Monthly Archives: July 2012
Scientists are supposed to change their minds when the balance of evidence changes. In my experience, this doesn’t always happen, but one very respected scientist who has changed his mind, not once but twice, and very publicly, is Prof Richard Muller of the Berkeley Earth Land Temperature Project, UC Berkeley, and Lawrence Berkeley National Laboratory.
Three years ago, he was among the few remaining respected scientists to reject the IPCC (Intergovernmental Panel on Climate Change) analysis of current climate, and unconvinced that significant climate change was happening at all, let alone that it might be driven by human activity. Not surprising, then, that a consortium of those with an interest in denial funded his BEST (Berkeley Earth Surface Temperature) project, to carry out a completely independent, assumption-free, analysis of the data. They got more than they bargained for.
First, BEST concluded, in findings published last year, that warming is indeed taking place as asserted by the overwhelming majority of the climate science community. Now, even more significantly, BEST has taken the position, in a paper submitted to The Third Santa Fe Conference on Global and Regional Climate Change, that CO2 is the most significant driver, that the IPCC estimate of the effect of CO2 (3oC warming for each doubling of CO2 concentration) is accurate, and that the amount of warming from the 1950s to the 2000s (0.87 +/- 0.05 oC) is if anything slightly more than the IPCC estimate.
Moreover, the BEST publications analyse and dismantle all the standard objections to this work. Yes, there are effects due to volcanoes. I don’t think anyone denies this. The 1991 Mount Pinatubo eruption led to summers bad enough to force up the price of potatoes, but earlier events, such as the eruptions of Laki in 1783, Tambora in 1815, and Cosiguina in 1835, were much more significant. We know this from accounts at the time, and can quantitatively estimate the intensity of the eruptions by the amount of sulphate in ice cores. The late 18th and early 19th century data are good enough to provide a scaling factor (0.15 oC cooling per gigatonne emitted sulphate), showing that, by contrast, the overall effect of volcanoes in the 20th century has been insignificant. No, there is no significant effect attributable to the Sun. No, there are no artefacts due to the number and location of climate stations, although this has not stopped WattsUp, a Koch-funded enterprise, from raising this yet again in response to Muller. There is some variability connected with oscillations in the Atlantic, which may be responsible for the 0.17 oC variation from the simplest model. This model, which attributes all change to a linear volcanic effect, and a logarithmic CO2 effect, is remarkably successful. In the light of Muller’s work there is no excuse for invoking alleged scientific uncertainty to delay urgent consideration of the effects of further increasing CO2 concentrations, and the appropriate policy responses.
There are some particular words of caution. We don’t understand why the difference between day and night time temperatures decreased from 1900 to 1987, but then started rising again. We can’t be certain that present temperatures exceed those of the Mediaeval Warm Period, so beloved of climate “sceptics”, although it seems clear that if things continue as they are, the issue will be beyond all doubt. Warming has not led to more hurricanes, and the heat wave afflicting the United States this summer is local rather than global.
Muller’s approach includes the effects to date of one important feedback, the positive feedback due to the fact that ocean warming leads to increased concentrations of water vapour, the most significant of all greenhouse gases. However, of necessity, it neglects effects that have not yet kicked in, most of which can only add to our concerns. A tiny minority of climate scientists still maintain that increased cloud cover will moderate the effects of warming, but the evidence (see Science 2009, 325, 376, for a discussion) now shows that the opposite is true. Melting of sea and land ice will speed up warming, by reducing the Earth’s albedo, the fraction of incident sunlight that is reflected straight back into space, since exposed ground, crops, and open ocean absorb more energy and snow and ice. There is the prospect of release of methane from thawing tundra, and increased release of carbon dioxide from soils, as bacterial activity increases with warming. The only negative feedback in prospect is the greater reflectivity of deserts, as compared with cultivated land, but that is the last thing we should be looking forward to.
Thus Muller’s approach offers us the lowest credible estimate of what is in store for us. Despite which, opposition parties in Australia and the US, including one US presidential candidate, and a vocal faction within the United Kingdom’s governing Conservative Party, continue, and may be expected to indefinitely continue, in their denial that any real problem has been shown to exist.
