I respect you . . . I don’t want to infect you

I was an HIV/AIDS educator for a time. I remember the phrase “it ain’t love without a glove” running around. It was a reference to condom use. Our trainers told us that if person A had unprotected sex with person B it would be like person A having sex with everyone person B ever had sex with! Unprotected sex was not just sex with someone but with someone’s entire sexual history.

It was a graphic depiction of the nature of disease transmission.

COVID-19 is of course quite a bit different than HIV. But what’s being asked of us is the same. With HIV education we asked young people to protect themselves but we also made it clear they needed to protect others! Taking precautions, communicating honestly, and abstaining from certain behaviors takes effort. But if you care about yourself and the other people in your life you will put forth the effort.

If we want to reduce the threat of this virus we have to stop interacting with people. It is the best and most effective thing we can do.

This is hard. We need each other. We need close contact with friends and family. We need a healthy society that we can work and play in. We need goods and services. But we have to delay gratification. We have to inhibit our natural spontaneity. We have to isolate ourselves, as best we can.

We used to tell our students that you had to assume your partner had a sexually transmitted disease, that way you’d certainly protect yourself. And we reminded them that they could be carrying a disease and unwittingly infect someone if they were unprotected. They didn’t want to be that person, did they?

If you assume you are infected with COVID-19 you will take precautions not to spread the virus, like proper social distancing and self-isolation. This protects other people. And guess what? It protects you, to.

Isolation and social distancing are acts of respect. You are saying to your neighbors “I want you to be safe.” And at the same time you are looking out for your own health and well-being. Who can argue with that?

Remember:

“It ain’t love without a glove.”

 

Xenobots

If you didn’t already think you were living in a sci-fi world now you have no choice but to succumb to its inevitability.

A research team from several East Coast institutions (University of Vermont, Tufts University, and Harvard University) recently demonstrated “living” robots made from biological materials.

Their paper has a rather modest title: A scalable pipeline for designing reconfigurable organisms.

These folks aren’t as excited about what they created so much as they are about the process and what it suggests for future creations.

Stem cells were harvested from Xenopus laevis (African clawed frogs) as well as progenitor cardiac cells which were then manipulated mechanically and shaped into designs, creating “creatures” of about 1 mm in size. (The heart tissues are contractile and provide a crude locomotion.) The designs were done in silico and subjected to an evolutionary algorithm that winnowed out un-workable architectures and provided models for assembling the living-tissue robots.

The computational requirements to model the designs and test them in virtual environments were immense and done on the so-called “DeepGreen” supercomputer at the University of Vermont. The actual biological assembly was the least complicated part of the process. The “surviving” designs were further analyzed and improved in succeeding trials. The goal was to create novel organisms capable of four things: locomotion, object manipulation, object transport, and collective behavior. From the study:

Here, we demonstrate a scalable approach for designing living
systems in silico using an evolutionary algorithm, and we show
how the evolved designs can be rapidly manufactured using a
cell-based construction toolkit. The approach is organized as a
linear pipeline that takes as input a description of the biological
building blocks to be used and the desired behavior the manufactured
system should exhibit (Fig. 1). The pipeline continuously
outputs performant living systems that embody that behavior in
different ways. The resulting living systems are novel aggregates of
cells that yield novel functions: above the cellular level, they bear
little resemblance to existing organs or organisms.

“They bear little resemblance to existing organs or organisms.”

This is not Jurassic Park! This is something else entirely and the focus is on reproducibility, that is, industrial-scale applications.

What might such things be good for? Again, from the authors:

Given their nontoxicity and selflimiting
lifespan, they could serve as a novel vehicle for intelligent
drug delivery (28) or internal surgery (29). If equipped to express
signaling circuits and proteins for enzymatic, sensory (receptor),
and mechanical deformation functions, they could seek out and
digest toxic or waste products, or identify molecules of interest in
environments physically inaccessible to robots. If equipped with
reproductive systems (by exploiting endogenous regenerative
mechanisms such as occurs in planarian fissioning), they may be
capable of doing so at scale. In biomedical settings, one could envision
such biobots (made from the patient’s own cells) removing
plaque from artery walls, identifying cancer, or settling down to
differentiate or control events in locations of disease. A beneficial
safety feature of such constructions is that in the absence of specific
metabolic engineering, they have a naturally limited lifespan.

In the future—which is closer all the time—medicines will be customized to the patient. Extraction of materials from the earth, whether for remediation (waste cleanup) or resource mining, will be done without risking human workers.

I’m surprised this story didn’t generate more interest. I think it is pretty damn amazing and I hope I live long enough to see such schemes become economically feasible.

