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Miscellaneous Items from 2012:                        to enlarge a photo, click on it

Watch the dog's tail    Science blogging    Duh and Doh    Farming slime molds    Do pets make us happy?   The big companies   Bloody Beavers      The savanna look   Too dumb to know it      A moral issue    The big warming around the corner     Ready to say goodbye to bees?    Re-runs   New way to explain extreme weather      Doing the arithmetic      Events of AD 774     Harry's little trick     A very old flower    Fraud found using stats
What is it about nines?    There will be 'omes everywhere     Prehistoric artists    Big History    

Watch the dog's tail

The left-brain right-brain thing is almost all silly hype. Stuff about logical verses creative, linear verses parallel and so on has not stood up to testing. But there is something that has. Left-brain 'approach' and right-brain 'aversion' has turned out to be true of many birds and mammals and is less clear in humans but seems to be colouring our difference in the use of the two hemispheres. For example, when eating birds like to position themselves so that the vision and sound from the food goes to the left-brain and the information from the least protected direction goes to the right-brain. The same pattern in frogs and monkeys and every vertebrate tested for it – and my big favorite, dogs
Stanley Coren say:
“Since tail wagging is meant as signal a dog will only wag its tail when other living beings are around-e.g. a person, another dog, a cat, a horse or perhaps a ball of lint that is moved by a breeze and might seem alive. When the dog is by itself, it will not give its typical tail wags, in the same way people do not talk to walls.”
“There are many combinations, including the following common tail movements:
● A slight wag-with each swing of only small breadth-is usually seen during greetings as a tentative "Hello there," or a hopeful "I'm here."
● A broad wag is friendly; "I am not challenging or threatening you." This can also mean, "I'm pleased," which is the closest to the popular concept of the happiness wag, especially if the tail seems to drag the hips with it.
● A slow wag with tail at 'half-mast' is less social than most other tail signals. Generally speaking, slow wags with the tail in neither a particularly dominant (high) nor a submissive (low) position are signs of insecurity.
● Tiny, high-speed movements that give the impression of the tail vibrating are signs the dog is about to do something-usually run or fight. If the tail is held high while vibrating, it is most likely an active threat.”
But here is the new thing:
“We can now add another newly discovered, feature of dog tail language that may surprise attentive pet owners as much as it surprised scientists like me. It now appears that when dogs feel generally positive about something or someone, their tails wag more to the right side of their rear ends, and when they have negative feelings, their tail wagging is biased to the left...It is important to understand that we are talking about the dog's left or right viewed from the rear as if you are facing in the direction the dog is viewing. That means that if you are facing the dog and drew an imaginary line down the middle of his back that positive right-sided signal would appear as tail swings mostly curving to your left...Since the left brain controls the right side of the body and the right brain controls the left side of the body, activity in one half of the brain shows up as movements on the opposite side of the body.”

Science blogging
What is it all about? What science bloggers do is to comment on science news or explain scientific theories. The bloggers are either working scientists, working authors/journalist or, like me, dedicated followers of some corner of science. A few are advocates for a cause but treat the science honestly.
There is a style of science blogging that is newish and called research blogging. “Cognitive Daily, a blog written by a husband-and-wife team of Dave and Greta Munger, quickly grew a very large audience. But more importantly – and that is easy to see looking back with 20-20 hindsight – Cognitive Daily ushered in a new style of science blogging, what we now call research blogging: picking up a scientific paper (usually, but not always, one very recently published in a peer-reviewed journal, though a few bloggers specialize in older, more historical literature) and explaining what it really means. Many, many new science bloggers liked this format and started emulating Dave and Greta’s style, and today this style of blogging is almost synonymous, at least for some audiences, with science blogging as a whole.”
This style of blogging is taken up by aggregator sites. The first was Researchblogging. I submit every third posting to this site, which means that a third of my posts are comments on original papers rather that abstracts, press releases, books or other bloggers. “The emphasis is quality over quantity. Our 29 editors monitor the site to ensure that the posts all meet our community-based standards for discussing authoritative research...Unlike many other sites, ResearchBlogging doesn’t aggregate every post written by its member bloggers. Instead, it focuses only on those that cite and discuss peer-reviewed research. Like anyone else, science bloggers can write about politics, their vacation plans, or the latest editorial cartoon, but when they take the time to seriously discuss journal articles, they place a special bit of code in their post, which alerts our system.” The Researchblogging site is a sort of gold standard for serious science bloggers.
I also submit all posting to the ScienceSeeker aggregator. It does not require citing original papers but has a high standard of bloggers. It “first appeared on the science blogging aggregation scene in January 2011 at ScienceOnline2011, to an enthusiastic reception. It was the brainchild of Bora Zivkovic, Anton Zuiker, and Dave Munger, who hoped to provide an interface to the world of science blogging that would include independent bloggers who were not associated with a network. The site was intended to provide one central place to list (almost) every science blog active on the web.” This site gives independent bloggers the sort of listing that ScienceBlogging aggregator gives to networks of science bloggers.
I treat my blogging almost like a job rather than a little hobby. I keep an aim in mind, have a set of standards come dos-and-don'ts, keep to a restricted area of science, and post in a regular schedule. I spend 3 to 4 hours a day reading and writing, mostly reading. So I am glad that there are these aggregators to submit my posts to and have them read by people interested in my little area of consciousness. I don't pretend to be a working researcher or an accomplished author, just doing my best to finding developments in the field and putting them in context as plainly and clearly as I can.
Here are the links to the site I have mentioned: http://charbonniers.org my blog, Thoughts on thoughts; http://www.researchblogging.com Research Blogging; http://scienceseeker.org Science Seeker; http://ScienceBlogging.org Science Blogging.