I find this frightening.
This post is also available at http://www.thetwentyfirstfloor.com/?p=4457
Part I,Dalton and Darwin
Don’t say “Darwin” when you mean “evolution”. Don’t say “theory of evolution” when you mean the established historical facts of change over time and common descent. And above all, don’t say “Darwin’s theory of evolution” except in the historical context of the evolution of ideas. If you do, you are guilty of scientific, logical, historical, and pedagogical errors, and playing into the hands of our Creationist opponents.
Dalton is to the modern atomic theory, and the modern atomic theory is to chemistry, as Darwin(not to forget Wallace) is to evolution, and as evolution is to biology. But we don’t call our present perspective on atoms “Dalton’s theory”, and indeed, unless we are speaking historically, it sounds odd to even talk about “atomic theory” when we discuss atoms. So why should we refer to “Darwin’s theory”, and indeed why should we talk about the “theory of evolution” when we really mean the fact that evolution has taken place? I argue here that we shouldn’t, and that, given the ongoing opposition to the central facts of biology, it is actively damaging to do so.
John Dalton produced his “atomic theory” in the early 19th century. He arrived at it by way of a theory of gas pressure that we now know to be totally erroneous. Wielding Occam’s Razor rather too energetically, he assumed that the simplest compound between two elements contained just one atom of each, so that water would have the formula HO. He rejected what now seems to us perhaps the most striking validation of his theory, Gay-Lussac’s observation that gases combine according to simple ratios, because it pointed towards what later became known as Avogadro’s Hypothesis, which in turn required some gaseous molecules to be divisible, and when it came to gaseous elements Dalton had not grasped the distinction between atoms (the fundamental particles of chemical composition) and molecules (the fundamental particles of gas pressure). It was half a century before his theory was generally accepted, and even then some remained sceptical, on the grounds that no one had ever observed the effects of individual atoms or molecules, until in 1905 Einstein pointed out that that was exactly what people were doing when they looked at Brownian motion. These days, however, individual atoms are routinely observed by the methods of high resolution transmission electron microscopy, and scanning tunnelling microscopy, both of which depend on concepts far beyond any available to Dalton.
Charles Darwin produced his theory of the mutability of species as the result of natural selection (he did not himself use the term “evolution”) in the mid-19th century. Central to the theory is the existence of sufficient heritable variation to explain the diversity of life, and a major stumbling block is the prospect that favourable variations will disappear through dilution. He appealed to the experience of animal breeders, but as a solution to the problem of dilution this is grossly unfair, since breeders can and do deliberately select rare variants to breed between. He lamented the absence of fossil evidence, in terms still quoted by creationists despite the tons (literally) of such evidence that have been unearthed (literally, again) in the intervening 150 years. He was unaware of the digital nature of inheritance, as established by his contemporary, Gregor Mendel, but not widely known until that work was rediscovered (or more accurately, perhaps, reinterpreted) at the beginning of the 20th century. He fully realised that evolution required many millions of years, and had no good answer when Lord Kelvin, his “ogre”, used thermodynamic arguments to show (correctly) that the then known sources of energy could only have kept the sun shining for a mere 20 million years or so. He had no inkling of the nature of the genetic material, and could not have conceived of the methods of molecular biology that now allow us, using much the same kind of evidence that the courts use to establish paternity, to compare related species and to chart their divergence in exquisite detail. Least of all did he have any notion of the source of the variations of which evolution depends, or of how the supply of variants is constantly replenished by mutation, a process that we can now observe at the level of an individual’s DNA.
The first half of the 20th century saw the formation of what became known as “the neo-Darwinian synthesis”, bringing together by the 1940s the concept of selection and the methods of population genetics. (The expression “neo-Darwinian” should now properly be restricted to the evolutionary thought of that time, although Creationists persist in applying it to current biology, for reasons to be discussed in part II). The second half saw an explosion in our understanding of inheritance, based on laboratory studies, while the final decades saw breakthroughs in our understanding of human evolution, with the discovery of the fossilised remains of over a dozen species of our early relatives in eastern and southern Africa. By the end of the 20th century, evolution denial could fairly be compared with Holocaust denial. Given what we have learnt from molecular biology in the present century, it could now more fairly be compared with denying that Hitler ever invaded Poland in the first place.