The Year Zero

You know, the year that was before AD 1 and after 1 BC.

Well, there wasn’t one.

There is no Year Zero. Our modern calendar starts with Year One. Anno Domini means “in the Year of Our Lord” so it marks the birth of Jesus of Nazareth. Whether Christ was actually born in that year is irrelevant. A 6th-century scholar named Dionysius Exigenus created the Anno Domini system and most of the modern world uses that marking point. Nowadays we call it the Common Era as opposed to the Christian Era, so we say CE 1 and 1 BCE (Before the Common Era), but the starting place is the same. The Romans would have called that year 754 AUC. That stands for ab urbe condita or “from the founding of the city.”

So if Year One was the first, and there was no Year Zero, when did the first decade end? Year Ten, of course. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. That’s ten years, that’s a decade.

So that means the second decade started in Year Eleven. And went for ten years: 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. It ended in Year Twenty.

I’m sure you see where I’m going. The first decade was AD/CE 1-10 and the second was AD/CE 11-20. Then 21-30, 31-40, 41-50, etc. There’s a rule: decades start on years with a “one” at the end and they stop with years with a “zero” on the end. That means this current decade started on 01 January 2011 and will end on 31 December 2020.

But people don’t like that scheme. We are much happier to start our counting at zero and end it at nine. Year 2010 starts the twenty-tens or the twenty-teens or whatever it’s called and Year 2019 ends it. Hence all the “Best of the Decade” lists coming out.

I’m not sure why people like that kind of counting better. Maybe it’s the digits. From 2010 to 2019 you only change the ones place. With 2020 you have to change the tens place as well. Perhaps it is more intuitive to visualize a decade that way, flipping over one number at a time until you run out.

There’s nothing wrong with starting at zero when counting. It’s the same number of leaps, the same number of things, you are just using a different numeral to represent the stopping point.

So if people want to count decades from 0-9 instead of 1-10 that’s OK. The only confusion is for those folks from the first decade (CE/AD 1-10). They have to be a nine-year decade, a nonade or novemade or something. Since there is no Year Zero they go 1, 2, 3, 4, 5, 6, 7, 8, 9 and call it good. In Year Nine they would publish their “Best of the Nonade” (the one-and-only nonade) lists. Then we could get on track and call Year Ten the start of the second decade (10-19) and it will all dovetail nicely with our 2019 end-of-the-decade stuff.

Whether you are a pedantic scholar and refuse to celebrate the End of the Decade until next year, or a party animal who loves those lists and can’t wait to ring in The New Decade, I hope you have a wonderful New Year in CE/AD 2020!

What it really means

I used to tell my students that a weather forecast was pretty simple. If it said “40% chance of rain tomorrow” that meant if ten of them went outside, four of them would get wet. They were usually skeptical of this interpretation, to which I give them a lot of credit. After all, they would hear stuff from teachers all day long, and of the stuff they actually listened to, much of it was bullshit. That’s just the nature of schooling: a lot of bullshit gets spread around. Humans are a bullshitting species—we can’t help ourselves.

But it always got me thinking about what such a weather forecast actually meant. Statements of probability are attractive because they are unambiguous. Or ought to be. “It might rain tomorrow” is not very useful. “There’s a really good chance it will rain tomorrow” is a little better.

People may prefer “it will” or “it will not” rain, but hardly anyone is ever that certain. Besides, life is unpredictable. We know this. Probabilities are the best we can do.

So what does a “40% chance of rain tomorrow” really mean? Does it mean 40% of the area will be rained upon? All forecasts are organized by areas, so that seems a reasonable take. Perhaps it means it will rain 40% of the time. So in a 24-hour day you’d get 9.6 hours of rain. I don’t like that one, and I’m not sure why, but I could see someone interpreting it that way.

I would always follow up my initial foray into probabilities with another version of “40% chance of rain tomorrow.” I told my students that if we could replay the day 10,000 times it would have rained in 4000 of them.

That’s a little whimsical, we get to play god and mess with time, but computer simulations allow us to think like that. You have to check your models against nature, so you better go back and see how well they did!

Turns out the National Weather Service has an official definition for this so we don’t have to fret (PoP is Probability of Precipitation):

Mathematically, PoP is defined as follows:

PoP = C x A where “C” = the confidence that precipitation will occur somewhere in the forecast area, and where “A” = the percent of the area that will receive measureable precipitation, if it occurs at all.

