Elk Reduction

In the winter of 1964, some time after Christmas, an old bull elk stumbled down through the steaming terraces of Mammoth Hot Spring. It was a bitter cold and windless night in the far northwest corner of Wyoming. Snow was smeared in streaks and patches on the frozen ground, except for the hot zones where the geothermal water oozed. In the silence, you could hear the tiny hissing and burping of the boiling water striking the cold January air. The elk passed in and out of ragged wisps of steam. His ribs and shoulder blades pressed out through his scruffy hide. He was starving. Like a ghost, he drifted across the road with the steam, and took up a position behind a dark clump of juniper. His head drooped towards the ground. I know, because I saw him there the next morning. The juniper he picked was about 50 feet from the path that I took with my brother each day to school. Together with a gang of 4 or 5 other kids in brown work boots, blue jeans and quilted down parkas, we climbed up the broken travertine terrace and spotted the elk.

We eyed each other. Time was running short for all of us. The elk was dying. We were late for school. We continued up the mountain with a few fitful backward glances, our destiny well within our own means. The elk swung his head slowly, waiting for his. On our way home from school, we raced down the mountain, feet skidding and arms flailing, to see if the elk was dead. Not yet. He stood still, trembling slightly, staring at us with eyes that seemed to have gone milky with cataracts. We shuffled our feet, disappointed – then continued on down to our houses in their neat set of double rows in the valley below.

elk

In the evening, my Dad reloaded his cartridges. They were shiny yellow brass, long and sensuous like a lipstick, with dark scars where the burning gunpowder left its residues. They stood in line on a small round tray, while the new black powder poured down into each of them in turn, a carefully measured little pile of black sand. Then Dad would press down on a small metal handle, and a bright copper bullet was pressed snugly into the end of the shell. Now instead of standing there with its gaping mouth hanging open, each cartridge was capped with this glittering, lethal, aerodynamic crown. Bullets were cool.

Every morning on my way to school, I could look up and see a helicopter thumping overhead. It was Dad, flying away up the Lamar valley on his way to work. During the course of the day, he would fire most of those reloaded cartridges into the elk that he spotted from the helicopter. That killed them quicker than starvation, which was their other choice. The rangers called this activity elk reduction. There were no wolves in the park then, and few other predators. The coyotes were so stuffed on dead elk that they couldn’t be bothered to attack them while they were still standing. So the elk stood and waited. For the ones who were still far from the roads, where no one would see them, the helicopters might come. Those who drifted in close to the roads and houses, like the one next to our school path, were on their own. The news media of that time were nothing like the snarling hoard that scavenges for sensationalism everywhere today. But the rangers knew better than to create an incident in full view of the road.

It was against the policies of Yellowstone Park and the Department of the Interior to feed animals in the park. So no one brought the starving bull anything to eat. It was not against park policy to shoot the animals, however. That hadn’t been against the rules for a long time. That’s what had happened to the wolves. By the time I lived there, they were all gone. When bears misbehaved, by coming right into the campgrounds and begging for food, that’s what happened to them too. First they would make a big public show of darting the bear with a hypodermic full of succinyl choline. It made the bear get soggy and fall asleep. Then the rangers would hustle the limp body into a pickup, arguable to be taken to a safer place. The tourists loved it. Often, the bear never woke up. If it was one who was coming back into the campgrounds over and over, they made sure it didn’t wake up. It was my Dad’s job to drag the bear carcasses away into the woods where tourists wouldn’t see them. Most of the horses wouldn’t do it. They bucked, shied, looked crazy in the eyes and ran off. Rex the wonder horse, an old palomino gelding who lived at the south entrance to the park, would pull bears. Rex would stand patiently if a small boy approached him, drawn by the salty, sweet smell of his warm yellow hide. My eyes came just to the level of his powerful chest. I would bury my face in his mane, and he would look around calmly, making a small, wet sound with his nose. He was telling me not to worry. I gave Rex his name, which was the same as the one written on my own plastic riding horse. It was mounted on springs to a metal frame, and I would rock back and forth on it for hours, pulling imaginary bears out into the back woods.

The bears were dumped about a half mile behind the barn, near on old pioneer grave. The girl buried there was named Betsy Roebottom. The bears were left not far from Betsy’s simple headstone. I knew where they were, because sometimes Dad let me ride on the back of the saddle, holding on to the taut pull rope as if it was an important job that needed done. The bears were strung out in a ragged line under the dense lodgepole pines. Some were just bones. Ravens stood on top of them and yelled at us.

