News and Views

Not much to say about a city that everyone except Gisele and I have been to before. White House, Capitol, Smithsonian, Memorials, …

We chose this time to come so we could see the cherry blossoms, and there are quite a few around, but otherwise it’s a bad time. Lots of other people also want to see the cherry blossoms, and lots of kids are on spring break. It took us about a half hour to get into the Air and Space museum today, and it was wall to wall people. Still worth the visit, of course.

Our hotel is kind of interesting, I guess. It’s on the “National Trust for Historic Preservation” list of “Historic Hotels of America”, one of 260. Built in 1929, it’s hardly ancient, but it is quaint and is clean and neat. It’s on Pennsylvania Avenue, about a 10 minute walk from the White House, so it’s in a convenient location.

We did a lot of walking on the first day, but have since got smart and have used the Metro a lot more. There is a station about 5 minutes from our hotel.

Dale wanted me to talk about weird people, but unfortunately we haven’t met any. I’ll keep my eye open for one, just for you Dale.

Maybe Library of Congress tomorrow…?

Yesterday morning we woke up to find a dense fog covering the “Valley of the Sun”. Les and I had already planned a hike, so I picked him up and we drove out to the south side of South Mountain. We had to drive slowly in places because of poor visibility.

To you folks who live in rainier climates, fog is a common occurrence, but it is rare here in the Sonoran desert.

As we started up the trail we couldn’t see even the outline of the sun, but as we climbed higher and higher the fog began to thin and the sun became visible, though still not too bright to look directly at. Finally, as we reached about 1000 feet above the desert floor we broke out of the fog into clear blue sky.

Just above the fog, looking northeast towards the TV towers on the peak of South Mountain. Tempe is somewhere to the right of the towers under the white blanket.

Looking west towards the Sierra Estrellas, over a sea of cloud.

The little valley we had come up through was filled with fog.

Playing basketball (of course) Wednesday morning, when I reached in to steal a pass. Instead, the ball impacted the tip of my pinkie which immediately started bleeding. It didn’t hurt much, so I wrapped it up and kept playing.

That day was OK, though it hurt a little to type with that finger. I assumed it was just another jammed finger, of which I have had plenty.

The next day the whole hand started swelling and hurting. It got so bad that I had to take oxycodone in order to sleep last night. So this morning I went to an Urgent Care center and had x-rays taken.

They splinted it, prescribed pain and antibiotic medication, and said I should see an orthopedic surgeon. Not sure if I will bother. Nothing to do but wait till it heals, 3-4 weeks.

Update: I made an appointment with a hand surgeon for Monday. Dr Haber is the hand surgeon for ASU and the Phoenix Suns, so I should be in good hands…

There was a cheese factory in Cuba, NY, the town I was born in. I grew up eating this cheese in everything from toasted cheese sandwiches to macaroni and cheese. It is unique and delicious.

Living in Arizona I don’t get much opportunity to eat Cuba cheese any more, but I recently came into acquisition of two and a half pounds of the precious substance.

The problem is that the Cuba Cheese Factory doesn’t use mold inhibitors in their products, and it shows. The cheese will start showing mold in a week or two, and there’s no way I can eat 2.5 pounds of cheese that quickly. Once I cut into the wrapper the clock starts ticking and the mold starts growing.

One solution we have tried in the past is freezing. This does stop the mold, but it renders the cheese crumbly and seems to modify the taste a little. It’s better than mold, but not ideal.

This time we’re trying something new: Wax. I bought some cheese wax, cut the big loaf into quarter-pound pieces and dipped each piece into the melted wax. The heat of the wax is supposed to kill any mold that may have started. I’ll store these pieces in the refrigerator and only cut into each piece as we finish the last one.

It’s the first time I’ve tried this so I can’t be sure how well it will work. Maybe enough spores survived the dipping and when I remove the wax I’ll find huge mold growths. I’ll find out in a few weeks.

