Fairhaven, The River

Aviation News

Today's Aviation Week had three relevant articles.

1. Another article on upgrading aircraft to use digital telemetry, GPS, etc.  This time it was discussion of the steps that Delta is taking with some of their aircraft.  Nothing new or radical is reported.  It's just another article how to upgrade at reduced cost.  Long term (assuming the FAA mis-managers don't completely ruin things) the digital upgrades should reduce fuel use, air pollution, noise pollution, and flight times.  Switching from voice to text messaging makes sense for all the routine flight control.  There are two pilots and messaging doesn't interfere with flying the way it does with driving.  It's faster and avoids the confusion over exact numbers that sometimes affects the voice controls.  It also carries a lot more messages per second over the limited radio channels.
2. A report on prototype effort by British Airways, as part of joint effort with Solena Fuels and GreenSky London, to build a $500 million plant to convert waste biomass into fuels.  It's to be built in Tilbury and go operational in 2016.  The plant will take 565,000 metric tons of sorted municipal waste and generate 50,000 tons jet fuel, 50,000 tons diesel, 20,000 tons naptha, and 50 megawatts excess electrical power.

   The feedstock is dry sorted municipal waste. That means metals, glass, and other recyclables have been removed.  (Technically it's called refuse derived fuel - RDF).  Part of the deal is the attraction of using something that somebody else collects and pays you to take, as are airline commitments to reduce carbon impact.  These fuels count as bio-fuels with no carbon impact.

   It's a plasma torch gasification, so plastic, tires, etc. can be processed.  It uses the usual syngas F-T processes, with the latest chemical reactor and catalyst designs.

3. An article about the complaints about latest idiocy on carbon tax for aviation.  The European Parliament has clearly said that they will collect tax on aviation travel outside Europe, has created a bureaucratic monster, and all the non-EU countries (US, Russia, China, etc.) have reacted with immense hostility. This choice abrogates promises to use ICAO international processes for aviation CO2 controls. One of the absurdities is that a charter airline that flies one 747 per week is considered de minimus carbon contributor and avoids most of the paperwork.  A business jet operator that flies one business trip per month is not considered de minimus and must follow the full bureaucratic procedures.

   The annual paperwork cost (filings, people, etc.) is estimated at $100K/yr.  For an airline this is just another piece of the regulatory burden.  For business jet operators this is a big extra cost.  There is a series of "free" allowances.  Again, even for small airlines the cost of filing and qualifying is justified by the value of the allowances.  For business jet operators, the filing cost exceeds the value of the allowances.

   The laws justification was CO2 emissions, but clearly the regulations are designed to eliminate private aviation and business jet operations in favor of commercial airlines.  Extending the reach outside Europe is a simple power and money grab by the EU Parliament.

Proper Statistics

I was reminded at the FDA summit of proper statistical evaluation methodology.  The study was one looking at the impact of color calibration of monitors on the accuracy and speed of dermatology diagnosis.

Step one, they measured the inherent variability of the system by testing the same doctors, same equipment, and same patient records.  This showed that when the test conditions are the same, the doctors reached the same diagnosis about 85% of the time.  From a statistical perspective this sets the baseline for assessing the effect of the changes being studied. 

It also reminded me of a gap in most of the IT studies that I've seen.  None started with the inherent variability measurement.  Few actually took independent measurements.  Most of the studies on the impact of IT on healthcare operate from anecdote or movie script stories.

So when reading another movie script story about how much some IT improvement will change medical diagnosis and treatment efficacy, I will wonder about it's relevance.  If there is an inherent 15% disagreement when presented the same data with the same equipment, how many sample points and what kind of measurement methodology is needed to indicate a statistically significant effect?  It depends on the variations found, but most likely hundreds of independent samples are needed.

And, as an added note for the big data lovers, see the latest on using Google to track the flu.  It doesn't show that google tracking is irrelevant.  It does show that you need to do a lot more consideration of the situation than is part of the movie script scenario used in the PR stories.

FDA Color Summit

The FDA, ICC, DICOM, and AAPM held a two day summit on issues related to color and color management in medical imaging.  These are my initial conclusions about the present situation.  There will be further discussions and conversations about what should be done.