Without their key predators, the elk population exploded. The park was being stripped of forage. Elk were starving. It hadn’t occurred to the employees of the Park Service back in the 1920’s. They thought of predators as bad park citizens who caused unnecessary pain and suffering. They also thought of themselves as the masters of the Park, who could easily manage this unruly system and make it better. When a wolf attacked and throttled a week-old elk calf, they interpreted that as a bad thing. And it was, if you were the elk calf. It seems odd, looking back, that the rangers seemed to identify personally with a large grazing animal, and not with a small, highly social predator that hunted cooperatively in packs. Because really, that’s exactly what the rangers were themselves. Perhaps they looked on the wolves as competitors trying to invade their territory.

By the time I was living there, the park rangers knew that they weren’t the masters of anything. They couldn’t even get the government to pay for the bullets that they used to kill off the elk. But I think Dad liked to reload his cartridges – he probably would have done it anyway. The rangers also knew by then that the animals that had no guns were better ecosystem managers than the animals who did. It was a joke. All of the rangers understood that in 1964, in Montana, no one was going to get permission to bring back a predator like the wolf. At night, other rangers would come to the house and talk about it while they drank beer and Mom baked them cookies. They sounded bitter and angry and defeated, and I couldn’t understand why they didn’t just go get some wolves. As I got older, I would begin to know the NPS, the IRS, the DEA, the FDA, FEMA, INS, HSA – all of them. I am often stopped from getting on airplanes for improperly exposing my liquids. Now I see what was stopping the rangers. Forty years would go by before they would finally get enough momentum to do what was right. Many of the ones drinking beer in my father’s house would not live long enough to see it happen.

The next day, the elk had moved. Maybe he went off in the night for a drink of water. We found him out in the open, lying down, still looking at us with those glazed eyes. For one last day, he lay there like a statue. The next morning it was snowing lightly, and coyotes and ravens were milling around him in the frosty morning air. His stomach was torn open, and his head was finally down on the ground. Dark, round, empty sockets stared blankly off into space. Magpies bickered about who got to perch in his antlers. We threw rocks at the coyotes, and then milled around his body ourselves, poking at it with sticks. Satisfied, we raced off to tell our parents.

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Why Obama Should Not be King

Kirk_Obama_Cartoon

Shortly before his policies in the Middle East imploded on themselves, dragging Obama into his latest, twitchy, defensive, mouse-in-a-corner foreign policy debacle, he was trying to focus our attention on climate policy. In keeping with his other recent regal edicts, he ordered the EPA to order the states to order their power companies to reduce carbon dioxide emissions by 30% over the next 15 years. To emphasize the obviousness of this move, he snarked that anyone who opposed his policy must think the moon was made of green cheese.

Curious to know what effect this policy might really have on the amount of CO2 in the atmosphere, I turned to the well known Keeling Curve. (See Figure 1.) Each day, the concentration of carbon dioxide at the summit of Mauna Loa is determined, with an accuracy of 10 parts per billion, and reported to the general public via the NOAA website.

Atmospheric CO2 Concentration vs. US Energy-Related CO2 Emissions

 

 Figure 1

On June 2, the day of Obama’s proclamation, the concentration was 402.15 ppm. Just now, the concentration is 397.76 ppm, or 0.039776%. In the last two months, the value has plummeted as photosynthesis in the northern hemisphere summer dominated the carbon cycle in what can only be described as the planet Earth inhaling. For as long as man has made these measurements, starting in the 1960s, there has been a pulsatile, seasonal rise and fall in the measured concentration of atmospheric CO2. This got me thinking… who is really in charge of atmospheric CO2 anyway? And how much CO2 are we talking about?

The EPA reports the total US energy-related CO2 emissions in the latest full year were 5.290 x 109 kg. If you plot the amount of US energy-related emissions for the last 15 years against the Mauna Loa data, you can see right away that there is no correlation. The r-value is -0.45, which means that as US emissions gradually declined by about 12% since 2007, the amount of CO2 in the atmosphere marched steadily upward. There are at least two plausible reasons for this. Unlike the Mauna Loa data, which is a precise number measured by calibrated scientific instruments, the EPA number is, basically, a guess. No one sits atop the chimneys of power plants metering out the emitted gasses, and no one really keeps track of the fuel burned by locomotives pulling mostly coal cars but also some cement cars… you get the point. But if one concedes the point that the EPA estimate is at least in the ballpark, it is plausible that this amount of CO2 simply isn’t significant, in the grand scale of things. So let’s think about that…

In order to find the mass of the entire atmosphere, one must multiply the surface area of the Earth (5.1 x 1014 m2) by the pressure exerted by the atmosphere at the surface (101,325 Pa (or N/m2)) and divided by the force of gravity (9.81 N/kg), giving 5.2 x 1018 kg.