When I was in my teens our family spent several vacations at Rocky Point in Mexico. It was a sleepy little Mexican village, and we camped on the beach, either in a trailer that we hauled down there, or in tents, or just on a tarp on the sand. We spent several idyllic weekends there in my youth.

Last week my family went down to Rocky Point again and spent 3 nights. What a difference! There are huge luxury condos up and down the beach. The town doesn’t seem much different, with many dirt roads, but it is certainly larger. We stayed on Sandy Beach, while in my teens we camped at Shell Beach. We didn’t get a chance to visit Shell Beach, so I don’t know how much it has changed there.

Right in front of our resort. It looks the same in the other direction. That’s Gisele looking at sea shells.

The heat wasn’t working in the first condo we took (a 3 bedroom/2 bath — about 1600 sq ft) and it was freezing cold. They tried to find us another one that night, but the heat wasn’t working in the other ones they tried, so we were stuck. I turned the electric oven on and opened the oven door, put on extra blankets and we slept OK.

The next day they moved us to a nicer condo (3 bedroom/3 bath — about 2000 sq ft) and instead of charging us more they gave us back part of the rent for the first night, so for two nights we got to sleep in a very nice condo on the 7th floor with nice views of the beach.

We chose a particularly cold time to visit the beach, with night time temperatures around freezing, days mid-50s and windy. The boys and I soaked a little in a hot tub, but it wasn’t the optimal time for a visit to Rocky Point. On the other hand, the crowds were very thin

I unfortunately brought something home with me, with the resulting diarrhea, head ache, chills and fever (101.1). I don’t feel bad-bad, just not very good.

After the iDigBio conference (“Hackathon”) in Gainesville, we came to Orlando to play.

3 1/2 days at Disney World were lots of fun. Big crowds Saturday evening at the Magic Kingdom, and pretty big crowds Sunday at Epcot, but by Monday at Animal Kingdom and Tuesday at Hollywood Studios, we pretty much just walked on to any ride or entertainment without waiting. We still had to weave through the winding queue lanes, but they were empty almost all the way to the rides.

Today we went out on an air boat into the Everglades, or a portion of the Everglades near Orlando. It was lots of fun zooming over the water and lily pads and through the reeds; those air boats can go almost anywhere there is water.

Ready to go! The head sets served to muffle the sound of the engine, and allowed us to all talk and hear the guide.

No way through here except with an air boat. We went.

We saw several alligators, a couple of them approaching 10 feet long, and almost ran over a group of one-foot babies that quickly swam out of the way.

This was a big one — approaching 10 feet long. He was about 20 feet from the boat. We saw others out of the water, but not quite this close.

There are two alligators in this picture, though hard to see the second. The one you can see stretched across the middle was 8 or 9 feet long. His head is on the left — you can just make out his nose sticking past the small tree trunk.

There was lots of other wildlife, including a water moccasin (no picture), a few turtles and lots of birds.

I think this was a cormorant. We saw lots more, along with blue herons, ducks, egrets, and more.

Tomorrow we are planning to go to Kennedy Space Center in the morning and afternoon, then to see a showing of Cirque du Soleil in Downtown Disney in the evening. Friday we go back home.

It’s pronounced “I Dig Bio”, and that’s what I’ve been working on for the past three days. I’ve been in Gainesville at the University of Florida which is sponsoring a “Hackathon” for iDigBio.

iDigBio is a collaboration (funded by the National Science Foundation) between universities and museums all over the world with a focus on digitizing natural science collections, hence the name “Integrated Digitized Biocollections”. This particular hackathon had about 25 attendees mostly from the US, but Australia and Scotland were also represented. We met to discuss and develop programs and processes to help simplify and automate the digitization process.

Filed away in basements and cabinets all over the world are hundreds of millions or billions of plant, animal, insect, mineral and other specimens collected over the past few centuries. Up to now, these specimens were only available to a few researchers and even then one had to either travel to the specimen or ship the specimen to the researcher. This current effort is to upload to the internet pictures and details about each of the specimens to make them available not only to researchers but also to the general public. It is a big effort and without some automation almost impossible. Another approach to the problem is “crowd sourcing” — using volunteer “citizen scientists” to help, and that was also a major topic of this meeting. An example of a crowd sourced project is “Notes From Nature” where volunteers have just passed one million transcriptions.