• sRGB and consumer grade equipment presents important issues
  • Use of sRGB and consumer grade equipment is inevitable.  It has nearly 100% penetration for patients and providers.  It is cheap, and they know how to use it.
  • sRGB and consumer grade equipment is inadequate. Examples:
    • The sRGB color gamut does not include the colors found in fresh blood.  This is not important to consumers, but it matters in surgery and some other medical uses.
    • Typical human vision has the ability to discriminate color and contrast with 10-12 bit resolution.  Consumer equipment is only 8 bit resolution.
    • Mobile equipment lacks calibration capability and lacks manufacturer claimed specifications.  PC class equipment has some calibration and claimed specifications, but most is limited to 8 bit data paths.
    • Measurements of consumer equipment indicates huge quality problems for acquisition (e.g., camera variability) and modest problems for displays.  The typical errors for consumer cameras were 20-40 delta E.  A typical person says that two colors do not match when the delta E exceeds 3-5.
• Huge variability is also introduced by other acquisition variations: lighting, positioning, preparation, etc. all matter and introduce significant effects.
• Displays used to be a big problem.  Now they are a modest problem, and with calibration become a small problem.  Calibrated color monitors had measured delta E around 3.
• Clinical trials and anecdotal evidence indicate that:
  • Diagnostic efficacy is not affected by the variability of monitors, nor by some of the acquisition issues.  Skill, experience, and the eye-brain complex compensate for the variations.
  • Diagnostic speed is significantly affected.  (This is statistical significance.)  The measured diagnostic tasks were performed 50% faster on calibrated monitors.  This is likely significant in the context of medical workflow, capacity, etc.
  • User fatigue is reduced on calibrated monitors.  This was not quantitatively assessed, but was consistently reported by the subjects.
• The goals and requirements of various medical activities are substantially different and not well enunciated.  There are needs like "consistency", "looking natural", matching memories of color, etc.  The needs vary significantly in different disciplines.  Pathology slide staining, dermascopic exams, endoscopic exams, and laproscopic surgery all have different needs.
• Issues like focus, depth of field, lighting, etc. are similarly important and poorly controlled sources of variability.  Color is not easily separated from these issues.
• The relationship with multi-spectral imaging is unresolved.  E.g., a slide stain is a series of spectral spikes that correspond to the stain, yet it is being represented by a tri-stimulus value.  This is combined with other stains and the inherent broadband spectrum of the underlying tissue.  This kind of mapping of spikes onto tri-stimulus is problematic due to numerical stability issues.

Two book reviews

First, Iron Curtain by Anne Applebaum.  This is a very good history of how the Soviet Union took over Eastern Europe in the years 1944 to 1956.  It really only covers East Germany, Poland, and Hungary in any detail.  The other countries get just brief mentions. The steady imposition of a police state, destruction of any alternative civil society, and transition to a totalitarian state is detailed.  The public reactions and adaptations are covered.  It's not a catalog of dates and events.  It's a catalog of techniques and results.  It's a depressing book because the historical result is depressing.  It's also a good history of material that is often not covered.

Second, The Drowning Girl: A Memoir, by Caitlyn Kiernan.  This is a Nebula 2012 nominee, and in my opinion should be the winner.  It's hard to categorize this book.  It could be called a horror/fantasy ghost story.  It could be called a character study.  It's not for someone who wants a story with a plot and several interesting characters that moves from a straightforward start to a finish.

The Drowning Girl is a memoir by a schizophrenic author, told first person.  Something happened, perhaps involving a ghost or perhaps a siren, or perhaps it was all delusions.  The author struggles with the events, writing, rewriting, exploring, getting distracted, and even at the end of the book the conclusion is

"You know now that you'll never be sure what happened?"

"Yeah, I know now.  I know that."

The viewpoint of insanity is well presented and human.  The few characters are complex and real.  The events and how people reacted unfolds piecemeal as it's told, retold, gaps filled, lies corrected, lies added, and eventually you guess at possible explanations.  Perhaps there was a ghost.  I think not.  Perhaps there was a siren.  That mythology fits better for me.  Perhaps it was the insanity.  That's possibly the case.  The goal of the book is not to resolve that mystery.

Insanity is not a happy story, and this is not a happy story.  But there is a character exposition and a character arc, and the telling is very well done.

