Big Bang Bother For Bible Believers

BBC News - BBC explains Big Bang discovery using a sock

Once again, when scientist shone a light in a gap in our understanding they found no god in it. And shining a light in this case is especially apt, as it was light that was analysed. There is even talk of a Nobel Prize. While, as is normal with significant science, the results are to be subjected to intense scrutiny and other teams will try to replicate them, it looks very much as though scientists of the PICEP2 Project led by Prof John Kovac of the Harvard-Smithsonian Center for Astrophysics have found the data verifying the inflation model of the Big Bang.

Inflation was basically inserted in the Big Bang theory as the best explanation for things not quite adding up. It proposed that, during the initial few moments of the Big Bang, the Universe expanded exponentially at faster than light speed until it was about the size of a marble. Not much of an inflation you might think, but bear in mind a fraction of a billionth of a second earlier, the entire Universe had been packed into something so small that it would have been indistinguishable from nothing. What inflation did was offer an explanation of how the three 'quantum' forces of weak and strong nuclear forces and electromagnetism became stripped away from the fourth, gravity, allowing the Universe to continue to expand and not collapse immediately under its own gravity. Basically, gravity had lost control. This went a long way to explaining why we have something from nothing. The total of the three 'quantum' forces exactly equates to gravity, so, in terms of fundamental forces, the Universe was and still is zero.

The problem was, it was an educated guess the best evidence for which was that nothing seemed to contradict it and it explained a great deal. This is, of course, only circumstantial evidence - not enough to convict in a court of law. What was needed was the smoking gun.

Selfish Genes and Attractive Cannibals

Pennsylvanian grass spider Agelenopsis pennsylvanica

Zoologger: Female spider kills male to attract a mate - life - 11 March 2014 - New Scientist

Examples of females eating their mates during and after mating are well known in the animal world especially amongst the carnivorous insects and arachnids, like the praying mantis and the black widow spider, but it's rare to find an example of where this tendency actually makes the female more attractive to the male. In fact, at first sight, this would appear to run counter to what evolutionary theory tells us should happen.

But, with a little bit of thought and application, it is quite possible to come up with perfectly rational scenarios where this is exactly what evolving 'selfish' genes might produce. It might also be an example of evolution in progress where competing strategies might not have produced a winner yet.

I can't for the life of me see how it can be explained as the intelligent design of an all-wise and all-loving creator though. Maybe there is a creationist who can help me out here by suggesting one other than by invoking the universal cop-out that we can't hope to understand the mind of this magic creator but we should just accept that it's all for the best, because everything done by God er... The Intelligent Designer is perfect.

This particular example involves a harmless (to humans) common spider - Agelenopsis pennsylvanica or Pennsylvanian grass spider - which inhabits the northern United States down to Tennessee and Kansas. The species is one of the largest of thirteen similar Agelenopsids which live in grass and make a sheet web with a funnel at one end leading to a hole in the foliage, where they hide. The web isn't sticky like most spider webs but the spider is fast and rushes out of the funnel to grab any passing prey which walks on the web so alerting the owner to its presence.

But, to get to his potential mate, a male A. pennsylvanica needs to get across this web and close enough to the female to deliver his sperm package without triggering the attack response in his mate. Unfortunately he often fails and ends up as a meal.

Unlike the black widow where at least mating often takes place before she eats her mate, and the mantis where it normally at least gets under way, then the male makes do without his head as the female reaches round and eats it, finishing the rest off later when mating has finished, most male A. pennsylvanica who get eaten get eaten on the initial approach. Field studies have shown that, in urban areas, females are approached between zero and three times by males in the three-week breeding season so eating them seems a shortcut to extinction by celibacy yet 38% of females eat the first male to approach.

Now a team led by Jonathan Pruitt of the University of Pittsburgh in Pennsylvania, USA, has shed some light on what's going on here. They captured 100 wild females and divided them into two groups of 50. One group were fed wounded males; the other crickets - their normal prey. Between 20 and 24 days later they gave 20 male spiders a choice of females. 75% of them picked the females which had eaten a male.

They also found that the cannibal females produced more and better quality eggs which were more likely to hatch. They had obviously got some nutritional benefit from eating a male. The key finding however was that females normally only eat one male after which they can be approached with relative safety. 38% of females ate the first male to approach them but only 5% ate a second male. They seem somehow to be sending out the message that they have already had lunch to prospective mates.

