DNA: A Matter of Trust

In combat, we trust our buddies with our lives. We have their back and they have ours. When submitting to surgery, we trust the medical team with our lives, and usually that trust is not betrayed. But should we be willing to trust strangers with our very essence, our DNA?

Recently I was trying to solve a plot problem in the science fiction thriller, Triangle. The storyline relied on a particular individual being singled out by the government for monitoring, not for what he had done, but for who he was.

After finishing the novel, I went back to tie up loose ends in the plot. One such loose end involved a question: How could the government know that this one person out of millions had an unrecognized super power? He was a main character in the book and so I could not ignore that question. Certainly it helps the reader suspend disbelief if the plot elements are plausible, at least superficially.

I did not have to puzzle over that question very long before an advertisement for Ancestry DNA popped up on my computer screen.

That was it!

And so the following text flowed quickly.

The characters in this conversation are Sally Simpkin  (AKA Pippi Longstocking) and Joshua Nilsson, identified below by their initials. She was trying to explain to Nilsson why she and her employers had been monitoring him.

SS: “[The government] detected that you had a high probability of having certain prescient capabilities.”
JN: “Forgive me for being a bit skeptical. Why can’t you tell me [how]?”
SS: “I’m not even cleared to know the process. I just took the assignment. It had something to do with a DNA sample you submitted.”
JN: “DNA? The only DNA I’ve submitted was for genealogy research.”

Triangle was published on May 21, 2017. On May 25, the following BBC headline appeared in my browser.

Ancestry.com denies exploiting users’ DNA. “A leading genealogy service, Ancestry.com, has denied exploiting users’ DNA following criticism of its terms and conditions.”

So, is this author also prescient like Nilsson? Or is this blogger merely a bit jaded.

Genealogy services have a difficult time competing in the world market. After all, there are only so many retired folks trying to trace their family history and solidify their genetic place in the world before their demise. Speaking for myself, I started my genealogy research years ago, picking it up from my grandmothers who told tales of Civil War Colonels and Carpet Bagger treachery, and murder. In fact, I’ve posted on this blog before about some of my discoveries.

With the advent of computers and the availability of free records from the Mormon Church, the ease of doing genealogical research exploded. Some of the software and services were either free or inexpensive. Of course, “free” doesn’t do much for a service provider’s cash flow. So, into each CEO’s mind comes, sooner or later, thoughts of monetization. How could Facebook’s Zuckerberg and others turn a free service into something that can make them gazillions? In the case of genealogy services, they started by charging a monthly access fee, and in one case, by enticing viewers to keep paying fees by waving images of fig leaves to attract their attention. That was a strange but brilliant ploy that worked very well on this researcher.

The next step in monetization is now universal: sell ads to companies who want access to the growing body of amateur genealogists. The final ploy, and by far the most ethically troubling, is selling information about users of computer services. First there were those pesky cookies, but now there is blood, or saliva more exactly.

For some companies, it is not enough to know what users search for. There is now a market for information about who you are, your very genetic essence, which is hidden even to you. But some companies like 23andme, Ancestry, MyHeritage, GPS Origins, Living DNA, and Family Tree DNA, let you take a peek into your genes, for a price.

The ironic thing is, this most personal information is not only freely given, but people actually pay the DNA harvesters to harvest their most sacred self. And of course, once that has been done, your genetic-identity can be sold (read the fine pint). While we are urged to protect ourselves from identity theft, isn’t it odd that we are at the same time being enticed into giving away our most precious identity of all, our DNA? And we seem to be doing so gladly, blithely unaware of the implications for us and our progeny.

But don’t let the natural skeptic in me show through too strongly. I do, after all, have faith that everything we’re being asked to store in the “cloud” is actually as secure as cloud storage facilities (whatever those are) claim. And I’m sure the secrets buried deep in our genes are forever kept private, and safe from hackers.

But then, there is that troubling Orwellian Consent Form.

Oh well, Sally Simpkin’s monitoring assignment in Triangle is purely fictional. Surely, no government would really have an interest in our genes.

Or would it?




U.S. Navy Diving and Aviation Safety

Blood pressure is not the only silent medical killer. Hypoxia is also, and unlike chronically elevated blood pressure, it cripples within minutes, or seconds.