My involvement and invitation came about because of programs I developed at Arizona State University to help automate the digitization of their plant specimens. Nearly one hundred thousand records passed through my program, SALIX, and I am now working on a web version of this program that can (hopefully!) be used by institutions all over the country and world.

It’s been an interesting and fun three days working with experts in the field. I’ve learned a lot and, I hope, contributed to the effort. There’s still a lot to do!

Tomorrow Gisele and I leave Gainesville and drive to Orlando where we’ll spend a few days at Walt Disney World.

There’s a lot of talk about “Net Neutrality” lately.

Basically, net neutrality means that those who provide and control the internet cannot adjust speeds or give preference based on content or other criteria. They have to remain “neutral” to the content.

Here’s a useful analogy: Compare an electricity utility and cable (or satellite) TV. For electricity you pay a monthly bill and get electricity that you can use however you want; lighting, TV, computer, air conditioning. You pay more to use more, but how you use it is entirely up to you. The power company can’t offer you more reliable power if you install a certain brand of air conditioner. With cable TV you also pay a monthly bill, but the cable company has much more control about what is available to watch. You can choose a “package” of programs and add on premium channels, but the company assembles the packages, and they often depend on financial agreements between the cable company and the networks.

Right now the internet is more like a utility company. You pay a monthly fee for service, but how you use that service is entirely up to you. Your ISP (Internet Service Providers like Cox or Comcast) can’t throttle your speeds for Amazon streaming movies but speed them up for Netflix movies, for example. This is the way the internet has functioned since the beginning with a few temporary exceptions, but things may be about to change.

In April of this year the FCC (which has jurisdiction over the internet) was reported to be considering changes to make the internet more like cable TV. One proposed change is that ISPs (Internet Service Providers like Cox or Comcast) can start charging internet companies like Netflix a surcharge to get a faster connection. Since Netflix uses about a third of all the bandwidth of the internet, it almost seems plausible that they might have to pay a little more for a reliable, fast connection. But the big concern I have is that a small start-up company providing some kind of video service might not have the budget to pay for a fast connection, and wouldn’t be able to compete on a level playing field. This would stifle competition and innovation.

And from the consumer’s perspective, I pay a premium for a faster connection already. Let me decide how to use that bandwidth.

The strongest opposition to net neutrality comes from the ISPs. Cox Cable would love to charge Netflix a fee for a fast connection. I can foresee situations like the current one between Dish Satellite and CNN: While they have been negotiating a contract for several weeks, I can’t watch CNN. If Cox and Netflix were negotiating their contract, would I be able to stream movies, or would Netflix be slowed to a crawl, or even blocked?

I can see a possibly acceptable compromise to net neutrality: Allocate bandwidth generally based on content type. For example, allow video streams (e.g. Neflix) priority over email. This sounds reasonable: I’d rather my email be delayed by a few seconds than have to wait while my movie stops and buffers. But this doesn’t help the cable companies at all; in fact it adds a layer of complexity to their systems, so I’m sure they would fight strongly against this approach.

An amusing side note to this discussion is that after Obama recently came out in favor of net neutrality, there were a few knee-jerk reactions from his usual opponents. Glen Beck mistakenly complains that the government wants to control the internet and says that with net neutrality the government will be able to “choke down his speeds”, which is exactly backwards. His guest asks why we would want the government intruding into the free internet which is working so well. Net neutrality keeps the internet free as it is now.

Ted Cruz calls net neutrality “Obamacare for the Internet“, that it would be government control of the internet. Politifact gives him a half-true, since net neutrality would allow the government control to the extent that they could prohibit favoritism and enforce neutrality rules.

