Saturday, 31 May 2014

13,000-year-old American

Flooded cave hides Naia, a 13,000-year-old American - life - 15 May 2014 - New Scientist

As Francis Collins, himself a Christian, observed in his otherwise quite silly book, The Language Of God, "Young Earth Creationism has reached a point of intellectual bankruptcy, both in its science and in its theology". This point is made forcefully by recent discovery in a submerged cave in Mexico of the 13,000 year-old skeleton of a girl who was about 15 years-old when she died, almost certainly by falling into the hole before it was flooded as sea-levels rose at the end of the last ice-age.

She was found in Hoyo Negro (Black Hole) in the vast complex of caves in the Yucatan Peninsula known as a the Sistema Sac Atun along with the remains of about twenty-six other animals, representing both living and extinct species.

Nicknamed Naia after a mythological Greek water nymph, she is one of the most complete skeletons of an early Native American to be found. She is also the sixth oldest and is telling us a great deal about these earliest colonisers of the New World. Her dental caries suggest she ate an acidic diet of fruit and maybe honey from the surrounding forest rather than being a member of a tribe of big game hunters. Her slight build suggests her diet was deficient in protein and that she went hungry a great deal of the time. Life was by no means easy for these people.

I have not thought there was compelling reason or evidence that the anatomical differences between ancient and modern peoples in the Americas needed to be explained by anything more than evolutionary processes.

David Meltzer, anthropologist,
Southern Methodist University in Dallas, Texas
Her mitochondrial DNA shows that in her female line she was closely related to the people from Siberia who are believed to have lived in Beringia between Siberia and Alaska when sea-levels were lower and from whom the Native Americans are almost certainly descended, maybe from just a handful of people who migrated either down the coast or across ice-sheets or through a proposed ice-free passage over land. Her long, narrow skull and short facial features are closer to that found in the southern Pacific rim, Africa and Australia rather than being typical of modern Siberians and Native Americans. While these physical features have prompted some to suggest that she may be from an earlier migration and that modern Native Americans may be descendants of later, possibly multiple migrations but DNA is the clincher here. It shows all Native Americans, like Naia, are from Siberia and this in turn suggests the differences in the skull and facial features is due to evolution in America.

So we see how the evidence is continue to pile up against creationism, and especially the Bible-literalist who believe Earth is only a few thousand years old and all people on it are descended from a small family who were the sole survivors of a global flood about 4,000 years ago. Within that model there can be no possible explanation of why a 13,000 year-old skeleton of a girl came to be in a submerged cave in Mexico, why she appears to have had the physical characteristics of people from Africa, Australia and Southeast Asia but the DNA of Siberians and modern Native Americans and none of these are problems for the standard scientific theory of human evolution, a changing Earth with rising and falling sea-levels and changing climate, and above all, environmentally driven evolution or even random genetic drift in the descendants of a small founder population.

And yet, despite this mounting evidence against it, and despite not being able to explain these frequent scientific discoveries without misrepresenting the science, Young-Earth Creationism continue to be the explanation of choice for the Christian political right, for fundamentalist Christian churches and for Islamic clerics of all flavours and a Young-Earth creationist is far more likely to be elected to political office in the USA, the most powerful and economically developed country in the world, than is a scientist who advocates for Darwinian evolution and accepts that Earth is 4 billion years old and exists in a Universe that has existed for 13.82 billion years. Those most capable of assimilating the complex data needed to make major policy decisions are effectively debarred from holding public office because they don't have enough ignorance and don't believe the refuted and absurd Bronze Age myths.

As Francis Collins goes on to say of Young-Earth Creationism, "Its persistence is thus one of the great puzzles and great tragedies of our time".

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Why Science Grows And Religions Stagnate

A couple of interesting articles in the science literature this week showing how science works and why it ultimately corrects it errors, whether because of mistaken claims or deliberately false ones, and above all why it continues to grow and develop. I wonder if any keen theologists can cite examples of religions being extended and kept on track by a similar process.

The first, in Scientific American, concerns the recent announcement of the detection of evidence of gravity waves as predicted by the inflation model of the Big Bang. This model explains a great deal about the observable universe such as why widely separated areas of the Universe that could never have been in contact with one another given the limitations imposed by the velocity of light, appear broadly the same. However, inflation remained a hypothesis pending definitive evidence supported only by the fact of its mathematical elegance and that it explained what can be observed.

Then last March, as reported in this blog and elsewhere a team working on the Background Imaging of Cosmic Extragalactic Polarization 2 (BICEP2) experiment at the South Pole announced that they had found the evidence in the form of gravity waves, or more precisely, evidence for gravity waves; the smoking gun of inflation.

Now, however, and in the finest traditions of a major discovery, some serious questions are being asked and as yet not being fully answered. Doubts have been expressed about the validity of the conclusions from the data which the team have not yet made available for public scrutiny, nor have they produced a promised 'systematics' paper setting out possible sources of error although one was promised. Another problem for the science community is that, although the peer-review process is underway the team have not yet published their findings in a science journal.

Note that no-one is suggesting any dishonesty or falsification of data here, only questioning the validity and reliability of the conclusions from the data and whether it is the conclusive evidence for inflation that it was hailed as initially. As always, the concern is not whether the evidence agrees with the conclusion but whether the conclusion follows from the evidence. This is a crucial difference and one which can't be overstated.

The second article, this time in Science Magazine, is on a different scale altogether and deals with a strong suspicion of dishonesty and data manipulation or falsification. Although not formally proven there is growing concern about the work of Jens Förster, a Dutch researcher in psychology who resigned recently from the University of Amsterdam. As reported by Frank van Kolfschooten in Science Magazine, doubts had been raised about the statistical probability of his results being genuine and not the result of data manipulation to produce the desired results. One enquiry by the University of Amsterdam concluded that they were 'virtually impossible' whilst another concluded that there had been data manipulation in a 2012 paper.

Förster had accepted the charge of data manipulation but claimed the data used was from research in Germany, mostly at Jacobs University Bremen between 1999 and 2008 and suggested an unidentified and over-enthusiastic assistant had changed the data. However, emails have now emerged from 2009 which appear to be discussing the details of the experimental method to be used and which clearly post-date the pre-2008 German research claim. The offer of a professorship at Ruhr University, Bochum, Germany, supported by a €5 million grant from the German Alexander von Humboldt Foundation, has now been postponed.

So, in both these examples we see the scientific community using the scientific method to ensure that both genuine mistakes and deliberate falsifications are identified and investigated with all sides of the argument being heard before a final conclusion is reached - and the sanctions which inevitably follow from exposed deliberate falsification which can bring a reputation into disgrace and a career to a sudden end.

The reason for this, and the reason why it raises such concern in the scientific community is because the entire point of science is to arrive closer to the ultimate truth and to ensure that any conclusions are only and precisely what the evidence supports, nothing more and nothing less. It does not matter how badly one wishes that there was data to support a favourite hypothesis or how much one wishes to be the first to provide an elusive proof of a hypothesis, and it does not matter how much one researcher might put his own career prospects above his respect for truth, honesty and integrity, or how easily one researcher falls for the temptation to just change the data a little to show the world the 'truth' as he/she sees it, or to flatters his/her boss with the brilliance of his methods. None of this adds to the strength of the conclusion. The only thing that matters is the truth.

