Appendix A To Essay 11-01 -- Scientists Change Their Minds..., er..., Yet again


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This Appendix used to belong to Essay Eleven Part One; it has been moved here since that Essay was becoming unwieldy.


In this section, I will be posting examples (in addition to those already listed in the main body of the above Essay) where scientists have radically changed their minds, or where they have overthrown, questioned or rejected established dogma -- or, indeed, where they are about to do so.


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(1)   Return Of Lamarck?


(i)  Genomes Modified By The Environment


(ii) Acquired Characteristics Inherited?


(2)   Is Everything We Know About The Universe False?


(3)   Plate Tectonics On The Slide?


(4)   Heisenberg For The High Jump?


(5)   Quantum Mechanics -- Probably Defective?


(i)  Mathematical Foundations Shaky


(ii) Probability "As Useful To Physics As Flat-Earth Theory"


(6)    Is It Higgs Or Not? Does It Even Matter?


(7)    Supersymmetry Bites The Dust?


(8)    Neuroscience -- Having A Nervous Breakdown?


(9)    Is Much Of Science Wrong?


(10)  Saturated Fats Might Not Be Bad For You After All


(11)  Gravitational Waves Discovered? Yes! Er..., Oops..., No!


(12)  Time To Wave 'Goodbye' To 'Dark Matter'?


(13)  The Periodic Table -- About To Decay?


(14)  Should We Ditch The Current Theory Of The Solar System?


(15)  Cosmological Principle Ready For The Scrapheap?


(16)  Cosmic Expansion In Crisis?


Summary Of My Main Objections To Dialectical Materialism


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Lamarck Makes A Comeback


Genome Modified By The Environment


For over a hundred years we had been told that the environment can't alter the genome, and that anyone who accepted Lamarckism was branded as some sort of heretic, but now we find out that maybe Lamarck was right:


"Conditions in the uterus can give rise to life-long changes in genetic material. People in their sixties who were conceived during the Hunger Winter of 1944-45 in the Netherlands have been found to have a different molecular setting for a gene which influences growth. Researchers from the LUMC are the first to demonstrate this effect. They published their findings this week in PNAS Online Early Edition, together with colleagues from Columbia University.


"During the Hunger Winter (the Dutch famine of 1944-1945) the west of the Netherlands suffered from an extreme lack of food. It now appears that the limited food intake of mothers who were pregnant during this period altered the genetic material of embryos in the early stages of development. The effects of this can still be observed some sixty years later. These alterations are not changes in the genetic code, but a different setting for the code which indicates whether a gene is on or off. This is known as epigenetics. One of the main processes in epigenetics is connecting the small molecule methyl to DNA.


"The researchers compared the degree of methylation of a piece of DNA, the IGF2 gene, of people who were conceived in the Hunger Winter with that of their brothers and sisters. They chose this particular gene because it plays an important role during gestation. People in their sixties who were conceived during the Hunger Winter have less methyl groups on the IGF2 gene than their siblings. This did not apply to children of the Hunger Winter who were in later stages of gestation when the famine occurred. They did have a lower birth weight than their siblings, but the IGF2 gene was not 'packaged' differently. This indicates that epigenetic information is particularly vulnerable in the early stages of pregnancy.


"'The next question is whether the epigenetic change which has been identified is a "scar" on the DNA because of lack of food, or a specific adaptation to the shortage of food,' comments Prof Eline Slagboom. Researcher Dr Bas Heijmans: 'Epigenetics could be a mechanism which allows an individual to adapt rapidly to changed circumstances. Changes in the DNA sequence occur by chance and it takes generations before a favourable mutation spreads throughout the population. By then, a temporary famine is long past. It could be that the metabolism of children of the Hunger Winter has been set at a more economical level, driven by epigenetic changes.' This could explain why children of the Hunger Winter suffer more frequently from obesity and cardio-vascular diseases. The research was partly financed by the Netherlands Heart Foundation and the EU network LifeSpan." [Leiden University Report, October 2011. Quotation marks altered to conform with the conventions adopted at this site.]


"Epigenetics: Genome, Meet Your Environment

"As the evidence accumulates for epigenetics, researchers reacquire a taste for Lamarckism


"Toward the end of World War II, a German-imposed food embargo in western Holland -- a densely populated area already suffering from scarce food supplies, ruined agricultural lands, and the onset of an unusually harsh winter -- led to the death by starvation of some 30,000 people. Detailed birth records collected during that so-called Dutch Hunger Winter have provided scientists with useful data for analyzing the long-term health effects of prenatal exposure to famine. Not only have researchers linked such exposure to a range of developmental and adult disorders, including low birth weight, diabetes, obesity, coronary heart disease, breast and other cancers, but at least one group has also associated exposure with the birth of smaller-than-normal grandchildren. The finding is remarkable because it suggests that a pregnant mother's diet can affect her health in such a way that not only her children but her grandchildren (and possibly great-grandchildren, etc.) inherit the same health problems.


"In another study, unrelated to the Hunger Winter, researchers correlated grandparents' prepubertal access to food with diabetes and heart disease. In other words, you are what your grandmother ate. But, wait, wouldn't that imply what every good biologist knows is practically scientific heresy: the Lamarckian inheritance of acquired characteristics?


"If agouti mice are any indication, the answer could be yes. The multicoloured rodents make for a fascinating epigenetics story, which Randy Jirtle and Robert Waterland of Duke University told last summer in a Molecular and Cell Biology paper; many of the scientists interviewed for this article still laud and refer to that paper as one of the most exciting recent findings in the field. The Duke researchers showed that diet can dramatically alter heritable phenotypic change in agouti mice, not by changing DNA sequence but by changing the DNA methylation pattern of the mouse genome. 'This is going to be just massive,' Jirtle says, 'because this is where environment interfaces with genomics.'


"Epigenetics Explained


"This type of inheritance, the transmission of non-DNA sequence information through either meiosis or mitosis, is known as epigenetic inheritance. From the Greek prefix epi, which means 'on' or 'over', epigenetic information modulates gene expression without modifying actual DNA sequence. DNA methylation patterns are the longest-studied and best-understood epigenetic markers, although ethyl, acetyl, phosphoryl, and other modifications of histones, the protein spools around which DNA winds, are another important source of epigenetic regulation. The latter presumably influence gene expression by changing chromatin structure, making it either easier or more difficult for genes to be activated.


"Because a genome can pick up or shed a methyl group much more readily than it can change its DNA sequence, Jirtle says epigenetic inheritance provides a 'rapid mechanism by which [an organism] can respond to the environment without having to change its hardware.' Epigenetic patterns are so sensitive to environmental change that, in the case of the agouti mice, they can dramatically and heritably alter a phenotype in a single generation. If you liken the genome to the hardware of a computer, Jirtle explains, then 'epigenetics is the software. It's the grey area. It's just so darn beautiful if you think about it.'


"The environmental lability of epigenetic inheritance may not necessarily bring to mind Lamarckian images of giraffes stretching their necks to reach the treetops (and then giving birth to progeny with similarly stretched necks), but it does give researchers reason to reconsider long-refuted notions about the inheritance of acquired characteristics. Eighteenth-century French naturalist Jean Baptiste de Lamarck proposed that environmental cues could cause phenotypic changes transmittable to offspring. 'He had a basically good idea but a bad example,' says Rohl Oflsson, Uppsala University, Sweden.


"Although the field of epigenetics as it is known today (that is, the study of heritable changes in gene expression and regulation that have little to do with DNA sequence) has been around for only 20 years or so, the term epigenetics has been in use since at least the early 1940s. Developmental biologist Conrad Waddington used it back then to refer to the study of processes by which genotypes give rise to phenotypes (in contrast to genetics, the study of genotypes). Some reports indicate that the term is even older than Waddington, dating back to the late 1800s. Either way, early use of the term was in reference to developmental phenomena.


"In 2001, Joshua Lederberg proposed the use of more semantically, or historically, correct language. But it appears that today's use of the term is here to stay, at least for now, as are its derivatives: epiallele (genes with different degrees of methylation), epigenome (the genome-wide pattern of methyl and other epigenetic markers), epigenetic therapy (drugs that target epigenetic markers), and even epigender (the sexual identity of a genome based on its imprinting pattern).


