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.

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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.

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Patients in Waiting

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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.

http://www.youtube.com/watch?v=ZIVWdbnT-WU

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Lose Weight…and your poop will glow in the dark too!

laboratory ratSean Davies had a problem to solve: If you genetically modify enteric bacteria to make them more healthful, how can you quickly check to see if they’re happily growing away inside your experimental rat? The solution he chose could represent the pinnacle of scientific achievement in its own right – he incorporated bioluminescence into the same bacteria. Those rats that were successfully colonized by the modified E. coli could be detected at a glance – because their poop now glowed in the dark.

Sean did not start out to create the next GM novelty item. Working in the Vanderbilt Department of Pharmacology and with collaborators at Texas A&M and CNRS in France, he recognized that not all gut bacteria are created equal. Many recent studies have demonstrated that the gut microbiota can predispose an individual to metabolic disorders, including obesity. So why not engineer a gut microbe specifically to be a health-promoting bug?

Rat Diagram

Four weeks after ingesting a dose of these high-tech probiotic bacteria, lab rats on a high fat diet gained 20% less weight than their controls, who not only got fat, but also had boring bowel movements. Taking a cue from the field of endocannabinoids, the lipid substances that are your body’s own version of THC, the researchers surmised that a genetically modified gut microbe could be designed to produce a normal signal of satiety. The gene for N-Acylethanolamine (NAE) synthesis was transfected into the normal human commensal E. coli N1917, along with the luciferase gene so it was easy to check on how these new bugs were thriving. NAE works in the gut to induce a feeling of fullness and anorexia, normally in response to a high fat meal.

A preliminary report of the study was presented on November 4, 2013 in San Juan, Puerto Rico at the 13th International Conference on Bioactive Lipids. Sean hopes to publish a full description of these exciting results in the Journal of Clinical Investigation, no doubt to glowing reviews.

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I’m only two pages into the latest children’s book on learning one’s colors, and my 3-year old hits a snag. “Corn is NOT yellow!” he shouts indignantly. For several weeks now, he’s been going with me to the garden and bringing back armfuls of native corn, then sitting and husking them one leaf at a time until the kernels come into sight. Then, with “Oooohs!” and “Aaaahs!” worthy of a fireworks display, everyone admires the deep reds, purples, pinks, and greens that make up the true colors of maize.

Enough people have asked me about this recently that I thought I would take a stab at a topic so complicated that it won Barbara McClintock a Nobel prize. Maize is the ultimate transgenic exhibitionist, flagrantly moving bits of its genes around with each generation. This is not recombination – it is unguided transposition engineered by ancient parasitic bits of DNA that stick themselves in and out of the maize pigmentation genes at random. It made me smile when golden rice became all the buzz recently, as I’ve watched many generations of maize revert back and forth from white to golden without Greenpeace getting lathered up about it.

That’s as good a place to start as any, because the carotenoids are expressed mainly in the endosperm, forming the base color of the kernel. See the illustration for the names and locations of the various seed layers. The endosperm forms the substance of the corn kernel, and it is the canvas, while the thinner pericarp and aleurone layers are like paint layered over this base color. Corn has a robust production of deep yellow carotenoids including zeaxanthin (Fig1), and these genes are either disabled by the insertion of transposons, giving a white background, or intact, giving yellow.

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Empty Promises

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An Animal Products Export Certificate (APEC) is a bland, illegible form bearing an impressive signature in blue ink. Required on all international shipments of research proteins and antibodies, an APEC informs the overseas importer that “These products have been obtained in a manner that precludes any chance of contamination or infectious disease. Promise.” Unfortunately, the United States Department of Agriculture is the only issuer of APECs, so since the time of the partial government shutdown, they are no longer available. For a small research biotech business, that means an abrupt halt to product sales to Korea, Japan, and elsewhere.

