their time and money?

Well, among other things, they deal with the consequences of a worldwide customer base:

The official update feed from the Google Apps team: Google Calendar adds support for 8 new languages

.... Google Calendar now supports Google Calendar now supports US English, UK English, French, Italian, German, Spanish, Danish, Dutch, Norwegian, Finnish, Swedish, Russian, Chinese (Simplified), Chinese (Traditional), Hindi, Indonesian, Korean, Japanese, Thai, Filipino/Tagalog, Portuguese (Brazil), Portuguese (Portugal), Turkish, Hungarian, Serbian, Ukrainian, Bulgarian, Latvian, Romanian, Lithuanian, Slovenian and Polish...

Language support is feature 0 for most users (excluding the Dutch, who all speak and write six languages from birth). On the other hand, a port to Chinese doesn't get my Outlook 2003 sync working.

Obviously, Google needs to do this work. A port to Chinese is a thousand times more important in terms of human value and Google's future than fixing Outlook Calendar sync.

It is interesting though, to consider the consequences of having a worldwide support task. It suggests new features will be deployed with increasing care and deliberation - no matter how much development money is available. Software development does not scale linearly with resources, as Microsoft has amply shown. At some point a extra billion dollars buys only a small increment in functional improvement.

I wonder if Google's global burden will open opportunities for less constrained competitors...

The rights of non-man

A mildly incoherent essay appeared in the NYT recently. The topic was the relative rights of different classes of human people, and the extension of some of those rights to non-human people.

First some excerpts that are more coherent than the original, then some history of my own ...

Ideas and Trends - When Human Rights Extend to Nonhumans - NYTimes.com

... the environment committee of the Spanish Parliament last month to grant limited rights to our closest biological relatives, the great apes — chimpanzees, bonobos, gorillas and orangutans.

The committee would bind Spain to the principles of the Great Ape Project, which points to apes’ human qualities, including the ability to feel fear and happiness, create tools, use languages, remember the past and plan the future...

If the bill passes — the news agency Reuters predicts it will — it would become illegal in Spain to kill apes except in self-defense. Torture, including in medical experiments, and arbitrary imprisonment, including for circuses or films, would be forbidden.

The 300 apes in Spanish zoos would not be freed, but better conditions would be mandated...

... Mr. Singer ... left out lesser apes like gibbons because scientific evidence of human qualities is weaker, and he demanded only rights that he felt all humans were usually offered, such as freedom from torture — rather than, say, rights to education or medical care.

... even in democracies, the law accords diminished rights to many humans: children, prisoners, the insane, the senile. Teenagers may not vote, philosophers who slip into dementia may be lashed to their beds, courts can order surgery or force-feeding.

Spain does not envision endowing apes with all rights: to drive, to bear arms and so on. Rather, their status would be akin to that of children.

... Spain’s Catholic bishops attacked the vote as undermining a divine will that placed humans above animals. One said such thinking led to abortion, euthanasia and ethnic cleansing...

If we're still around fifty years from now, this will be an obscure event on a history exam, with the context of "of course this is obvious".

It's a more than mildly interesting question.

Eons ago I wrote an ambitious essay for a philosophy class; I attempted to create a species-neutral mechanism for assigning rights and privileges. Every scheme I came up with, and those I've read since, had uncomfortable consequences. It wasn't merely that one ended up giving lesser rights to my species than to better behaved robots and aliens, the rights of many impaired humans overlapped with not only apes, but also cats, dogs and squirrels.

In a later medical school essay I accepted the inevitable, and wrote that all ethical systems are merely post-hoc explanatory frameworks for enforcing and extending biologically and culturally evolved mores. The species-specific assignment of rights then is not a challenge to reason, it's merely politics.

Still. Many things that were once accepted mores are now despised. Even the homophobia of my youthful culture is passing into the night.

We know the road we're going down. If our civilization survives, sometime in the next century we'll grow our protein from tissue cultures, not from animals.

Franklin quote: new to me

Lessons in Love, by Way of Economics - NYTimes.com: "Ben Franklin summed it up well. In times of stress, the three best things to have are an old dog, an old wife and ready money."

Emily laughed, so maybe it's safe to post.

Unintended consequences: medication co-pays and combination therapy

In the course of a board review program I've been reviewing ten years of medication development ...

Gordon's Notes: Family Medicine Board Review from the AAFP, ABFM and free - with podcasts

... I've long had an information-geek's admiration for the printed version of Monthly Prescribing Reference. Despite its evil ad-funded roots, there's a real genius to the density and layout of the content, refined by generations of customer feedback. It also has the virtue (and sin) of being always topical and exceedingly brief.

So I started my review by reading this cover to cover. Each time I come across a medication that's new to me, or a familiar one that unlocks a domain of forgotten knowledge, I add it to my core med review sheet. This sheet is also an interesting overview of what's changed in medicine over the past decade. There was more activity in the treatment of Parkinson's Disease, for example, than I would have guessed...

Other than observing the desperate attempts to find something Tumor Necrosis Factor inhibitors are good for, I was struck by the explosion of combination meds.

What explains this? Is it patient demand? Is it pharma desperation due to a shrinking development pipeline?

It was Emily who suggested a motivation that could explain the development all by itself.

Medication co-pays.

The most common co-pay schemes strongly incent patients to minimize the number of their chronic prescriptions, with much less incentive to minimize the cost of prescriptions. On the other hand, combination meds are very profitable for pharmaceutical companies.

I suspect the payors who designed co-pay schemes didn't have have these outcomes in mind.