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The end of Bioinformatics?! No comments yet

The End of Bioinformatics?!

I read with some interest the announcement of the Wolfram Alpha.  Wolfram intends to be the end all and be all data mining systems and some say, makes bioinformatics obsolete.

Wolfram’s basis is a formal Mathematica representation.  It’s inference engine is a large number of hand-written scripts that access data that has been accumulated and curated.  The developers stress that the system is not Artificial Intelligence and is not aiming to be.  For instance,  a sample query,

“List all human genes with significant evidence of positive selection since the human-chimpanzee common ancestor, where either the GO category or OMIM entry includes ‘muscle’”

could currently be executed with SQL, provided the underlying data is there. 

Wolfram won’t replace bioinformatics.  What it will do is make it easier for a neophyte to get answers to his or her questions because they can be asked in a simpler format.

 I would guess Wolfram uses one or more these scripts to address a specific data set in conjunction with a natural language parser.  These scripts would move this data to a common model that could then be modeled on a web page.

But why not AI?  Why not replace all those “hand-written” scripts, etc.  with a real inference engine.

I rode the first AI wave.  I was a member of the first of 25 engineers selected to be a part of the McAir AI Initiative at McDonnell Aircraft Company.  (”There is AI in McAir”).  In all, 100 engineers were chosen from engineering departments to attend courses leading to a Certificate in Artificial Intelligence from Washington University in St. Louis.

One of the neat things about the course was the purchase of at least 30 workstations (maybe as many as 60) for a young company called Sun that were loaned to Washington University for the duration of the course.  Afterwards, we got a few Symbolics machines for our CADD project. 

Other than Lisp and Prolog, the software we used was called KEE (Knowledge Engineering Environment).  Also, there was a DEC (Digital Equipment Company) language called OPS5.

The course was quite fast-paced but very extensive.  We had the best AI consultants available at the time lecture and give assignments in epistemology, interviewing techniques, and so on. I had a whole stack of books.

The only problem was that no money was budgeted (or so I was told) for AI development for the departments for the engineers when they returned from the course eager to AI everything.  A lot of people left.

Anyway, my group of three developed a “Battle Damage Repair” system that basically “patched up” the composite wing skins of combat aircraft.   Given the size and location of the damage, the system would certify whether the aircraft would be able to return to combat, and would output the size and substance of the patch if the damage wasn’t that bad.

One interesting tidbit:  We wanted to present our system at a conference in San Antonio and had a picture of a battle-damaged F-15 we wanted to use.  Well, we were told that the picture was classified and, as such, we couldn’t use it.  Well, about that same time, a glossy McAir brochure featuring our system and that photo were distributed at the AAAI (American Assn. of Artificial Intelligence) to thousands of people. 

Another system I developed dealt with engineering schematics.  These schematics were layered.  Some layers and circuits were classified.   Still another system scheduled aircraft for painting and yet another charted a path for aircraft through hostile territory, activating electronic counter measures as necessary.

I guess the most sophisticated system I worked on was with the B-2 program.  The B-2 skin is a composite material.  This material has to be removed from a freezer, molded into a final shape and cooked in a huge autoclave before it completely thawed. 

We had to schedule materials, and the behavior of that material under various circumstances, as well as people and equipment.  The purpose was to avoid “bottlenecks” in people and equipment.  I was exposed to the Texas Instruments Explorer and Smalltalk-80 on an Apple.  I’ve been in love with Smalltalk ever since.

The system was developed, but it was never used.  The problem was that we had to rank workers by expertise.  That’s union workers and that wasn’t allowed. 

It was a nice system that integrated a lot of systems and worked well.  Our RFP (Request for Proposals) went out to people like Carnegie-Mellon.  We had certain performance and date requirements that we wanted to see in the final system.  We were told that the benchmarks would be difficult, in not impossible, to attain.  Well, we did it, on our own without their help.

We also had a neural net solution that inspected completed composite parts. The parts were submerged in water and bombarded with sound waves.  The echoes were used by the system to determine part quality.

AI promised the world, and then it couldn’t really deliver.  So it kind of went to the back burner.

One problem with the end and be all.  It will only be as good as your model.  It will only be as good as the developers can determine the behavior of the parts and how they interact with the whole.  Currently, this is a moving target and is changing day to day.  Good luck.

Links -

Will Wolfram Make Bioinformatics Obsolete? - http://johnhawks.net/weblog/reviews/genomics/bioinformatics/wolfram-alpha-bioinformatics-2009.html

Women in Flight Test No comments yet

Women in Flight Test

I spent some 10 plus years in engineering.  As a woman in engineering it was daunting.  As a woman in    Avionics Flight Test, it was even more so.

I was working as a systems programmer at McDonnell-Douglas (now Boeing) in St. Louis, Missouri.   Our project consisted of 6 compilers that supported a completely integrated database system for hospitals.  A woman on our team was married to a section chief who worked at McDonnell Aircraft.  McAir (as it was commonly called) manufactured the F-4, F-18, and F-15 aircraft.   As our project was in trouble, she said her husband said Flight Test was looking for someone who could develop database systems and do other programming for the Ground Support Systems (GSS) unit.