So… in the case of the forecast above, if the forecaster knows precipitation is sure to occur ( confidence is 100% ), he/she is expressing how much of the area will receive measurable rain. ( PoP = “C” x “A” or “1” times “.4” which equals .4 or 40%.)

But, most of the time, the forecaster is expressing a combination of degree of confidence and areal coverage. If the forecaster is only 50% sure that precipitation will occur, and expects that, if it does occur, it will produce measurable rain over about 80 percent of the area, the PoP (chance of rain) is 40%. ( PoP = .5 x .8 which equals .4 or 40%. )

In either event, the correct way to interpret the forecast is: there is a 40 percent chance that rain will occur at any given point in the area.

I suspect a lot of folks will find that unsatisfying, but this mathematical view is at least a precise definition. And it seems to cover both the “area” part and the “time” part.

So what does it all really mean? I think a bunch of meteorologists get together at lunch and look out the window and argue about whether or not it will rain tomorrow. Finally they agree to state it as a probability, and experience tells them how often they’ve been wrong. So “40% chance of rain tomorrow” really means “we get this right four out of ten times!”

Our Vehicular Future

Buying a new car introduced me to the next-generation safety systems. All cars have seat restraints, air bags, anti-lock brakes, and other such improvements from the early days. We take these upgrades for granted now, but I remember a time when disconnecting the seat belt buzzer was the first thing people did to a new car! Now we have computer-assisted driving that can protect us from inadvertent lane changes, alert us to cross traffic, and even take control of the brakes and steering in an emergency.

We opted not to pay for those upgrades in our vehicle choice, but that’s mostly due to the cost difference, and that fact that we don’t drive a lot. And we don’t typically drive on crowded freeways or in dense urban environments where the safety features would play better. Also, there was a certain annoyance factor that was part of the decision. There are a lot more distractions in today’s automobiles! Seems like we need the computers to protect us from our distractions. I will say that I really like backup cameras—seems like every car has those now.

With all the talk and hype about autonomous driving you don’t hear much about the successes. It is going to be a while before a robot can take you in your car on a nice, safe trip. Right now the cars just aren’t smart enough for prime time. But there’s one place where autonomous vehicles are not just the future, but the living present, and that is in mining.

Caterpillar has self-driving trucks, big massive ore-haulers, that work not only continuously but safely as well. They’ve recently reached a milestone at a mine in Western Australia: a billion tons of ore hauled successfully without an operator in the vehicles. They expect to have 175 autonomous trucks in operation at that site by next year. These are seriously big trucks:

cat 2

But it’s the software that makes them go, and Caterpillar designed theirs to work with other brands of vehicles, too. Smart move. Lots of companies make mining trucks.

Another place where robot drivers are establishing themselves is agriculture. Autonomous tractors can do much of the work on a modern farm. What was science fiction when I was a boy is actually happening in the real world today.

Of course no one wants the robot-computer system to take over completely. The Boeing 737-MAX tragedies were caused by a “glitch” in the software. That’s a geek word, and it fits, but it seems too cavalier. That problem in the programming sent hundreds of innocent people to their deaths.

But people died when only humans flew planes. Now they are such complex beasts the pilots have to have the tech to help them. Our cars, it seems, are becoming like that as well.

I want the computer-robots to take over. I want to go on long drives where I don’t have to drive at all, where I can just stretch out in the back, sip whiskey, smoke a fattie, and watch the scenery. I doubt I’ll be around when that becomes a reality, but it sure sounds good.

The people who are mining the minerals we need to build cars and roads and the folks growing the food we need to live are going autonomous. Why should they have all the fun?

FIVE Nobel Prizes in SCIENCE!

I read this newspaper called the Capital Press. It is one of the few West Coast independents left. It is based in Eugene, Oregon, comes out twice a week weekly, and reports on agriculture and such things. In yesterday’s mailing we got one of those advertising inserts that comes from another planet. I wrote about the “chemtrails” guy last year, and this new stuff is right up there. Here’s one of the best lines:

Highly-engineered and computer-driven, this immune-modulator has earned five Nobel prizes in science.

Dude! An immune-modulator! I gotta get me one!

The stuff they are selling on this professional-looking 8-1/2 x 11 two-sided glossy sheet is an aerosol supplement called Liquid Gold Rx. They list the 38 ingredients thusly:

alfalfa, wild celery, anise, lemon balm, basil, greater burdock, celery, dill, hyssop, rock weed, fennel, ginger, cola nitida, marjoram, great mullein, Abyssinian myrrh, parsley, dog-rose, rosemary, saffron crocus, sage, elder, tea plant, garden thyme, turmeric, verbena, white willow, black cherry, yarrow, garlic, artichoke, motherwort, hop, red raspberry, hawthorn, elecampane, fennel bulbs, juniper

They feed alfalfa to cattle.