Duh and Doh
When we go past new year all sorts of lists appear: top 10 lists of every kind of event in the previous year. I saw two blog posts (apparently unconnected), one called Duh and the other Doh. The first was a list of very obvious scientific papers and the other a list of very obvious retractions of papers in 2011. I think that if this is the worst of the useless and the faulty for the year, it is not bad compared to the huge number of papers published in a year (probably around a million).

First the Duh list by Stephanie Pappas:
Unsafe sex is more likely after drinking - for every 0.1-milligram-per-milliliter increase in study participants' blood alcohol levels, there was a 5 percent increased likelihood of having unprotected sex.
Men appear confident by suppressing fear, pain and empathy - tamping down those emotions might make someone seem more formidable.
Smoking pot and driving isn't safe – people who drove within hours of smoking pot were twice as likely to have accidents.
Pigs love mud – they are not pretending.
Fashion magazines glorify youth – magazines rarely feature women over 40.
People with generous partners have happy marriages – it would be interesting to know which causes which.
Parents don't think their kids are doing drugs - Most parents believe at least 60 percent of 10th-graders drink alcohol, only 10 percent thought their own teen did.
People aren't doing anything in particular on the Internet - 53 percent of people ages 18 to 29 get online at least once on any given day just to pass the time.
Restricting driver's licenses decreases teen fatalities - Restrictions such as limits on the number of passengers a teen can ferry around and rules against night driving decreased fatal crashes by 13 percent and 9 percent, respectively.
Most shoppers ignore nutrition labels - 1 percent looked at information about total fat, trans fat, sugar and serving size on nearly all labels, even though between 20 percent and 31 percent of people said they looked at each of those categories when they shopped.
Presidents outlive their contemporaries - Money, knowledge and good health care tend to buy health and longevity.

Now the Doh list by Christopher Wanjek:
Los Angeles marijuana dispensaries lead to drop in crime - The RAND Corporation retracted its own report in October after realizing its sloppy data collection. They did not include data from the L.A. Police Department. Isn't that where you would expect to go for crime figures?
Butterfly meets worm, falls in love, and has caterpillars – Refuters based their arguments entirely on well-known concepts of both basic evolution and the genetics of modern worms and butterflies. How did the paper get published in the first place?
Treat appendicitis with antibiotics, not surgery – The article was attacked for its science, the authors defended and the publication took out the article but not for its science but for plagiarism – chicken.
Litter breeds crime and discrimination – The author Diederik Stapel may have faked data in at least 30 papers and has been suspended from his post while being investigated. It is too bad that his many theories were featured in the New York Times and sounded so good.
Chronic fatigue syndrome is caused by a virus – This is a long story. There is still some physicians who do not accept CFS as a physical disease. Then there was a paper associating CFS with a virus (XMRV) seeming to prove CFS was real. But no other lab could reproduce the results. The authors refused to retract the paper. A Science editorial distanced itself from the paper. The authors issued a partial retraction and removed data from contaminated samples. Science did a full retraction and continues its investigation of the data. It seems that the heated controversy over the nature of CFS complicated the correction of an innocent mistake.


Farming Slime Molds
You all know my soft spot for slime molds. Here is highlights of a blog on a paper in Nature, Primitive agriculture in a social amoeba by Brock and others.
Farmer Joe Dictyostelium - by Elio
The practice of agriculture is not limited to humans: ants, termites, and snails all grow fungi, and who knows who else does something similar. But not many have claimed that such activities are to be found among simpler organisms. Now we have a report that slime molds have also gone down the road to agriculture. Dictyostelium discoideum, the best studied of the cellular slime molds, is a social amoeba that thrives by grazing on bacteria. Given ample bacterial food, these organisms grow as single cells. When food becomes scarce, they aggregate into pretty, differentiated fruiting bodies (called sorus, plural sori) consisting of a round mass of spores held up by a stalk. The spores eventually become dispersed, to repeat the cycle at a new site.
What is new here is that about one third of 35 clones of this species collected in the wild do something extra, namely they carry bacteria with them as they differentiate. They even include them within their sori—like packing a lunch, sort of. Once released, the spores have the ready opportunity to enjoy the source of food providently supplied for them. But non-farmers eat up all the available food before differentiating, whereas the farmers leave about half of the bacteria uneaten. It’s a little bit like humans not eating a whole grain harvest, but carrying some along when migrating to provide seeds for future sowing.
This sounds mighty prudent, but it comes with costs. The farmer amoebae don't travel as far before differentiating, thus are less likely to make it to a locale with more abundant food. And their sori contain fewer spores. If the spores find themselves in places with abundant bacteria, the advantage of carrying the bacteria along may disappear entirely. This was the case when they were grown on agar plates with plenty of food in the form of their preferred bacteria. However, in experiments closer to real-life using two arboretum soil samples, the farmers did better than the non-farmers, and produced more spores. The authors suggest that clones of this species consistently employ one of these two strategies, either farming or not farming. Each may have an economic advantage, just like with people. Not eating all your seeds is prudent for the future, but eating them all makes you better fed today. 
Now let me pick a nit. Calling this agriculture, even "primitive agriculture" as in the title of the featured paper, seems like a bit of a stretch. In contrast to the tending of the fungal gardens by the ant or termite farmers, these amoebae do not cultivate their bacteria. And the term is rife with anthropocentric connotations that could lead one down a slippery teleological path. Nevertheless their kind of farming does involve multiple changes to enable these slime molds to become farmers. In truth, in this blog we use anthropocentric terminology all the time. But, no matter, this does not detract one whit from a fine paper.