In order to find out how much of that is CO2, you simply multiply that number by the Mauna Loa percentage for the date you have in mind. On June 2, the day Obama declared atmospheric marshal law, there was 2.091 x 1015 kg of CO2 in the air. Eight weeks later, there is 2.068 x 1015 kg, for a net reduction of 2.3 x 1013 kg. Meanwhile, US power plants were emitting 8.1 x 108 kg. That’s five orders of magnitude smaller. Houston, I think we have an answer to the problem.

There is 400,000 times more CO2 in the atmosphere than is generated by the US power industry in one year. Over the last 8 weeks, the net negative flux of the natural carbon cycle was nearly 30,000 times larger than the tiny positive contribution from US power plants. Visually explained, because the US power industry generated CO2, the large black rectangle representing all of the carbon pulled out of the air by natural forces in June and July has this little white hole in it, as illustrated below. Obama is proposing, at some cost, to make that hole 30% smaller in 15 years. I hope that any persons looking to this president for decisive actions (the Yazidis and Ukrainians come to mind) will have a look at this graphic.

pixelinthedark

In June and July 2014, the white square represents the US power industry carbon output relative to the magnitude of the natural carbon cycle.

Since global atmospheric CO2 concentration and US energy-related CO2 emissions have had no correlation with each other for 15 years, it can be expected that they will remain without any correlation for the next 15 years as well. Since the annual flux through the carbon cycle is so much larger than US power emissions, stating that reducing US power plant emissions 30% will reduce global warming is like stating that a boy peeing in the Mississippi river will flood New Orleans. Any true scientist can state, with conviction, that there will be no detectable impact of this EPA policy on the amount of CO2 measured in the atmosphere. Any reasonable observer could likewise state that impacts on the economy and power industry, whatever their magnitude (which may be considerable) cannot be justified by any balancing environmental benefit.

Some years ago, Mark Twain noted, “In politics, people’s beliefs and convictions are in almost every case gotten at second hand, and without examination, from authorities who have not themselves examined the questions at issue, and whose opinions about them are not worth a damn.”

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Exterminating the Parasitic CEO

Don’t be like these guys…

It is June and time for that twisted corporate introspective agony called the Annual Employee Performance Review. There is something slightly Maoist in the idea that, once every year, each employee-supervisor pair should turn on each other and start rank ordering their superlatives and deficiencies like some poor couple in marital therapy. It’s been my experience that more harm than good comes of this. Since I also do my own scathing self-review (Organization: Abysmal. It is demotivating to many of those who work around me to see to what degree my own work is in a shambles.), I had a chance to comment on my own compensation.

I make $300,000 per year running a company of about 300 people with global annual revenues of about $40 million. Fortunately, the New York Times recently reviewed CEO compensation in a piece that I picked up on Twitter, allowing me to make some comparisons and develop two simple guidelines for setting appropriate CEO pay.

  1. The CEO should never be paid more than 1% of gross revenue. At an astonishing 47% of gross revenue, the leader of the NYT survey is consuming his parent company feet first and his lips are slurping at his own ass.
  2. The CEO should never be paid more than 10 times the compensation of the lowest paid entry-level college graduate in that company. I don’t care how stuffed your Rolodex, how merrily you multitask, how bluetoothed your smartphone and laptop, how energized you emerge in the office at 5:00 am after leaving a mere 4 hours earlier—you don’t do the work of more than 10 people. No, you don’t.

Virtually all of the corporate CEOs compensating themselves at rates shooting past $100 million each year are doing so not because they have earned it or because they deserve it—they do it because they can. That is the same reason Viktor Yanukovych built himself a mansion containing a white Steinway piano modeled after the one presented to Yoko Ono by John Lennon. That is also why Muammar Gaddafi and Saddam Hussein [fill in any excess you find most grotesque].