So why does the name of Darwin still provoke controversy, why do people still speak of “the theory of evolution”, when as often as not they are referring, not to theory, but to the established historical facts, why does it matter, and how should we respond? These topics will be the subject of my next posting on this subject, “Naming and Framing”.
(You will find more on Dalton and his times, and on Kelvin and the age of the earth, in my book, From Stars to Stalagmites, and the arguments in these two posts are developed at greater length in an article that I wrote with Britt Holbrook; Putting Darwin in his Place; the Need to Watch our Language. ) This post first appeared on The 21st Floor
 Two volumes of hydrogen combine with one volume of oxygen to make two volumes of steam. If, as required by Avogadro’s Hypothesis, equal volumes of gas contain equal numbers of molecules, then each molecule of oxygen must contain (at least) two atoms, as shown in the way we now write this equation: 2H2 + O2 = 2H2O
 Imagine a favourable red variant in a population of white flowers. Under the blending theory of inheritance then current, its first generation offspring will be deep pink, the second generation somewhat paler, and so on until the descendants are indistinguishable from the general population.
 See Genesis; the Evolution of Biology, Jan Sapp, OUP, 2003, pp 117-122
This post originally appeared on The 21st Floor
I don’t normally bother with the Creationist newssheet, Evolution News and Views, but the recent article there by David Klinghoffergoes beyond what I am willing to suffer in silence. Klinghoffer himself, of course, is a senior fellow of the Discovery Institute, and the author of How Would God Vote? Why the Bible Commands You to Be a Conservative. I do not know his academic credentials – I seem to remember that he is a lawyer, but neither his biography on the Discovery Institute website, nor his Wikipedia entry (which follows that biography rather closely), give any details, and I hope that some readers can tell us more about this.
I also think it worth noting that Klinghoffer’s article has nothing to do with Intelligent Design, misguided though that may be. Like so much Discovery Institute material, it is an attack on the well-established facts of common ancestry. In other words, what is being advocated is, in the strictest and narrowest sense of the word, creationism. And not even creationism as a philosophical or religious position, but as an interpretation of the facts of biology, in a manner that has been intellectually unsustainable since around 1830.
Anyway, to business: in my own recent posting here I describe why, when announcing their finding in 2010, the discoverers of Au. sediba chose, on reflection, to include it in the genus Australopithecus rather than in the genus Homo. That 2010 account does, however, give a long list of ways in which Au. sediba is closer than Australopithecus to modern humans, and the title I chose for my piece (An Almost Human Tragedy) reflects this. I also described the most recent, rather surprising, finding; that the diet of Au. sediba ignored available grasses, in favour of woodland products such as tree bark.
Now here is what Klinghoffer has to say about this same finding:
Another Human “Ancestor” Bites the Dust Bark
…Sure enough, the cooling trend [concerning the importance of Au. sediba] is now plainly in evidence, with Nature reporting that the creatures had a very notable characteristic in common with chimps, not humans, that had not previously been recognized: their diet, highlighted by tree bark and wood. This was found thanks to an analysis of tooth enamel and dental tartar and microwear. The NY Times lets its readers down softly:
“Dr. Berger was an author of the new journal report. Few other paleoanthropologists agree with Dr. Berger’s contention that the new species is the most plausible known ancestor of archaic and modern humans. [Emphasis added by Klinghoffer]. Dr. [Amanda G.] Henry’s group said that studies of additional fossils from the Malapa caves “will provide a better understanding of the dietary ecology of Au. sediba.””
The discoverer of the fossils, Lee Berger of theUniversityofWitwatersrandinJohannesburg, says the new species, known as Australopithecus sediba, is the most plausible known ancestor of archaic and modern humans. Several other paleoanthropologists, while disagreeing with that interpretation, say the fossils are of great importance anyway, because they elucidate the mix-and-match process by which human evolution was shaped.