Do pets make us happy?
I have been to people's houses where there is no non-human living thing, not even a gold fish or a cactus plant. To add to this, some lived in apartments in city centers and would be lucky if they saw a tree or a pigeon some days. I have wondered how they keep their sanity (which they do seem to do).
As I grow older I get to feel more deprived whenever I am without a pet and a bit of garden.
People with pets often believe that the pets make them happier. But when measured, pet owners and non-pet owners do not differ in happiness or in depression. However, pet owners are less lonely and have more self-esteem. They also may be healthier. But happier – no.
People without pets often believe that pets are used to make up for less social contact. But it has been shown that the more that people felt that their social needs were fulfilled by their dogs, the more they also felt that their social needs were fulfilled by other people. There is no difference in the number of friends that pet owners have compared to non-owners. The order in which dog owner's rate their social support is: closest friends, parents, dog, siblings, other friends.
I have thought that the unconditional love of a pet is very important. It is the hardest thing to obtain except from parents and very young children. Even our spouses and close friends love us for reasons – their love is conditional on us being somewhat worthy of it. There are times when unconditional love is just what is needed. I think that is why some people are so attached to their cats. A cat's love is even more unconditional then a dog's because a cat is a less dependent animal – they don't feel they need us.
So why do pets not make us happy? Actually I don't think anything much changes how happy we are in the long term. We return to our own set point for happiness. We get some money and we are happier for a while and then back to normal. We fight with a friend and we are less happy for a while and then back to normal. Set points change slowly of course but that takes more than a pet.

The big companies
Three systems theorists at the Swiss Federal Institute of Technology in Zurich have taken a database listing 37 million companies and investors worldwide and analyzed all 43,060 transnational corporations and share ownerships linking them. They built a model of who owns what and what their revenues are and mapped the whole edifice of economic power.
They discovered that global corporate control has a distinct bow-tie shape, with a dominant core of 147 firms radiating out from the middle. Each of these 147 own interlocking stakes of one another and together they control 40% of the wealth in the network. A total of 737 control 80% of it all. The top 20 are below. There are many reasons for tightly bundled nodes and connections: anti-takeover strategies, reduction of transaction costs, risk sharing, increasing trust and groups of interest.

Here are the top 20:
Barclays plc
Capital Group Companies Inc
FMR Corporation
State Street Corporation
JP Morgan Chase & Co
Legal & General Group plc
Vanguard Group Inc
Merrill Lynch & Co Inc
Wellington Management Co LLP
Deutsche Bank AG
Franklin Resources Inc
Credit Suisse Group
Walton Enterprises LLC (holding company for Wal-Mart heirs)
Bank of New York Mellon Corp
Goldman Sachs Group Inc
T Rowe Price Group Inc
Legg Mason Inc
Bloody Beavers
Being from Canada, I am supposed to have a soft spot in my heart for the beaver. But... they can be annoying. If they hear running water, a nice little stream, they go mad. Running water must be stopped at once, dam building begins and it does not stop until there is no sound of running water. So when paper.li had a problem and put up this notice – I laughed out loud and took a screenshot. Someone has to find the beaver that has stopped the flow of data and get rid of the dam.


The savanna look

savanna Savanna has a look. Grass and few widely spaced trees dotting it. The trees are oddly shaped with a flat top and no lower branches. They all seem the same height. Along any little streams or ponds there are taller and shorter trees close together like a woods. The main tree is the acacia thorn but there are others that grow the same way. The thorn trees can grow flat-topped in the grass, tall in the woods and like a big ball in some other places.
Why the few trees on the savanna? It is dryish and so the new saplings grow slowly and most are killed by herbivores or fire before they are big enough to protect themselves. The grass fires and most of the animals kill trees that are less than 2 or 3 meters high. The saplings shot straight up as fast as the climate allows until they are out of reach of the grass fires and the shorter animals. Then they spread out horizontally. Why horizontally? It is because they are not competing with close neighbours for light and because their defense against giraffes is to have a very wide umbrella of thorns protecting the middle of the tree's crown from grazing. So low water, high light, heavy grazing, and frequent fire is what produces the savanna look.
The photo is one we took at dawn near the Rift Valley with a Marabou stork waking up for the day.

Too dumb to know it
graphIncompetent people don't know it – they think they are above average. So if someone is not very smart, they are not smart enough to know it. If they have a poor sense of humour, they do not have enough sense of humour to know it. The same applies to social and emotional intelligence, language skill, logic. Lack of ability makes it difficult to notice one's deficiency.
The very top performers underestimate their skill and the very bad performers greatly overestimate theirs. So everyone thinks they are above average whereas about half are going to have to be below average, that is what average means. Here is a graph by a researcher (Dunning) who tested people in a number of areas, ranked them, divided them into four groups and then asked them to guess their place in the ranking.
This accounts for the fact that when people do not understand something, they think it is simple or easy; they simply do not understand it well enough to see the difficulties.
But there is another ingredient in this situation. When we judge our own actions we are very aware of the constraints and difficulties that we faced and make allowance for that. (it was too cold, I was not feeling well, etc.) But when we judge other's actions we are often not aware of their circumstances and assume that they choose to do whatever they did, the way they did it without any constraints. We therefore tend to judge others harder than we judge ourselves. By doing this we underestimate their smarts and skill compared to our own.
It explains a lot!!