"Terminology aside, biologists have long entertained the notion that certain types of cellular information can be transmitted from one generation to the next, even as DNA sequences stay the same. Bruce Stillman, director of Cold Spring Harbor Laboratory (CSHL), NY, traces much of today's research in epigenetics back to Barbara McClintock's discovery of transposons in maize. Methyl-rich transposable elements, which constitute over 35% of the human genome, are considered a classical model for epigenetic inheritance. Indeed, the epigenetic lability of Jirtle's agouti mice is due to the presence of a transposon at the 5' end of the agouti gene. But only over the past two decades has the evidence become strong enough to convince and attract large numbers of epigenetics researchers. '[Epigenetics] has very deep roots in biology,' says Stillman, 'but the last few years have been just an explosion in understanding.'


"Methylation And More


"One of the prominent features of DNA methylation is the faithful propagation of its genomic pattern from one cellular or organismal generation to the next. When a methylated DNA sequence replicates, only one strand of the next-generation double helix has all its methyl markers intact; the other strand needs to be remethylated. According to Massachusetts Institute of Technology biologist Rudy Jaenisch, the field of epigenetics took its first major step forward more than two decades ago when, upon discovering DNA methyltransferases (DMTs, the enzymes that bind methyl groups to cytosine nucleotides), researchers finally had a genetic handle on how epigenetic information was passed along. Now, it is generally believed that DMTs bind methyl groups to the naked cytosines based on the methylation template provided by the other strand. This is known as the maintenance methylase theory.


"But even a decade ago, says Wolf Reik of the Babraham Institute, Cambridge, UK, 'a lot of epigenetics was phenomenology, and so people looked at it and said, well, this is all very interesting, but what's the molecular mechanism?' Reik points to recent evidence suggesting a critical link between the two main types of epigenetic regulation, DNA methylation and histone modification, as one of the most interesting recent developments in the field. Because of that link, researcher Eric Selker and colleagues at the University of Oregon, Portland, have proposed that there may be more to methylation propagation than maintenance, despite 25 years of evidence. In 2001, Selker and coauthor Hisashi Tamaru showed that dim-5, a gene that encodes a histone H3 Lys-9 methyltransferase, is required for DNA methylation in the filamentous fungus, Neurospora crassa. The histone enzyme is, in turn, influenced by modifications of histone H3. So even though DNA methylation is guided by a DNA methyltransferase encoded by dim-2, it still takes orders from the chromatin.


"In a study by CSHL researchers Robert Martienssen, Shiv Grewal, and colleagues, evidence suggests that histone modifications are, in turn, guided by RNA interference (RNAi). Using the fission yeast Schizosaccharomyces pombe, the researchers deleted genes that encode RNAi molecular machinery and observed a loss of histone H3 lys-9 methylation and impaired centromere function. 'This new understanding has created a lot of excitement,' says Stillman....


"Lamarckism Revisited


"Normally, the fur of agouti mice is yellow, brown, or a calico-like mixture of the two, depending on the number of attached methyl groups. But when Duke University researchers Jirtle and Waterland fed folic acid and other methyl-rich supplements to pregnant mothers, despite the fact that all offspring inherited exactly the same agouti gene (i.e., with no nucleotide differences), mice who received supplements had offspring with mostly brown fur, whereas mice without supplements gave birth to mostly yellow pups with a higher susceptibility to obesity, diabetes, and cancer. The methyl groups bound to a transposon at the 5' end of the agouti locus, thereby shutting off expression of the agouti gene, not just in the murine recipient but in its offspring as well.


"Although the study demonstrates that, at least in mice, folic acid supplementation in pregnant mothers reduces the risk of their babies having certain health problems, Jirtle warns that the results cannot be extrapolated to humans. 'Mice are not men,' he emphasizes. But he doesn't downplay the proof of principle. The take-home message is not that folic acid supplements are a good thing. Rather, environmental factors such as nutritional supplementation can have a dramatic impact on inheritance, not by changing the DNA sequence of a gene or via single-nucleotide polymorphism, but by changing the methylation pattern of that gene. 'It's a proof of concept,' says Donata Vercelli, University of Arizona, Tucson. 'That's why it's so important.'


"According to Vercelli, the environmental susceptibility of epigenetics probably explains why genetically identical organisms such as twins can have dramatically different phenotypes in different environments. She points to the agouti mice, as well as another recent cluster of studies on a heat shock protein, Hsp90, in Drosophila melanogaster, as 'model systems that have very eloquently demonstrated' the critically important role that epigenetic inheritance plays in this kind of gene-by-environment interaction.


"Hsp90 regulates developmental genes during times of stress by releasing previously hidden or buffered phenotypic variation. Douglas Ruden of the University of Alabama, Tuscaloosa, says he noticed some weird fruit fly phenotypes -- things like appendage-like organs sticking out of their eyes -- at about the same time that a paper appeared in Nature connecting Hsp90 activity in Drosophila to genetic variation. In that paper, Suzanne Rutherford and Susan Lindquist, then at the University of Chicago, presented compelling evidence that Hsp90 serves as an 'evolutionary capacitor,' a genetic factor that regulates phenotypic expression by unleashing 'hidden' variation in stressful conditions. Even after restoring normal Hsp90 activity, the new phenotypes responded to ten or more generations of selection. The scientists concluded that, once released, even after normal Hsp90 activity was restored, the previously buffered variation persisted in a heritable manner, generation after generation.


"When the Lindquist paper came out, Ruden says he thought, 'Ah, I'm probably seeing the same thing.' He was doing some crosses, 'and I started to see this weird phenotype.' But Ruden and collaborators concluded that their strange eye phenotype was due to something other than, or in addition to, the sudden unleashing of hidden genetic variation. Indeed, the researchers used a strain of flies that had little genetic variation, and yet was still capable of responding to 13 generations of selection even after normal Hsp90 activity was restored. Because of the genomic homogeneity of their flies, combined with observations that mutations encoding chromatin-remodeling proteins induced the same abnormal eye phenotype, the investigators concluded that reduced levels of Hsp90 affected the phenotype by epigenetically altering the chromatin.


"Although it is hard to imagine that an appendage-like structure sticking out of the eye would be adaptive in times of stress, Vercelli says that epigenetic change clearly can be environmentally induced in a heritable manner, in this case by alterations to Hsp90. The morphological variations in the eye were probably only the most obvious of many phenotypic differences caused by the chromatin changes.


"In a written commentary, evolutionary biologist Massimo Pigliucci said that Ruden's experiment was 'one of the most convincing pieces of evidence that epigenetic variation is far from being a curious nuisance to evolutionary biologists.' Pigluicci doesn't go so far as to say that the heritable changes caused by Hsp90 alterations are Lamarckian, but Ruden does. 'Epigenetics has always been Lamarckian. I really don't think there's any controversy,' he says.


"Not that Mendelian genetics is wrong; far from it. The increased understanding of epigenetic change and the recent evidence indicating its role in inheritance and development doesn't give epigenetics greater importance than DNA. Genetics and epigenetics go 'hand in hand,' says Ohlsson. In the case of disease, says Reik, 'there are clearly genetic factors involved, but there are also other factors involved. My suspicion is that it will be a combination of genetic and epigenetic factors, as well as environmental factors, that determine all these diseases.'" [Pray (2004). Quotation marks altered to conform with the conventions adopted at this site. Spelling changed to UK English. Bold emphases and some links added. References included in the original article have been omitted.]


On this, see Carey (2011) and Francis (2012).


Acquired Characteristics Inherited?


The New Scientist, January 2015, again:


"We used to think evolution had to start with random mutations -- now walking fish and bipedal rats are turning our ideas on their head


"'To be honest, I was intrigued to see if they'd even survive on land,' says Emily Standen. Her plan was to drain an aquarium of nearly all the water and see how the fish coped. The fish in question were bichir fish that can breathe air and haul themselves over land when they have to, so it's not as far-fetched as it sounds.


"What was perhaps more questionable was Standen's rationale. Two years earlier, in 2006, Tiktaalik had become a global sensation. This 360-million-year-old fossil provides a snapshot of the moment our fishy ancestors hauled themselves out of the water and began trading fins for limbs. Standen thought forcing bichir fish to live almost entirely on land could reveal more about this crucial step in our evolution. Even if you were being kind, you might have described this notion as a little bit fanciful.