Just sayin’.

I suppose we all want to be immunized from the dangers of living. And this aerosol supplement—yes you really do spray it in your mouth, 4x daily—will fight off the toxins and replace it with all the goodness from the “eleven herbs and spices.”

Here’s how it works:

Upon contact with your saliva, the body immediately recognizes LGRx as the perfect, uncontaminated superfood and opens the blood vessels. The liver responds by removing the toxins you’ve taken in from your blood . . .

You know, the usual stuff. But at least they’re honest:

Every individual varies, but within 30 to 60 days, everyone will have his or her own unique experience to share.

Yes. That is exactly what will happen. Every person will have a unique experience. Whether they want to share them is another matter, in fact several may want to when they discover they’ve been ripped off.

One side of the sheet is almost entirely devoted to glyphosate (the stuff in Round-up) and how this fabulous product neutralizes the negative effects of exposure to herbicides. Targeting their ag-oriented audience, I’m sure.

Snake oil is alive and well in the American West.

Let’s put the future behind us

What’s the best kind of prediction? The one you know will come true? Or the one you can’t lose on?

Here’s what I mean:

What do you want this year, Scorpio? What are you passionate about? Your dreams are the focus of 2019, and guess what? Some of them could come true in a big way!

That’s from horoscope.com and by the way I was born on the 13th of November so that makes me a Scorpio. I note that some sites now include Ophiuchus, the Physician or Serpent-bearer, in their list of zodiac signs. That makes thirteen instead of the usual twelve. Even the astrologers have to recognize physical reality once in a while! But that’s later in November, my sun is still in Scorpius.

scorpius_600

That’s the best kind of prediction. Some of my dreams “could” come true! They could! If they do, the prognosticators were right. If they don’t, the prognosticators were still right. That’s like flipping a two-headed coin, man. That’s the way to win in the business of astrological forecasting.

Did you know there is a new field called superforecasting? I’ll bet the astrologers could teach those guys a thing or two about hedging your bets. And if the horoscope-types adopted some superforecasting strategies I suspect they’d be right more frequently. Not that it matters, horoscopes are always right, that is, they work by self-fulfillment. You don’t want reality to intrude too far into the prediction racket.

Superforecasters are the type of people who treat everything as testable hypotheses. Certainty is their enemy, oddly enough. They have to be flexible and adaptable, and they adjust their outlook when they get new information. They don’t have biases, or if they do, they have workarounds. Astrology (and other rackets like Freudian analysis) are the opposite—they have an answer for everything. The logic is circular, and the solutions can always be found in a careful re-reading of the text.

The future is heady stuff. You have to be really smart, or a con artist, or both. More likely both.

I say stick to the present.

Big science, small results

In January of 1986 the Space Shuttle Challenger exploded seconds after liftoff, destroying the spacecraft and killing the crew.  Lots of finger-pointing followed but eventually the infamous O-rings became the focus of the investigation. Panel member Richard Feynman famously dropped the O-ring material into his ice water during the hearings. And he got a clear and unambiguous result—the goddamn stuff hardened!

Feynman was a “let’s see what happens” kind of guy, and that was one of those moments where a simple experiment could cut through the B.S.

But big science isn’t so simple. Things like clinical trials involve not only an awful lot of money and time but generate mountains of data. All that information is hard to handle. It requires quite a bit of analysis before any real conclusions can be arrived at, and even then the results can be interpreted in multiple ways.

This is frustrating for regular folks. We want clear and unambiguous evidence that acai berries will protect us from cancer or that meditation will lower our blood pressure.  Big science is particularly hard on journalists who want to write about “breakthroughs” and other dramatic things. Big science isn’t very dramatic. It is slow and incremental. Conclusions are couched in vague or conditional language (“the evidence seems to suggest . . .”). Scientists are like everyone else, they want fame, fortune, and glory, but as a general rule they are circumspect about grand, far-reaching statements.

Part of the problem is that scientists are not statisticians. Most experiments require significant statistical analysis. The data have to be examined and processed, and these mathematical skills are often outside the realm of the scientists’ expertise.

Designing experiments is hard. A scientist has to have the free-thinking, synthetic brain of the artist to explore all the necessary questions. And he or she has to have the constraint-driven, analytical mind of the engineer in order to turn those questions into proper experiments. You have to be imaginative and rigorous at the same time.