A moral issue
Jim Hansen is the director of NASA's Goddard Institute for Space Studies and has just won the Edinburgh metal. He used the occasion to say that climate change is a moral issue on a par with slavery.
“The latest climate models had shown the planet was on the brink of an emergency. Humanity faces repeated natural disasters … The situation we're creating for young people and future generations is that we're handing them a climate system which is potentially out of their control. We're in an emergency: you can see what's on the horizon over the next few decades with the effects it will have on ecosystems, sea level and species extinction … Current generations have an over-riding moral duty to their children and grandchildren to take immediate action. This as an issue of inter-generational justice on a par with ending slavery. Our parents didn't know that they were causing a problem for future generations but we can only pretend we don't know because the science is now crystal clear. … We understand the carbon cycle: the CO2 we put in the air will stay in surface reservoirs and won't go back into the solid earth for millennia. What the Earth's history tells us is that there's a limit on how much we can put in the air without guaranteeing disastrous consequences for future generations. We cannot pretend that we did not know. … It can't be fixed by individual specific changes; it has to be an across-the-board rising fee on carbon emissions. We can't simply say that there's a climate problem, and leave it to the politicians. They're so clearly under the influence of the fossil fuel industry that they're coming up with cockamamie solutions which aren't solutions. That is the bottom line."

The big warming around the corner
In a nut shell:
  1. Carbon dioxide has risen enough already to melt some of the Arctic and Antarctic ice. Even if carbon dioxide emissions started to drop overnight, there would still be melting in polar regions for some time. But emissions are not dropping; they are rising faster than ever. Polar regions are warming faster than other latitudes.
  2. The melting of arctic ice liberates large amounts of methane. The permafrost and tundra is rich in methane. In some places it will sustain a flame as it leaks out when the permafrost is disturbed. Recent warming has resulted in plumes of methane bubbles rising in shallow parts of the Arctic Ocean. The release of methane will increase as melting/warming continues.
  3. The amount of methane in polar regions and its escape has been underestimated. Recently a team identified about 150,000 methane seeps in Alaska and Greenland lakes along the margins of ice cover. A Siberian study found more than 100 fountains, some more than a kilometer across emitting methane into the atmosphere. The region stores vast quantities of the gas in different places - in and under permafrost on land, on and under the sea bed.
  4. Methane is about 24 times more powerful a greenhouse gas compared to carbon dioxide. So the effect of rising carbon dioxide as it causes the increased release of methane will be a jump in temperature rise and rate of temperature rise – a big jump. The warming will feed the warming.polar bear
Many people have used the same metaphor – here M Mukerjee, “Remember how Wile E. Coyote, in his obsessive pursuit of the Road Runner, would fall off a cliff? The hapless predator ran straight out off the edge, stopped in midair as only an animated character could, looked beneath him in an eye-popping moment of truth, and plummeted straight down into a puff of dust. Splat!” We may be running in thin air right now.
One of the mass extinctions in the past, possibly the greatest, was the End-Permian extinction. It was not caused by a big meteor or a cool sun or lots of volcanos. It was caused by the combination of global warming, acid rain, acidification of the ocean, and drops in oxygen – sounds familiar. These were enough to kill 90% of the species on land and sea. It took 10 million years for life to start coming back from the abyss. If we have enough nerve to metaphorically look down, this is the sort of 'splat' we might see.
The melting bear in oil is a work by Takeski Kawano brought to her facebook friends' attention by Judith Copithorne. click to enlarge.