"Today, it seems positively inspired. The bichirs did far more than just survive. They became better at 'walking'. They planted their fins closer to their bodies, lifted their heads higher off the ground and slipped less than fish raised in water. Even more remarkably, their skeletons changed too. Their 'shoulder' bones lengthened and developed stronger contacts with the fin bones, making the fish better at press-ups. The bone attachments to the skull also weakened, allowing the head to move more. These features are uncannily reminiscent of those that occurred as our four-legged ancestors evolved from Tiktaalik-like forebears.


"What is really amazing about this experiment is that these changes did not come about after raising generations of fish on land and allowing only the best walkers to breed. Instead, it happened within the lifetime of individual fish. Simply forcing young fish to live on land for eight months was all it took to produce these quite dramatic changes. We have long known that our muscles, sinews and bones adapt to cope with whatever we make them do. A growing number of biologists think this kind of plasticity may also play a key role in evolution. Instead of mutating first and adapting later, they argue, animals often adapt first and mutate later. Experiments like Standen's suggest this process could even play a role in major evolutionary transitions such as fish taking to land and apes starting to walk upright.


"The idea that plasticity plays a role in evolution goes back more than a century. Some early biologists thought that characteristics acquired during an animal's lifetime could be inherited by their offspring: giraffes got their long necks by stretching to eat leaves, and so on. The French naturalist Jean-Baptiste Lamarck is the best-known advocate of this idea, but Darwin believed something similar. He even proposed an elaborate mechanism to explain how information about changes in the body could reach eggs and sperm, and therefore be passed on to offspring. In this way, Darwin suggested, plasticity produces the heritable variations on which natural selection can work its magic.


"With the rise of modern genetics, such notions were dismissed. It became clear that there is no way for information about what animals do during their lifetime to be passed on to their offspring (although a few exceptions have emerged since). And it was thought this meant plasticity has no role in evolution. Instead, the focus shifted to mutations. By the 1940s, the standard thinking was that animals mutate first and adapt later. A mutation in a sperm cell, say, might produce a physical change in the bodies of some offspring. If the change is beneficial, the mutation will spread through the population. In other words, random genetic mutations generate the variation on which natural selection acts. This remains the dominant view of evolution today.


"The dramatic effects of plasticity were not entirely ignored. In the 1940s, for instance, the Dutch zoologist Everhard Johannes Slijper studied a goat that had been born without forelegs and learned to hop around, kangaroo-like, on its rear legs. [It seems that a dog in the UK can do likewise -- RL.] When Slijper examined the goat after its death, he discovered that the shape of its muscles and skeleton looked more like those of a biped than a quadruped. Few biologists considered such findings relevant to the evolutionary process. The fact that changes acquired during an animal's lifetime are transient seemed to rule out that possibility. If Standen's better-at-walking fish were bred and the offspring raised in a normal aquarium, for instance, they should look and behave like perfectly ordinary bichirs.


"Transient response


"But what if the environmental conditions that induce the plastic response are themselves permanent? In the wild, this could happen as a result of alterations in prey animals, or in the climate, for instance. Then all the members of a population would develop in the same, consistent way down the generations. It would look as if the population had evolved in response to an altered environment, but technically it's not evolution because there is no heritable change. The thing is, the only way to tell would be to 'test' individuals by raising them in different circumstances.


"In this way at least, plasticity can allow animals to 'evolve' without evolving. The crucial question, of course, is whether it can lead to actual evolution, in the sense of heritable changes. 'You can plastically induce generation after generation,' says Standen, who is now at the University of Ottawa in Ontario, Canada. 'At some point, can you remove the environmental conditions that induced the change and have the organisms remain changed?' The answer, surprisingly, seems to be yes. In the 1950s, British biologist Conrad Hal Waddington showed that it is feasible in an experiment involving fruit flies. Waddington found that when pupa are briefly heated, some offspring develop without crossveins in their wings. He then selected and bred those flies. By the 14th generation, some lacked crossveins even when their pupa were not heated. A physical feature that began as a plastic response to an environmental trigger had become a hereditary feature.


"How is this possible? Plastic changes occur because an environmental trigger affects a developmental pathway in some way. More of a certain hormone may be produced, or produced at a different time, or genes are switched on that normally remain inactive, and so on. The thing is, random mutations can also have similar effects. So in an environment in which a particular plastic response is crucial for survival, only mutations that reinforce this response, or at least do not impede it, can spread through a population. Eventually, the altered developmental pathway will become so firmly stabilised by a genetic scaffolding that it will occur even without the environmental trigger, making it a permanent hereditary feature.


"Waddington called this process genetic assimilation. It may sound like Lamarckism, but it is not. The acquired characteristics don't shape the genetic changes directly as Darwin proposed, they merely allow animals to thrive in environments that favour certain mutations when they occur by chance (see diagram). Waddington's findings have been regarded as a curiosity rather than a crucial insight. But in the past decade or two, attitudes have begun to change. One reason for this is a growing appreciation of the flexibility of genes. Rather than being rigidly pre-programmed, we now know that the environment influences many aspects of animals' bodies and behaviour.


"Such discoveries have led some biologists to claim that developmental plasticity plays a major role in evolution. A few, such as Kevin Laland at the University of St Andrews, UK, even argue that the conventional 'mutate first, adapt later' picture of evolution needs a rethink (Nature, vol 514, p.161). Most biologists have yet to be convinced. The sceptics point out that genetic assimilation does not overturn any fundamental principles of evolution -- in the long run, evolution is all about the spread of mutations, whether or not plasticity is involved. Yes, say the proponents of plasticity, but the key point is that plasticity can determine which mutations spread (New Scientist, 12 October 2013, p 33), so its role should be given the prominence it deserves. 'Several major recent evolutionary textbooks do not even mention plasticity,' says Laland.


"It may play a role occasionally, respond the sceptics, but it's a minor one at best. 'There is little debate that genetic assimilation can happen,' says Gregory Wray of Duke University in Durham, North Carolina. 'But there is unfortunately very little support for its role in nature.' This is what makes Standen's work on the bichir so significant. It implicates plasticity in a major evolutionary transition: fish turning into four-legged land animals (Nature, vol 513, p.54). Plasticity will soon be implicated in another major transition too -- the one our ancestors made from four legs to two about 7 million years ago. As part of his PhD dissertation, Adam Foster, now at the Northeast Ohio Medical University in Rootstown, has been making rats walk on a treadmill. 'I had a custom harness system built so I could modify the load experienced by the hind limbs,' he says. Some rats had to walk on their hind limbs, while others walked on all fours. Each rat exercised on the treadmill for an hour a day for three months, and then Foster examined their skeletons.


"He found that the 'bipedal' rats had developed longer legs than standard quadrupedal rats, and that their thigh bones had larger femoral heads -- the ball in the hip joint. Both features are associated with the transition to bipedalism in our hominin ancestors. Foster hopes to publish the results later this year. 'I think Adam's research is really compelling,' says Jesse Young, an anatomist at Northeast Ohio Medical University. 'As he was getting it going, I was a bit sceptical. You couldn't predict it would reveal anything useful.' While the work of Standen and Foster suggests that developmental plasticity could play a role in major evolutionary transitions, it is only suggestive. Indeed, these studies do not even show that the plastic changes seen in the bichir fish and rats can be fixed by mutations. Demonstrating this kind of genetic assimilation would certainly be tricky, says Standen. It would not be practical with the bichir fish she studied. 'As wonderful as they are, they're frustrating fish,' says Standen. 'They take the better part of a decade to mature, and even then they're really difficult to breed in captivity.'


"The fossil record is usually no help either. It is possible that some of the changes seen as fish colonised the land were a result of plasticity rather than genetics, says Per Ahlberg of the University of Uppsala in Sweden who studies the transition to land. For Ahlberg, the trouble is that there is no way to prove it. 'There's no evidence that will allow us to choose between the two,' he says.