Contrast this to what we witness daily in theology and especially fundamentalist theology and apologetics where the only thing that matters is that the argument arrives at the 'right' conclusion; the conclusion that faith tells them is the right one. This allows apologists like William Lane Craig to get away with blatantly false arguments, circular reasoning, repetition of refuted arguments to a different audience and glaring misrepresentation of statistical methods such as Baye's Theorem which, used correctly would have proved the probability of Jesus resurrecting from the dead was virtually zero, as shown here, not the virtual certainty he claimed to the delight of his Christian audience eager for confirmation of their bias.

This is the simple faith fallacy which allows Muslims, Christians, Jews, Shintoists and Hindus to look at the same evidence and arrive at entirely different conclusions, and why that conclusion never changes. It's also why no evidence that might change that conclusion is ever recognised or taken into account. It doesn't support the conclusion therefore the evidence is wrong, and why when asked for the evidence for their god, all supporters of all religions can, with equal confidence and with a sweep of the arm tell you to, "Look around! The evidence is everywhere". The evidence is everywhere because it is simply deemed to be evidence; their faith tells them so. And it's also the reason that what's presented as a serious science text book for Christian schools can come up with this extraordinarily bigoted statement presented as a basic principle of science:

  1. 'Whatever the Bible says is so; whatever man says may or may not be so,' is the only [position] a Christian can take..."
  2. If [scientific] conclusions contradict the Word of God, the conclusions are wrong, no matter how many scientific facts may appear to back them.
  3. Christians must disregard [scientific hypotheses or theories] that contradict the Bible.

William S. Pinkerton, Biology for Christian Schools

The conclusion is sacred so the facts must be ignored. If science had staggered along with that philosophy we would still be in the Bronze Age arguing about the best shape for wheels and arrowheads, and you couldn't be reading this. Religions, with their sacred conclusions and fixed dogmas, offering nothing more than comforting certainties, the delusion of false 'knowledge' and excuses for hate and ignorance, have no choice but to become increasingly irrelevant as human society progresses without them.

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Thursday, 29 May 2014

Closing The Gaps - Early Bird Shows Evolution

The fossil bird with its revealing stomach contents (insert)
Credit: © Senckenberg
Eocene fossil is earliest evidence of flower-visiting by birds

We have an interesting discovery reported this week in Biology Letter of a fossil bird which seems to be the earliest known avian nectar-feeder. It shows how evolution is driven by environmental opportunity as diversifying species move into and exploit the opportunities offered by new and evolving niches as the ecosystem they are part of develops, and how cooperation is at least as likely an outcome as are arms races and competition as 'selfish' genes are selected naturally because they produce more descendants.

Two researches, Gerald Mayr of the Ornithological Section and Volker Wilde of the Palaeobotanical Section, of Senckenberg Research Institute and Natural History Museum Frankfurt, Germany have cooperated in examining a fossil bird (Pumiliornis tessellatus) from the middle Eocene of Messel found at Messel, Germany and have shown it to almost certainly be the first known example of a nectivorous bird.

It has long been recognised that flowering plants or angiosperms, and nectar-feeding insects co-evolved as symbiotic relationships - the insects get nectar and the plants get their pollen spread to other flowers of the same species. This process minimises the waste of untargeted wind-blown pollen dispersal and the environmental restrictions of using motile male gamete found in lower plants such as mosses, ferns and liverworts, all of which require a damp environment so the motile gametes have something to swim in.

It's easy to understand how this system could have evolved from crawling insects and ground-hugging plants to flying insects and the wide rage and form of flowering plants now free to move into drier habitats. All this took place prior to the 160 million years ago from when we have the first definite fossil record of flowering plants which are believe to have diverged from the gymnosperms 240-202 million years ago. The major period of rapid diversification seems to have been around 120 million years ago.

Pollen grains in the stomach.
See original paper for explanation.
Meanwhile, the first true birds were diverging from the theropod dinosaurs about 150 million years ago, so they grew up with flowering plants, so so speak, and these provided them with the same ecological niche some insects had moved into, most notably and probably initially a wasp from which the bees have evolved. It's not surprising therefore that some birds such as the humming birds moved into this niche becoming smaller and more bee-like in the process (as incidentally, some other insects such as moths and butterflies, have).

Birds are important pollinators, but the evolutionary history of ornithophily (bird pollination) is poorly known. Here, we report a skeleton of the avian taxon Pumiliornis from the middle Eocene of Messel in Germany with preserved stomach contents containing numerous pollen grains of an eudicotyledonous angiosperm. The skeletal morphology of Pumiliornis is in agreement with this bird having been a, presumably nectarivorous, flower-visitor. It represents the earliest and first direct fossil evidence of flower-visiting by birds and indicates a minimum age of 47 million years for the origin of bird–flower interactions. As Pumiliornis does not belong to any of the modern groups of flower-visiting birds, the origin of ornithophily in some angiosperm lineages may have predated that of their extant avian pollinators.

Mayr. G. & Wilde. V.; Eocene fossil is earliest evidence of flower-visiting by birds; Biol. Lett. May 2014 vol. 10 no. 5 20140223; doi: 10.1098/rsbl.2014.0223

As the authors point out, this fossil only provides a minimum estimate for the evolution of ornithophilous (literally, bird-loving) plants but no pre-Eocene plants show any of the characteristics of ornithophilous plants and no earlier avian fossils show adaptation to a nectivorous diet. There is also an interesting reference to the remains of small insects amongst the pollen grains in the bird's stomach, possibly ingested accidentally, as occurs with present-day nectar feeders. However, this could give a clue about the evolution of nectar-feeding in this particular bird having possibly evolved from foraging for insects especially those exploiting the supply of nectar.

I wonder if creationists are able to explain why every single fossil meshes so neatly into our understanding of how evolution works, what it produces and the time-scale over which it operates, and never ever supports their special creation by magic a few thousand years ago notion. Every single discovery seems to be closing the gaps in which they try to fit their ever-shrinking little gods. That should be enough to convince any normal person that their daft notion is wrong, or at least to sow a few seeds of doubt about the wisdom and knowledge of the technologically backward and scientifically illiterate Bronze-Age hunter-gatherers who believed in magic and who came up with it in the first place.

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Wednesday, 28 May 2014

Sticky Problem For Creationists

Nosil Lab of Evolutioary Biology, University of Sheffield, UK
Is Evolution Predictable? | Science/AAAS | News

Here's one of those nice little pieces of scientific research that so infuriates creationist loons and sends them into deep denialism or a frenzied casting around for a way to dismiss it because it doesn't support their sacred conclusions.

One of the interesting questions in evolution is, just how predictable is it? Could we rewind the clock say ten million years and get the same result we have today? Or is there so much randomness in the process that small random differences both in the environment and the evolving individual species would add up eventually to major differences? And this of course is assuming that the main or only component of evolutionary change is natural selection and all change is adaptive. But, if random genetic drift is as important as some people think, then evolution could not be predictable except perhaps in conditions of intense selection pressure.