I suggest watching the video short (its just a couple minutes).  If your reaction is "that was odd, I would like to know more." it's a book to read.  If your reaction is "that was wierd, what a waste of time." don't read the book.

History repeats with sulfur pollution

The patterns from the 1950's  through 1970's sulfur controls are repeating in the ocean shipping world, where sulfur and NOx limits are being tightened.  There is a mix of scrubbers and fuel shifts to LNG taking place.  Of course the amounts of sulfur and human impact are much smaller.  In the 1950's dozens of people died from the toxic sulfur levels in some of London's fogs.  Now, the worry is long term subtle damage to the environment.  It's still interesting to see steady progress while the patterns repeat.

Weather Forecasting and Healthcare Risk discussions

Healthcare risk explanations will face the same kind of issues as weather forecasting.  Professional weather forecasting tailors the presentation and the forecast to the user. That can cause problems after the fact because a scientific user's preferences are not the same as a public user's.  These differences are usually related to differences in how predictive probabilities are understood.  Healthcare will need to learn how to deal with the same problem.  A patient's listening and understanding is different than the scientific understanding.

We're looking at another big North Atlantic storm.  I used to deal with these professionally.  We had customers that were experiencing this:

That's what it looks like for situations like this.

Sometimes the forecast involves "A record setting level of speculation".  This phrase was used recently in a public forecast.  It's amusing and helps convey uncertainty to the public.   Weather forecasting includes explicit understanding and attention to presenting uncertainty and measuring accuracy in the face of uncertainty.  This is not a familiar subject to the public.

When I was younger I worked for a company that had a weather forecasting division.  It had both commercial and public clients.  A typical commercial customer was a shipyard that needed to thread large empty ships through a narrow channel.  They wanted forecasts for crosswinds at the channel, giving direction and speed.  We also routed ships and aircraft around or through weather.  A typical public customer was a local radio station that wanted 55 second spots for their listening area.

In both cases there was close attention paid to forecast accuracy.  In the case of the commercial customer accuracy was measured against weather instruments at the channel.  For the public it was measured by pollsters asking listeners about the accuracy of yesterday's or last week's forecasts.  We were very aware of the difference.  You would see very different forecasts for the commercial customers from the public forecasts in the same areas.

The commercial forecast accuracy measured just the ability to predict specific weather events.  It was based on scientific measurement and scientific understanding of probability.

The public forecast accuracy measured the public memory, the effectiveness of the broadcast, the phrasing, and the ability to predict weather events.  This is dramatically different.  The public forecasts are carefully adjusted with guidance from the polls and public feedback.  But when someone reviews a specific forecast and compares it with scientific measurements it is obvious that the two do not match.  This reflects the difference between accurate scientific statements of probability and statements that the public understands.

Part of the difficulty, and the source for a regular stream of research reports on weather forecasting, is the inability to express uncertainty in a way that is both scientifically accurate and understood by the public.  The public hears what it wants to hear, and does not have a good concept of uncertainty.  It's gotten worse and worse.

Professional baseball management and weather forecasting are uncommon in requiring a conscious understanding of statistics and uncertainty as a core part of the skill.  I notice this gap in the terrible difficulties that modern medicine has with discussing uncertainty and risk.  Most healthcare professionals avoid statistics and uncertainty discussions at all costs.  The result is statements that are neither understood by the patients nor scientifically accurate.

I expect healthcare will need to learn to use the same kind of public feedback that weather forecasters use.  This will take time, but it's clear that patients are not understanding the words said by the doctors.  I also expect the same kind of conflict between scientifically accurate statements and statements that are understood by the patients.

Software Risk (and the end of the world)

When I was in college I made some book shelves from boards and cider blocks rescued from a dumpster.  In my first job after college, I worked with a guy who made custom crafted bookshelves that sold for tens of thousands of dollars.  We would occasionally discuss the difficulty that software has with user recognition of the difference between home built and custom crafted, and the difficulty that users have in deciding what level is appropriate for the job.

Now we have discussion of how bad excel spreadsheets made the financial crisis much worse, how this is due in part to home built vs custom crafted, and how custom crafted is no assurance of quality.

Everyone is still struggling with the problem.