"More evolvable


"Other biologists are more enthusiastic. It has long been suggested that different parts of the skeleton are more plastic and 'evolvable' than others, says William Harcourt-Smith of the American Museum of Natural History. 'So a foot bone or a hand bone might give you more useful info than a hip bone, for instance.' Work like Foster's could reveal if this is indeed the case and help us interpret the fossil record of human evolution. 'These experiments do have validity,' Harcourt-Smith says. 'They can help us understand whether traits are plastic or not.'


Take the honeycomb structure in the heads of our long bones. It is lighter and weaker than it was in our extinct cousins such as the Neanderthals. A study out last month compared the bones of hunter-gatherers and early farmers in North America. It concluded that our bones became weak only when our ancestors' lifestyles changed (PNAS, 'We could have a skeleton as strong as our prehistoric ancestors,' says team member Colin Shaw of the University of Cambridge, UK. 'We just don't because we're not as active.' It's possible that similar kinds of skeletal structural change seen in prehistory have been misinterpreted as signs of speciation when they really just reflect developmental plasticity, says Shaw -- perhaps especially so in hominin evolution. Humans are unique, he points out. 'Our first line of defence against environmental insult is culture. When that's not adequate -- for instance if the clothing you can make is not good enough to keep you warm -- then arguably the second line of defence is plasticity. Only after that fails might you actually get genetic selection.'


"All this still leaves open the question of whether genetic assimilation can 'fix' traits that first appear as a result of plasticity. A decade ago, Richard Palmer at the University of Alberta in Edmonton, Canada, found a way to search for evidence in the fossil record. Most animals have some asymmetric traits. In our case, it's the position of the heart and other organs, which is encoded in our genes. But in other species, asymmetries are plastic. For instance, the enlarged claw of male fiddler as likely to be on the left as on the right. What Palmer showed by examining the fossil record of asymmetry in 68 plant and animal species is that on 28 occasions, asymmetries that are now hereditary and appear only on one side started out as non-hereditary asymmetries that appeared on either side (Science, vol 306, p.828). 'I think it's one of the clearest demonstrations that genetic assimilation has happened and that it is more common than expected,' says Palmer.


"There is a caveat here, though. The ancestral non-hereditary asymmetries may have been a result of random genetic noise, says Palmer. So while his work does show genetic assimilation in action, it was not necessarily fixing traits due to developmental plasticity. There is no simple way to prove the evolutionary importance of developmental plasticity, says Mary Jane West-Eberhard of the Smithsonian Tropical Research Institute in Costa Rica, whose work has been particularly influential. 'Evolutionary biology that is concerned with evolution and speciation in nature necessarily depends on indirect proof -- an accumulation of facts that support or deny a hypothesis,' she says. At the moment, the facts that are accumulating seem to support the hypothesis. Expect lots more results soon: Standen's success is inspiring others. 'I've already had people ask me what other critters we could try this on,' says Standen. 'Everybody is friendly and excited and interested. It's fun -- it's the way science should be.'" [Barras (2015), pp.26-30. (This links to a PDF.) Quotation marks altered to conform with the conventions adopted at this site. Some links added, and several paragraphs merged to save space.]


August 2015: We now read this from The Guardian:


"Study of Holocaust survivors finds trauma passed on to children's genes

"Helen Thomson, The Guardian, 21/08/2015

"New finding is first example in humans of the theory of epigenetic inheritance: the idea that environmental factors can affect the genes of your children

"Genetic changes stemming from the trauma suffered by Holocaust survivors are capable of being passed on to their children, the clearest sign yet that one person’s life experience can affect subsequent generations. The conclusion from a research team at New York's Mount Sinai hospital led by Rachel Yehuda stems from the genetic study of 32 Jewish men and women who had either been interned in a Nazi concentration camp, witnessed or experienced torture or who had had to hide during the second world war. They also analysed the genes of their children, who are known to have increased likelihood of stress disorders, and compared the results with Jewish families who were living outside of Europe during the war. 'The gene changes in the children could only be attributed to Holocaust exposure in the parents,' said Yehuda.

"Her team's work is the clearest example in humans of the transmission of trauma to a child via what is called 'epigenetic inheritance' -- the idea that environmental influences such as smoking, diet and stress can affect the genes of your children and possibly even grandchildren. The idea is controversial, as scientific convention states that genes contained in DNA are the only way to transmit biological information between generations. However, our genes are modified by the environment all the time, through chemical tags that attach themselves to our DNA, switching genes on and off. Recent studies suggest that some of these tags might somehow be passed through generations, meaning our environment could have and impact on our children's health.

"Other studies have proposed a more tentative connection between one generation's experience and the next. For example, girls born to Dutch women who were pregnant during a severe famine at the end of the second world war had an above-average risk of developing schizophrenia. Likewise, another study has showed that men who smoked before puberty fathered heavier sons than those who smoked after. The team were specifically interested in one region of a gene associated with the regulation of stress hormones, which is known to be affected by trauma. 'It makes sense to look at this gene,' said Yehuda. 'If there's a transmitted effect of trauma, it would be in a stress-related gene that shapes the way we cope with our environment.'

"They found epigenetic tags on the very same part of this gene in both the Holocaust survivors and their offspring, the same correlation was not found in any of the control group and their children. Through further genetic analysis, the team ruled out the possibility that the epigenetic changes were a result of trauma that the children had experienced themselves.

"'To our knowledge, this provides the first demonstration of transmission of pre-conception stress effects resulting in epigenetic changes in both the exposed parents and their offspring in humans,' said Yehuda, whose work was published in Biological Psychiatry.

"It's still not clear how these tags might be passed from parent to child. Genetic information in sperm and eggs is not supposed to be affected by the environment - any epigenetic tags on DNA had been thought to be wiped clean soon after fertilisation occurs. However, research by Azim Surani at Cambridge University and colleagues, has recently shown that some epigenetic tags escape the cleaning process at fertilisation, slipping through the net. It's not clear whether the gene changes found in the study would permanently affect the children's health, nor do the results upend any of our theories of evolution.

"Whether the gene in question is switched on or off could have a tremendous impact on how much stress hormone is made and how we cope with stress, said Yehuda. 'It's a lot to wrap our heads around. It's certainly an opportunity to learn a lot of important things about how we adapt to our environment and how we might pass on environmental resilience.' The impact of Holocaust survival on the next generation has been investigated for years -- the challenge has been to show intergenerational effects are not just transmitted by social influences from the parents or regular genetic inheritance, said Marcus Pembrey, emeritus professor of paediatric genetics at University College London.

"'Yehuda's paper makes some useful progress. What we're getting here is the very beginnings of a understanding of how one generation responds to the experiences of the previous generation. It's fine-tuning the way your genes respond to the world.'

"Can you inherit a memory of trauma?

"Researchers have already shown that certain fears might be inherited through generations, at least in animals. Scientists at Emory University in Atlanta trained male mice to fear the smell of cherry blossom by pairing the smell with a small electric shock. Eventually the mice shuddered at the smell even when it was delivered on its own. Despite never having encountered the smell of cherry blossom, the offspring of these mice had the same fearful response to the smell -- shuddering when they came in contact with it. So too did some of their own offspring.

"On the other hand, offspring of mice that had been conditioned to fear another smell, or mice who'd had no such conditioning had no fear of cherry blossom. The fearful mice produced sperm which had fewer epigenetic tags on the gene responsible for producing receptors that sense cherry blossom. The pups themselves had an increased number of cherry blossom smell receptors in their brain, although how this led to them associating the smell with fear is still a mystery." [Quoted from here; accessed 22/08/2015. Several paragraphs merged to save space. Quotation marks altered to conform with the conventions adopted at this site. Links in the original. Bold added.]


However, it should be noted that there are serious problems with the above research; on that, see here.

Is Everything We Know About The Universe Wrong?


In 2010, we read this from the BBC:


"Is Everything We Know About The Universe Wrong?


"There's something very odd going on in space -- something that shouldn't be possible. It is as though vast swathes of the universe are being hoovered up by a vast and unseen celestial vacuum cleaner.


"Sasha Kaslinsky, the scientist who discovered the phenomenon, is understandably nervous: 'It left us quite unsettled and jittery' he says, 'because this is not something we planned to find'. The accidental discovery of what is ominously being called 'dark flow' not only has implications for the destinies of large numbers of galaxies -- it also means that large numbers of scientists might have to find a new way of understanding the universe.