A lot of clinical trials use something called NHST—null hypothesis significance testing. Here’s how it goes: you create a hypothesis, something like “drug XYZ will shrink bladder tumors.” But you don’t really test that, at least not at first. You create the null hypothesis, which is just saying that your experimental hypothesis is invalid. “Drug XYZ will have no effect on bladder tumors.” Then you run your test.

This seems sort of backwards but it is just a way of cross-checking. You don’t want to get ahead of yourself. If the null hypothesis is not supported, that is, it is refuted by the results, you can go forward. It’s like the train conductor checking your ticket and saying it is OK and that you can continue your journey.

The problem is that you knew this already. You knew the null hypothesis was invalid. After all, you’d played around with drug XYZ beforehand and knew it had promise for shrinking tumors. That’s why you designed the trial! You aren’t going to waste valuable lab time on a fruitless endeavor.

The problem comes when you get the result you expected. That is, the null hypothesis is not supported. Now you have to see if the data back up the experimental hypothesis. And this is where you need the math geeks. There is a lot of noise out there. It is not always easy to get the signal, to pull it out of the background.

Researchers don’t go into these investigations blind. They have mathematical models of the phenomena they study and they use these to make projections. They know, in advance, what the data ought to look like. They make predictions with the models. And they test the “significance” of the data, that is, they see if the numbers they got are close to what they predicted. If they get the “statistical significance” they hoped for then they can conclude their experimental hypothesis is valid.

Maybe. Sometimes there are flaws in the experimental design. There are variables that were not accounted for. There are alternative explanations for the results. And it is easy to fall into the logical trap of “the null hypothesis is false so that must mean my hypothesis is true.” Which of course is nonsense as there could be many useful competing hypotheses.

So they learn two things from all this. One, they confirm what they knew from before. Two, that they have to run another experiment to see if the results were just noise or not!

That’s not very exciting. Demonstrating an unequivocal outcome in front of a bunch of bureaucrats and politicians is much cooler.

Big science does not live up to its name. Its results are usually pretty damn small!

It’s a secret!

Here’s a story that the US is engaged in “secret talks” with one of Nicolas Maduro’s cronies. The guy’s name is Diosdado Cabello and it is reported that he has had preliminary talks via intermediaries with a Trump Administration official. Here’s my favorite line from the article (italics mine):

It’s not clear if Maduro knows of and/or has endorsed such talks between Cabello and a contact linked to the U.S. administration, the AP says.

Hmm. I found out about these “secret” talks on the internet! All I was doing was perusing my normal news sites (this time oilprice.com).

Gee, how big of a secret can these things be? I mean, they are on the internet! Nothing is a secret on the internet! Doesn’t Maduro have guys who can read? Can’t they find out about the “secret talks” the same way I did?

I can only conclude that this is really bad journalism. If you are reporting it, it is hardly a secret. Or it was never a secret at all! The writer is calling them “secret talks” because that’s more dramatic than just “talks.” Either way, it’s hella stupid.

The Caryatids

The_Caryatids_Bruce_Sterling

I don’t know how I missed this ten-year old Bruce Sterling novel as I am usually tuned in to his latest stuff. It turns out to be the best book I’ve read in a while! Sterling has one of those overly-fertile minds and stuff spills out of him so fast it can hardly be contained on the page. Sometimes his novels are so energetic and enthusiastic he forgets to finish them and they peter out disappointingly. The ride is usually worth it though, even if the structure of the book is sometimes a little lacking.

In The Caryatids he solved his plot problem with an ‘afterword’ and an ‘epilogue’ which tie together the different threads of the narrative rather neatly and give the story a satisfying conclusion.

The story, as usual, is set in a dystopian near-future and involves clones, orbital colonies, surveillance technology, and a host of other typically Sterlingesque notions. My favorite thing was his description of a state-of-the-art LA freeway system that is robust enough to withstand major earthquakes. It’s not just a bunch of roads but an intelligent, adaptive network. Residents are encouraged to head for the freeways in a natural disaster as they will be the safest spots!

Sterling’s world is dominated by corporations and other private entities as most nation-states have collapsed from the climate crisis. What’s interesting about The Caryatids is its hopeful, encouraging tone. Despite all the disasters people demonstrate remarkable resiliency and continue to be creative in the face of new problems.

The best SF isn’t so much about the future as it is about the times right now. Sterling is tuned in to contemporary trends and twists them around and amplifies them so that we get a better look at them. He’s always stimulating and illuminating and The Caryatids has some of his best stuff and reminded me of his early Shaper/Mechanist works like The Schismatrix.

By the way “caryatids” are female figures in architecture that serve as pillars. They are Greek in origin.

caryatid