Ready to say goodbye to bees?
Everyone agrees that we need bees – ecosystems in the natural world need them, and farmers, gardeners, honey producers need them. In the US they pollinate $15 billion worth of crops. They are being killed by particular insecticides but no one is outlawing those chemicals.
The problem is neonicotinoid type insecticides such as imidacloprid which were introduced in the early 1990s and are now the most heavily used insecticides in the world (Gaucho, Prestige, Admire, Marathon, Cruiser, Platinum, Actara, Helix, Adage, Meridian, Centric, Flagship, Poncho, Titan, Clutch, Belay, Arena, Confidor, Merit, Ledgend, Pravado, Encore, Premise, Assail, Intruder, Adjust and Calypso etc.). Its use correlates with the death of bees since its introduction. Honey bees are suffering colony collapse and wild bubble bees are becoming rare, in some cases extinct. The chemical is used on cotton, corn, grains, potatoes, rice, vegetables and more. It was, of course, tested before it was licensed but the testing was for the level that was safe for contact with bees. It passed the test but the problem is not contact. The residue levels of the insecticide are perfectly safe for bees to come in contact with.
But the bees actually eat the insecticide and that is because that the insecticide incorporates itself in the nectar and pollen of plants (most insecticide do not do this). The bees take the poison in and take it back to the hive to feed the queen and young. But even here, although this may be hard on the bees, they might survive it. Some people say the bees would; they are spokespersons for the chemical companies for what its worth.
So why do the bees disappear? Neonicotinoids target the nervous system in insects. There are several clues to how whole hives just die or disappear. One is that although adult bees may be able to survive, the next generation that developed on poisoned food are not able to survive. Another is that the bees when foraging lose their sense of direction and cannot find their way back to the hive. Whatever it is, there have been trials in the US, France and UK that show that neonicotinoid kills honey bee hives as they overwinter and kill bubble bee queens.
Trial 1 showed that repeated low-dose (legal) exposures can kill whole hives of bees.
In trial 2, 20 brand new hives were set up in 4 clusters, far enough apart to not mingle. In each cluster the bees were given sugar syrup. 4 hives in each cluster had imidacloprid added to their sugar and one did not. They were fed like this from the start of July to the end of September and then all hives got the pure sugar syrup. Mid-December the hives went into wintering mode. The first hive collapsed at the end of December and by late February only one hive fed insecticide was not empty. There was no sign of bacterial, virus or mite disease. The control hives were healthy except one which was suffering dysentery but not dead.
Trial 3, fed hives a related insecticide, thiamethoxam and found that it weakened the bees, the hives failed to prosper. Bees that were fitted with trackers were not navigating well compared to controls.
Trail 4, fed wild type bumble bees the insecticide in trace amounts and found that they were less able to produce queens and start new colonies. There was an 85% drop in the number of queens in each generation.
Trail 5, small, single doses of imidacloprid fed to bees made them more 'picky eaters', poorer dancers, poorer at remembering and learning. They are being made into dumb and uncommunicative bees.
Because the first die off noticed in Europe was where and when treated corn seed was used. Attempts were made to improve the seed drills but it made no difference. Now in some places there is a ban on seed corn treatment.
The companies are not withdrawing their products and are disputing the scientific results. Farmers are not avoiding these insecticides much. Only partial and piecemeal bans are in place. Meanwhile about a third of American bees are already gone. (I don't know what the figure is for Europe). Honey producers are going out the business. And crops are not being fully pollinated (almonds, apples, grapes, soybeans, cotton are amongst the crops at risk).
What is happening with bee colonies is no longer a 'mystery'. The mystery is why these insecticides are not completely banned.

This is the time of year for bad, bad television – the Jubilee events, the run up to the Olympics, the Euro2012 football from Ukraine, tennis non-stop from French Open, Queens and then Wimbledon, the Tour de France and so on. What I wouldn't give for some old, good re-runs.
I have assumed that it is my age that make re-runs enjoyable. As I get older I get more annoyed by high voltage entertainment. I want something interesting and engaging but that has very little suspense, shock or extremely strong emotions. I never was happy with having my emotions played with for no real purpose and stopped going to movies years ago. I do watch movies on TV sometimes but I know that I can just turn the program off if I feel manipulated. Anyway, I thought it was me and my age that made me so fond of re-runs.
No, apparently, most people enjoy re-runs. I'm not odd at all. And their reason are probably the same as mine too. We have a guaranteed outcome – if it was good the first time, it will not be bad a second time around. I can know just what to expect and therefore know whether I am in the mood for it. I also find that knowing where the story is going, I notice many things that I missed the first time, little subtle details, even slightly different stories emerge. Some re-runs are even a bit nostalgic.
There are people who peek at the ending of a book before reading it. Good idea! If we can enjoy the same painting or music over and over, why should literature or drama be different. And far from being my age, I recall that children just love to hear the same story over and over. They know every word and still enjoy it one more time.

New way to explain extreme weather
A new concensus is growing in climate science. Climate change cannot be used to explain any single weather event, but climate change can be used to explain the probability of a class of weather events. Up until now scientists have just said, when asked, that a cause and effect line cannot be drawn between climate change and this flood or that drought.
Now 400 scientists from 48 countries have address this problem in a report.
“Authors of the study found that a heat wave is now around 20 times more likely during a La Nia year than it was during the 1960s, and that frigid Decembers are half as likely to occur now compared to 50 years ago. 'While it remains hard to link single events to human-caused climate change, scientific thinking has moved on and now it is widely accepted that attribution statements about individual weather or climate events are possible,' the report added.' Scientists liken carbon's role in climate change to the effect of steroids on a baseball player. While steroids are likely the cause of improved performance, a natural variability in the player's swings must be accounted for.'” - Big Think
“Last year's record warm November in the UK – the second hottest since records began in 1659 – was at least 60 times more likely to happen because of climate change than owing to natural variations in the earth's weather systems, according to the peer-reviewed studies by the National Oceanic and Atmospheric Administration in the US, and the Met Office in the UK. The devastating heatwave that blighted farmers in Texas in the US last year, destroying crop yields in another record "extreme weather event", was about 20 times more likely to have happened owing to climate change than to natural variation.” - The Guardian
“We are much more confident about attributing [weather effects] to climate change. This is all adding up to a stronger and stronger picture of human influence on the climate.” - UK Met Office
But this does not mean that all extreme weather can be confidently be blamed on climate change. If the patterns that caused the sort of weather point to the probability of the event not being extraordinary then it can not be explained by climate change. If there is a very high probability that climate change is involved than that climate change is now used in explanations (not avoided as previously).
Take-home is that we really are looking at the future when we have extreme rain, extreme drought, extreme heat, extreme wind.