At my interview, I was told, “We manufacture high-tech war machines that might kill innocent women and children.  So, I don’t want any wimps or pacifists working for me.”

I wondered at the time if my interviewer was wearing cammo underwear.

I was accepted.   At the time I was one (if not the first) woman professional working at McAir Flight Test.

My desk was on the fourth floor on the West end of a hanger.  Flight Test had offices and labs on the East and West ends of the hanger. Since our unit was the first set of desks one encountered when accessing our area, I was assumed to be a secretary and asked all sorts of questions.  The fix was to turn my desk around so everybody was looking toward the interior and my desk was facing the window.  I got an up-close look at the planes taking off and landing as they were just clearing the building.  Take offs were bad because the fumes from the jet fuel were overwhelming.  I would have to ask the person I was talking to on the phone if they would hold because I couldn’t hear them over the noise.

The hush houses were less than 100 yards away.  You couldn’t hear the noise (that’s what hush houses do), but the thud-thud-thud vibration of the engines became a bit much at times.  Oh yeah, our hanger sat right on top of the Flight Test fuel dump.

The first project was to develop a database system to track the equipment used by Flight Test.  The original system consisted of a 6-ft. by 20-ft. rack of index cards in pull-down trays. Each piece of equipment had a card which stated what it was, where it was, etc.

Every time a Flight Test program was scheduled, all the parts for that program had to be tagged and their index cards updated.  This would take anywhere from 3 days to a week under the old card system.

The new system did it in a few hours and produced timely reports on all parts and their locations.

Next system was a database system for Flight Test electronics like Vishay resistors, etc.

Another project was providing the documentation and training aids for the Digital Data Acquisition System for the F-18.  This system directly connected the plane’s computer system and uploaded mission information and, subsequently, downloaded mission results.

The old system was called the “taco wagon”.  It was a large roll-about cart.  These carts cost about $300K and used a card reader to upload mission info.

Our system replaced the “taco wagon” with an early Compaq laptop that cost about $3K.

Then Flight Test submitted my name as one of two people for a special program.  The other person from Flight Test was an ex-Air Force major who flew F-15s.

I went through the program and upon returning to Flight Test was asked to make a presentation to our executives.

The major and I made our presentation and opened it up to questions.  Our VP asked the major a question that started with the phrase, “As Flight Test’s designated expert in this area…”.
Later, I told my section chief what happened.  He said and I quote, “Flight Test is not ready for a woman to be expert at anything.”

These are two of the most glaring examples.  There were lots of others.

However, when I left, the VP said, “We will tell your story around the campfires.”

I took that as the highest compliment.

After Flight Test, I worked on AI projects before returning to Flight Test.

The Dee Howard Company in San Antonio ran an ad in Aviation Week for Flight Test Engineers.  I answered the ad.  Alenia (the world’s largest aerospace company, headquartered in Italy) had a stake in Dee Howard.  They were taking on a new project, the UPS 727QF.  The FAA had mandated that all cargo aircraft had to cut their engine noise levels.  UPS decided to re-engine their 727 aircraft with new, quieter, Rolls-Royce Tay 650-powered engines.  Dee Howard was to do the work and conduct the testing.

At the time of the contract, the count of planes to be re-engined was given as 60 plus.  The number actually re-engined has been given as 44 and 48.

Previously, Dee Howard was known for customizing aircraft interiors.  The interior of the 747 that NASA uses to ferry the space shuttle was done by the company.  They also fitted an emir’s 747 with a movie studio, solid gold toilet fixtures, and a complete operating studio.  The tale was that the emir, who had a bad heart, had a living heart donor traveling with him at all times.  Anyway, it makes a nice story.

I was hired in and proceeded to work on the system for the new program.

We were the first to replace all 3 engines on the 727.  Previously, only the two external engines were replaced, the tail engine was left as is.  We were going to replace all three.

We were to have two planes.  The critical plane was to have a new data acquisition system.  The other plane was to use a system from Boeing - ADAS.  Originally designed in 1965, ADAS had 64K memory, filled half a good sized room, used 8-inch diskettes, and the measurements were programmed by way of EEPROM.

The new acquisition system was better.  We bought a ruggedized cabinet and started adding boards.   PC-on-a-chip wasn’t quite there, but we did have PC-on-a-board and we could set things up via a PC interface.  To analyze the PCM data stream I used BBN/Probe instead of the custom software that was used on the previous system.

First flight came.  The system came up and stayed up.  Except for the one time, the flight engineer turned the system on before power was switched from the APU to the aircraft (the 8=mm tape recorder died), it worked every time.

On the fighters, flight test equipment was mounted on pallets in the bomb bay.  It was neat to ride on the plane during a test flight.  An airplane, with all the seats and padding removed, is your basic tin can.