Abstract
Precopulatory sexual cannibalism is an extreme form of sexual conflict that can entail significant costs to the cannibalized individual and a variety of costs and benefits to the cannibal itself. Characterizing these costs and benefits is fundamental to our understanding of how this behavior evolves. Using the spider Agelenopsis pennsylvanica, we tested the reproductive consequences of precopulatory sexual cannibalism by staging cannibalization events and comparing the performance of experimental cannibals against natural cannibals (i.e., those that cannibalized on their own) and non-cannibals. We found two performance benefits associated with precopulatory sexual cannibalism: first, experimental cannibals were more likely to produce egg cases than non-cannibals, and second, egg cases from experimental cannibals and natural cannibals were significantly more likely to hatch than those produced by non-cannibals. We then tested whether males were more likely to approach the webs of experimental cannibals vs. non-cannibalistic control females. Our data demonstrate that sexual cannibalism increases female attractiveness to males. Although this result seems counterintuitive, in fact, rates of precopulatory sexual cannibalism were much lower in females that had already cannibalized their first male: 38% of sexually naïve females engaged in precopulatory sexual cannibalism, whereas only 5% of females engaged in cannibalism a second time. Thus, males that approach cannibals receive two benefits: they are less likely to be cannibalized precopula, and they have the possibility of mating with females that have a higher probability of producing viable egg cases. Taken together, our data suggest that precopulatory sexual cannibalism affords females numerous benefits and may have a hand in shaping male mate choice decisions.

Pruitt, J. N., Berning, A. W., Cusack, B., Shearer, T. A., McGuirk, M., Coleman, A., Eng, R. Y. Y., Armagost, F., Sweeney, K., Singh, N. (2014),
Precopulatory Sexual Cannibalism Causes Increase Egg Case Production, Hatching Success, and Female Attractiveness to Males.
Ethology. doi: 10.1111/eth.12216

So what's going on here?

Well, the gene theory of evolution tells us that whatever 'strategy' produces more copies of genes in future generations will come to predominate in the species gene pool. It seems that, like black widows and mantises, providing the female with a free meal from which she can build more viable eggs will produce more surviving copies of the male genes. Males play no part in rearing the offspring and have no utility value to either female or offspring. The genes have no concern for the individual welfare of their carriers so these extreme forms of altruism can be expected in the right circumstances.

So, at some point in their evolutionary history, A. pennsylvanica probably went through a stage in which males were eaten postcopula by a percentage of females. Meanwhile, with no way of knowing whether the female was a cannibal or not, males had no choice but to run the risk (not that this is a conscious decision, of course), but if the offspring acquired some advantage there was not only no evolutionary pressure to do away with cannibalism but there may well have been evolutionary pressure to retain it.

Then, with a ready supply of males, there was some advantage to the females in eating the first male before mating - maybe the additional time to assimilate whatever they got from them before producing eggs. These over-eager males were now at a significant disadvantage because they provided sustenance but not to their offspring so there was now a much stronger reason for males to avoid cannibal females in terms of perpetuation of their genes.

So, males had a reason to evolve ways of discriminating and females had a reason to evolve ways of overcoming this tendency and they had the means - they could use something from their dead suitor to signal to the males that they were now safe to approach. So, females who provide this signal and males who can detect it and respond to it, both derive a benefit in terms of more high-quality eggs and more offspring carrying the genes for it.

This system appears to give a significant advantage to females and to males who wait for the safety signal, so the fact that 62% of females are not cannibalistic suggests there are ongoing evolutionary arms races here between different strategies. Males appear to have two strategies - to make an early approach which is successful in 62% of cases but the eggs are of lower quality, or wait for the safety signal and be successful with the remaining 38% of females but with better quality eggs. Meanwhile females also have two different strategies - eat the first male and produce more high-quality eggs with the second if one comes by and if it detects your signal, or mate with the first one and produce lower quality eggs. Self-evidently, the system can't move to one where all the males play the waiting game because that strategy would be bound to fail. If it happened locally, that population would go extinct, so removing all their genes from the gene-pool.

It may well be that the arms races simply haven't run their course yet, or the different competing evolutionary drivers have arrived at an equilibrium, but we may be seeing evolution in progress here. We are certainly seeing evidence of selfish genes doing what selfish genes do - making copies of themselves with no regard to what effect their strategy for doing so has on individuals, just so long as it gives the most copies.

Any creationist prepared to take up my challenge or will it be silence again as usual when faced with real examples of real evolution instead of the usual infantile parodies you normally attack?

'via Blog this'

---

How Evolution Changed Our Minds

American-born primatologist Alison Jolly, who sadly died on 6th February in Lewes, East Sussex, UK, was a Visiting Scientist at the University of Sussex and was instrumental in changing our view both about the role of social interaction in evolution and the role of gender in group leadership.

She was the first to report that females are dominant in some primate species, an observation based on her study of lemurs in Madagascar, where, unlike prosimians in the rest of the world, they have evolved in the absence of true monkeys to fill the niche occupied by true monkeys elsewhere. We now know that many primate groups are led by females, not males, so there is nothing inherently male about the ability to dominate and lead a group.

Edible Frogs and Unintelligent Design.