Hypoxia, a condition defined by lower than normal inspired oxygen levels, has killed divers during rebreather malfunctions, and it has killed pilots and passengers, as in the 1999 case of loss of cabin pressure in a Lear Jet that killed professional golfer Payne Stewart and his entourage and aircrew. Based on Air Traffic Control transcripts, that fatal decompression occurred somewhere between an altitude of 23,000 feet and 36,500 ft.

In most aircraft hypoxia incidents, onset is rapid, and no publically releasable record is left behind. The following recording is an exception, an audio recording of an hypoxia emergency during a Kalitta Air cargo flight.

Due to the seriousness of hypoxia in flight, military aircrew have to take recurrent hypoxia recognition training, often in a hypobaric (low pressure) chamber.

As the following video shows, hypoxia has the potential for quickly disabling you in the case of an airliner cabin depressurization.

Aircrew who must repeatedly take hypoxia recognition training are aware that such training comes with some element of risk. Rapid exposure to high altitude can produce painful and potentially dangerous decompression sickness (DCS) due to the formation of bubbles within the body’s blood vessels.

In a seminal Navy Experimental Diving Unit (NEDU) report published in 1991, LCDR Bruce Slobodnik, LCDR Marie Wallick and LCDR Jim Chimiak, M.D. noted that the incidence of decompression sickness in altitude chamber runs from 1986 through 1989 was 0.16%, including both aviation physiology trainees and medical attendants at the Naval Aerospace Medical Institute. Navy-wide the DCS incidence “for all students participating in aviation physiology training for 1988 was 0.15%”. If you were one of the 1 and a half students out of a thousand being treated for painful decompression sickness, you would treasure a way to receive the same hypoxia recognition training without risk of DCS.

With that in mind, and being aware of some preliminary studies (1-3), NEDU researchers performed a double blind study on twelve naïve subjects. A double-blind experimental design, where neither subject nor investigator knows which gas mixture is being provided for the test, is important in medical research to minimize investigator and subject bias. Slobodnik was a designated Naval Aerospace Physiologist, Wallick was a Navy Research Psychologist, and Chimiak was a Research Medical Officer. (Chimiak is currently the Medical Director at Divers Alert Network.)

Three hypoxic gas mixtures were tested (6.2% O2, 7.0% and 7.85% O2) for a planned total of 36 exposures. (Only 35 were completed due to non-test related problems in one subject.) Not surprisingly, average subject performance in a muscle-eye coordination test (two-dimensional compensatory tracking test) declined at the lower oxygen concentrations. [At the time of the testing (1990), the tracking test was a candidate for the Unified Triservice Cognitive Performance Assessment Battery (UTC-PAB)].

As a result of this 1990-1991 testing (4), NEDU proved a way of repeatedly inducing hypoxia without a vacuum chamber, and without the risk of DCS.

The Navy Aerospace Medical Research Laboratory built on that foundational research to build a device that safely produces hypoxia recognition training for aircrew. That device, a Reduced Oxygen Breathing Device is shown in this Navy photo.

070216-N-6247M-009 Whidbey Island, Wash. (Feb 16, 2007) Ð Lt. Cmdr. James McAllister, from San Diego, Calif. sits in the simulator during a test flight using the new Reduced Oxygen Breathing Device (ROBD). The ROBD is a portable device that delivers a mixture of air, nitrogen and oxygen to aircrew, simulating any desired altitude. Combined with a flight simulator the ultimate effect replicates an altitude induced hypoxia event. McAllister is the Director of the Aviation Survival Training Center at Whidbey Island. U.S. Navy photo by Mass Communication Specialist 1st Class Bruce McVicar (RELEASED)
Whidbey Island, Wash. (Feb 16, 2007) Lt. Cmdr. James McAllister, from San Diego, Calif. sits in the simulator during a test flight using the Reduced Oxygen Breathing Device (ROBD). The ROBD is a portable device that delivers a mixture of air, nitrogen and oxygen to aircrew, simulating any desired altitude. Combined with a flight simulator the ultimate effect replicates an altitude induced hypoxia event. McAllister is the Director of the Aviation Survival Training Center at Whidbey Island. U.S. Navy photo by Mass Communication Specialist 1st Class Bruce McVicar.