Chromebook C7 Experience (It's the right choice)

After using it for about two months and taking it on some travel, I've decided that this is a suitable machine.  It's a bit awkward traveling with two computers, but having both machines available is worth it.  My original impressions hold true.  It's got annoyances and inconveniences, but for $200 I can tolerate them.  It's fast enough for the way I use it.  They keyboard is OK.  The size is good.  The screen is good.  The linux environment is good.

In an earlier post I describe the Chromebook and what I've done with it.  Since then, I've taken it on several trips.  It's capable of being a complete system for personal travel.  On business trips it can co-exist with the corporate laptop.  Carrying both is a bit inconvenient.  The laptop bag is on the heavy side and gets bulky.  But it's acceptable.  The convenience of having a complete personal Linux system that I can use at the same time as the corporate system is good.  I find myself using it more than I expected.

It still has annoyances.  I've found a fix for the hypersensitive touchpad.  It was waking the system up even when it was lid closed in the laptop bag.  But, you can take the touchpad completely out of the wakeup system.  I've not found a suitable fix for the problem of my thumbs triggering cursor relocation while I type.  I can put in a touchpad suspend so that it is disabled for a couple seconds after each keystroke.  That almost fixes the problem.  But it also disable things like control-click, because holding the control key down disables the touchpad.

The battery life is also somewhat short.  It's good for four hours.  There were discussions on some blogs about another battery working.  The system uses the Acer AL12B32 battery.  The Acer AL12X32 is mechanically compatible and was listed as an equivalent with twice the capacity.  It's almost but not quite.  I got one.  It's mechanically a fit, it powers the computer, and the software reports it as OK.  But it will only trickle charge.  Looking at more details, the AL12B32 is a 14.5 volt battery and the AL12X32 is a 11.8 volt battery.  It won't charge fast.  There may be some driver or firmware tweak to fix this, but I don't find anything on the net yet.

Still, when these are the kind of problems I've got, it's a great deal for $200 plus $40 for the extra memory.

Email environment

I've switched to mu4e for email for a while.  It's got a lot in common with notmuch.  The motivation for switching is the UI for reading mail.

I find that the search capabilities of both notmuch and mu4e are good.  The combination of tagging, probabilistic free text search, and email header awareness makes it much more effective than any of the traditional email clients that I have tried.  I'm now a little bit spoiled by having the ability to do a free text search on all 25,000 emails in my archive in less than 100 milliseconds. (The contrast with the glacial often broken Lotus Notes that I must use for work is painful.)  The one important difference is that tags are in the mail index for notmuch, while tags are in X-headers in the emails for mu4e.  So mu4e must modify the email file to add or remove a tag.

My motivation for switching is that the email reader for notmuch is a style that I do not like.  I prefer a style more like that of "mutt". 

• I want a split view, so that I can see both the list of emails matching my query.  A typical query is "unread".
• I want the split view to be the same for everything.  I want to see an email tree in the index.  Notmuch only shows one line with a read/unread count for each thread.
• Thread view.  Both email readers pay attention to the email headers to figure out threads.  (Lotus Notes thread support is completely borked.  MS Outlook tends to get confused by threads.  The result is that email conversations with corporate folks are more difficult.  They fall into the "new mail in front, copy everything behind" mode because that's the only threading method that is reliable with these broken systems.

After trying notmuch and mu4e long enough to be reasonably expert I've switched to mu4e.  The email reader is more important than the differences in tag and search.  There may be a way to add index-only tags to mu4e with a lot less effort than changing the mail reader. I don't like modifying the original email.  It feels wrong to me.

Switching back and forth was easy because they both use a maildir format for storing emails.

Chromebook C7 Experience (Initial Review)

Summary: The Acer Chromebook C7 works as an ultralight Linux system and I will continue using it.  There are plenty of annoyances and it is not for everyone.  It is for people who can tolerate annoyances and who like to tinker with things.  The $200 price compensates for a lot of annoyances.  If you can't handle annoyances or don't want to tinker with things, get an Ultrabook ($800+) or Mac Air ($1300+).

I got a Chromebook C7 and have replaced the ChromeOS with Ubuntu linux.  It will replace my aging Mac Pro laptop.  This began as an experiment.  I was willing to risk $200 on this.  It's working and I'm now committing to it.

I evaluated my needs by examining all the applications on my Mac Pro and on my corporate laptop.  This established what I want from a travel machine.