Pelophylax kl. esculentus. Image: Grand-Duc, Wikipedia.

Here's a puzzle for the 'Intelligent Design' movement. All you have to do is explain the intelligence behind the design and say why ID is a better explanation than that offered by evolution theory.

Here are the facts (I hope that word hasn't put the IDiots off!):

The Edible Frog (Pelophylax kl. esculentus) is a name for a common European frog, also known as the Common Water Frog or Green Frog (however, this latter term is also used for the North American species Rana clamitans). It is used for food, particularly in France for the delicacy frog legs...

P. esculentus is endemic to Europe. It naturally occurs from the northern half of France to western Russia, and from Estonia and Denmark to Bulgaria and northern Italy. It is introduced in Spain and the United Kingdom. The natural range is nearly identical to that of P. lessonae...

Pelophylax kl. esculentus is the fertile hybrid of the Pool Frog (Pelophylax lessonae) and the Marsh Frog (Pelophylax ridibundus), hence the addition of the "kl." (for klepton) in the species name.

During the ice ages, the population of the common ancestor of both species was split into two. These populations diverged, but remained genetically close enough to be able to create fertile hybrids. However, when edible frogs mate with each other, their offspring are often malformed, so there are no pure populations of edible frogs.

The hybrid populations are propagated predominantly by female edible frogs mating with males of one of the parental species (P. kl. esculentus × P. lessonae or rarely × P. ridibundus).

Hybridogenesis implies that gametes of hybrids don't contain mixed parental genomes, as normally occurs by independent chromosome segregation and crossover in meiosis (see also second Mendel's law, recombination), but intact one of them or two. Usually because one entire genome of the parental species is excluded prior to meiosis during gametogenesis.

Source: Wikipedia - Edible frog.

P. lessonae. Image:Piet Spaans.

P. ridibundus. Image: © Marie-Lan Nguyen.

Typical hybridization between pool frog (P. lessonae), marsh frog (P. ridibundus)
and their hybrid - edible frog (P. kl. esculentus, P. lessonae x P. ridibundus) in a
native LE (lessonae-esculentus) hybridogenetic population invaded additionally by
P. ridibundus. Predominant matings are P. kl. esculentus females x P. lessonae
males and P. ridibundus females x P. lessonae males. P. kl. esculentus x P. kl.
esculentus crossings result in inviable P. ridibundus tadpoles and are not shown here.
Large circles - adult frogs, small circles - gametes.,
x - lack of gametes containing genome of one of parental species.

On a technical note, some authorities dispute the statement that there are no pure populations of P. esculentus because triploid P. esculentus individuals are common and can produce fertile offspring and so form pure populations, however these populations tend to be short-lived.

The reason this 'green frog complex' has arisen during the course of evolution is because during the production of gametes the frogs chromosomes do not exchange genes and so mix up their genomes. In P. esculentus there is one complete P. ridibundus set and one complete P. lessonae set. In a triploid form there will be two sets of one and one of the other. So, when they mate with one or the other parent species, they can produce offspring with the complete genome of eitherP. ridibundus or P. lessonae, or more P. esculentus.

Okay, so that's all straightforward so far. Nothing there that can't be explained in terms of evolution and perfectly natural things with no magic required. So, the question for creationists then is, why would an intelligent designer create edible frogs in such a bizarre and unorthodox fashion when it had designed a perfectly sensible way to produce other species with perfectly normal sexual reproduction? The supplementary question of course, is how is whatever explanation you manage to come up with better than the scientific one and what does it explain that the scientific one doesn't?

Incase you're wondering, I have eaten frog's legs. I found them slightly unpleasant tasting. Maybe I was unfortunate but I probably won't be eating them again through choice.

'via Blog this'

---

Human Evolution is Speeding Up

Human Evolutionary Change 100 Times Higher in Past 5,000 Years

A popular theme on creationist websites is that no-one has ever seen evolution occur. Well, it's certainly true that no-one has ever seen a creationist parody version of evolution occur, but then they wouldn't do, would they. The parody was designed to be ludicrous; that's the point of parody.

For a successful snake-oil salesman, the trick is to fool your audience into believing the parody is the real thing and that must be the simplest thing in the world to achieve, given that the target audience is not only largely ignorant of science but proudly so and is eager to be fooled because what they crave most is confirmation, no matter how spurious.

An ancillary theme to this is endless debate about if and why human evolution has stopped. Even some serious scientists will wade in with explanations about why human evolution is no longer happening because we've removed all the natural selection mechanisms by isolating ourselves from our environment and even keep people with genetic defects alive long enough to have children when they would have died in childhood just a few years ago. The latter argument is often used either to try to justify eugenics or to smear those who accept the evidence for evolution as secret eugenicists, in some sort of attempt to argue from consequences. Even if it were true, abusing evolutionary theory in pursuit of a social or political agenda does not render the theory wrong anymore so than the undesirability of nuclear war renders atomic theory wrong or the harm which comes from stepping off a high building renders the theory of gravity wrong.