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Click to view APEC

If one reads an APEC carefully it becomes clear that nowhere on this document are there results from any test. No test for BSE, no tests for viruses, infectious agents – nothing. In fact, what’s written there is basically nonsense. For example: “LDL Uptake Cell-Based Assay raised in rabbit, goat, bovine.” One gets a garbled visualization of something part goat and part rabbit being birthed by a cow. The actual product, pictured at the end of this post, is a tidy plastic wrapped box.

The Animal Products Export Certificate is best described as an empty promise. Promises that are in short supply, since it is only the government that makes and requires them. APECs are quite the money maker, actually, as it costs my company $51 for each one, for each overseas customer, for every shipment we send to them. Plus the cost of overnight mail coming to and from the USDA. All that has come to a halt now, as we and our customers wait for the USDA to come chugging back to life. Meanwhile, October sales are down 7%.

Getting a License to Export your Thoughts. The logical extension of requiring export permits and licenses for everything came to pass in 2011, when Ron Fouchier of Erasmus Medical College in Rotterdam was required by the Dutch government to obtain a license to export his “thoughts” in the form of a manuscript, to Science magazine in the United States. Done under protest and then appealed to the courts, this startling form of repression was upheld on September 20, 2013 by the Dutch court, citing an obscure EU regulation. Liberal thinkers who have felt a certain smugness watching businesses cope with this costly and pointless burden of paperwork should remember a version of the timeless Martin Niemöller quote: “When the Nazis came for the trade unionists, I did not speak out, because I was not a unionist…”

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Testicle Size in Parenting and Sexual Selection

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Thanks goes to Laura Deming for pointing out another recent paper whose title, “Testicular volume is inversely correlated with nurturing-related brain activity in human fathers,” proved irresistible to PNAS, enabling them to overlook stunning intellectual flaws. 

Problems include: Selection bias. Participants were self-selected by reading ads and fliers, then deciding to participate in a parenting study. If the father was not cohabiting with the mother, he was disqualified. This removed from the study pool an important number of fathers who give no care to their children, do not answer ads about parenting studies, and who do not cohabitate with the mother of their children. Having eliminated the crucial bottom end of the study population, the authors then lopped off the much more interesting top end – fathers who do not cohabitate with the mother but provide 100% of the care and support for their children – yes, single dads do exist.

Now stuck with this muddle-in-the-middle study population, the authors compounded the error by failing to control for age. The parameters they studied – testosterone level and testicular volume – are linearly related and decline proportionately by up to 50% in the population of males between ages 21 and 55 that they studied. This resulted in a series of scattergrams that, quite bluntly, do not support either their title or their conclusions.

Most important, this study fails the “Duh” test. The average testicle of 40cc is not a significant metabolic drain. Enlarging it by 2 standard deviations to 65cc is not a large investment. But it is difficult to imagine why a male would grow a testicle of 65cc when instead he could have added 25cc of gray matter to the area of his brain devoted to figuring out what women want. If he is a social moron, it is unlikely he will ever get to use his large testicles. More important, simply possessing them exposes him and his evolutionary strategy of parental non-involvement to his potential mates. The Life History Theory these authors were hoping to probe makes it clear that human females are crucially dependent on the support of their mate for successful reproduction. If women could determine accurately whether a possible spouse would be a helpful and attentive partner by simply feeling his balls, then women in barroom dating scenes would have their hands under the table, not fiddling with cigarettes or shot glasses. Women would frown at anything resembling a bulge in a man’s pants, and men would be binding their privates in an effort to conceal unsightly testicular volumes.

Let’s do a quick study. Not a careful scientific one – let’s just work at the level of members of Departments of Psychiatry and Anthropology publishing in PNAS. Women readers are encouraged to fill out the attached survey, which is designed to determine whether female humans pay any attention to the “fact” that the most committed, nurturing fathers have the smallest testicles.

Use this link to access the survey: https://www.surveymonkey.com/s/testesblog

View the original blog post, Science is Not Your Enemy

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Fighting Climate Change by Killing Eagles

Why isn’t the wind industry subject to the Bald and Golden Eagle Protection Act?