"Dark flow is the latest in a long line of phenomena that have threatened to rewrite the textbooks. Does it herald a new era of understanding, or does it simply mean that everything we know about the universe is wrong?" [Quoted from here. Bold emphases added.]


"14 billion years ago there was nothing; then everything exploded into existence and the universe was born, but a new generation of cosmologists are questioning this theory. Cosmologists have created a replica of the universe by using equations; it's called the standard model of cosmology and it's the reason behind the Big Bang theory; however, this model is now doubted. Professor Alan Guth's theory challenges the Big Bang by stating that the universe started out small, allowing the temperature to even out everywhere, before expanding on a massive scale.


"Stars nearer the edge of a galaxy move just as fast as those in the centre. This made cosmologists think that galaxies needed more gravity, but the only way to get more gravity was to create it. Astrophysicist Dan Bauer is hunting for dark matter half a mile under the dark plains of Minnesota in order to trace and record it more effectively. The discovery that the universe is speeding up suggests that a new force is powering the universe. This force is known as dark energy, and cosmologists have no idea what it is.


"The combination of the standard model, inflation and dark matter has given way to a new theory called dark flow. The nature of this theory could show that our universe isn't the only one. The standard model of cosmology has withstood much criticism, therefore making the theory stronger; however it could still be totally wrong." [Quoted from here, where the BBC programme in question can be accessed. Bold emphases and links added.]


Plate Tectonics On The Slide?


August 2012: The New Scientist has yet more disconcerting news to offer its readers:


"Plate tectonics can't explain all the earthquakes, volcanoes and landscapes of Earth, so what else is shaping its surface?


"'A lot of people (sic) thinks that the devil has come here. Some thinks (sic) that this is the beginning of the world coming to a end.'


"To George Heinrich Crist, who wrote this on 23 January 1812, the series of earthquakes that had just ripped through the Mississippi river valley were as inexplicable as they were deadly. Two centuries on and we are no closer to an understanding. According to our established theory of Earth's tectonic activity, the US Midwest is just not the sort of place such tremors should occur.


"That's not the only thing we are struggling to explain. Submerged fossil landscapes off the west coast of Scotland, undersea volcanoes in the south Pacific, the bulging dome of land that is the interior of southern Africa: all over the world we see features that plate tectonics alone is hard pressed to describe.


"So what can? If a new body of research is to be believed, the full answer lies far deeper in our planet. If so, it could shake up geology as fundamentally as the acceptance of plate tectonics did half a century ago.


"The central idea of plate tectonics is that Earth's uppermost layers -- a band of rock between 60 and 250 kilometres thick known as the lithosphere -- is divided into a mosaic of rigid pieces that float and move atop the viscous mantle immediately beneath. The theory surfaced in 1912, when German geophysicist Alfred Wegener argued on the basis of fossil distributions that today's continents formed from a single supercontinent, which came to be called Pangaea, that broke up and began drifting apart 200 million years ago.


"Wegener lacked a mechanism to make his plates move, and the idea was at first ridiculed. But evidence slowly mounted that Earth's surface was indeed in flux. In the 1960s people finally came to accept that plate tectonics could not only explain many features of Earth's topography, but also why most of the planet's seismic and volcanic activity is concentrated along particular strips of its surface: the boundaries between plates. At some of these margins plates move apart, creating rift valleys on land or ridges on ocean floors where hotter material wells up from the mantle, cools and forms new crust. Elsewhere, they press up against each other, forcing up mountain chains such as the Himalayas, or dive down beneath each other at seismically vicious subduction zones such as the Sunda trench, the site of the Sumatra-Andaman earthquake in December 2004.


"And so plate tectonics became the new orthodoxy. But is it the whole truth? 'Because it was so hugely successful as a theory, everybody became a bit obsessed with horizontal motions and took their eye off an interesting ball,' says geologist Nicky White at the University of Cambridge.


"That ball is what is happening deep within Earth, in regions far beyond the reach of standard plate-tectonic theory. The US geophysicist Jason Morgan was a pioneer of plate tectonics, but in the 1970s he was also one of the first to find fault with the theory's explanation for one particular surface feature, the volcanism of the Hawaiian islands. These islands lie thousands of kilometres away from the boundaries of the Pacific plate on which they sit. The plate-tectonic line is that their volcanism is caused by a weakness in the plate that allows hotter material to well up passively from the mantle. Reviving an earlier idea of the Canadian geophysicist John Tuzo Wilson, Morgan suggested instead that a plume of hot mantle material is actively pushing its way up from many thousands of kilometres below and breaking through to the surface.


"That went against the flow, and it wasn't until the mid-1980s that others began to think Morgan might have a point. The turnaround came when seismic waves unleashed by earthquakes began to reveal some of our underworld's structure as they travelled through Earth's interior. Seismic waves travel at different velocities through materials of different densities and temperatures. By timing their arrival at sensors positioned on the surface we could begin to construct a 3D view of what sort of material is where....


"If we can do that, will history repeat itself, the doubters be won over, and another hotly disputed model become the new orthodoxy? [Professor Dietmar] Müller certainly thinks so: 'Geology is on the cusp of another revolution like plate tectonics.'" [Ananthaswamy (2012), pp.38-41. Italic emphasis in the original; bold emphases added. Quotation marks altered to conform with the conventions adopted at this site. Several links also added.]


Heisenberg For The High Jump?


September 2012: The BBC reported as follows:


"Pioneering experiments have cast doubt on a founding idea of the branch of physics called quantum mechanics. The Heisenberg uncertainty principle is in part an embodiment of the idea that in the quantum world, the mere act of observing an event changes it. But the idea had never been put to the test, and a team writing in Physical Review Letters says 'weak measurements' prove the rule was never quite right. That could play havoc with 'uncrackable codes' of quantum cryptography.


"Quantum mechanics has since its very inception raised a great many philosophical and metaphysical debates about the nature of nature itself. Heisenberg's uncertainty principle, as it came to be known later, started as an assertion that when trying to measure one aspect of a particle precisely, say its position, experimenters would necessarily 'blur out' the precision in its speed. That raised the spectre of a physical world whose nature was, beyond some fundamental level, unknowable. This problem with the act of measuring is not confined to the quantum world, explained senior author of the new study, Aephraim Steinberg of the University of Toronto.


"'You find a similar thing with all sorts of waves,' he told BBC News. 'A more familiar example is sound: if you've listened to short clips of audio recordings you realise if they get too short you can't figure out what sound someone is making, say between a "p" and a "b". If I really wanted to say as precisely as possible, "when did you make that sound?", I wouldn't also be able to ask what sound it was, I'd need to listen to the whole recording.'


"The problem with Heisenberg's theory was that it vastly predated any experimental equipment or approaches that could test it at the quantum level: it had never been proven in the lab.


"'Heisenberg had this intuition about the way things ought to be, but he never really proved anything very strict about the value,' said Prof Steinberg. 'Later on, people came up with the mathematical proof of the exact value.'...


"Prof Steinberg and his team are no stranger to bending quantum mechanics' rules; in 2011, they carried out a version of a classic experiment on photons -- the smallest indivisible packets of light energy -- that plotted out the ways in which they are both wave and particle, something the rules strictly preclude. This time, they aimed to use so-called weak measurements on pairs of photons, putting into practice an idea first put forward in a 2010 paper in the New Journal of Physics.


"Photons can be prepared in pairs which are inextricably tied to one another, in a delicate quantum state called entanglement, and the weak measurement idea is to infer information about them as they pass, before and after carrying out a formal measurement. What the team found was that the act of measuring did not appreciably 'blur out' what could be known about the pairs.


"It remains true that there is a fundamental limit of knowability, but it appears that, in this case, just trying to look at nature does not add to that unavoidably hidden world. Or, as the authors put it: 'The quantum world is still full of uncertainty, but at least our attempts to look at it don't have to add as much uncertainty as we used to think!'


"Whether the finding made much practical difference was an open question, said Prof Steinberg.