Your Ancestors Mated With Chimpanzees

Human Ancestors May Have Interbred With Chimpanzees

To anyone who understands how evolution works, the news that humans and chimpanzees interbred for a considerable period as the two species diverged from a common ancestor will come as no surprise. Evolution is not normally a sudden event or single act of speciation but a long, slow process in which it is impossible to say precisely where one species became two.

From the chimpanzees' point of view, their ancestors mated with humans. I wonder if they would also find the idea fascinating but at the same time slightly disturbing, even a little distasteful.

Scientists comparing human and chimpanzee genomes have found that their X-chromosomes last shared a common ancestor about 5.1 million years ago but all the others appear to have diverged about 6.3 million years ago. In other words the X-chromosome is 1.2 million years younger than the rest of our genome.

It's as though we diverged twice. In fact, this may well be what happened. We began to diverge about 6.3 million years ago, probably into different habitats, but remained similar enough to be able to interbreed when we came into contact for about a million years before finally diverging completely about 5.1 million years ago.

Abstract
The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

Nick Patterson, Daniel J. Richter, Sante Gnerre, Eric S. Lander and David Reich;
Genetic evidence for complex speciation of humans and chimpanzees;
Nature 441, 1103-1108 (29 June 2006) | doi:10.1038/nature04789

I think the most interesting thing [is] this idea that long, extended gene flow seems to have occurred and that this might be a creative mode of evolution.

David Reich, Geneticist,
Harvard Medical School, MA, USA

And this illustrates how speciation is not the creationist parody event. In this infantile parody, evolution is a single event where one entire species changes into a different one through a series of discrete intermediate stages, or more bizarrely one member of one species gives birth to a different species which then goes on to reproduce, presumably with itself, to form a new species.

Apparently creation pseudo-scientists assume their target audience will believe that millions of serious biologists delude themselves into thinking these are realistic scenarios and are either too stupid to see how implausible they are or are simply all conspiring to mislead people for some political or religious reason.

In fact, it's the creationist frauds who are lying for political and/or religious reasons and many of them will have taken the ICR oath that their 'research' and writings will always be in full accord with the biblical account of Creation in Genesis, as a condition of funding and publication. But this tactic plays to the ego needs of an audience of people who want to believe that their ignorance of science gives them a greater understanding of reality than all that studying and research, and who see science as elitist and scientists as all more than a little bonkers.

This is contributing to the idea that species are kind of fuzzy. They become real over time, but it takes millions of years. We probably had a bit of a messy origin.

James Mallet, Geneticist,
University College, London, UK

Speciation is often a very slow process of gradual divergence across a large geographical range as different populations respond to local change or simply drift genetically more quickly than their genes can flow across the entire population. That's not to say it can't be a fairly sudden divergence if one part of a population becomes isolated for some reason, for example the newly-discovered river dolphin, Inia araguaiaensis, which became isolated when geological events led to a population becoming isolated in a branch of the Amazon river system.

Where speciation happens gradually this can lead to the phenomenon of the 'ring species' where the species gradually changes across its range to form a cline but where breeding can occur in some overlapping areas. This appears to have been the situation with evolving humans and chimpanzees for over a million years and it appears to have been the situation with diverging human populations later on where modern humans and archaic forms seem to have interbred and closely related species like Homo sapiens, H. Neanderthalensis and the so-far unnamed 'Denisovans' seem to have interbred so that genes could occasionally flow between species.

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.

W.S. Pinkston, J.A. Graham, G. Kuzmic and C. Vogt;
Biology for Christian Schools;
Bob Jones University Press

And of course, in species where sex has a social and recreational role, as well as a reproductive one, this tendency to interbreed would likely have been more marked than where sex depends more on hormones and visual or other sensory stimulation and serves a purely procreational function.

What you will never get a creationist to acknowledge is that this mode of evolution not only would not produce the 'missing link' they keep demanding science produce but that we should not expect to find any. We would expect the fossil evidence to be exactly what it is - a slightly muddled, fuzzy picture with no strong demarcations and a series showing gradual change over millions of years, just as the DNA evidence is reflecting.

This will give scant comfort to those who require evolution to be a childishly simplistic process of sudden change such as one might see in a biology book for the unfortunate children of Christian fundamentalists.

[Footnote] The above discovery was made seven years ago at the time or writing. Love and kisses to the first person who can find any reference to it on a creationist website or in any of their publications.

'via Blog this'

---

Tweet Link

Something Big and Nasty In Russia

Pithovirus sibericum

Biggest-ever virus revived from Stone Age permafrost - life - 03 March 2014 - New Scientist

A couple of scientists have found something big and potentially nasty lurking in the permafrosts of the Siberian tundra, something that could point to a threat to humans and something that raises some fundamental questions about 'life' itself, at least so far as creationists loons and, to be fair, many normal people think of it.