To help understand this a little better, a group from the Nosil Lab for Evolutionary Biology, University of Sheffield, UK, examined the differences in the DNA of a widespread species of Californian stick insect, Timema cristinae. This species has evolved two ecotypes adapted to living on different hillside plants. One with a broad body which lives on broad-leaved plants and one with a long, thin body with a central stripe, adapted to narrow-leaved plants. Although the same species, these can be seen as a species in the process of diverging into two daughter species.

Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess of coding genes with specific molecular functions. Regions of parallel genomic divergence in nature exhibited exceptional allele frequency changes between hosts in a field transplant experiment. The results advance understanding of biological diversification by providing convergent observational and experimental evidence for selection’s role in driving repeatable genomic divergence.

Víctor Soria-Carrasco, Zachariah Gompert, et al; Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation;
Science 16 May 2014: Vol. 344 no. 6185 pp. 738-742 DOI: 10.1126/science.1252136

I think it says that repeatability of evolution is very low.

Andrew Hendry, evolutionary biologist, McGill University, Montreal, Canada
As expected, they found many genetic differences between the two ecotypes, but they also found a wide difference between what appeared to be the the same ecotype collected from different hillsides. Only 17 percent of their DNA had changed in the same way. This indicates that a lot of the change is initially random and then selection works on that randomness to arrive at the same adaptive change, but by different routes and with different genes.

They've actually been able to dig down into the genome and find out a little bit more about [parallel evolution]. [The work] is really starting to give us some mechanistic understanding of the molecular basis of evolution.

Tim Coulson, population biologist, Oxford University, UK
So the team then transferred members of each ecotype onto the 'wrong' plant and analysed the DNA of their offspring to see how the frequency of different alleles had changed from those in their parents. These shifts would be due to selection pressure with those more advantageous to the parents making them more likely to breed and so increasing in frequency in the offspring with a corresponding decrease in their less-favourable counterparts. The result was a significant increase in those genes associated with differences in the two ecotypes. In other words, in a single generation, selection pressure had pushed the species towards the ecotype normally living on the host plant onto which they had been transferred.

These results indicate that divergent selection plays a role in repeated genomic divergence between ecotypes. Furthermore, our results suggest that, although repeated evolutionary scenarios (i.e., replaying the tape of life) would likely result in idiosyncratic outcomes, there may be a repeatable component driven by selection that can be detected, even at the genome-wide level and during the complex process of speciation.

Víctor Soria-Carrasco, Zachariah Gompert, et al; op cit

It would be interesting to hear what one of the loons at the Discovery Institute or the Institute for Creation Research has to says on this subject. Here we see not only environmentally-driven speciation in progress but we can see significant change in the frequency allele of key genes involved in this divergence being measurable in a single generation. If this does not constitute experimental evidence for evolution and an observed instance of speciation in progress so far as they are concerned, then it's probable that there is no evidence that they would accept. It's the equivalent of watching a stone fall to Earth while denying that gravity exists.

The only way this can be dismissed as evidence for evolution is simply to ignore it altogether, or to redefine evolution as something other than the standard scientific description of ".. any change in the frequency of alleles within a gene pool from one generation to the nex" (Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974).

Any creationist up for trying for an explanation? If so, please try to spell correctly and use proper English grammar.

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Sunday, 25 May 2014

Starting From The Conclusion

Recently, I've been reading A Manual for Creating Atheists by Peter Boghossian. Its purpose is to create 'Street Epistemologists' who can casually engage people in gentle, non-threatening conversations about faith and sow the seeds of Atheism by asking the right questions or making the right point at the right place in a conversation. The weak-point in theistic argument is of course the thing they regard as their strength - their faith in faith as a valid way to determine truth.

But, without evidence, faith is nothing more substantial than pretending to know things you don't know. In effect, the conclusion is whatever the 'faithful' want it to be. As Peter Boghossian goes on the say:

Friday, 23 May 2014

DNA Shows Big Bird Evolution

Emu-style birds have abandoned flight six times - life - 22 May 2014 - New Scientist

Given what we now know of how birds evolved from the therapod dinosaurs, it would be tempting to look at the big flighteless birds like the emu, ostrich, moa, the extinct giant elephant bird or Aepyornis maximus of Madagascar, and not so big New Zealand kiwi, which we collectively call the ratities, and assume they may have missed out on flight altogether and simply distributed themselves on foot from their ancestral homelands somewhere around Africa when the major landmasses were still joined up, marking then out as not very far removed from the early proto-avians and feathered dinosaurs.

However, DNA analysis, which is proving such a powerful tool for answering these little questions and resolving disputes about the precise details of evolution, shows they may not be closely related at all and may have evolved from flying birds on at least six different occasions. Their similar appearance may simply be an example of convergent evolution where broadly similar environments produce broadly similar solutions.

A team lead by Alan Cooper of the University of Adelaide in Australia has sequenced the mitochondrial DNA of the Madagascan Aepyornis maximus and other flightless birds and has shown the the closest relative of A. maximus is the New Zealand kiwi and not the moa as had been assumed from their appearance. Kiwis and A. maximus shared a common ancestor about 50 million years ago, which is some time after New Zealand and Madagascar were last in contact, so the only way they could have their current distribution was by flying. Similarly, the moas, which were thought to be more closely related to A. maximus turns out to be closer to the South American aerial tinamou. Again, this separation is more easily explained if both shared a flying common ancestor.

The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.

Kieren J. Mitchell1, Bastien Llamas1, Julien Soubrier, Nicolas J. Rawlence1, Trevor H. Worthy, Jamie Wood, Michael S. Y. Lee1, Alan Cooper.
Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution
Science 23 May 2014: Vol. 344 no. 6186 pp. 898-900 DOI: 10.1126/science.1251981

The suggestion is that these birds evolved during a brief spell between the extinction of dinosaurs and the evolution of large mammals when they moved into a vacant niche for large terrestrial animals. In all but one instance this involved becoming large in the process. The reason kiwis remained small was because the niche had already been occupied by moas.

So here we see how well the DNA evidence is meshing neatly with the geological evidence for continental drift and the paleontological evidence for the extinction of dinosaurs and the rise of large mammals to replace them. Just like every other test of Darwinian evolution thrown up by new scientific discoveries (Darwin knew nothing of DNA or continental drift of course) the theory is not only passing with flying colours but is strengthened and confirmed by it. There are probably no other scientific theories that can claim that, not even fundamental 'laws' like Newton's Laws of Motion, the theory of gravity and the Law of Conservation of Matter which were all overthrown by Relativity.

Creationists still like to pretend this theory is no more than a guess with no supporting evidence, teach this denialism to their unfortunate children and want to be able to teach it to our more fortunate children at public expense.

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Wednesday, 21 May 2014

You Got Your Gut Bacteria From Mother's Mouth

Baby's first gut bacteria may come from mum's mouth - health - 21 May 2014 - New Scientist

A lovely example of how through evolution of 'selfish' genes over a prolonged period, humans, and very probably other placental mammals, have formed a mutually cooperative alliance with bacteria. Science has long recognised the role our microbiome of bacteria and fungi play in maintaining our health, and especially the role certain bacteria have in our gut where they are essential for absorbing some nutrients and vitamins.