The role model of the CEO should be that of a statesman, not a tyrant. His personal ambitions should be modest, while his ambitions for his staff and their enterprise should be unlimited. So if you want a raise, masters of the universe, add $5 million to your corporate sales, add $5,000 to the pay of your newest and brightest—and I’m sure you can do the math from there.

Yanukovych_piano

The piano of Viktor Yanukovych, President of Ukraine from 2010 to 2014.

Note added in proof: Application of these CEO rules to my own pay caps compensation at $340,000/yr. However, it was determined that my pay change will be 0.0%. The time being wasted writing and researching irrelevant topics for my personal blog as well as the time spent idly chatting on social media such as Twitter were duly noted. That is, performance issues have delayed the full actualization of my reward potential. Only HR could make it sound so positive.

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Phenotyping and the Bucketmouth Beard

genome

genome

When the Personal Genome Project(PGP) launched and the first ten volunteers were inducted, it was clear that they were intent on more than just genomics. Most of us were photographed with a little 10cm ruler taped to the middle of our foreheads. This had the effect of making us all look (and feel) as if we were being hauled in for a DUI, but I think that was inadvertent. The only use that could arguably be made of that little bar grid was to phenotype us. That is, the PGP wanted to make an effort to describe and measure exactly the look, feel, shape and dimension of the protoplasmic projection of those genomes they were sequencing. That set the bar very high indeed.

As we have come to realize, phenotyping is easier said than done, and it doesn’t exactly roll off the tongue in the first place. I can extract at least a couple bits of crude phenotype from those early PGP photos. (For reference, see my earlier blog post Patients in Waiting) Interpupillary distance (how far apart are your eyes) is an important human metric. It undoubtedly follows a bell shaped Gaussian distribution, and a narrow one, because if it’s too short, you look cross eyed and stupid. If it’s too wide, you look bug eyed and alien. Two important points quickly emerge. There are numerous phenotypic designations already in common usage, and they are usually offensive. Scientists wanting to tease apart the many genetic and embryonic influences on craniofacial development that determine our interpupillary distance need to be able to talk about it without being hissed at by enforcers of the politically correct. Niceties aside, it’s pretty clear that Steve Pinker, PGP-6, and James Shirley, PGP-10, are the cross-eyed and bug-eyed outliers of our particular group.

Interpupillary outliers

Interpupillary Outliers

The author and his son share a SNP in intron 86 of the HERC2 gene, controlling expression of the adjacent OCA2 gene, and predicted to result in a blue colored iris.

My son and I share an SNP in intron 86 of the HERC2 gene, controlling expression of the adjacent OCA2 gene, and predicted to result in a blue colored iris.

You can also assess skin pigmentation, just based on whether you are whiter than your strip or your strip is whiter than you. James Shirley and Rosalyn Gill are probably our diversity winners, but melanization can be measured more precisely than this.

pigment

Melanization Outliers

All that is missing from this phenotypic analysis is precision, reproducibility, a common accepted semantics, and a testable underlying theory of genetic contribution. In addition, many people actively subvert accurate phenotyping by altering their appearance with cosmetics, surgery, prosthetics, dentistry and the coloring and shaving of hair. Only George Church of the original PGP-10 gave us a full view of his facial hair phenotype.

I was mildly curious about this, so I grew out my own beard. Nothing like a World Series on the line or anything – I just wanted to have an accurate phenotype. There’s been a lot of discussion around our labs about what a beard is for in the first place. Is it a microbiome warehouse of stray composting food particles  so you can mix probiotic bacterial spores into your mouth while you eat with your fingers? Is it the opposite of a love handle – a hate handle that you can grab and jerk on if you’re not receiving the full attention of the owner?

Imagine my surprise when mine grew out – the first time I had seen it since college – and it had bands in it. Seriously – from ear to chin, it goes dark-white-dark-white and then back up the other side in the same order. Not all people can grow a beard. Not all of them who do grow one have a striped one. WTF? I probably would have just left that thought to the dustbin of time and the ravages of senile dementia, but the next day on TV I saw an interview with Shane Smith, founder of Vice Media. It was an “I am your father Luke!” kind of moment.

shanekirk1_

So I took a few photographs and made some observations. I now think your beard is there to make you look authoritative and scary. If I open my mouth really wide and say something really mean, like “What the f*** is going on here??!!” the black bands make it look like my mouth is maybe 5 times bigger than it really is. I have a bucketmouth beard. Is this genetic? Looking back at the PGP, George Church kind of has one too. But I think both of us will recall that our beards were originally solid, not striped.