"'The jury is still out on that. It's certainly more than a footnote in the textbooks; it will certainly change the way I teach quantum mechanics and I think a lot of textbooks. But there's actually a lot of technology that relies on quantum uncertainty now, and the main one is quantum cryptography -- using quantum systems to convey our information securely -- and that mostly boils down to the uncertainty principle.'" [Quoted from here. Minor typos corrected; paragraphs merged to save space. Several links added. Quotation marks altered to conform with the conventions adopted at this site. Italic and bold emphases added.]


Quantum Mechanics Defective? -- Probably


Mathematical Foundations Shaky


September 2012: We encountered this disturbing news in the New Scientist:


"What if you constantly change the ingredients in your raw batter, but the baked cake is always lemon? It sounds like something from a surrealist film, but equivalent scenarios seem to play out all the time in the mathematics of the quantum world.


"Nobel prize-winner Frank Wilczek and colleague Alfred Shapere say we can't ignore the absurdity of the situation any longer. It's time to get to the bottom of what is really going on, and in the process cement our understanding of the fundamental nature of the universe.


"They are part of a broader call to arms against those who are content to use the maths behind quantum mechanics without having physical explanations for their more baffling results, a school of thought often dubbed 'shut up and calculate'.


"'I don't see why we should take quantum mechanics as sacrosanct,' says Roger Penrose of the University of Oxford. 'I think there's going to be something else which replaces it.'


"Einstein's widely accepted theory of special relativity states that nothing can travel faster than the speed of light. But the phenomenon of quantum entanglement seems to flout that speed limit by allowing a measurement of one particle to instantaneously change another, even when the two are widely separated. Einstein famously called this 'spooky action at a distance'.


"'It's very disturbing,' says Wilczek of the Massachusetts Institute of Technology. 'It bothered Einstein. It should bother everybody.'


"To underline what they mean Wilczek and Shapere of the University of Kentucky in Lexington, examined a quantum system affected by a key aspect of special relativity: simultaneous events might not look simultaneous to all observers.


"If two fireworks go off at exactly the same time in neighbouring towns, a spectator will be able to see both simultaneously. To an observer moving from one town to the other, one firework will seem to explode first. What holds true for you depends on your frame of reference -- that is, it's relative.


"Now add a third firework. If there's a reference frame in which it goes off at the same time as only one of the other two, you'd think there should be another reference frame in which all three happen simultaneously. Surprisingly, that is not how it works mathematically. Instead the calculations only work for 4 of the 6 possible orderings (


"The team then applied this test to the quantum world. When particles are entangled, they share a 'wave function'. Physically measuring one of the particles 'collapses' all the possibilities encoded in the wave function into a single value, instantly affecting any entangled partners.


"Based on the new maths, if you have three entangled photons and you measure photon A, you can have reference frames where measuring A affects C, or measuring A impacts B, but never where measuring A happens before the effects on both B and C. This implies that measuring photon A can influence events that happened in the past, creating a mathematical paradox. 'That's the tension: how can you have such large effects on the mathematical objects without physical consequences?' Wilczek says...." [New Scientist 22/09/2012, p.13. The on-line article is slightly different from the printed version. Quotation marks altered to conform with the conventions adopted at this site. Some links added.]



Probability "As Useful To Physics As Flat-Earth Theory"


October 2015: Physicist, David Deutsch had this to say in recent issue of the New Scientist:


"Probability is as useful to physics as flat-Earth theory


"You can't explain how the world really works with probability. It's time for a different approach


"Probability theory is a quaint little piece of mathematics. It is about sets of non-negative numbers that are attached to actual and possible physical events, that sum to 1 and that obey certain rules. It has numerous practical applications. So does the flat-Earth theory: for instance, it's an excellent approximation when laying out your garden.


"Science abandoned the misconception that Earth extends over an infinite plane, or has edges, millennia ago. Probability insinuated itself into physics relatively recently, yet the idea that the world actually follows probabilistic rules is even more misleading than saying Earth is flat. Terms such as 'likely', 'probable', 'typical' and 'random', and statements assigning probabilities to physical events are incapable of saying anything about what actually will happen.


"We are so familiar with probability statements that we rarely wonder what 'x has a probability of ½' actually asserts about the world. Most physicists think that it means something like: 'If the experiment is repeated infinitely often, half of the time the outcome will be x.' Yet no one repeats an experiment infinitely often. And from that statement about an infinite number of outcomes, nothing follows about any finite number of outcomes. You cannot even define probability statements as being about what will happen in the long run. They only say what will probably happen in the long run.


"The awful secret at the heart of probability theory is that physical events either happen or they don't: there's no such thing in nature as probably happening. Probability statements aren't factual assertions at all. The theory of probability as a whole is irretrievably 'normative': it says what ought to happen in certain circumstances and then presents us with a set of instructions. It is normative because it commands that very high probabilities, such as 'the probability of x is near 1', should be treated almost as if they were 'x will happen'. But such a normative rule has no place in a scientific theory, especially not in physics. 'There was a 99 per cent chance of sunny weather yesterday' does not mean 'It was sunny'.


"It all began quite innocently. Probability and associated ideas such as randomness didn't originally have any deep scientific purpose. They were invented in the 16th and 17th centuries by people who wanted to win money at games of chance.


"Gaming the system


"To discover the best strategies for playing such games, they modelled them mathematically. True games of chance are driven by chancy physical processes such as throwing dice or shuffling cards. These have to be unpredictable (having no known pattern) yet equitable (not favouring any player over another). The three-card trick, for example, does not qualify: the conjurer deals the cards unpredictably (to the onlooker) but not equitably. A roulette wheel that indicates each of its numbers in turn, meanwhile, behaves equitably but predictably, so equally cannot be used to play a real game of roulette.


"Earth was known to be spherical long before physics could explain how that was possible. Similarly, before game theory, mathematics could not yet accommodate an unpredictable, equitable sequence of numbers, so game theorists had to invent mathematical randomness and probability. They analysed games as if the chancy elements were generated by 'randomisers': abstract devices generating random sequences, with uniform probability. Such sequences are indeed unpredictable and equitable -- but also have other, quite counter-intuitive properties.


"For a start, no finite sequence can be truly random. To expect fairly tossed dice to be less likely to come up with a double after a long sequence of doubles is a falsehood known as the gambler's fallacy. But if you know that a finite sequence is equitable -- it has an equal number of 1s and 0s, say -- then towards the end, knowing what came before does make it easier to predict what must come next.


"A second objection is that because classical physics is deterministic, no classical mechanism can generate a truly random sequence. So why did game theory work? Why was it able to distinguish useful maxims, such as 'never draw to an inside straight' in poker, from dangerous ones such as the gambler's fallacy? And why, later, did it enable true predictions in countless applications, such as Brownian motion, statistical mechanics and evolutionary theory? We would be surprised if the four of spades appeared in the laws of physics. Yet probability, which has the same provenance as the four of spades but is nonsensical physically, seems to have done just that.


"The key is that in all of these applications, randomness is a very large sledgehammer used to crack the egg of modelling fair dice, or Brownian jiggling with no particular pattern, or mutations with no intentional design. The conditions that are required to model these situations are awkward to express mathematically, whereas the condition of randomness is easy, given probability theory. It is unphysical and far too strong, but no matter. One can argue that replacing the dice with a mathematical randomiser would not change the strategy of an ideally rational dice player -- but only if the player assumes that pesky normative rule that a very high probability of something happening should be treated as a statement that it will happen.


"So the early game theorists never did quite succeed at finding ways of winning at games of chance: they only found ways of probably winning. They connected those with reality by supposing the normative rule that 'very probably winning' almost equates to 'winning'. But every gambler knows that probably winning alone will not pay the rent. Physically, it can be very unlike actually winning. We must therefore ask what it is about the physical world that nevertheless makes obeying that normative rule rational.


"You may have wondered when I mentioned the determinism of classical physics whether quantum theory solves the problem. It does, but not in the way one might expect. Because quantum physics is deterministic too. Indeterminism -- what Einstein called 'God playing dice' -- is an absurdity introduced to deny the implication that quantum theory describes many parallel universes. But it turns out that under deterministic, multi-universe quantum theory, the normative rule follows from ordinary, non-probabilistic normative assumptions such as 'if x is preferable to y, and y to z, then x is preferable to z'.