Although NEDU is best known for its pioneering work in deep sea and combat diving, it continues to provide support for the Air Force, Army and Marines in both altitude studies of life-saving equipment, and aircrew life support systems. Remarkably, the deepest diving complex in the world, certified for human occupancy, also has one of the highest altitude capabilities. It was certified to an altitude of 150,000 feet, and gets tested on occasion to altitudes near 100,000 feet. At 100,000 feet, there is only 1% of the oxygen available at sea level. Exposure to that altitude without a pressure suit and helmet would lead to almost instantaneous unconsciousness.

OSF FL 900
A test run to over 90,000 feet simulated altitude.

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  1. Herron DM. Hypobaric training of flight personnel without compromising quality of life. AGARD Conference Proceedings No. 396, p. 47-1-47-7.
  2. Collins WE, Mertens HW. Age, alcohol, and simulated altitude: effects on performance and Breathalyzer scores. Aviat. Space Environ Med, 1988; 59:1026-33.
  3. Baumgardner FW, Ernsting J, Holden R, Storm WF. Responses to hypoxia imposed by two methods. Preprints of the 1980 Annual Scientific Meeting of the Aerospace Medical Association, Anaheim, CA, p: 123.
  4. Slobodnik B, Wallick MT, Chimiak, JM. Effectiveness of oxygen-nitrogen gas mixtures in inducing hypoxia at 1 ATA. Navy Experimental Diving Unit Technical Report 04-91, June 1981.


A Geometric Mind

By Impronta – Own work, CC BY-SA 3.0, https://commons.wikimedia.org

I challenge you to describe the following images in terms of simple geometric shapes: shapes such as rectangles and circles, and flat surfaces called planes.

If you see one of those shapes in the image, then mentally note it.

You may not be able to completely define the image with those simple shapes, but at least note those parts of the image where you can see a plane, or a rectangle, or a circle.

The shapes are not likely to be seen dead on; they may be seen at an oblique angle.

Color is an interesting variable in the images, but it is not the primary focus of this exercise. The ability to use geometrical shapes is the point of this post.

The first such shape is Figure 1.

Copyright John R. Clarke.


The next shape is Figure 2. Do you see a lighted plane on the left partially obscured by an extruded rectangle, otherwise known as a rectangular prism or cuboid?



Figure 3. Yet another image, somewhat similar to Figure 2:



And a fourth image, Figure 4.

Copyright John R. Clarke.


Now, lets try some variations on the theme.


















The four images immediately above are identical to the first four images, but by seeing them in this order you may detect that there are only two unique images.

The images on the right are simply the images on the left rotated 180°; that is, they are turned upside down.

And yet most people identify an entirely different geometry, depending on which way the images are rotated.

So, seeing is believing …

… or is it?

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I do not know if this visual phenomenon has a name or not: I accidentally discovered it when looking at images to post on a laboratory wall. One figure looked unfamiliar; I was confused by it, until I happened to rotate it.

As the French say, voila. It was an optical illusion caused by our brain’s tendency to look for familiar shapes in unfamiliar and potentially confusing images.

There is a literature on the illusions of inverted images where images have been digitally manipulated (sometimes called the Thatcher Effect), but the images above have not been altered in any way.






How Will You Try to Kill Me?

Émile Jean-Horace Vernet-The Angel of Death

It’s been over three years since I posted a cautionary tale about oxygen sensors in rebreathers, and the calamities they can cause. Since then, the toll of divers lured to their death has been steadily mounting. In one week alone in April 2016, at almost the same geographical latitude in Northern Florida, there were two diving fatalities involving rebreathers. It is an alarming and continuing trend.

I know a highly experienced diver who starts each dive by looking at his diving equipment, his underwater life support system, and asking it that title question: How will you try to kill me today?

This deep cave diver, equally at home with open circuit scuba and electronic rebreathers, is not a bold cave diver. He is exceptionally cautious, because he is also the U.S. Navy’s diving accident investigator. He has promised me that his diving equipment will never end up in our accident equipment cage.

He and I have seen far too many of the diving follies where underwater life support systems fail their divers. But the crucible in which those fatal failures are often born are errors of commission or omission by the deceased.

Carelessness and an attitude of “it can’t happen to me” seem all too prevalent, even among the best trained divers. Divers are human, and humans make mistakes. Statistically, those accidents happen across all lines of experience: from novice divers, to experienced professional and governmental divers, and even military divers. They all make mistakes that can, and often do, prove fatal.