What Chantal Abergel and Jean-Michel Claverie of Aix-Marseille University, Marseille, France found was a previously unknown virus and the largest ever found, so large it is visible under a normal light microscope. It was taken from 30,000 year-old permafrost and proved to be perfectly viable.

The virus, a Pithovirus sibericum, so called because it resembles a Greek pithos or large earthenware jar, complete with a plug keeping its contents in, is 30% larger than the previous largest known virus, pandoravirus, also found by the same team, but has only a fifth of pandoravirus's 2500 genes. Those 500 genes are never-the-less enough for pithovirus to invade amoebae and turn them into machines for making for pithoviruses, and in a unique way, or at least in a way not seen before. The normal virus way of making more viruses is to invade a cell, or even just inject its DNA (or RNA) into the host cell, and then hijack the host genes and convert them into genes for making viruses.

Pithovirus, however, enters an amoeba and migrates to a vacuole (basically a chamber enclosed in a membrane inside the cell) and attach itself to the vacuole membrane, then removes the plug and empties its contents into the vacuole, where they then use their own DNA to make viruses, using the amoeba as a source of raw materials.

There are three competing theories of virus origins, which are not necessarily exclusive in that any could be correct for a given group of viruses.

If on top of this we are now also seeing a possible release of potentially viable pathogenic viruses that are otherwise not living today, this will certainly add a whole further and new dimension to the thawing problem. It may mean that we are confronted not just with indirect climate warming impacts from thawing permafrost, but also direct human-health-related issues.

Torben Christensen, Lund University, Sweden

• The Progressive Hypothesis, which sees the virus as a gene which has broken free and now exists as an independent entity, able to move between cells and integrate itself into the genome. It seems that a great deal of the human genome may have originated from these 'retroviruses' which have become a permanent fixture.

• The Virus-First Hypothesis in which the virus is seen as having evolved directly from early replicators, and cells are seen as organised collections of virus-like particles, which viruses can use but have never become fully integrated into.

• The Regressive Hypothesis where the virus is seen as an extreme form of parasitic reduction, rather like the bacteria which became incorporated into early cells to become organelles like mitochondria and chloroplasts.

Pithoviruses are definite candidates for the third type.

Thirty percent of the world's oil reserves are thought to be hidden under the permafrost, along with gold and other key minerals, so exploration is bound to increase, so we must be careful to take precautions when prospecting – if people become sick with strange symptoms, it might be wise to quarantine and clear them of dangerous new infections before sending them back.

Jean-Michel Claverie

Fortunately, the newly-discovered virus is a specialised parasite of the amoeba and appears to be harmless to human and mouse cells in cell cultures. Fortunate that is because of the ease with which they could be 'revived' after 30,000 years, simply by thawing them out and giving them a supply of amoebae. There is no reason at all why this should not be true of a potentially dangerous pathogen, maybe even ones we have never, as modern humans, encountered before. And this raises the possibility that climate change which is currently thawing out permafrosts and freeing up the viruses held in suspended animation for tens and maybe hundreds of thousands of years may be freeing up dangerous pathogens.

As I mentioned above, not only does this present a problem for us, but the ease with which these viruses can be 'revived' (and I use the term loosely because there was no revival other than thawing needed) presents a problem for people who assume 'life' is some quality or substance which distinguishes 'living' things from inorganic substances; that somehow its presence marks the difference between a rock and a human or between a plank and a tree. We've all seen them come rushing excitedly onto the Internet fully primed by some creationist scam site or fundamentalist religious site, to ask their 'killer' question, "How did the first life arise from non-life?", only to tiptoe quietly away when asked how they are defining life, often after posting some gibberish about souls or breathing.

Successful revival of any kind of ancient virus is always newsworthy. My own group finds bacteria present at all depths in deep ice in the Antarctic and Greenland. The pithovirus is so large that we might be able to see it in ice cores more than 100,000 years old at their bases.

Buford Price, University of California at Berkeley, USA

What these viruses show is that something can exist for at least 30,000 years and probably for very much longer than that, as nothing more than lifeless chemicals and membranes, doing nothing that would be recognised as living because the temperature was too low for the chemical reactions to occur, and can become 'living' again simply by raising the temperature sufficiently for the chemical processes to resume. This is exactly what would happen if a biochemical reaction in a test tube were to be put in a deep freezer for a year and then thawed out. It would simply carry on where it left off yet no one would seriously argue that the test tube and its contents are alive.

So, where was 'life' in these viruses for 30,000 years? Of course, it wasn't there since the viruses did not need to manage entropy and the anatomy and physiology was not doing any chemistry, so there was no life as most people would recognise it.