"You could conceive of Earth as being literally flat, as people once did, and that falsehood might never adversely affect you. But it would also be quite capable of destroying our entire species, because it is incompatible with developing technology to avert, say, asteroid strikes. Similarly, conceiving of the world as being literally probabilistic may not prevent you from developing quantum technology. But because the world isn't probabilistic, it could well prevent you from developing a successor to quantum theory. In particular, constructor theory -- the framework that I have advocated for fundamental physics, within which I expect successors to quantum theory to be developed -- is deeply incompatible with physical randomness.


"It is easy to accept that probability is part of the world, just as it's easy to imagine Earth as flat when in your garden. But this is no guide to what the world is really like, and what the laws of nature actually are." [Deutsch (2015); quotation marks altered to conform with the conventions adopted at this site. Several paragraphs merged to save space. Emphases in the original.]


If this is so, it is hard to see how Bell's Theorem can survive, and with that out goes 'Quantum Entanglement'.


Is It Higgs Or Not? Does It Even Matter?


November 2012: The New Scientist back-tracked yet again:


"So we've finally found it. Or have we? Four months on, the identity of the particle snared at the Large Hadron Collider [LHC -- RL] remains unclear.


"It may indeed be the much-vaunted Higgs boson. Or it might not. Finding out will require a welter of tests hard to do in the messy environment of the LHC's proton collisions (see 'Particle headache: why the Higgs could spell disaster' -- reproduced below, RL).


"What's needed is...wait for it...a successor to the LHC. Physicists have already started dreaming of another huge particle smasher, this time based on electrons, to finally pin down the Higgs.


"In these straitened times that won't be an easy sell, especially as the LHC still feels so shiny and new. But a successor was always part of the long-term plan and will eventually be needed to make more progress. Whatever the LHC found, the public was captivated. Now is a good time for physicists to start -- subtly -- making their case." [Editorial, New Scientist, 10/11/12, p.3.]


"Particle headache: Why the Higgs could spell disaster


"Matthew Chalmers


"If the particle discovered at CERN this July is all we think it is, there are good reasons to want it to be something else.


"So Peter Higgs didn't get this year's Nobel for physics after all. It would have been the Hollywood ending to a story that began half a century ago with a few squiggles in his notebook, and climaxed on 4 July this year with a tear in his eye as physicists armed with a $6 billion particle collider announced they had found the particle that bears his name. Or something very like it anyway.


"Higgs wasn't the only one feeling a little emotional. This was the big one, after all. The Higgs boson completes the grand edifice that is the 'standard model' of matter and its fundamental interactions. Job done.


"If only things were that simple. As particle physicists gather in Kyoto, Japan, next week for their first big conference since July's announcement, they are still asking whether that particle truly is the pièce de résistance of the standard model. And meanwhile, even more subversive thoughts are doing the rounds: if it is, do we even want it?


"Higgs's squiggles aimed to solve a rather abstruse problem. Back in the early 1960s, physicists were flushed with their ability to describe electromagnetic fields and forces through the exchange of massless photons. They desperately wanted a similar quantum theory for the weak nuclear force, but rapidly hit a problem: the calculations demanded that the particles that transmit this force, now known as the W and Z bosons, should be massless too. In reality, they weigh in at around 80 and 90 gigaelectronvolts (GeV), almost 100 times meatier than a proton.


"The solution hit upon by Higgs and others was a new field that filled space, giving the vacuum a positive energy that in turn could imbue particles with different amounts of mass, according to how much they interacted with it. The quantum particle of this field was the Higgs boson.


"As the standard model gradually took shape, it became clear how vital it was to find this particle. The model demanded that in the very early hot universe the electromagnetic and weak nuclear forces were one. It was only when the Higgs field emerged a billionth of a second or less after the big bang that the pair split, in a cataclysmic transition known as electroweak symmetry breaking. The W and Z bosons grew fat and retreated to subatomic confines; the photon, meanwhile, raced away mass-free and the electromagnetic force gained its current infinite range. At the same time, the fundamental particles that make up matter -- things such as electrons and quarks, collectively known as fermions -- interacted with the Higgs field and acquired their mass too. An ordered universe with a set hierarchy of masses emerged from a madhouse of masslessness.


"It's a nice story, but one that some find a little contrived. 'The minimal standard model Higgs is like a fairy tale,' says Guido Altarelli of CERN near Geneva, Switzerland. 'It is a toy model to make the theory match the data, a crutch to allow the standard model to walk a bit further until something better comes along.' His problem is that the standard model is manifestly incomplete. It predicts the outcome of experiments involving normal particles to accuracies of several decimal places, but is frustratingly mute on gravity, dark matter and other components of the cosmos we know or suspect to exist. What we need, say Altarelli and others, is not a standard Higgs at all, but something subtly or radically different -- a key to a deeper theory.


"Questions of identity


"Yet so far, the Higgs boson seems frustratingly plain and simple. The particle born on 4 July was discovered by sifting through the debris of trillions of collisions between protons within the mighty ATLAS and CMS detectors at CERN's Large Hadron Collider. For a start, it was spotted decaying into W and Z bosons, exactly what you would expect from a particle bestowing them with mass.


"Even so, a definitive ID depends on fiddly measurements of the particle's quantum properties (see 'Reflections on spin'). 'The task facing us now is ten times harder than making the discovery was,' says Dave Newbold of the University of Bristol, UK, a member of the CMS collaboration.


"Beyond that, a standard-model Higgs has to decay not just into force-transmitting bosons, but also to matter-making fermions. Here the waters are little muddier. The particle was also seen decaying into two photons, which is indirect proof that it interacts with the heaviest sort of quark, the top quark: according to the theory, the Higgs cannot interact directly with photons because it has no electric charge, so it first splits into a pair of top quarks and antiquarks that in turn radiate photons. Further tentative evidence for fermion interactions comes from the US, where researchers on the now-defunct Tevatron collider at Fermilab in Batavia, Illinois, have seen a hint of the particle decaying into bottom quarks.


"But equally, the CMS detector has measured a shortfall of decays into tau leptons, a heavier cousin of the electron. If substantiated, that could begin to conflict with standard model predictions; ATLAS is expected to present its first tau-decay measurements in Kyoto next week. Both ATLAS and CMS see more decays into photons than expected, perhaps signalling the influence of new processes and particles beyond the standard model.


"It is too early to draw any firm conclusions. Because we know the new particle's mass fairly well -- it is about 125 GeV, or 223 billionths of a billionth of a microgram -- we can pin down the rates at which it should decay into various particles to a precision of about 1 per cent, if it is the standard Higgs. Because of the limited number of decays seen so far, however, the measurement uncertainty on the new particle's decay rates is more like 20 or even 30 per cent. By the end of the year, ATLAS and CMS will have around two and a half times the data used for the July announcement, but that still won't reduce the uncertainty enough. Then the LHC will be shut down for up to two years to be refitted to collide protons at higher energies. 'We're probably not going to learn significantly more about the new particle in the immediate future,' says Newbold.


"What physicists would like to fill this vacuum is a new collider altogether. The LHC is not exactly ideal anyway: it smashes protons together, and protons are sacks of quarks and other innards that make measurements a messy business. Researchers are lobbying for a cleaner electron-positron collider, possibly in Japan, to close the Higgs file, but that too is a distant prospect.


"So we are left with a particle that looks like the standard Higgs, but we can't quite prove it. And that leaves us facing an elephant in the accelerator tunnel: if it is the standard Higgs, how can it even be there in the first place?


"The problem lies in the prediction of quantum theory, confirmed by experiments at CERN's previous mega-accelerator, the Large Electron Positron collider, that particles spontaneously absorb and emit 'virtual' particles by borrowing energy from the vacuum. Because the Higgs boson itself gathers mass from everything it touches, these processes should make its mass balloon from the region of 100 GeV to 1019 GeV. At this point, dubbed the Planck scale, the fundamental forces go berserk and gravity -- the comparative weakling of them all -- becomes as strong as all the others. The consequence is a high-stress universe filled with black holes and oddly warped space-time.


"Conspirators sought


"One way to avert this disaster is to set the strength of virtual-particle fluctuations that cause the problem so they all cancel out, reining in the Higgs mass and making a universe more like the one we see. The only way to do that while retaining a semblance of theoretical dignity, says Altarelli, is to invoke a conspiracy brought about by a suitable new symmetry of nature. 'But where you have a conspiracy you must have conspirators.'