Doing the arithmetic
From numbers published by Bill McKibben, we have a very clear picture of what is happening with climate change.
The upper limit of climate change that the world agreed to in Copenhagen 2009 was 2 degrees Celsius (3.6 Fahrenheit); "we agree that deep cuts in global emissions are required... so as to hold the increase in global temperature below two degrees Celsius." Since then it has become clear that 2 degrees is too high. The problems are far more serious than was realized in 09. So far the rise has been 0.8 degrees and this has caused effects that science had not expected in 09. But 2 degrees is the limit, agreed by 167 countries.
But the 0.8 degrees is not fixed. If we stopped putting any carbon into the air at this point, the temperature would rise another 0.8 degrees, the effect of previously released carbon continuing to overheat the planet. So we are three-quarters of the way to the two-degree target.
So how much carbon can we put into the air and still have a hope of coming in under the limit of 2 degrees. The most favourable number seems to be about 565 gigatons of carbon dioxide by mid- century; by many models that would squeeze us in under 2 degrees. Last year the world put 31.6 gigatons into the atmosphere. If emissions go on as usual, rising 3% per year, we will use up our headroom in 16 years.
If all the fossil fuel reserves that are known and proven by the the energy companies and countries what we get is 2795 gigatons. In other words the world as a whole has plans to burn 5 times as much carbon as the planet (and the human race) can accept. And people are still looking for more reserves. Even if the number have some small errors, this is clearly an untenable situation.
What do these numbers mean for the energy companies (and countries dependent on oil and gas)? We have five times as much oil and coal and gas on the books as climate scientists think is safe to burn. We'd have to keep 80 percent of those reserves locked away underground to avert disaster. But the reserves are the companies main assets and if they were effectively cut by 80%, company stocks would sink like rocks. They are in the wind by about $20 trillion. And many countries are counting on their cut of this future fuel.
So what energy companies/countries want is for this plain arithmetic to not be understood by the population. Short-term politics and short-term economics are the pressure on everyone who could do something about the situation. The big shareholders are people with money but they do not spend it on finding ways to burn less carbon – the money is spent on denying that there is a problem, thwarting efforts to deal with the problem and of course looking for even more reserves. Instead of investing in non-carbon forms of energy and becoming forward-looking companies/countries; they spend on PR, lobbying, lawyers, politicians and continuing business as usual.
Our future is being bought and thrown away by greedy men.

Goals of the American Petroleum Institute from 1990s memo quoted in Steve Coll's book
- Average citizen “understands” (recognizes) uncertainties in climate science
– Recognition of uncertainties becomes part of the “conventional wisdom”
– Media “understands” (recognizes) uncertainties in climate science
– Media coverage reflects balance on climate science and recognition of the validity of viewpoints challenging current “conventional wisdom”
– Those promoting the Kyoto treaty [a global effort to reduce greenhouse gas emissions] on the basis of extant science appear to be out of touch with reality.
I guess the list has had all items checked off - too bad for humanity.

Events of AD 774
A lot of things happened in AD 774. For example Charlemagne defeated the Lombards and added Italy to his empire. In that year the Northumberland king changed from Alhred to Aethelred. In the year 774 AD Kukai, founder of Shingon Buddhism in Japan was born. But the event of cosmic importance was recorded by the Anglo-Saxon Chronicle, "In the year 774 AD, appeared in the heavens a red crucifix, after sunset; the Mercians and the men of Kent fought at Otford; and wonderful serpents were seen in the land of the South-Saxons."
A Japanese group headed by Fusa Miyake noticed that tree rings dated to AD 774-775 had 20 times the normal rate of variation in C14. This is only known to be produced by gamma rays from supernova or giant solar flares. They found reference to abnormal increases of C14 in European and North American trees from that time and increases of beryllium10 in ice cores. They looked for historic records of some possible event and found none. So it was a little mystery – the unknown massive cosmic event of AD 774. It should have been seen but apparently wasn't. This mystery was featured on a Nature podcast.
In California, a biochemistry student, Jonathon Allen, listened to the podcast and he was interested in history. "I knew that going that far back, there's very limited written history," he says. "The only things I'd ever seen or heard of were in religious texts and 'chronicles' that listed kings and queens, wars and things of that nature." He checked the Anglo-Saxon Chronicle for 774 and found the reference to the red crucifix and got in touch with the Japanese group.
The big question was why was this supernova not seen as a new bright star for a period of time on earth. It seems it was probably behind the sun and so was not directly seen. But there was certainly something going on in the sky near the sun. It made enough of an impression to be mentioned again. Mike Baillie, another tree ring researcher found another historical record. The 13th-century English chronicler Roger of Wendover is quoted as saying: "In the Year of our Lord 776, fiery and fearful signs were seen in the heavens after sunset; and serpents appeared in Sussex, as if they were sprung out of the ground, to the astonishment of all."

Harry's little trick
Harry and I have a little joke about the Ukraine being the center of civilization. (Else why did God speaks Church Slavonic? Why is Ukrainian onomatopoeic?) Until recently Harry had some evidence – the steppe in the region of the Ukraine was the place of origin of the Indo-European languages – so obviously that was the source of civilization. Now he has to change his tune.
Some upstart scientists have run the IE languages through software used in genetics with words taking the place of genes. And then they used epidemiological software with language spread rather than disease spread. They showed that it was more likely that Indo-European started in Anatolia 8000 years ago rather than the steppe 6500 years ago. It was spread by early farmers rather than Kurgan horsemen.
When I told Harry this he remembered as a boy he could turn into a Turk. It was his party piece as a very small boy. He sang the song and then did a somersault.
Tepr ya Turrok
N cosak
Bo ya vzh chyelkom

This is a rough version in latin letters rather than cyrillic for those of you who can speak Ukrainian. Harry's says the Ukrainian is remembered from his childhood and might not be that accurate.
It would translate as “Now I'm a Turk not a Cossack because I'm already completely turned over. So now I can tease him about being prepared for even a change in the home of civilization.