There is no reason to suppose that the first replicators were anything more than chemical reactions which occurred inevitably because the conditions were right, just as any other chemical reaction occurs. There was no initial 'life' because 'life' doesn't exist either as an entity or a characteristic in its own right and certainly not as some undefined magic ingredient. To ask where life came from is as daft as asking who set fire to the sun.

'via Blog this'

---

Einstein's Lost Theory

Einstein's Lost Theory Uncovered - Scientific American

Any interesting draft paper has been discovered which throws considerable light on both Albert Einstein's thinking and on his personal integrity in scientific matter. The paper written in German was apparently 'hidden' in full public view at the Albert Einstein Archives in Jerusalem and may be seen here. It had been wrongly classified as the draft of another paper.

Almost any religious apologist worth his salt will have thrown out the claim that Albert Einstein believed in God, quoting his "God doesn't play dice with the Universe" argument against quantum theory. This is usually deployed when the argument is going badly and the only ploy left is to try to make their detractor look like they're just too stupid to see the sense of the argument. If Einstein, one of the most intelligent and scientifically literate of people, believed in God, then who are you to disagree?

Einstein, of course, was always at pains to point out that by 'God' he meant nature - the God of Spinoza; the forces which produce the universe as we see it - but religious apologists are never slow to 'mistake' a metaphor for a statement of fact, unless it comes to defending an absurd statement of 'fact' in the Bible or the Qur'an, in which case they are clearly metaphors, often for something too obscure and ineffable for mere humans to understand. God didn't always want to be understood so he wrote a book to be misunderstood in, apparently.

What Einstein was clearly doing here was expressing his personal distaste for a theory which appeared to throw a large dose of randomness into the mix. Quantum theory appeared to say that we shouldn't expect the Universe to be predictable, with clear causality and that events can occur without cause. Einstein's Universe was unchanging and ran on basic rules which, with sufficient diligence and observation, couples with the right analysis, we should be capable of discovering.

We present a translation and analysis of an unpublished manuscript by Albert Einstein in which he explored a 'steady-state' model of the universe. The manuscript, which appears to have been written in early 1931, demonstrates that Einstein once considered an expanding cosmos in which the mean density of matter is maintained constant by a continuous formation of matter from empty space. This model is very different to previously known Einsteinian models of the cosmos (both static and dynamic) but anticipates the later steady-state cosmology of Hoyle, Bondi and Gold in some ways. We find that Einsteins steady-state model contains a fundamental flaw and suggest that it was discarded for this reason. We also suggest that he declined to try again because he realised that a successful steady-state model would require an amendment to the field equations. The abandoned model is of historical significance because it reveals that Einstein debated between steady-state and evolving models of the cosmos decades before a similar debate took place in the cosmological community.

Cormac O Raifeartaigh, Brendan McCann, Werner Nahm, Simon Mitton;
A steady-state model of the universe by Albert Einstein; arXiv:1402.0132v2 [physics.hist-ph]

But, both Einstein's Relativity, and quantum theory, seemed to be showing that the Universe not only had a randomness at the very small scale but that it actually began as a very small random event. In a way, Einstein was anticipating the still unresolved conflicts between Relativity and Quantum Mechanics which has recently caused Stephen Hawking to revise his thinking on black holes.

[The manuscript was probably] a rough draft commenced with excitement over a neat idea and soon abandoned as the author realized he was fooling himself.

James Peebles, cosmologist.
Princeton University, New Jersey, USA

The paper was written in 1931, apparently during a visit to California, and appears to have been written quite quickly, as though following a sudden flash of insight, only to be revised later.

By 1931, the Big Bang appeared to have been confirmed by Edwin Hubble's discovery of the Red Shift in the 1920's but Einstein still seemed to be searching for ways around this and had hit on an idea which Fred Hoyle also proposed almost 20 years later - that the Universe was expanding but it had always been expanding and would continue to expand forever - the so-called steady state theory which only required some slight tweaking of Einstein's Relativity equation to remain consistent with Relativity.

Einstein appeared to have been toying with this idea in this draft paper then, as he thought it through, he realised he had made errors in the maths and that it wouldn't work. At any rate, he abandoned the idea, never completed the paper and never mentioned the idea again.

Hoyle's theory was eventually falsified by astronomical observation but not before he had made a spectacle of himself by publically trying to taunt a young Stephen Hawking by asking him why the background radiation required by the Big Bang theory had not been found - "because it's not there perhaps? Hmmm?" - just before it was discovered.

'via Blog this'

---

Cthulhu Lives!

New Octopus-like Protists in Termite Guts Named for HP Lovecraft Cosmic Monster ‘Cthulhu’ | The Artful Amoeba, Scientific American Blog Network

As everyone knows, Cthulhu is a tentacle-faced titanic god-monster who sleeps in a mythic undersea lair called R’lyheh, dreaming of the day he will emerge to destroy humanity. We'll, everyone who reads H.P. Lovecraft's stories knows.