before and after

So here is my theory: Beards are secondary sexual characteristics of males that initially signal the onset of sexual maturity, the adequacy of whole body testosterone activity and the desire to advertise oneself as a suitable mate. Beards are initially solid in color, and the fullness and density of the beard can be used to advertise vigor, health and adequate strength and nutrition. As men age, those who are continuously in a position of authority as a group leader or chief undergo epigenetic changes that enhance the loss of  beard follicular melanin in a banded pattern. (George has been the head of Harvard’s Church lab since 1986; I have been CEO of Cayman for 35 years; Shane is a whippersnapper but he’s the founder of Vice) This banded, bucketmouth beard increases the intimidating appearance of facial gestures and reduces the physical effort required to maintain order among unruly subordinates. This is an easily testable hypothesis, although no biochemical basis is proposed. In short, you can’t be the boss until you’ve earned your stripes.

I’m really curious how common this sort of beard pattern is in the general population. Curious enough, that I’ll send a FREE Philips Norelco Vacuum Beard Trimmer to my favorite 5 photographic examples of a bucketmouth beard. Submit your beard one of the following ways:

Post the picture on Twitter and mention me, @KirkMMaxey

Email the picture to my address, KirkMike157@gmail.com

There was an elegant paper in Science recently that described precisely the underlying embryology and endocrine biochemistry leading to the stripes and bands on King Cheetahs and Mackerel Tabby cats. A single gene mutation distinguishes the cat on the left from the one on the right. However, at least four additional genes work in tandem to establish the striped pattern.  My wish for the Personal Genome Project is that it will someday let us know as much about ourselves as we do about our cats.

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Winter of our Disrespect

lighthouseOn a cold February morning recently I checked the Great Lakes Environmental Research site and found that only one of the Great Lakes had any waves on it. Superior, Erie, Huron, and Ontario were frozen solid. A small peanut of Lake Michigan remained partially liquid and filled with floe ice. The same map also shows me that I could drive a snowmobile straight from St. Joseph, Michigan to Chicago, Illinois avoiding all the traffic on the interstate. On one hand I’m exhilarated, because I may personally witness in the winter of 2014 the first complete freeze of the Great Lakes in recorded history. Yet on the other hand, I’m disgusted by the chicanery, incompetence, self-righteousness and posturing of the so-called “climate scientists” who assured us that the opposite of this bitter weather would prevail in the 21st century. It is not so much that they made such a prediction and were wrong. My emotional overtone springs from the fact that, through politicization of their alarmism, they were just ginning up the funding mechanisms to allow them to spend poorly even larger sums of money in the service of predicting future climates badly.

Contempt is a poor prognostic indicator for any future reconciliation between disputing sides in a conflict. Upon reflection, it is surprising that I would find myself in such an intractable state of disagreement. I myself am a scientist. I’m naturally sympathetic towards other people who study things in detail and make discoveries about those systems or objects, even when those discoveries are counterintuitive or unexpected. I actually do read the peer reviewed literature that pertains to climate, and find many of the authors publishing there to be competent scientists making credible observations, carefully restricting their conclusions to those that are supported by their data. I also browse through news reports and social media, reading what various advocates and journalists say and write about climate. This led me to follow a recent Twitter post by Carl Zimmer, that took me to 173 pages of congressional testimony by Andrew E. Dessler,  that brought me to the crystalline, cathartic comprehension of the source of this winter’s ill will.

But first I want to point out the work, unnoticed in the press and generally unheralded, of some real climate scientists.

geomar

Professor Christian Berndt is a German scientist working at the GEOMAR Helmholtz Center for Ocean Research in Kiel, Germany. In January of this year, he and his group published a detailed study of the release of methane from submarine arctic sediments off Svalbard Island in the North Atlantic. In 2008, passing ships had noticed vigorous outgassing of methane in a narrow zone of water about 400 meters deep, and this was interpreted by some as the onset of catastrophic methane hydrate dissociation caused by global warming. Methane matters, because it is 30 times more opaque to infrared radiation as CO2 is. The GEOMAR team made several expeditions to the area, made parametric echosounder profiles of the area, photographed the bottom sediment features of the gas release sites, and made a continuous 21-month bottom water temperature observation at the site. They observed carbonate precipitate crusts up to 40cm thick indicating that methane had been oozing from these sediments for at least 3,000 years, and that it was being oxidized by benthic microbes. Based on the recorded temperature profile, the authors deduced that there is a seasonal growth and decay of methane hydrate deposits along the continental shelf that has been stable for many centuries. This work was characterized by the generation of much new data through direct observation, not by computer modelling of existing data. The conclusions were limited, in that the authors admit that we do not have any precise knowledge of the global methane budget. We do not know how much methane is released worldwide or where it comes from; we do not know why the atmospheric concentration of methane stopped increasing about 15 years ago, or why it began increasing again in the last few years. But we do know, thanks to their data, a lot more about this one source, and that it is not coupled in any way to global warming.