A very old plant
old seedThis flower was produced from seed that had been in the Siberian permafrost for 32,000 years. The seed holds the record for the oldest seed to germinate into a healthy plant.
The researchers were studying ancient soil composition in an exposed Siberian riverbank in 1995 when they discovered the first of 70 fossilized Ice Age squirrel burrows, some of which stored up to 800,000 seeds and fruits. Permafrost had preserved tissue from one species—a narrow-leafed campion plant—exceptionally well, so researchers at the Russian Academy of Sciences recently decided to culture the seeds to see if they would grow. Team leader Svetlana Yashina re-created Siberian conditions in the lab and watched as the refrigerated tissue sprouted buds that developed into 36 flowering plants within weeks. The frozen plants, blooming again after millennia in the freezer, seeded a new generation.
It is very slightly different from the modern form of this plant.

Fraud found using stats
Uri Simonson has made a name for himself by identifying fraudulent scientific papers using statistics. Data can be just too good. The odds of such 'nice' numbers is just too long. This has been done a number of times lately (but maybe not as often as it should). Sometime ago, I read that Mendel's famous pea experiments, the experiments that launched genetics, were too good but would be just right statistically if he had done each experiment twice and reported the average of each data point. We can forgive Mendel – it was 150 years ago and he was an amateur scientist as a side-line to being a monk-gardener.
There are many ways that a scientist can sort of cheat that would not be called fraud. One, outliers can be included when there is good reason for cutting them, or, they can be excluded when there is no good reason to cut. A single outlier can make a big difference to many stats. Two, experiments that give some evidence of an effect but are not quite significant can be repeated until one passes the significance test. That sort of thing accounts for 'regression to the mean'. There is a surprising paper but the effect reported is less and less with each paper that looks at it – until the effect has just disappears. Statistically there are always going to be unusual results and if the results are statistical artifacts rather than real effects, they will be washed out in later runs - typical regression to the mean. If a scientist has a surprising result, then he should be suspicious, and repeat the experiment until he is sure that it is or is not safe to publish it.
election stats
Stats can be used to look at elections and see if they were fairly done. The trick is to plot the % vote for the winning party against the % turnout for each voting station. Normally this gives a round or oval blob of points (one point for each station). If the results are being fiddled, the blob will have a smeared tail towards the top right. In extreme cases there will be a small second blob in the top right. I think this analysis should be done on all elections as normal precaution. It would stop the common, easy ways to rig elections.
Another tool in finding fraud is Benford's Law. In many systems there is a simple relationship between the frequencies of various digits. Suppose that you are measuring something that is growing, at say 20% per year. 100, 120, 144, 173, 207, 249, 299, 358, 430, 516, 619, 743, 891, 1070. You can see that the first digit is 1 for 5 numbers; 2 for 3 numbers; 3 4 5 6 7 and 8 for 1 each; and no 9. This is just a little example of how the digit frequencies can be unequal. The law: in lists of numbers from many (but not all) real-life sources of data, the leading digit is distributed in a specific, non-uniform way. According to this law, the first digit is 1 about 30% of the time, and larger digits occur as the leading digit with lower and lower frequency, to the point where 9 as a first digit occurs less than 5% of the time. Benford's law also gives the expected distribution for digits beyond the first, which approach a uniform distribution as the digit place goes to the right.
Benford used a number of sources in his publication of his law: surface areas of rivers, US populations, physical constants, molecular wieghts, entries in a mathematical handbook, numbers in an issue of Readers' Digest, street addresses, death rates. There are few natural systems that break this law.
It has been used to uncover fraud and has stood up in court. People who make up numbers tend to pick digits randomly, close to the same frequency for all the digits. So fictional book keeping and reporting can often be checked by simply comparing the ratio of 1 to 9 in first digits. Of course, not everyone bent on fraud may be ignorant of Benford and pick their numbers more carefully.

What is it about nine?
When I was little, my grandfather showed me an arithmetic trick that had to do with nines. It was a way to check an answer to an addition, subtraction, multiplication or division to see if it is correct. I asked Mom or a teacher or someone about it and they said it was an old thing that wasn't taught anymore. So I ignored it. (And it was very old, in fact ancient) Later in tech training I was taught to use a venier and again encountered the nine thing. Years later, studying computer science, I was learning about check sums and a lecturer said that modular arithmetic was the basis of the old method called 'casting out nines'. There was nothing magical about nine except it was one less than the counting base 10. So here is a nice little puzzle to figure out how this pattern happens.


And another:
Write down any 3 digit number, then reverse it, subtract the smallest from the biggest. The result will be a number with 9 in the middle and the first and last digit adding up to 9.