Our little Cthulhu (Cthulhu macrofasciculumque, that is) is rather smaller and may not have such grandiose dreams as the fictional one but inhabits a strange lair, has tentacles and is at least real. The strange lair it inhabits is the gut of a Cuban subterranean termite (Prorhinotermes simplex) and termite guts are just about as strange as it gets on Earth, even allowing for the deep, dark recesses of the Pacific floor.

The thing about termites and their guts is that termites live almost entirely on the cellulose and lignin of dead wood, which are notoriously difficult to digest, being a highly stable large polymers of glucose. What termites have done is to harness the huge evolutionary power of single-celled organisms with their rapid generation time, which gives them great powers to solve complex problems using nothing but the genetic algorithm - problems like how to digest cellulose. This worked for termites and continues to work perfectly well, so there has been no evolutionary pressure on the termite genes to evolve their own solution. Genes will form alliances with whatever works and are not limited to those in the animal they happen to find themselves in. So, termites and their gut biome have become inextricably bound together by evolution, just as we have with our gut biome, as I blogged about earlier.

Termites are not the only animals to solve this problem that way. Many ruminants who live on grass and leaves use the same method and have guts modified to act like fermentation chambers where bacteria and other protist do much of the work in return for a sheltered environment and a supply of raw materials.

Each species of termite acts like an isolated ecosystem with very little contact with the outside world and, not surprisingly, evolution has proceeded in its own direction there, producing a whole range of organisms not found elsewhere and often only very remotely connected with common ancestors of related species.

C. macrofasciculumque has a bunch of 20 flagella which it uses for propulsion by paddling. Unlike normal flagella which rotate at the rear like a propeller, these flagella are at the front and row rather like the arms in a breaststroke. They come together on the forward stroke to reduce resistance and spread out on the backward, power stroke. There may also be a standard propeller flagellum at the rear.

Meanwhile, in a related species of the Cuban subterranean termite, the Eastern subterranean termite (Reticulitermes flavipes), we find another very similar, and clearly related (though not that closely, hence it has a different generic name) protist, which has been named after Cthulhu's secret daughter (the fictional Cthulhu, that is). Cthylla microfasciculumque does the same job in R. flavipes as its counterpart does in P. simplex but it has only five tentacles compared to its better-endowed relative and has a definite propeller flagellum.

These protists are part of a much larger group called the parabasalids which includes not only simple, single-celled species but some bigger, multicellular organisms, and one, Trichomonas vaginalis, which is a sexually transmitted parasite in humans. They all appear to have evolved from a single common ancestor and are usually associated with complex, multicellular animals, either parasitically or symbiotically. It appears that the bigger ones may have evolved several times from the smaller ones.

It almost seems churlish to ask creationists and intelligent designers, what on Earth they imagine their 'Intelligent Designer' was thinking of when it came up with these organisms and this system for digesting dead wood, when it could have provided termites and other plant-eaters with a well-designed digestive tract in the first place.

I doubt I'll get any, but answers below, please.

'via Blog this'

---

How Our Gut Microbes Have Shaped Our Evolution

Ancient Poop Had Antibiotic Resistance Genes, Too

There is a war going on in your guts. Mostly you won't feel a thing unless, as happens occasionally, the wrong side gains the upper hand. The war is, maybe surprisingly, not between you and the billions of bacteria that live in your gut but between them and invaders.

Our guts are unique in that each of us has our own population of bacteria and other single-celled organisms all coexisting in balance with one another but in ratios unique to each of us. We acquire our gut 'flora' very early in life - within days and week after birth - and each population quickly establishes its unique mixture, like a micro ecosystem, which is exactly what it is.

When a foreign organism enters our gut the local population actively resists it by evolving antibiotics. The invaders respond by evolving resistance and the defenders respond by evolving even stronger antibiotics.

Bacteriophage P2 using Transmission Electron Microscope (Mostafa Fatehi)

Part of this microbiome are parasitic viruses called bacteriophages, or 'phages' for short, which attach themselves to the a bacterium and inject their contents into it where they take over its reproductive system to make more phages. These then move on to infect other bacteria, often with pieces of bacterial DNA included in their genome, some of which may be genes for making antibiotics. Not all the bacteria are killed in the process otherwise the population would be wiped out in a few hours. Over the years bacteria have evolved to live with their parasites and their parasites have evolved to live with their hosts. And bacteria may well be getting something in return.

The viruses are acting as transports to spread bacterial genes through the population, carrying things like genes for antibiotic resistance. With a good supply of phages, in the presence of antibiotics, resistance will quickly spread throughout the population and, significantly, the phage population will act as a reservoir of bacterial antibiotic genes evolved in earlier times.