And the original paper in Science actually said, in the Abstract,
Combined craniodental and postcranial evidence demonstrates that this new species shares more derived features with early Homo than any other australopith species and thus might help reveal the ancestor of that genus
…and, in the body of the paper (p 203, column 3),
We can conclude that combined craniodental and postcranial evidence demonstrates that this new species shares more derived features with early Homo than does any other known australopith species, and thus represents a candidate ancestor for the genus, or a sister group to a close ancestor that persisted for some time after the first appearance of Homo [my added emphasis].
The situation is exactly as I described it, with no great claim to originality, in my earlier account here:
The problem is no longer one of finding a missing link, but one of tracing an individual branch (the one that led to us) through a densely forking bush. It is always notoriously difficult to distinguish closely related species, because of individual differences. Even when we can, we have no way of being sure which extinct species lie on our direct ancestral line; it is difficult to tell the difference between our great-grandfather and our great-great-uncle, or between one great-great-uncle and another.
In short, then, on the basis of newspaper accounts and apparently without having read the original literature, Klinghoffer gleefully demotes Au. sediba from a position that most workers in the field had never even claimed for it, in the belief that the evolutionary account is thereby in some way undermined. Actually, the boot is on the other foot; the loser is the religious doctrine of separate creation. For if the 20 or so known distinct australopithecine and other early hominin species are not related by common descent, and were therefore doomed to extinction without progeny, why were they ever created in the first place?
Some time a little less than 2 million years ago, an adult female of the family of apelike creatures to which humans are related by descent was walking through the woodland of southern Africa with her younger companion (child? brother?) when the soft soil gave way beneath their feet. They were plunged down a sinkhole almost 100 feet deep into an underground cavern, and killed (let us hope) instantly. Fragments of their skeletons were first discovered in 2008 and described in the scientific literature in 2010. Burial in the cavern had protected their bodies from predators, and the continuing infall of rubbish into the sinkhole meant that some fragments were unusually well-preserved. It was even possible to examine the teeth in enough detail to study these animals’ (people’s?) diet. Being distinct from but clearly related to Australopithecus Africanus, their species has been given the name Australopithecus sediba. This follows the admirable new fashion of incorporating words from local languages into the names of fossil species; sediba is a seSotho word meaning “fountain”.
Malapa Cave, scene of these events, is one of a group of caves in South Africa that now form the South African Cradle of Humankind World Heritage Site. The surrounding rock is dolomite, laid down in the late Archaean (a little over 2.5 billion years ago), and fractured much more recently by tectonic forces. Water flowing through these fractures has hollowed out a series of caves, while surface run-off seeping from above has given rise to sinkholes, such as the one involved in this tragedy. Animals including carnivores are often drawn to such sinkholes, attracted by the smell of water or of decaying flesh, with deadly results. Debris falling into the sinkhole forms a cone, burying their remains. Water running through the cave deposits layers of flowstone, calcium carbonate containing traces of uranium, and uranium-lead dating of these layers enable us to bracket the age of the sediments lying in between them. Additional dating information comes from palaeomagnetism (the Earth’s magnetic field changed direction several times during the period of interest, affecting the magnetisation of sediments). Further confirmation comes from other associated fossil remains; the cave also contains bones of horses, which did not arrive in this part of the world until 2.6 million years ago, and of the sabretoothed cat Megantereon, which became extinct roughly one million years later.
Au. sediba is distinct from Au. Africanus in many ways, so much so that the discoverers think it worthwhile to discuss whether it should actually be included in the genus Homo. On the whole, they think not, because the cranial capacity of around 420 cm3 is in the range associated with australopithecines, or even chimpanzees, rather than the more than 600 cm3 for all species classified as Homo. Moreover, Au. sediba has long arms, and ape-like shoulder bones, suggesting that it was partly arboreal. Nonetheless, the shape of the skull, the relatively small size of the back teeth, and the shape of the pelvis and hip region are decidedly more human than those found in Au Africanus.