"At the moment, most physicists see those conspirators in the hypothetical superpartners, or 'sparticles', predicted by the theory of supersymmetry. One of these sparticles would partner each standard model particle, with the fluctuations of the partners neatly cancelling each other out. These sparticles must be very heavy: the LHC has joined the ranks of earlier particle smashers in ruling them out below a certain mass, currently around 10 times that of the putative Higgs.


"That has already put severe pressure on even the simplest supersymmetric models. But all is not lost, according to James Wells of CERN's theory group. If you don't find sparticles with low masses, you can twiddle the theory, to an extent, and 'dial them up' to appear at higher masses. 'We expected that the Higgs would be found and that a supporting cast would be found with it, but not necessarily at the same energy scale,' he says. [Tweaking the 'epicycles'? -- RL.]


"Even so, the goalposts cannot be shifted too far: if the sparticles get too heavy, they won't stabilise the Higgs mass in a convincingly 'natural' way. Sparticles are also hotly sought after as candidates to make up the universe's missing dark matter. Updates will be presented in Kyoto next week, and there is also hope for indirect leads to supersymmetry from measurements of anomalies in the decay rates of other standard-model particles. If nothing stirs there, all eyes are on what happens when the LHC roars back early in 2015 at near double its current collision energy. A revamped LHC should be able to conjure more massive sparticles from thin air, or perhaps even more radical particles such as those associated with extra dimensions of space. These particles amount to another attempt to fill the gap between where the Higgs 'should be' -- at the Planck scale --- and where it actually is.


"The weirdest scenario of them all, though, is if there is nothing but tumbleweed between the energies in which the standard model holds firm and those of the Planck scale, where quantum field theories and Einstein's gravity break down. How then would we explain the vast discrepancy between the Higgs's actual mass and that predicted by quantum theory?


"Teetering on the brink


"One solution is to just accept it: if things were not that way, the masses of all the particles and their interactions strengths would be very different, matter as we know it would not exist, and we would not be here to worry about such questions. Such anthropic reasoning, which uses our existence to exclude certain properties of the universe that might have been possible, is often linked with the concept of a multiverse -- the idea that there are innumerable universes out there where all the other possible physics goes on. To many physicists, it is a cop-out. 'It looks as if it's an excuse to give up on deeper explanations of the world, and we don't want to give up,' says Jon Butterworth of University College London, who works on the ATLAS experiment.


"But a second fact about the new particle gives renewed pause for thought. Not only is its 125 GeV mass vastly less than it should be, it is also about as small as it can possibly be without dragging the universe into another catastrophic transition. If it were just a few GeV lighter, the strength of the Higgs interactions would change in such a way that the lowest energy state of the vacuum would dip below zero. The universe could then at some surprise moment 'tunnel' into this bizarre state, again instantly changing the entire configuration of the particles and forces and obliterating structures such as atoms.


"As things stand, the universe is seemingly teetering on the cusp of eternal stability and total ruin. 'It's an interesting coincidence that we are right on the border between these two phases,' says CERN theorist Gian Giudice, who set about calculating the implications of a 125 GeV Higgs as soon as the first strong hints came out of the LHC in December last year.


"He doesn't know what the answer is. In any case, finding any new particles will change the game once more. 'There are many questions in the history of science whose answers have turned out to be environmental rather than fundamental,' says Giudice. 'The slightest hint of new physics and my calculation will be forgotten.' So that is what all eyes will really be on in Kyoto. Higgs's squiggles seem to have become reality -- but for a more satisfying twist to the tale, we must hope some other squiggles show similar signs of life soon." [New Scientist, 10/11/12, pp.34-37. Several links added. Quotations marks altered to conform with the conventions adopted at this site. The on-line version has a different title to the published article. Bold emphases added. Typo corrected.]


Update November 2014: It looks like the Higgs Boson might not have been discovered, after all; here is what Science News had to say:


"Techni-Higgs: European Physicists Cast Doubt on Discovery of Higgs Boson


"Nov 10, 2014 by


"'The CERN data are generally taken as evidence that the particle is the Higgs particle. It is true that the Higgs particle can explain the data but there can be other explanations, we would also get these data from other particles,' said Dr Mads Toudal Frandsen of the University of Southern Denmark, the senior author of the study published in the journal Physical Review D ( preprint).


"The study does not debunk the possibility that CERN physicists have discovered the Higgs boson. That is still possible -- but it is equally possible that it is a different kind of particle.


"'The current data is not precise enough to determine exactly what the particle is. It could be a number of other known particles,' Dr Frandsen said. 'But if it wasn't the Higgs particle, that was found in CERN's particle accelerator, then what was it? We believe that it may be a so-called techni-Higgs particle. This particle is in some ways similar to the Higgs boson -- hence half of the name.'


"Although the techni-Higgs particle and Higgs boson can easily be confused in experiments, they are two very different particles belonging to two very different theories of how the Universe was created.


"The Higgs particle is the missing piece in the theory called the Standard Model.


"This theory describes three of the four forces of nature.


"'But it does not explain what dark matter is -- the substance that makes up most of the universe. A techni-Higgs particle, if it exists, is a completely different thing,' the scientists said.


"'A techni-Higgs particle is not an elementary particle. Instead, it consists of so-called techni-quarks, which we believe are elementary. Techni-quarks may bind together in various ways to form for instance techni-Higgs particles, while other combinations may form dark matter,' Dr Frandsen said.


"'We therefore expect to find several different particles at CERN's Large Hadron Collider, all built by techni-quarks.'


"If techni-quarks exist, there must be a force to bind them together so that they can form particles. None of the four known forces of nature (gravity, the electromagnetic force, the weak nuclear force and the strong nuclear force) are any good at binding techni-quarks together.


"'There must therefore be a yet undiscovered force of nature. This force is called the technicolor force. What was found last year in CERN's accelerator could thus be either the Higgs particle of the Standard Model or a light techni-Higgs particle, composed of two techni-quarks.'


"More data from CERN will probably be able to determine if it was a Higgs or a techni-Higgs particle.


"'If CERN gets an even more powerful accelerator, it will in principle be able to observe techni-quarks directly.'" [Taken from here; accessed 11/08/2015. Quotation marks altered to conform with the conventions adopted at this site. Bold emphasis alone added. Several paragraphs merged.]


And we also read the following:


"God particle may not be God particle: Scientists in shock claim


"'Data not precise enough to determine exactly what it is'


"A new scholarly paper has raised suspicions in boffinry circles as to whether last year's breakthrough discovery by CERN was indeed the fabled, applecart-busting Higgs boson. The report from the University of Southern Denmark suggests that while physicists working with data from the Large Hadron Collider (LHC) did discover a new particle, the data might not point to the fabled Higgs boson, but rather to a different particle that behaves similarly.


"'The CERN data is generally taken as evidence that the particle is the Higgs particle. It is true that the Higgs particle can explain the data but there can be other explanations, we would also get this data from other particles,' said associate professor Mads Toudal Frandsen. 'The current data is not precise enough to determine exactly what the particle is. It could be a number of other known particles.'


"The Southern Denmark researchers suggest that the particle discovered by the LHC may not have been the Higgs boson, but rather a 'techni-higgs' particle that's composed of 'techni-quarks.' Such a particle might behave similarly to the Higgs particle but in fact is very different from the genuine Higgs boson. If the researchers are right, their report would discredit the claims of discovery of the Higgs boson, which has been sought because its existence would fill vital holes in the Standard Model of physics.


"The researchers claim that although their findings may disprove the Higgs boson discovery, they also pave the way for the discovery of another force -- one not yet uncovered -- that would be responsible for binding the techni-quarks into particles, including those that form dark matter. The group says that more data is needed to establish whether the particle observed by CERN was indeed the Higgs boson or otherwise. One way, they say, would be for CERN to build an even larger collider to better observe the particles and provide more evidence as to the existence of the theorized techni-quarks." [Quoted from here. Accessed 11/08/2015. Links and capitals in the original. Some paragraphs merged to save space; quotation marks altered to conform with the conventions adopted at this site. Bold emphasis added. See also here.]


"CERN May Not Have Found The Higgs Boson