It is exceedingly rare that a life support system fails all by itself, since by design they are robust, and have either simple, fool-proof designs, or redundancy. In theory a single failure should not bring a diver to his end.

The “head”, triplicate oxygen sensors, oxygen solenoid and wiring leading to the rebreather CPU. Image from jj-ccr.com.


Are oxygen sensors trying to kill you? That depends on how old they are? Are they in date? Ignoring the expiration date on chocolate chip cookies probably won’t kill you, but ignoring the expiration date on oxygen sensors may well prove fatal. Complex systems like rebreathers depend upon critical subsystems that cannot be neglected without placing the diver at risk.

Oxygen sensors are usually found in triplicate, but if one or more are going bad during a dive, the diver and the rebreather can receive false warnings of oxygen content in the gas being breathed.  We have seen a rebreather computer “black box” record two sensor failures, and it’s CPU logic deduced that the single working sensor was the one in error.

The controller’s programmed logic forced it to ignore the good sensor, and thus the controller continued to open the oxygen solenoid and add oxygen in an attempt to make the two dying sensors read an appropriately high O2. Eventually, the diver, ignoring or not understanding various alarms he was being given, went unconscious due to an oxygen-induced seizure. His oxygen level was too high, not too low.

Unlike fuel for a car or airplane, you can have too much oxygen.

Oxygen sensors do not fail high, but they do fail low, due to age. Rebreather manufacturers should add that fact into their decision logic tree before triggering inaccurate alarms. But ultimately, it’s the diver’s responsibility to examine his own oxygen sensor readings and figure out what is happening. The analytical capability of the human brain should far exceed the capability of the rebreather CPU, at least for the foreseeable future.

JAKSA high pressure 6-volt solenoid used in a Megalodon rebreather. NEDU photo.

Oxygen addition solenoids hold back the flow of oxygen from a rebreather oxygen bottle until a voltage pulse from the rebreather controller signals it to open momentarily. The oxygen flow path is normally kept closed by a spring inside the solenoid, holding a plunger down against its seat.

But solenoids can fail on occasion, which means they will not provide life giving oxygen to the diver. The diver must then either manually add oxygen using an addition valve, or switch to bailout gas appropriate for the depth.

Cut-away diagram of a 24-volt Jaksa 200 bar solenoid.

Through either accident or design, divers have been known to invert their solenoid spring and plunger, thereby keeping the gas flow open. In that case, oxygen could not be controlled except by manually turning on and off the valve to the oxygen tank. Of course, knowing when oxygen is too low or too high would depend upon readings from the oxygen sensors.

Suffice it to say that such action would be extremely reckless. And if the oxygen sensors were old, and thus reading lower than the true oxygen partial pressure, the diver would be setting himself up for a fatal oxygen seizure. It has happened.

Assuming a solenoid has not been tampered with, alarms should warn the diver that either the solenoid has failed, or that the partial pressure of oxygen is dropping below tolerance limits.

But as the following figures reveal, if the diver does not react quickly enough to add oxygen manually, or switch to bail out gas, they might not make it to the surface.

The three figures below are screen captures from U.S. Navy software written by this author, that models various types of underwater breathing apparatus, rebreathers and scuba. In the setup of the model, an electronically controlled, constant PO2 rebreather is selected. In the next screen various rebreather parameters are selected, and in this case we model a very small oxygen bottle, simulating an oxygen solenoid failure during a dive. On another screen, a 60 feet sea water for 60 minutes dive is planned, with the swimming diver’s average oxygen consumption rate set at 1.5 standard liters per minute.

Screen shot 3Screen shot 2










On the large screen shot below, we see a black line representing diver depth as a function of time (increasing from the dashed grey line marked 0, to 60 fsw), a gray band of diver mouth pressure, and an all-important blue line showing the partial pressure of inspired oxygen as it initially increases as the diver descends, then overshoots, and finally settles off at the predetermined control level of oxygen partial pressure (in this case 1.3 atmospheres). Broken lines on the very bottom of the graph show automated activation of diluent add valve, oxygen add solenoid, and over pressure relief valve. Long horizontal colored dashes show critical levels of oxygen partial pressure, normal oxygen level (cyan) and the limit of consciousness (red).

Screen shot 1
Screen shot of UBASim results after an ill-fated 60 fsw dive.