Of course, there is no reason to think this system of mutual cooperation is unique to humans or even mammals since we share an essentially similar digestive system with all the deuterostome which are believed to have evolved some 558 million years ago, so it's a system which has been being refined and perfected for a very long time.

So how do we get our gut bacteria in early childhood? We have certainly acquired them within a few days of birth and it had been assumed babies are born with a sterile gut and acquire their bacteria from the mother's vagina during birth and from their general environment soon afterwards. Now, however a team led by Kjersti Aagaard of Texas Children's Hospital in Houston, Texas, USA has found that gut bacteria are present in meconium, the tary black fecal matter babies pass in the first day or two after birth which means they must have been present before birth.

Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA–based and whole-genome shotgun (WGS) metagenomic studies. Identified taxa and their gene carriage patterns were compared to other human body site niches, including the oral, skin, airway (nasal), vaginal, and gut microbiomes from nonpregnant controls. We characterized a unique placental microbiome niche, composed of nonpathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. In aggregate, the placental microbiome profiles were most akin (Bray-Curtis dissimilarity <0.3) to the human oral microbiome. 16S-based operational taxonomic unit analyses revealed associations of the placental microbiome with a remote history of antenatal infection (permutational multivariate analysis of variance, P = 0.006), such as urinary tract infection in the first trimester, as well as with preterm birth <37 weeks (P = 0.001).

Copyright © 2014, American Association for the Advancement of Science.

K. Aagaard, J. Ma, K. M. Antony, R. Ganu, J. Petrosino, J. Versalovic, The Placenta Harbors a Unique Microbiome.
Sci. Transl. Med. 6, 237ra65 (2014).

To try to understand where they came from the team then examined the placenta from 320 women after birth, taking tissue samples from deep in the placenta to minimise the risk of contamination. Not only did they find bacteria present but they included the gut bacteria essential for metabolising nutrients and vitamins. However when they checked the genetic profile of these bacteria the result was even more surprising. They most closely resembled the bacteria normally found in the mouth, not the vagina. The conclusion was obvious, if more than a little surprising - bacteria must have travelled from the mothers' mouths to the fetal intestines, yet the only route must be via the mother's blood to the placenta and then either into the amniotic fluid to be swallowed by the fetus, or via the fetal circulation into the developing gut.

The placenta has its own ecology and these were not the bacteria we were expecting. Most people would have expected it to be a vaginal flora.

James Kinross, colon surgeon,
Imperial College, London, UK
The team also found that some species of bacteria were more common in the placentae of women who had delivered before 37 weeks, i.e., prematurely, suggesting a link between bacteria and premature birth which ties in with other findings showing a link between gum disease in women premature births.

So, knowing how fond creationists are of my blog, here's a little something for them to ponder on, and explain if they can. Why would an intelligent, benevolent creator invent this idiotic mechanism to help animals with guts absorb essential nutrients and vitamins from their food in the first place when it could have designed an efficient gut and why did it come up with a mechanism for getting these bacteria into the guts of developing fetuses which entails the risk of premature births and babies being born with serious illnesses?

There is, of course, no problem in understanding this as an evolved system in which the benefits outweigh the risks and which 'favours' only those genes which result in more descendants. Our guts evolved in the presence of bacteria, some of which had a utility value in helping us absorb certain nutrients which in turn removed any pressure to evolve more complex solutions and so we became committed to that evolutionary pathway. Cooperative alliances between replicators, even replicators from different species, are absolutely what the selfish gene view of Darwinian evolution predicts.

I appreciate it can't be easy trying to force-fit these little pieces of scientific evidence into a primitive superstition, but never-the-less, I'd appreciate if it a creationist or two could try.

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Friday, 16 May 2014

Driving Ethical Evolution

I realise they are only doing it so they can bask in that nice warm glow of smug self-satisfaction but when Christians and Muslims pretend to be baffled by why Atheists don't go around raping and murdering people because we don't believe we are going to answer for our crimes to their imaginary friend, I wonder if they realise how ignorant they appear. Surely they only need to take a quick glance at reality to see it doesn't equate to their idiotic assertion, don't they? Here's an everyday example which refutes them entirely.

I have already blogged about this subject a few time (see Xeno's Religious Paradox, Religion: An Abdication of Moral Responsibility and Why Morality Evolved) and tried to make the point that, just like evolved related species, human cultures have broadly similar morals and ethics serving broadly similar purposes, yet differ in detail, just as you would expect of something that evolved over time, diversifying in response to local conditions to form varieties, subspecies and species.

This was brought home to me when I was driving in Naples, Italy over the last few days. If you've never driven there, it's something of an experience to put it mildly. Basically, the traffic is chaotic. The road-markings are absent or indistinct and are mostly ignored anyway as are speed limits, pedestrian crossings and red traffic lights by the first half dozen cars. People live in tenement blocks with no off-street parking, so roads are lined with parked cars - in fact, for the average visitor, parking is almost non-existent. This makes all but the widest roads barely wide enough for two cars to pass and yet slowing down seems to be regarded as something for softies. Driving is competitive, so you will be overtaken on either side if there is room, raced away from traffic lights, cut up on junctions, and nine out of ten cars will be battle-scarred. Our nearly new hire-car picked up its first scrape in a carpark in Sorrento. Luckily, I was fully insured otherwise I would have been 820 Euros out of pocket.

Horns are used frequently and yet headlights are rarely flashed. On the one occasion I flashed a car with a short flash, which in the UK unofficially means, "Go ahead, I'm giving way to you", I got a stare that would have turned a cockatrice to stone. And yet road-rage is rare, if my experience is anything to go by and the Neapolitans are generally actually considerate and helpful people, or so I found. It took me a couple of days to work out what was going on. and then it became much easier to drive. When in Naples, do as the Neapolitans do.

In Naples, you expect a car to pull out of a turning or to turn across your path because they assume you will give way to them. It's a social norm which is taken so much for granted that no one thinks anything of it. It's a bit like the old rule of the road you still see quite a lot in France where you give way to someone pulling out from the right. You are expected to push into a small gap or overtake either side if there is room. It isn't meant to be aggressive and it isn't taken as such. In the UK what could easily end up as a road-rage incident is the norm in Naples.

On the other hand, flashing your headlights in Naples is a big no-no. That's the equivalent of a rude stare and is assumed to be aggressive. In the UK, it's a sign of courtesy unless you give a long flash, or flash from behind, then it's aggressive. We all know this and take it for granted. Short flash to give way; long flash to get out of my way.

And we hardly ever sound a horn unless it's in anger. In Naples, a short toot simply means take care. Normally given when you want to warn of your presence - as a courtesy more than anything (in fact what it should mean in the UK according to the Highway Code, except that no-one uses it that way) and with much less of the aggressive connotations it has in the UK.

So, in two European countries, both predominantly Christian and both of which have had the motor car for about the same length of time, two very different cultures have developed so far as driving, sounding horns and flashing headlights are concerned. And these two different sets of ethics have evolved in less than a hundred years and mostly in the last fifty. One uses the horn extensively, assumes the right to cross another car's path and hardly ever flashes headlights because that shows aggression; the other flashed headlights as a courtesy, only normally sound the horn in aggression and crossing another car's path unless given permission to is a big insult which may well get an aggressive retaliation.