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By: Robert Bryce

For some environmentalists, the threat of climate change is so great that we must allow wind turbines to kill bald and golden eagles. The argument I’ve heard is that renewables, including wind energy, will reduce the amount of carbon dioxide in the atmosphere. Less carbon dioxide reduces the threat posed by climate change, which benefits eagles and other wildlife.

In other words, we have to kill eagles in order to save them.

If this sounds far-fetched, consider the notice that the U.S. Fish and Wildlife Service published in the Federal Register on Sept. 27. It seeks public comment on a proposed permit that will allow a wind project to kill up to five golden eagles over a five-year period, despite their protected status under the Bald and Golden Eagle Protection Act.

The permit is sought for the Shiloh IV Wind Project in Solano County, Calif. If it is granted, it would formally recognize a legal double standard that is already in existence with regard to wildlife protection in America.

Wind projects routinely violate the Bald and Golden Eagle Protection Act and the Migratory Bird Treaty Act, but no wind farm has ever faced a single prosecution. Meanwhile, companies in the oil and gas industry and other sectors are routinely indicted for violating those same statutes.

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Sam is My Hero

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Sam is a streamliner. Everyone knows who they are, although no one calls them that when the teachers are around. He’s one of the kids who wouldn’t be in the main high school if it weren’t for a special program. Most of the day he’s in his own classes with 8-10 other streamliners. But during class change, Sam comes out into the hall.

Sam talks to everyone. “What’s the capital of Nevada? Carson City. Carson City, Nevada.” Most of the people do not know what to say back to him. “Where is the Space Needle? Seattle. Seattle, Washington.” Sam has a wonderful fund of knowledge and likes to share it.

Sam is making a heroic effort to fit into one of the most intimidating social environments known to mankind – the American public high school. “Where’s track and field? Varsity track and field?” Sam has no hope of succeeding at this. The streamliners are treated like mice, kept for 50 minutes at a time in a nice warm cage, and then dropped for 10 minutes into a cold swimming pool. No normal person would do this to them. “What’s the capital of California? Sacramento. Sacramento, California.”

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Science is Not Your Enemy

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A labored defense of the practice of science – which we will define as scientism – was recently published under the title Science is Not Your Enemy by Stephen Pinker in New Republic magazine. A much more lighthearted approach by Tim Minchin takes sharper aim at anti-science in a video.

The only critics of scientism who take themselves seriously come from the extreme left and the extreme right. The middle ground is populated by the vast majority of mankind, who – although they do not always agree – cannot help constructing their arguments within the framework of science. Amy Harmon was both widely praised and harshly criticized by readers of her article on golden rice, critics felt that third world populations with vitamin A deficiency should grow and eat yams and carrots in home gardens. They did not dispute the structure and metabolism of retinoids, GPCRs and vision, dietary fats and vitamin absorption. So this is a policy issue, not an issue of scientism. Likewise, when Harmon wrote about attempts to express a defensin peptide in orange trees, her critics did not dispute the elegant contributions of microbiology in establishing the bacterium C. liberibacter asiaticus as the proximal cause of citrus greening. They also accepted AsianCitrusPsyllid1entomology’s premise that a psyllid insect vector spreads the disease. In a narrow dispute over policy, the critics simply wanted other scientific solutions to be tried, in preference to genetic engineering. Most opponents of climate change policy, including myself, do not disbelieve in barometric pressure or the infrared absorbance spectra of gasses. What we do argue about is science performed poorly. I am strongly opposed to selection bias, unvalidated computer models, inferred measurements, and conclusions not supported by data, to name just a few. One can oppose public policies based on flawed concepts without becoming an anti-scientist. My position would be that it makes one a more demanding, skeptical, and articulate scientist to point out the aspects of peer reviewed publications and public policy that have poor design, flawed data, and unjustified conclusions.

Let’s refocus this debate away from the idea that science is mankind’s best tool for creating and then perfecting an accurate view of reality. An embarrassed silence is a sufficient response for those questioning science itself. Let’s insist instead that people calling themselves scientists live up to the label. Scorn and derision should be heaped upon those who pretend to do science but are actually ideologues or shills for political movements and large, well-funded special interests.

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