Andrew Dessler gave testimony in the US Senate with respect to President Obama’s Climate Action Plan on January 17, 2014, the same day that Professor Berndt’s paper published in Science. By way of background, Mr. Dessler’s previous employment experience was with First Boston Corp in the investment banking industry, and then as a senior policy analyst in the Clinton White House. That is to say, he has apprenticed in the two largest criminal con games operating in America – banking and politics. A review of his sparse peer reviewed publications reveals that he is a climate modeler. That is, he does not actually study climate, he takes the data generated by real scientists such as Dr. Berndt and plugs it into computer games that he programs using public funding, yielding improbable projections of future climate that are almost certainly incorrect. A summary of more than 100 of these contradictory computer climate models recently appeared on  Steve Goddard’s Twitter feed.

It may be of little consequence what I think of Andrew Dessler, but what is so telling is what he thinks of himself. On the third page of his Senate testimony, which reads very much like a political position paper, there is a little footnote 1 after the sentence “The actual amount of warming over the last century roughly matches what is predicted by the standard model of climate.” Then, at the bottom: “1. Following particle physics and cosmology, I’ll refer to the mainstream theory of climate science as the Standard Model. A climate model is a single computational realization of the physics embodied in this standard model.” So…Mr. Dessler thinks of himself and his faulty computer model as being on a par with the Standard Model of particle physics. Not only does he rub shoulders and share the stage with Einstein, Bohr, Schrodinger, and Feynman, but also more recent Nobel laureates Sheldon Glashow, Steven Weinberg, and Abdus Salam. With a pompous grandiosity that induces vomiting, Dessler tries to paper over the absurdity of his jury rigged algorithms with the wizardry and precision of physics. He’s nothing if not generous – every single climate model that runs and generates ‘roughly the same amount of global warming’ gets to be equivalent in importance with the foundations of particle physics and the fundamental properties of all matter.

I am driving my 4×4 pickup through 20 inch snow now on the weekends, to cut firewood that I could have cut a lot more easily in September. My mare is due to foal in 4 weeks, and I can hardly afford to heat her barn with propane now that the price has doubled. I could have bred her a month later, and filled the propane tank in August. Michigan is having one of the coldest winters ever recorded. This was not predicted six months ago by long term weather forecasters. But in the 1990s, the opposite of this was vigorously predicted by climate forecasters. They were wrong. Humans are currently unable to predict either seasonal weather or  long term climate with an accuracy that allows actionable steps to be made by ordinary people. This state of affairs will likely continue, because the likes of Mr. Dessler consume an inordinate amount of the scarce public funding available to actually study climate. Unnoticed and underappreciated, the true scientists in the field who make no alarmist statements and who generate real measurements and data find their support being parasitized by thinly-veiled con men who anoint themselves as a bunch of Einsteins. A validated climate model is one that has accurately predicted  100 year average precipitation and temperature anomalies, to within 5%, over the entire planet 25 years in advance, in 4 out of 5 iterations. We have no validated models. Even if one that’s up and running is valid, we won’t know that for 125 years.  For the present, it would help if those who wish to pontificate about  future climate preface their remarks with the sobering truth: Man does not yet understand how climate works.

Trilobyte_Single

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Patients in Waiting

genome

The 10 high-profile volunteers currently having their genomes sequenced as part of the Personal Genome Project.

When people learn that I have been sequenced as part of George Church’s Personal Genome Project (PGP) they often say, “Wow- I’d like to be sequenced too!” My first response to them is, “Why – are you sick?” If the last decade has taught us anything, it’s that sequencing healthy people returns mainly raised eyebrows, but little more. Sequencing cancer patients and their tumors, on the other hand, can be life saving. Dr. Lukas Wartman probably saved himself from an early cancer death by being sequenced.