It's fair to assume that these have evolved as extensions of the human voice for a horn and a stare for headlights. Clearly, they must have had different nuances pre-motorcar to have acquired different meanings in the context of driving today. And then there is the assumed courtesy of giving way in Naples which is mostly absent in Britain although it's okay when permission has been given and permission often is given.

Nowhere in this evolution of driving ethics is there anything in the Bible that wasn't basic to all human cultures already - like the Golden Rule - and nowhere has religion contributed to their development, never to my knowledge has the Pope or the Archbishop of Canterbury ever expressed an opinion on the use of horns or headlights and there is no theological doctrine concerning giving way at a road junction, yet we have evolved ethics, and two very different sets of ethics in such a short space of time. We even take driving on the right or the left respectively as absolutely basic, right and proper and assume it's based on some sound reasoning or other.

And I could probably write a similar comparison for every country I have driven in in Europe and North America.

How do the sanctimonious religious bigots who like to pretend to occupy the moral high-ground and the creationists who claim not to be able to understand why anyone would be good without threats and rewards explain this? How does this equate to the Craigite claim that morality couldn't have come from nowhere, in a thinly disguised plagiarism of the Intelligent Design frauds who claim life couldn't have evolved? For a biologist or sociologists who understands the evolutionary memetic nature of human ethics, there is no difficulty in explaining it, though the exact cultural origins of it and the forces which caused it to evolve would be a fascinating subject for a doctoral thesis.

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Monday, 12 May 2014

Obscenities Of Sorrento - Church of St. Anthony

Tucked away in a small piazza alongside a busy road through beautiful Sorrento at the end of the Sorrentine Peninsula, south of Naples, Italy, you can find the Basilica di Sant'Antonino or the Church of St. Anthony. The inside is a tribute to the skilled craftspeople who made the marble inlay, much of it looted from surrounding villas of the Roman Imperial era, and the wooden marquetry which is used to decorate the 'Stations of the Cross' all round the walls and other features throughout the church.

And central to it all is that hideous depiction of a blood sacrifice of an innocent person that is somehow supposed to have given everyone who believes it absolution for something they didn't do either, turning the whole thing into a shrine to morbidly paranoid theophobia.

All along the sides of the main body of the church are shrines to various saints together with the traditional candles of various sizes and prices, and the money box for superstitious people to put their money in, apparently in the belief that if you give the church some money and light a candle, the saint will smile favourably on you and ask God to grant your wishes. Apparently, the smoke from the candle carries your thoughts up to Heaven where they don't seem to have invented emails, faxes or Facebook pages yet.

One of these shrines is dedicated to the newly canonised Karol Józef Wojtyła who, as Pope John Paul II put ex-Nazi Cardinal Ratzinger, later his successor, Pope Benedict XVI, in charge of covering up the world-wide scandal of systematic child sexual abuse by Catholic priests and nuns. It is not clear which unfortunate saint was ousted from his or her shrine to make room for the Catholic Church's frantic attempt to persuade world opinion that Wojtyła was far too holy to have knowingly allowed these abuses to continue, or of seeing the problem in terms of the potential damage it could do to the church's income streams moral authority of the church, rather than the damage it could do to those abused and bullied into silence and persecuted when they broke the Vatican's code of omerta.

Italy is a poor country as witnessed by it's poor roads, dirty, litter-strewn cities like Naples, appalling housing in over-crowded, rat and cockroach-infested tenements, and a shocking disregard for health and safety for either the workers or the public, and yet the Catholic Church can apparently afford to build, maintain and enrich churches like the Basilica di Sant'Antonino and stock it with valuable gold and silver ornaments, crystal chandeliers and art treasures with the money it hoovers up from the poor people of the world on a daily basis. This is an obscene display of wealth, power and abused authority; of conspicuous, flamboyant and arrogant consumption in the face of poverty.

Such a thing could only be tolerated by a superstitious people who are constantly reminded that any criticism of the Catholic Church or any daring to question it's dogmas, teaching and practices, no matter how grotesquely immoral, of it's clerics, will certainly be met with the most grotesque of eternal tortures with no hope of relief. The Vatican has a direct line to God and what the Pope says goes, just as much in heaven as on Earth. Like any other mobster protection racketeer, even a hint of dissent and disloyalty absolutely cannot and will not be tolerated.

As Stephen Fry said when debating the proposition that the Catholic Church is a force for good in the world:

Do you know who would be the last person ever to be accepted as a prince of the [Catholic] Church? The Galilean carpenter. That Jew. They would kick him out before he tried to cross the threshold. He would be so ill-at-ease in the Church... What would he think, what would he think of St. Peter’s? What would he think of the wealth, and the power, and the self-justification, and the wheedling apologies? ... The Pope could decide that all this power, all this wealth, this hierarchy of princes and bishops and archbishops and priests and monks and nuns could be sent out in the world with money and art treasures, to put them back in the countries that they once raped and violated, ... they could give that money away, and they could concentrate on the apparent essence of their belief, and then, I would stand here and say the Catholic Church may well be a force for good in the world, but until that day, it is not. Thank you.

No wonder the Catholic Church is haemorrhaging members and even in devoutly Catholic countries like Italy and Spain, where similar obscenities can be seen in every town and village, people are coming over to rationalist Humanism partly in disgust at the flagrant immorality of the Christian Church and those who use it for their own self-aggrandisement and as an excuse for claiming an undeserved power and authority the better to abuse it for their own ends.

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Sunday, 11 May 2014

Intelligent Design - Even Intelligent Pigeons Refute It

Bird brainiacs: The genius of pigeons - life - 04 May 2014 - New Scientist

More evidence emerged earlier this month that humans are far from unique in certain attributes that creationists like to present as uniquely human, God-given attributes such as intelligence, self-awareness, consciousness and inductive reasoning ability. Not only do we know that several apes and monkeys have these abilities but now feral pigeon, Columba livia, can be added to the list.

Feral or town pigeons are the descendants of pigeons which were first domesticated by Man about 5000 years ago from wild rock doves, which tend to inhabit rocky areas. The wild rock dove is now quite rare in many parts of its range. In the UK it is now restricted to north and West Scotland, some offshore islands and the coast of Northern Ireland. I have only ever seen two pairs; one in Oman, almost certainly the C. l. palaestinae subspecies, and one in the Tunisian Atlas Mountains. The feral form has adapted to living alongside humans for which it needed to be both flexible and opportunistic, both implying intelligence and the ability to learn. Similar attributes can be seen in rats, dogs and cats, for example. The variations in colour and markings to be seen in the feral form are almost certainly the result of human selective breeding.

Of course, ever since the famous psychologist B.F.Skinner showed with his operant conditioning experiments, we have known that pigeons will develop religion when 'rewards' become dissociated from actions. Like religious humans, operantly conditioned pigeons perform rituals apparently in the belief that they influence the outcome of what is actually a randomised and unpredictable system, just as humans sing, say prayers and adopt ritual body postures thinking they are influencing the future.

Now it seems that this is due to a limited form of simple reasoning ability which probably includes both self-awareness and the ability to 'philosophise', i.e to think about thinking and to be aware of their own knowledge - I'm taking about pigeons here, not religious humans, by the way.