There will be 'omes everywhere
Now that there are big computers with big memories, it is possible to find things out by brute force rather than clever elegance. And since the genome project, every really big data collection and sorting is called a something ome. It seems to have started with genome, a sort of pun on chromosome, but then the next big project carried the suffix on.
There is an old idea about science – that each science starts with a stage where things are just documented. In this way of looking at science, chemistry started with finding the describing new elements, compounds and reactions. More and more individual facts were collected but it was only later that patterns appeared and theories were constructed and tested. When geology started, people collected and characterize all the rocks they could find and described elements of landscape. Later came the how and why questions. In biology, taxonomy was first. But most biologists thought they were over that stage many, many years ago. But molecular biology/genetics was different and it is now doing its taxonomy. The 'omes just get this taxonomy stage out of the way in a hurry. Find everything and give each thing a place in a huge datebase, as an activity on which other activities can be based. It is a kind of mind boggling way to do things.
Here are some of the omes:
genome – a complete reading of the base pairs in DNA of an organism, finally all? organisms. Unsurprizingly, that didn't tell us much until we could figure out what the body does with this information. We needed a …
transcriptome – a complete reading of all the pieces of RNA that is transcribed from the DNA. Guess what – this was not too useful if we didn't know what the RNA was doing. Lots is making protein so...
proteome – a complete list of proteins in cells with their function and structure. Now we should have all the info needed but there are still problems. We don't know how things are controlled. …
epigenome – all the inheritance information that was not included in the genome
metabolome - all the other molecules not covered so far and their reactions, especially the end points of all the cells chemistry. This has given birth to reactome (all biochemical pathways) and interactome (all interaction between molecules in cells). The image is one of the very early drafts of a interactome.
Why limit this to what happens inside cells?
biome – a list of all ecosystems with their descriptions,
connectome – a map of all the connections in the brain. Even many biologists think this one is a just plain crazy idea.
Every and anything is now a candidate for 'oming if there is a fast, cheap way to collect the information (or even if there isn't).
This will probably go on and on until the world's disk space is all gone. For a 'ome to be useful there has to be ways to present the information so that researchers can find, compare, annotate and so on – good databases for mining. And access has to be open and free or cheap. The objects studied have to be relatively stable. But the sky is the limit. What about a languagome? A residencome?


Prehistoric Artists
How inventive were the artists in prehistoric times?
30,000 years ago artist were making images in the caves of France and Spain. (We visited one in the 60s but it is now closed to the public as I believe are most of them.) Often there is what looks like multiple attempts at the same animal over painted on the same spot. And you think 'oh well no one is perfect'. Marc Azema tried a flickering light like the light that might come from a burning torch – and the images came to life. In the flickering light the multiple images acted like a movie. He studied the images in detail and found that the animals would move in a very characteristic way for that particular type of animal. Whether they were looked at sequentially like a comic strip or view with a flicker like a movie, the artists were capable of separating a movement into components true to the actual animal. Here is a link to a video of the effect
You might think this was not that deliberate but Azema has 20 years of studying the effect and tons of evidence. Florent Rivere found palaeolithic small bone discs with animals drawn on them. They have holes in the center and if spun, the drawings are superimposed to give a movement.
So not only were Cro-magnon great draftsmen of animal anatomy, they found ways to show the movement as well. In fact, the Palaeolithic artists were more correct about animal gaits then recent artists. “Most quadrupeds have a similar sequence in which they move each limb as they walk, trot or run, and this sequence was studied and outlined in the early 1880s by Eadweard Muybridge. The authors examined prehistoric and modern artwork ranging from cave paintings of cows and elephants to statues and paintings of horses, elephants and other quadrupeds in motion to see how well these artistic depictions matched the scientific observations of animal motion. The majority of depictions of these animals walking or trotting had their legs incorrectly positioned, but the prehistoric paintings had the lowest error rates of 46.2%, whereas modern pre-Muybridgean art depicted animal motion incorrectly 83.5% of the time. This error rate decreased to 57.9% after 1887”.
There is also Iegor Reznikoff who visited the caves. He was in the habit of humming as he studied. He noticed the parts of the caves that resonated 'like cathedrals'. People had wondered why some parts of the caves had lots of paintings and others had none. Some paintings were in very hard to access parts of the caves. He mapped the painted areas and resonant areas for several caves and found they coincided.
There are many later examples of early people using acoustic engineering with some real skill.
It is not just an artful representation of nature that these ice age people showed. There is a figure of a man with a lion's head that is at least 40,000 years old. It is made from extremely hard mammoth ivory and is a foot tall. It is very skillfully made and it is estimated that it took about 400 hours. Some group feed and looked after the craver for months while he made the statue.
This taste for art and skill at producing it did not start suddenly with Cro magnon. 150,000 years ago people were using pigments, probably to paint themselves, their things, their shelters, and their special places. Nothing much remains except the stores of prepared pigment. But even that shows that it was already a big thing to them.

Big History
There is a new movement in teaching history – stop being nationalistic. Forget about British History, Canadian History, French History, American History; think instead about the History of Mankind. The idea is that of David Christian and it has been taking off as the new idea in Britain, Australia and the States. It is unlikely to fade away because Gates money is backing it.
Using a vast timescale and covering the whole world, this history traces the cause and effect patterns without the constraint of political borders - without the borders on subject matter either as it involves geology, climate, biology, disease and so on as well as politics, wars, and powerful people. They aim for course material for students anywhere in the world so that all share a common sense of history.
Here are some facts that were used to advertise a recent TV programs on BBC using the Big History approach:
The human body has changed more in the past 100 years than in the previous 50,000. Adults are 50% heavier and four inches taller.
100,000 years ago, there were barely enough people on Earth to fill a football stadium.
Ancient Rome was eight times more densely populated than New York today.
When Columbus "discovered" the New World, there were already 90 million people in the Americas, a third of the world's population.