The biggest surprise about Au. sediba is its diet. Thanks to the beautifully preserved back teeth of the juvenile, we can learn about this in three distinct ways. Firstly, and most obviously, there is the roughness and degree of wear and tear on the tooth surfaces. Secondly, there is the isotopic composition of carbon in the teeth. This requires a little explanation. We are talking about the stable isotopes of carbon, the exact amount of carbon-13 compared with carbon-12; the radioactive carbon-14 that must have originally been present has long since decayed to completely undetectable levels. One of the near-truths that I used to tell my classes when I was a chemistry teacher, was that different isotopes of the same element have identical chemical properties. This is not exactly so. As a result of what is called zero point vibrational energy, which is itself a consequence of quantum mechanical uncertainty, there is a small but definite tendency for the heavier isotope to concentrate in environments where the carbon atom is more tightly bound, and to react more slowly because reaction almost always involves loosening of bonds. For this reason, plants contain measurably lower concentrations of carbon-13 than the carbon dioxide they use in photosynthesis.
Not all plants are created equal. They can be divided into C3 and C4 types, depending on the pathway by which they fix carbon dioxide. The older C3 pathway involves conversion of carbon dioxide and the five-carbon sugar ribulose into two molecules of the three-carbon molecule glyceric acid (I have missed out some phosphate groups for simplicity). The C4 pathway involves an additional step, and, as the name implies, gives rise to 4-carbon products. C4 material is less depleted in carbon-13 than that formed by the C3 pathway. The C4 pathway is more advantageous than the much older C3 pathway under conditions of drought, or relatively low carbon dioxide abundance, and seems to have arisen independently 40 different times in the past 30 million years or so.
Finally, we can examine the actual dental tartar of these specimens. This contains phytoliths (Greek; phyton, plant; lithos, stone), fragments of non-crystalline silica formed within plants from silica dissolved in groundwater, and different plants give rise to differently shaped phytoliths.
The results were surprising. We know that C4 grasses abounded in the neighbourhood, from the presence of grazers such as the horse, and Megalotragus, a bovid related to the hartebeest, whose skeletons unsurprisingly give the carbon-13 abundances characteristic of animals living on such grasses. However, Au. sediba showed the highest degree of depletion of carbon-13 in any fossil related to humans, indicating something close to a pure C3 diet. The worn surfaces of the teeth (and remember that these teeth were small, compared with Au. Africanus) showed that their owner had been chewing on hard materials. Finally, the phytoliths recovered show that the diet included fruit, bark, and sedges. The importance of fruit and bark is consistent with tree climbing ability, but so far we have no idea why Au. sediba, or at least these two particular individuals, avoided the abundant C4 grasses.
Darwin, famously, lamented the inadequacy of the fossil record in his time, in words that continue to be quoted by Creationists, as if nothing had been discovered in the meantime.
Alfred Russel Wallace,Darwin’s friend and co-discoverer of the principle of Natural Selection, believed human intelligence to be the product of special intervention or purpose. When he wrote, there was a clear gap between humans and apes, the “missing link” of popular imagination.
It was in 1925, Raymond Dart, professor at the University of the Witwatersrand, described the skull of what would become known as the “Taung child“, found in what is now Botswana, the first virtually complete cranium of animal clearly intermediate between apes and humans, which he called Australopithecus Africanus
Since that time, excavations worldwide, but especially in South Africa and in the Horn of Africa, have vastly extended the range of known pre-human species. The problem is no longer one of finding a missing link, but one of tracing an individual branch (the one that led to us) through a densely forking bush. It is always notoriously difficult to distinguish closely related species, because of individual differences. Even when we can, we have no way of being sure which extinct species lie on our direct ancestral line; it is difficult to tell the difference between our great-grandfather and our great-great-uncle, or between one great-great-uncle and another. Nonetheless, the 2007 Yale University Press compendium, The Last Human, lists some 20 different species somewhere on or near the line of descent from non-human ape to human. The fact that neither Australopithecus sediba, nor Denisovans, are among them, is proof of how fast our knowledge is still developing, and, by inference, how much still remains to be discovered.
References: Discovery of Au. sediba and description of cave setting, Science 328, 195 and 205, 2010; diet, Nature doi:10.1038/nature11185, published online 27 June 2012. Discovery of Au. Africanus, Nature 115, 195, 1925.
This post first appeared on 21st Floor, at http://www.thetwentyfirstfloor.com/?p=4272