For example, Mike Columbo of Otago University, New Zealand, has shown the pigeons can memorise more than 100 images and recall them more than two years later. He also showed that they can handle numbers and subtle relationships between them. For example, pigeons trained to peck at a series of images of ascending numbers of object, when given a series of images with larger numbers of objects up to nine, still pecked them in ascending order.

They can also apply deductive reasoning logic such as working out that if person B is taller than person A and person C is taller than person B then person C is taller than person A. They can do this with up to five people. This was a logic puzzle upon which Aristotle mused.

Some researchers have also shown that they can recognise the style of different artists and distinguish a Monet from a Picasso. They can also distinguish between major styles or art such as cubism and impressionism.

In another experiment, pigeons were fed by two very similar people in terms of skin and hair colour, height and age but wearing different coloured coats. One person simply fed them whilst the other chased them. The pigeons quickly learned to tell the 'hostile' person from the neutral one. They even recognised the right person when they swapped coats.

Considered as plague in many cities, pigeons in urban areas live close to human activities and exploit this proximity to find food which is often directly delivered by people. In this study, we explored the capacity of feral pigeons to take advantage of this human-based food resource and discriminate between friendly and hostile people. Our study was conducted in an urban park. Pigeons were fed by two experimenters of approximately the same age and skin colour but wearing coats of different colours. During the training sessions, the two human feeders displayed different attitudes: one of the feeders was neutral and the second was hostile and chased away the pigeons. During the two test phases subsequent to the training phase, both feeders became neutral. Two experiments were conducted, one with one male and one female feeder and the second with two female feeders. In both experiments, the pigeons learned to quickly (six to nine sessions) discriminate between the feeders and maintained this discrimination during the test phases. The pigeons avoided the hostile feeder even when the two feeders exchanged their coats, suggesting that they used stable individual characteristics to differentiate between the experimenter feeders. Thus, pigeons are able to learn quickly from their interactions with human feeders and use this knowledge to maximize the profitability of the urban environment. This study provides the first experimental evidence in feral pigeons for this level of human discrimination.
© Springer-Verlag 2011

Belguermi A, Bovet D, Pascal A, Prévot-Julliard AC, Saint Jalme M, Rat-Fischer L, Leboucher G.;
Pigeons discriminate between human feeders.; Anim Cogn. 2011 Nov;14(6):909-14. doi: 10.1007/s10071-011-0420-7. Epub 2011 Jun 7.

Other experiments have shown that pigeons can plan ahead, are aware of their own knowledge, and can recognise themselves in a video.

The ability to recognize self has been known to be limited to some animal species, but previous research has focused almost exclusively on the animal's reaction to a mirror. Recent studies suggest that the temporal contingency between a subject's action and the corresponding visual scene reflected in a mirror plays an important role in self-recognition. To assess the roles of visual-proprioceptive contiguity in self-recognition, we explored whether pigeons are able to discriminate videos of themselves with various temporal properties. We trained five pigeons to respond to live video images of themselves (live self-movies) and not to video filmed during previous training sessions (pre-recorded self-movies). Pigeons learned to peck trial-unique live self-movies more frequently than pre-recorded self-movies. We conducted two generalization tests after pigeons learned to discriminate between the two conditions. First, discrimination acquired during training sessions was transferred to a test session involving live self-movies and new pre-recorded self-movies. Second, the same pigeons were tested in extinction procedure using delayed live self-movies and new pre-recorded self-movies. Although pigeons responded to delayed presentations of live self-movies more frequently than to new pre-recorded self-movies, the relative response rate to delayed presentation of live self-movies gradually decreased as the temporal discrepancy between pigeons' own behavior and the corresponding video increased. These results indicate that pigeons' discrimination of self-movies with various temporal properties was based on the temporal contiguity between their behavior and its visual feedback. The methodology used in the present experiment is an important step toward improving the experimental analysis of self-recognition in non-human animals.

Toda K, Watanabe S.; Discrimination of moving video images of self by pigeons (Columba livia);
Anim Cogn. 2008 Oct;11(4):699-705. doi: 10.1007/s10071-008-0161-4. Epub 2008 Jun 3.

The interesting thing is that bird intelligence, which has also been demonstrated in the crow and parrot families, seems to have evolved independently from mammalian intelligence and involves different parts of the brain, although the neurons involved seem to be very similar, as though there is only the one solution to the 'problem' of evolving intelligence at the cell level. Never-the-less, and to further embarrass the proponents of the intelligent design notion, nature appears to have 'invented the wheel' at least twice so far as evolving intelligence is concerned. It would be interesting to see how cephalopods (octopuses and squids) fare in intelligence tests and how that has evolved, because, with their known to be intelligent behaviour and ability to plan and their very different nervous systems, one thing we can be sure about is that nature has invented the wheel yet again with these moluscs.

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Thursday, 8 May 2014

Putting Two And Two Together

I was struck by a simple example both of how structure can emerge from chaos and completely without any design or intent, and how science can make logical but always provisional deductions from the known facts and observations. This was provided by something I noticed on a visit to Pompeii the other day. I was also struck by how scientific observation differs radically from theology in it's ability to work from the known to the unknown and so for the unknown to become the known.

For those who haven't heard of Pompeii, or believe he was a Roman Emperor, Pompeii was a major Roman town situated a few miles south of modern Naples and probably had it's origins as a pre-Roman Greek settlement just as Naples does. Together with the nearby town of Herculaneum it was destroyed by an eruption of the volcano Vesuvius in 79 CE, having already been damaged by an earthquake related to Vesuvius's seismic activity in 63 CE. The entire settlement was covered in hot volcanic ash from a plume which extended down Italy to beyond Amalfi in the south. People were suffocated and died where they slept as can be seen from the casts of their bodies found when the city was excavated.

Almost every street junction, and at regular intervals in almost every street there are these raised flat-topped oval stones standing up above the street paving and more or less level with the walkways either side. Narrower streets have sometimes two, usually three blocks while the wider ones might have four. Between these blocks can often be seen deep grooves in the paving usually becoming less distinct the farther up or down the street they are from the blocks.

Okay, so what can we reasonably deduce from these blocks and their position and frequency?

Well, their position, their distance apart - just about a single pace - and the fact that they have flat tops is almost certainly because they were stepping stones on which to cross the street. Why would they have needed stepping stones to cross a street on? Quite obviously because they didn't want to step onto the street itself.

So, conclusion number one is that the actual streets of Pompeii were not the sort of places one would want to walk in. In fact, the streets were not only the city's drains, they were also not very frequently cleaned and probably relied on heavy rains to keep them from filling up altogether. The only non-human source of power with which to move bulk quantities of goods around would have been horse and donkey power. The roads were not just the city's sewers they were also full of horse excrement. This we can provisionally deduce from the fact that they needed stepping stones to cross the street on.

Now, what does this have to do with the other thing that struck me - emergence of structures from chaos and without planning or intent?

Look again at those groves. They have been made by generations of wheeled carts going between the stepping stones and all being forced to take almost exactly the same path between the blocks. No one need have planned to have those groves there; they were produced by the chaos of the paths of thousands of carts over the centuries being forced to channel into a single grove by the presence of the stepping stones which were necessary at least partly because the carts were being drawn along the streets by horses. And, as the grooves got deeper so they would have kept the wheels in line longer and so would have tended to lengthen over time.