Rush Limbaugh complains that net neutrality is just a liberal ruse to control the internet. He falsely states that “The FCC has just asserted its authority to regulate the Internet”, which is of course wrong; the FCC has had jurisdiction over the internet for years. But that jurisdiction has been mostly limited to ensuring that everyone plays fair and that all streams are created equal. When Limbaugh says that the internet is working fine and doesn’t need to change, he is agreeing with Obama, though he apparently doesn’t know that and would never admit it.

My conclusion to this is that net neutrality has worked well for years and is beneficial to the consumer. Any large changes to the system would only benefit ISPs and backbone providers, and would be our loss.

When I retired from Intel 14 years ago I didn’t have any plans other than not doing what I was tired of doing. I had no idea of the opportunities that would open up for me.

Here’s a brief update on my “career” since then.

Arizona Neighborhoods
For several years, I helped my friend Don Bates develop a set of thousands of websites, each focused on one subdivision in the Phoenix area (AZNB.COM). That was fun and challenging, and I still help out with a little maintenance from time to time, but there haven’t been any major developments for a few years.

ASU
Soon after I retired I met the husband of one of Gisele’s friends. Les is a professor of plant biology at ASU (Arizona State University). I should say “was” since he just retired last month. Les and I both shared interest in hiking, which soon developed into a friendship and subsequently into a research partnership, with my part being mostly programming. Les and I have worked together on several projects, some of which led to published papers. For example:

PlantMap
— I wrote a program that queried the database of plants to plot locations where specific species were found on a map of Arizona. I later found that other teachers at ASU were using this program in their classes as an assignment. (Derek’s girlfriend, Stephanie, came to dinner one night telling how her biology professor gave the class an assignment to go to “daryllafferty.com…”. She was quite surprised, to say the least!)

Germination
— We developed another program that simulated plants growing in a desert environment. You could vary attributes such as how much water it needed, how quickly a seed would germinate after getting wet, how heat affected it, etc.. We presented this at a couple of biology conferences.

Proximity Correlation
— We recently created a program that would query the database of plants to find those that often grow together, in an attempt to describe “biomes” — typical environments such as Pine Forest, Chaparral, Riparian, etc. These biomes have been described before but just based on observation and intuition. Ours is the first attempt we are aware of that tries to quantify these ecosystems. One interesting feature is that if you have an animal or insect with location information you can add it to the list and determine which plants the animals were most likely to be associated with. We have just submitted a paper describing the project for publication in a major international journal, (TAXON).

SALIX
— One of my biggest projects was called “SALIX” (Latin for willow). Les is (was) the curator of the ASU Herbarium. A herbarium is like a museum or library where hundreds of thousands of plant specimens are collected and stored, each flattened and glued to a large sheet of heavy paper. On each sheet is a label indicating data such as the scientific name, who collected it, when and where it was collected (descriptively and often including latitude, longitude and elevation), other plants in the vicinity, and several other bits of information. There are no standards on how the information is arranged or labeled.

There is a big push in the scientific collections world to database this type of information and make it generally available for research. SALIX is a program that can read the label and identify the information, determining which is the collector’s name, when and where it was collected, etc. The program was used extensively at ASU for adding their specimens to the database. The alternative to a program such as SALIX is manually reading and typing the information into a form, which is slower and more prone to errors (typos) and abbreviated information.

Recently another major herbarium has provided us funding to create a web version of the program so that it can be used anywhere by anyone. I am deep into that project now, and hope to have a usable version by early next year.

Next month I’m flying to Florida State University (Gainesville) to participate in a working group developing methods to improve the databasing of scientific collections.

So if you’ve read this far you have a small idea of what I’ve been doing for the past 14 years. It’s been more fun than I ever imagined!

The doctor said I could start playing basketball on November 1. I figured today is close enough.

I’m a little out of shape, and my shot is off — especially later in the morning as my legs got more tired. But it felt good to get out and run again.

Now if I can just stay healthy for a while and stay out of the way of the big guys…