Genomic sequencing of children with unexplained illnesses also leads to heartwarming breakthroughs. The Beery brother and sister pair, Noah and Alexis, had severe dystonia from birth and could barely breathe or walk. Misdiagnosed and mistreated as having cerebral palsy, the medical and emotional cost of this failed diagnosis on the Beery family was huge.  Genomic sequencing revealed that they were complex heterozygotes for null mutations in the gene sepiapterin reductase, causing a known dopamine-linked dystonia that can be rescued by dietary supplementation. Properly treated, they now lead normal, healthy lives. Other similar pediatric miracles, such as solving a case of inflammatory bowel disease, come to mind.

The Beery Family

The Beery Family

Sequencing normal healthy people, in my experience, just tends to undermine the confidence one has in peer reviewed medical literature. I was on hand in Boston in 2008 when the first 10 completed sequences of the Personal Genome Project were rolled out. I had a special vested interest, in that mine was genome number 5. When the sequences were reported, we were all taken individually and counseled about a few of our “calls.” Remember – almost any genome will have something like 3 million SNP variants that differ with respect to the reference genome. So to say this was cherry picking, or barely skimming the surface, would both be understatements. Then they brought us back together to discuss the impact this had on us. John Halamka (PGP-2) was standing there looking sheepish because he was supposed to have an autosomal dominant neuropathy…but he didn’t. When I looked at my own data, I found mostly very vague GWAS associations. What does it really mean if you have a single nucleotide variant that is within an intron in a gene of unknown function, and that a GWAS study found it is associated with a 2.8% increase in the chance of rheumatoid arthritis, which I don’t have? Four of the first PGP-10 volunteers had mutations in the gene ELAC2 on chromosome 17, supposedly linked to prostate cancer. I was one of those – but I have a low PSA value and no history of any relative having prostate cancer for 4 generations. Fully 70% of the PGP-10 had mutations in the SP110 gene supposedly making us more susceptible to tuberculosis. Hmm. Lots of raised eyebrows and shrugged shoulders.

Looking deeper, I came across my KCNQ3 gene. The KCNQ genes are a family of voltage gated potassium channels, now numbering 1-5, working as heteromers with each other to generate the neuronal M-type current. I happen to have a single nucleotide mutation in one copy of KCNQ3, converting Arginine 777 to Glutamine. Scanning the literature, I found six other known human KCNQ3 mutants – Trp309Arg, Pro574Ser, Ala381Val, R330Cys, Gly311Val and Gly263Val – but not mine. All these other mutations lead to epileptic seizures, mostly BFNC or Benign Familial Neonatal Convulsions. They act as autosomal dominants, so only one bad copy of KCNQ3 is needed in order to have the seizure disorder. The only problem for me is…I’ve never had a seizure. What I’ve become is a “Patient in Waiting.” Otherwise called a hypochondriac made-to-order by too much genomic sequencing, or a person who is now startled by their smallest involuntary twitch.

The number of patients in waiting grows daily, as more humans are sequenced and more mutations are called…in healthy people who don’t have what the mutation is supposed to predict. I’ve included in this post the story of another such patient, a little girl named Laura Inestroza. Her story, and the fact that despite her genome, she does not have cystic fibrosis, were recently reported in The Wall Street Journal. So Laura, here’s to you, and to me, and to a long and healthy life for all of us who are proving that genes, for all that we know about them, are still keeping a lot of secrets.

Laura Inestroza, 4, was found at birth to have the genetic changes associated with cystic fibrosis, but she still has no symptoms. Michal Czerwonka for The Wall Street Journal By Amy Dockser Marcus

Laura Inestroza, 4, was found at birth to have the genetic changes associated with cystic fibrosis, but she still has no symptoms. Michal Czerwonka for The Wall Street Journal By Amy Dockser Marcus

To read the full WSJ article, Genetic Testing Leaves More Patients Living in Limbo, click here.

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Type I Diabetes – A Day in My Daughter’s Life

A parent easily falls into the trap of describing the most horrific of their adolescent children’s behaviors. There are always those loud and angry interactions of one brain soaked with testosterone interacting with another one soaking in 400 mg/dl glucose. That’s why it made me so proud when my sixteen year-old son, who loves photography, collaborated with his Type-I diabetic sister, and together they produced this video. It was a homework project that made all my years of parenting seem worthwhile. Please have a look, and pass this along to any kids you know who have recently been diagnosed with diabetes.

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