And now we can deduce a few more things here: the carts were very probably iron-rimmed or the wood they were made from would hardly have marked the black volcanic basalt the paving is made from, so they were Iron-Age people with an economy sufficient to support iron smelters, or to buy it from those who could. They also had specialist cartwrights and wheel-rights and needed to move goods around in bulk, so they probably had trade and traders and people with money to spend, so they had paid labour and professionals who were paid for their specialist services.

It's also very probably that the horses were shod with iron shoes to work on the hard basalt streets, which means blacksmiths and farriers.

That now begs an interesting question that doesn't have a ready answer but we can reasonably narrow it down to three possible answers, some more realistic than others. Look again at the groves. How would a cart drawn by a single horse negotiate these blocks? Did the horse pass between two of the blocks before moving across to bring the cart into line? Did it step up onto the block and down the other side to keep the cart in line - if so one would expect to see signs of wear on that block? Or were there two horses?

And there are a couple of things we can deduce now about the political organisation. To make this system work at all there would need to be an accepted standard wheel guage and minimum wheel size so the carts could always negotiate the blocks without becoming stuck. They need to be able to fit between the blocks and the axle needs to clear them and this suggests city authorities able to impose this standardisation on both cart and street design. Once this system had become established, it would be impossible to change it without major disruption, so, just like an evolving organism, Pompeii would have been stuck with a system which, good, bad or indifferent for future needs, could only change within very small limits without causing major disruption.

So there we have it. Using deductive logic based on scientific observation, we can deduce a great deal about the political, economic and social conditions of Pompeii, all from the incidence of a pattern of grooves worn in the streets and how they came to emerge from chaos with no design or intent at any point.

Of course, all this is provisional and contingent upon finding solid confirmatory evidence so we can never say we have proved it, only that it looks very possible, even highly likely.

This of course is not possible with theology where the conclusions are already in place and are sacred. No evidence or deductive logic can have any impact on what is 'known' with absolute certainty, despite their being no evidence at all for it. And so creationists keep telling us that order can come from chaos and that all structure must have been consciously designed for a purpose. Ironically, this keeps their understanding of the Universe where it was in the Bronze-Age when Pompeii was a small village, if it was there at all.

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Monday, 5 May 2014

So What Did The Neanderthals Ever Do For Us?

Left: Neanderthal. Right: Modern.
Did Europeans Get Fat From Neandertals? | Science/AAAS | News

More astonishing news from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where Svante Pääbo's team are continuing to analyse the Neanderthal genome from a specimen found in Denisova cave the Altai Mountains of Siberia and make comparisons with the genomes of different human groups and related anthropoid apes.

Working with partners in the CAS-MPG (Chinese Academy of Sciences (CAS) and German Max Planck Society(MPG)) Partner Institute for Computational Biology in Shanghai, China researchers have now found that not only do present-day European and Asian populations differ in their brain structure so far as their lipid content is concerned, but that the difference is very probably due to the occassional interbreeding between early modern humans and Neaderthals, probably on very few occassions somewhere in the Middle East.

Comparison of the Neanderthal genes found in the genomes of eleven different human groups from Europe, Asia and Africa revealed, not surprisingly since the interbreeding between Homo sapiens and Homo neanderthalensis occurred after the Euro-Asian H. sapiens left Africa, no Neanderthal genes were found in the African groups. However, the Europeans were found to have three times the number of genes involved in lipid catabolism than did Asians.

Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas.

Ekaterina E. et al; Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans
Nature Communications 5, Article number: 3584 doi:10.1038/ncomms4584

We think it’s a very strong effect with very profound physiological changes

Philipp Khaitovich
CAS-MPG Partner Institute for Computational Biology
So, the team then turned to looking for evidence of differences in fat catabolism in fourteen adult humans from Europe, Asia and Africa as well as 14 chimpanzees. Because of its ready availability in a tissue bank they looked first at brain tissue and found that Europeans have distinct differences in the concentrations of certain lipids in their brain tissues and in enzymes associated with lipid catabolism. The assumption is that this is related to the higher incidence of Neanderthal genes for lipid metabolism found in these European groups. None of these lipids or enzymes were found in chimpanzee brain tissue, suggesting that the mutations arose after the split between Pan and Homo.

Clearly much more has to be done on the functionality of this, but it’s tempting to think it’s linked with some of the differences in sugar metabolism that have been picked up already. Neandertals might have had adaptations to get through the stress of northern winters that moderns could pick up through introgression.

Chris Stringer, Paleoanthropologist,
Natural History Museum, London
The thinking is that the ability to rapidly metabolise fats may have been an adaptive trait Neanderthals evolved during their long spell in the colder Euro-Asian norther climate, enabling them to use fats as an efficient energy store. So, the out-of-Africa European H. sapiens effectively took a shortcut to evolution by interbreeding with neanderthals who has already done the evolutionary spade work, and this enabled them to spread quickly into the colder northern zones.

So, it seems that we Europeans owe an enormous debt of gratitude to our Neanderthal ancestors and we are only just beginning to find out what. They paved the way for us to leave our African cradle and to spread out across the world without taking the 250,000 they had needed to evolve the genes they passed on to us.

I wonder how the creationists manage to shoehorn these emerging facts of our evolutionary story, and the evidence of co-existence of two, three, possibly four distinct species of Homo, able to interbreed at least in parts of our range like a typical ring-species stage in a diverging, evolving population. How can these facts be made to fit into a mythical special creation just a few thousand years ago of a fully evolved single human species?

Any creationist with the courage to try for a rational answer is more than welcome to do so in the comments section below.

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Saturday, 3 May 2014

Creationism - Spreading the Poison

Skeleton of Columbian mammoth, Mammuthus columbi
George C. Page Museum, La Brea Tar Pits, Los Angeles, California
I don't usually comment on American politics unless it serves to illustrate the depths which Christian fundamentalist are plumbing in their increasingly frantic attempts to discredit science as the rapid growth in Atheism and non-belief continues.

A couple of examples reared their ugly little head in South Carolina recently.

The first one all started with a proposal by 8 year-old Olivia McConnell that the state adopt the Columbian mammoth as the official state fossil (no! seriously!). All well and good, you might think, and a nice little gesture to an 8 year-old, a nice acknowledgement of the Columbian mammoths claim to fame as the first vertebrate fossil to be found in North America, and just a bit of fun that no-one could object to.

But, in the USA, the mention of fossils triggers a knee-jerk response by the creationist lobby desperate to make sure people don't get the right idea about evolution, and elevates whatever it is to the point of high principle, complete with bible-waving, threats of hellfire and hysterical shrieking about religious freedoms. Step forward the loon's champion, Rep. Robert L. Ridgeway, III to strike a blow for Jesus and the Bible and, hopefully completely unnoticed, against the secular US Constitution.

Ridgeway proposes amendment 1-1-712A to the effect that, instead of simply being referred to in official documents as 'The Columbian Mammoth' must always be referred to as "'Columbian Mammoth', which was created on the Sixth Day with the other beasts of the field.".