• I rejected the tablet plus keyboard alternative.  An Android tablet plus keyboard could do about two thirds of what I want.  I'm not willing to give up the other third.  One thing that I really want is the ability to browse the web, refer to PDF, Word, and other documents, all as part of writing another document (using either emacs or an office system).  That's the one thing that tablets can't do easily.  They are really limited to showing one application at a time.
• The Mac Air and the PC Ultrabooks can do everything that I want.  These cost about $1400 or $800 respectively.  If the Chromebook experiment failed, I would have gone to a PC Ultrabook.
• The Chromebooks have the option of replacing ChromeOS with Linux.  The $200 model is the better choice for this than the $250 model.  The two deciding factors were storage space and CPU.  The $200 model has 320GB disk and an x86 CPU.  The $250 model has 16GB static RAM and an ARM CPU.  For the non-tinkering user, the $250 is a much nicer machine.  But if you want to install Linux on it you need to put linux onto a separate 16GB microSD, and you're very storage limited.  The ARM means a lot of cross-compiling of software because there are relatively few Linux packages compiled and configured for the ARM family.  There are many different incompatible instruction sets among the ARM family, so you need to target machine types, not just ARM.

Physically the C7 looks like a Mac Air designed and built by a PC vendor.  It's clunky, boxy, a bit heavier, a bit thicker, slower, and much shorter battery life.  On the plus side, it has intelligent security protections, 320GB storage, and many useful connectors (like VGA and wired Ethernet).  It's flimsy, which does lead to some annoyances.  I haven't broken anything, but it feels fragile.  The battery life is only 3-4 hours, but you can buy additional batteries and swap batteries if you want.

Installing the software is straightforward but requires following a lot of instructions carefully.  (Instructions with pictures, and the real instructions). You can't just boot from a CDROM or Flash stick.  You need to get the machine into developer mode, download and run ChrUbuntu as an experimental OS, repartition the disk, sign it, and get Linux stored onto disk.  The first download is 1.5GB which takes a long time even with a fast Internet connection.  Then, the first update to bring it up to current versions will download another 400 MB.  And forever you must accept warnings at boot time that you are running an experimental OS in developer mode.

I do expect other distributions to follow Ubuntu's path and configure versions that can be installed in this way, but they haven't done it yet.  For other versions you are much more on your own.  You get to go read the ChromeOS developer documentation and figure it out yourself.

I've installed another 500MB of software downloads for

• emacs
• truecrypt
• Skype, and
• XCFE4

These first three are because they are core applications that I want to use.  They were the highest risk of failure on this system.  The other missing applications are going to work if Linux works.  (Most of the 400MB is dependencies pulled in by Skype.  Skype is only available in 32-bit mode on Linux.  ChrUbuntu is 64-bit mode.  So the Skype package pulls in a mass of 32-bit mode library and compatibility support.)

I installed XCFE4 because this system needs a lightweight windowing system.  I tried Canonical's preferred Unity system that comes with ChrUbuntu.  I replaced it because:

• It places too many demands on the 1.1Ghz Celeron.  The clickpad was highly erratic.  Other features were slow or erratic.  Unity really needs a beefier CPU and GPU.  It's full of demanding eye candy.
• It interferes with my doing multiple things at once.  It's like the tablets.  It's set up to show one application at a time.  If you fight hard you can have multiple applications at once, but it was easier to switch than fight.

An example of the kinds of annoyances you must face and fix is a conflict between Unity login manager and XCFE4 over access to the power system controls.  These are known bugs.  They leave it unpredictable whether power status will be shown and whether lid closure will trigger standby or not.  I dealt with the first by installed "xosview" to show me system status.  Further examination of comments on the bug reports showed how to configure XCFE4 to not use the power control daemon.  Now power management works much better.  But there are still occasional glitches where the system powers up from standby despite the lid being closed.  I haven't figured out how to stop this yet.

I've got plenty of software installing and customizing to go, but I'm confident it will work.  The high risk stuff is working and indicates that the rest will work.  It's just going to take time to do.

It's got lots of annoyances and limitations, but for $200 I can accept them.  (Extra:  I've just added 8GB of RAM ($40) and it's doing fine.  Instructions are here.)