The oxygen solenoid fails 53.7 minutes into the dive, no longer adding oxygen. Therefore the diver’s inhaled oxygen level begins to drop. Rather than follow the emergency procedures, or perhaps being oblivious to the emergency, this simulated diver begins an ascent. As ambient pressure drops during the ascent, the drop in oxygen pressure increases.

In this particular example, 62.5 minutes after the dive began, and at a depth of 13.5 feet, the diver loses consciousness. With the loss of consciousness, the diver’s survival depends on many variables; whether he’s wearing a full face mask, whether he sinks or continues to ascend, or is rescued immediately by an attentive boat crew or buddy diver. It’s a crap shoot.

So basically, the rebreather tried to kill the diver, but he would only die if he ignored repeated warnings and neglected emergency procedures.

What about your rebreather’s carbon dioxide scrubber canister? Do you know what the canister duration will be in cold water at high work rates? Do you really know, or are you and the manufacturer guessing? What about the effect of depth, or helium or trimix gas mixes? Where is the data upon which you are betting your life, and how was it acquired?

Scrubber canister and sodalime. NEDU Photo
NEDU photo.












Sadly, few rebreathers have dependable and well calibrated carbon dioxide sensors; which is unfortunate because a depleted or “broken through” scrubber canister can kill you just as dead as a lack of oxygen. The only difference is a matter of speed; carbon dioxide will knock you out relatively slowly, compared to a lack of oxygen.

But if you think coming up from a dive with a headache is normal, then maybe you should rethink that. It could be that your rebreather is trying to kill you.





Where Things Move Quickly and Darkly

I came across a great article from the New Yorker with an interesting title. In fact, my interest lasted all the way to the end.

Spooked: What do we learn about science from a controversy in physics?

“Albert Einstein (Nobel)” by Unknown – Official 1921 Nobel Prize in Physics photograph. Licensed under Public Domain via Wikimedia Commons

If you get the feeling that science is not as pure of thought and logic as it pretends to be, then you will find some comfort in Adam Gopnik’s approachable review of the deeply hidden controversy surrounding what Albert Einstein called “spooky action at a distance.” Spooky action is the weirdest of all science, and makes telepathy and clairvoyance seem almost banal by comparison.

In my opinion, parts of Gopnik’s none-too-technical article remind me of the quote by Dr. Jason Parker, the protagonist in the science fiction thriller, “Middle Waters“. In a supposed speech to the open-minded Emerald Path Society, Parker said, “There are regions between heaven and Earth where magic seems real and reality blurs with the surreal. It is a place where things move quickly and darkly, be they friend or foe. The hard part for me is knowing the difference between them.”

Gopnik expressed that thought more prosaically by the following: “”Magical” explanations, like spooky action, are constantly being revived and rebuffed, until, at last, they are reinterpreted and accepted. Instead of a neat line between science and magic, then, we see a jumpy, shifting boundary that keeps getting redrawn.”

Gopnik goes on to say, “Real-world demarcations between science and magic … are … made on the move and as much a trap as a teaching aid.”

To be honest, I did leave out Gopnik’s entertaining reference to Bugs Bunny and Yosemite Sam. Again, if you have ever been suspicious of the purity of science, the New Yorker article is well worth the read.

Unlike the concerns of Einstein, Neils Bohr and the rest of the cast of early 20th century physicists, the anxiety of Jason Parker, the fictional hero, is not cosmological; it’s personal. It’s every bit as personal as it is for each of us when we sometimes question our sanity.

Yes, real life can be like that sometimes, when things intrude into our ordered lives, as quickly as a Midwest tornado, but with less fanfare and warning. But every bit as destructive. And it is at those points, those juxtapositions with things radical, unexpected, that we end up questioning our grip on reality.

After all, what could be more unexpected and unreal seeming than the notion that cosmological matter we can’t see, dark matter, could send comets crashing into the Earth, as Gopnik mentioned, and the  Harvard theoretical physicist Lisa Randall wrote about in her book Dark Matter and the Dinosaurs.

So, Jason Parker had every reason to be wary of things that move quickly and darkly. They can be a killer.

Sometimes, as in the case of Parker, those internal reflections do end up having a cosmological consequence. But even if they don’t, it’s a good idea to occasionally reexamine our lives for the things which may seem one day to be magical, and the next day to be very real.

In short, the magic should not be dismissed out of hand, because, after all, just like “spooky action at a distance” and “dark matter”, it may not be magic after all.