Amend Title To Conform

Whereas, giant mammoths used to roam South Carolina; and

Whereas, scientists have identified the fossils of about six hundred and fifty species of vertebrates in South Carolina to date; and

Whereas, it has been recognized that fossilized mammoth teeth were discovered in a swamp in South Carolina in 1725; and

Whereas, this discovery has been credited as the first scientific identification of a North American vertebrate fossil. Now, therefore,

Be it enacted by the General Assembly of the State of South Carolina:

SECTION 1. Article 9, Chapter 1, Title 1 of the 1976 Code is amended by adding:

"Section 1-1-712A. The Columbian Mammoth, which was created on the Sixth Day with the other beasts of the field, is designated as the official State Fossil of South Carolina and must be officially referred to as the 'Columbian Mammoth', which was created on the Sixth Day with the other beasts of the field."

SECTION 2. Subsequent to this act's effective date there is a moratorium on the enactment of legislation establishing official state symbols and emblems until such time as the General Assembly directly by legislative enactment removes this moratorium.

SECTION 3. This act takes effect upon approval by the Governor.

After due consideration by the Judiciary Committee, who had no objections, the amendment was carried without dissent by the House. Patriotic South Carolinians might like to consider the fact that not a single elected Representative saw any problem with every official reference to the State Fossil containing a piece of blatant propaganda, paid for by the South Carolinian taxpayers, for a religious view despite the Establishment Clause in the US Constitution. And nor did the Judiciary Committee! However, at least a majority of the Senate defended the Constitution and refused to concur by a vote of 72:30 and knocked it back to the House. The future of Ridgways' amendment now rests with a joint House-Senate committee on which the pro-loon House has a majority.

We wait with baited breath on the outcome of this important point of principle for those who want to ensure people get a misleading view of evolutionary biology and the history of Earth, even if it means breaking the law.

Meanwhile the loons are mounting a vigorous campaign to ensure the children in South Carolina's public schools are not taught the truth about evolution. The battle has crystallised around Section B-5.1 in the Biology curiculum for Fourth Grade students in the state's new draft science-teaching standards. It has the temerity to mention evolution and in particular natural selection and its key role in understanding biological diversity. This was guaranteed to send the loons into a mouth-frothed frenzy, so introduction of the curriculum has had to be delayed while while right to deny knowledge to children is debated.

If they succeed it should ensure that any South Carolina children who want to go on to a higher education in any biology-related subject will be educationally substandard and bound to struggle. Given the power of the fundamentalist loon lobby in South Carolina who consider the sacrifice of their children's future as something worth fighting for and just what Jesus would want, it's anyone's guess whether the ultra-patriotic, flag-draped Christian right are going to get away with another little subversion of the despised US Constitution.

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Friday, 2 May 2014

Stone Age DNA Refutes Another Bible Myth

Stone Age DNA shows hunter-gatherers shunned farming - life - 24 April 2014 - New Scientist

Some fascinating data emerged recently which is causing us to re-think a basic assumption about the early history of modern humans and how major changes in technology and political organisation spread. It should also cause creationists to reassess their creation myth if only that were permitted.

It had been assumed that agriculture spread from it's origins somewhere in modern southern Iraq because the idea was obviously so good that it was adopted by neighbouring peoples. In other words, the spread was assumed to be the spread of agricultural cultural rather than a spread of agricultural people.

Now a detailed study of the genomes sequenced from a small number of skeletons of early Stone Age people from Sweden has shown that hunter-gatherers were more genetically distinct from those of early Stone Age farmers from the same area than modern Scandinavians are from Italians. If the spread of agriculture had been cultural we would expect to see no significant difference. The study was conducted on the genomes of four skeletons from Stone Age farming settlements and seven coastal hunter-gatherer communities. Earlier isotope studies on the bones had show distinct differences in diet. It thus seems highly likely that it wasn't so much the idea of agriculture which radiated out from the Middle East, but agricultural people, who replaced the local hunter-gatherers.

So, what we have here is another little conundrum for our creationists friends.

Of course, as you might expect, it's hard to map reality onto their favourite creation myth if only because they don't appear to have allowed for a hunter-gather phase at all. This was very probably because the myth originated in people who were unaware of a hunter-gatherer past so saw no need to mention it, but let's overlook that little problem because, as we will see, there are some much bigger ones for them to worry about.

According to the creation myth, the small number of people who survived the Great Genocide Event when their god drowned everyone in a fit of pique because it loved them (work with me on this one!) must have been agriculturalists because they had already mastered the art of building huge, ocean-going liners and could travel the world collecting up all the different species from distant lands.

Then, within no more than six generations when a population of 50-60,000 would have been going some, were able to have a dedicated workforce concentrating on building a tower so high it could reach above the stars and so began to alarm God himself. This could only have been done with a vast agricultural support system to provide the builders and those producing the building materials with enough food and other necessities like clothes and tools without growing it or making them themselves.

This is simple, basic economics, stemming from the simple fact that the same person can't be both building a massive tower and tending to his garden, making things or foraging for food in the surrounding countryside. So, we know the Ark survivors were, or were certainly very soon and within six generations, fantastically productive agriculturalists. (Remember we are still in the creationist fantasy here, not the real world. Any resemblance to reality is purely incidental).

Now, as Pontus Skoglund of Uppsala University in Sweden and his colleagues have shown, a population of hunter-gatherers came from somewhere and spread from the Middle East into Scandinavia in advance of the agriculturalists and they were genetically very distinct from the agriculturalists who followed them. Taken in isolation, this study probably wouldn't mean much and could be explained away as sampling error. However, this is not the first study to reach this conclusion - similar results have been found in Germany and elsewhere.

Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains contentious. Population-genomic data from eleven Scandinavian Stone-Age human remains suggest that hunter-gatherers had lower genetic diversity than farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone-Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone-Age foraging groups were historically in low numbers, likely due to oscillating living conditions or restricted carrying-capacity, and that they were partially incorporated into expanding farming groups.

Skoglund, P., et al; Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers
Science 24 April 2014. DOI: 10.1126/science.1253448

The question then is where did these hunter-gatherers come from, and hunter-gatherers moreover that were from a very different genetic line to the agriculturalists who, presumably, were the descendant of Noah and his family? How did this genetic diversity arise so quickly, what with evolution being impossible and no new information being able to arise because it's forbidden by the Second Law of Thermodynamics or Information Theory, or whatever the currently fashionable creationist reason for declaring it impossible is?

Or, if impossible evolution occurred at the warp speed normally offered up to explain this apparent rapid genetic diversity in post-Flood living things, why do we see no transitional forms with genomes intermediate between that of the hunter-gatherers and the subsequent agriculturalists?

And, if we forget for a moment that the Ark survivors must have been agriculturalists already and say some of them must have given rise to the hunter-gatherers while others went of to discover agriculture, there wouldn't have been enough agriculturalists to even consider building that enormous tower, because we would be looking at a local population of a mere few thousand at the most, not nearly enough even to do the building, let alone to sustain an economy capable of supporting such a huge economically non-productive workforce.

I wonder how many creationist can solve this conundrum and how many of those who can't will accept that this little bit of science utterly refutes their biblical creation myth. Anyone prepared to bet that the answers to both these will be as close to zero as makes no difference?

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