I always got along with the technicians.  They are the ones who do the real work.  They make the engineer’s design come to life or markedly point out the error of his ways.

It was really nice to ask for such and such a cable or gadget and have it brought to my desk. The best (and worst) part of the program was field testing.  I got to go to lively places like Roswell, NM, Moses Lake, WA, and Uvalde, TX with 35 guys.  The length of the test depended on flying conditions.  We were usually stuck there for 3-4 weeks.

We also did some testing at home.  For one ground test, we taped tiny microphones to different places on the engines. The microphones were connected to the acoustic analyzer and DAT recorders.  The engines were then run at various levels.  I ran the acoustic analyzer for a few seconds for one set of mikes and flipped to record another mike set for a few seconds more.  I had to wear headphones for the noise. We had to yell anyway.  It was really hot, because this was San Antonio in July. We were on a unused runway at the airport, next to a well-traveled road.  The test took several hours.  The guys took the door off the head (which was right across from the open front access door) so I could watch the traffic when I used it.  (Did I tell you I had to clean the head when the test was over?)

As the revs got higher, the airplane moaned and groaned.  One engine finally belched.  We were lucky it didn’t catch fire!

Other testing conditions were just as much fun.  Roswell has the desert.  Desert dust at 35 knots is awful.  Tumbling weeds have nasty stickers.  Moses Lake had volcanic ash.  Mt. St. Helen’s dumped about a foot of ash at the Moses Lake airport.  Airport officials dumped the collected ash on a spot at the airport that they thought was unused.  One of our trucks got stuck in it.

At Uvalde, we had heat and gnats.  You inhaled them and they flew down your throat.

A local asked where the women went to the bathroom because there weren’t any trees.

Other than the conditions, there was the schedule.  The equipment had to be set up, calibrated, and ready to go at sun-up.  If conditions were good, we worked all day with a break for lunch and put everything away after dark.

Wake-up was 3 or 4 a.m.   We usually got back to the motel at dark, after we prepped the plane.  It got to the point of going out to get dinner or getting an extra hour’s sleep.

The testing was fun, too.  The plan was to fly over at different altitudes carrying varying weights.  (We had to unload 14 thousand pounds of ballast at one point, consisting of 50-lb. round lead weights with handles on each site.  I took my place in line with the guys.  Same thing with the car batteries for the transponders and loading and unloading the generator from the truck.)

The locals thought we might be flying in drugs, so they called the law, and the local sheriff came to call.

The testing, when in progress, was intense.  After set-up, the microphones were calibrated.  We had mikes at center line and other mikes on the peripheral.  I ran the acoustic analyzer.

I set the analyzer to trigger on a signal from the aircraft and turn on the tape recorders.  After the fly-over I had to download the data, pass it off to an engineer who analyzed it via a curve-fit program, and reset everything for the next fly-over.

The fly-overs came one after the other about 5-7 minutes apart.  We had to re-calibrate the mikes after a few, so we got an extra 5-10 minutes.  We got a break for lunch (with the gnats).

It was hard, dirty work.  But it was fun - and dangerous.  One test consisted of engine stalls on a 30-year old aircraft at 19,000 ft.  (it was too turbulent down below).   Another test had the aircraft stall during takeoff with different loads.  I was on board and loving it.

My supervisor said that “field testing separates the men and women from the boys and girls.” He was right.

One day we had a visitor in the lab.  One of the techs was working on something and let lose a string of expletives.  The visitor said the tech should be quiet because there was a lady present.  The tech looked at the visitor and said, “That’s no lady, that’s Pam!”  (You had to know the guys. I took it as a compliment.)

If you haven’t guessed, as a woman working in this environment, you have to have a thick skin.  You have to work really hard because you have to be really, really good.   But I think it’s all worth it.

It’s too easy to become a “he-she” or a “shim” (dress and act like the guys), but I didn’t.  I wore my hair longish and always wore make-up.  Even in the field.  I laid out my clothes the night before.  I could be up and ready to go in 5 minutes, complete with mascara, eye liner, sunscreen and blush.  I always had my knitting nearby.

It was hard work, but it all paid off.  The UPS plane was certified the latter part of 1992.

I’ve got some memories, some good, some not, but I know I made the grade.

Addendum -

The group working on this project was international in scope and I worked closely with most of them.    We had several people from the British Isles representing Rolls-Royce, including J. who spoke with a find Scottish accent.

I worked with two engineers from Alenia on the acoustics aspect of the program.     They hailed from Naples, Italy.   M. spoke excellent English.  E.  didn’t, but engineering is universal, so we were able to make it work.  Another acoustic team member was a Russian, L.  His English was also excellent.

I can honestly say that I know Fortran in Russian and Italian.   I had to grab whatever Fortran text I could find in a pinch and the Russian or Italian text was usually the closest.

We communicated with facilities in Italy, England, and France on an almost daily basis. The time difference was the only snag.

It was interesting to see how our American ways are interpreted by other cultures.

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