Scientists were fairly sure this war had been going on for millennia - from way back before we were human to before our ancestors had crawled out of the sea even, probably to a time when the first coelenterates evolved a gut and in doing so provided a new niche which microbes could exploit - but the problem was getting the evidence. Guts don't fossilize very well and even if they did, it would be impossible to know what contamination there had been from other bacteria and their viruses during decomposition. The same goes for faeces of course.

But now a team from the Research Unit on Infectious and Emerging Tropical Diseases (URMITE) in Marseille, France, led by Christelle Desnues, has analysed 14th-century human excrement from an archaeological site at "Place d'Armes", Namur, Belgium and has found that phage viruses in the faeces carried bacterial genes for antibiotic resistance from way back before we had antibiotics. These had originated in response to natural antibiotics produced in this ongoing warfare described above. It seems that our gut flora were producing these antibiotics long before we had discovered them, not for us, but for their own survival.

Abstract
Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a Middle Age site in Belgium using electron microscopy and metagenomics. Viruses that infect eukaryotes, bacteria and archaea were detected, and we confirmed the presence of some of them by ad hoc suicide PCR. The coprolite DNA viral metagenome was dominated by sequences showing homologies to phages commonly found in modern stools and soil. Although their phylogenetic compositions differed, the metabolic functions of the viral communities have remained conserved across centuries. Antibiotic resistance was one of the reconstructed metabolic functions detected.

Sandra Appelt, Laura Fancello, Matthieu Le Bailly, Didier Raoult, Michel Drancourt and Christelle Desnues; Viruses in a 14th-century coprolite; Applied and Environmental Microbiology, 7 February 2014; doi: 10.1128/AEM.03242-13

Our evidence demonstrates that bacteriophages represent an ancient reservoir of resistance genes and that this dates at least as far back as the Middle Ages.

Christelle Desnues

Desnues' team also found metabolic genes for processing fats and amino acids which could hint at the reason we've evolved tolerance for them in the first place and have evolved to live with them. So, a fascinating picture is emerging: we depend on our gut flora for our health but they can run out of control if not kept in check. This is done by semi-parasitic phage viruses which, in turn, help antibiotic resistance spread quickly through the bacterial population to prevent them being killed off altogether. All three life forms, humans, bacteria and viruses, have evolved a mutual interdependence which suits the survival needs of their respective genomes.

It's as if we need these phages as part of our microbiome. We evolved as humans to house [gut phages] for the functions they provide—that’s the coolest part.

Vincent Racaniello, microbiologist,
Columbia University

The downside of this is that when we try to use antibiotics, the phage viruses have a range of antibiotic resistance genes from earlier times which can be quickly spread through the population far more quickly than if the bacteria had to evolve them anew because, actually, this phase of the system evolved more because it benefited the bacteria and the viruses than it did humans.

This is reinforced by another discovery made by Christelle Desnues: the range of antibiotics carried by these 14th-century phages was wider than is normally found today. This is believed to reflect the relatively insanitary conditions in the 14th-century compared to today and so shows evidence of evolution of our gut flora in response to a change in our environment and so, indirectly, in theirs.

Incidentally, this refutes the argument commonly used by creationists that development of antibiotic resistance in response to antibiotic use is not an example of evolution because the bacteria must have had this resistance in the first place for it to be selected for. This argument assumes that there were no antibiotics in the environment before humans discovered and mass-produced them. This is of course false. Antibiotics have been produced by microorganism since before there were ever humans and probably before there were even multicellular organisms, but the bacteria themselves don't need to retain genes for resistance to every ancient antibiotic; they have viruses that do that for them.

Curiously, creationists who use this argument see no problem with effectively arguing that their benevolent, anthropocentric god has designed bacteria so they can resist our attempts to stop them killing us. The benevolence and anthropocentricity of this intelligent designer can apparently be turned on and off at will as the argument for it requires.

So now the question for creationists who believe in this intelligent designer who made everything just for us humans:

Why would an intelligent designer design this elaborate system, which also goes on in the guts of other species, just to help us digest fats and amino acids, which can run out of control and make us ill, and which is now helping bacteria win a battle with us over antibiotic resistance? Why didn't it design a simpler, more efficient and safer system?

Answers below please.

'via Blog this'

---

Income from ads will be donated to charities such as moderate centre-left groups, humanist, humanitarian and wildlife protection and welfare organisations.

A Fitting End To Religion?

Ecstatic epilepsy: How seizures can be bliss - health - 24 January 2014 - New Scientist

Only one of the following is a descriptions of religious experiences; the others are descriptions of a type of the aura experience by some epilepsy sufferers. I'll reveal which one later.

The immense joy that fills me is above physical sensations. It is a feeling of total presence, an absolute integration of myself, a feeling of unbelievable harmony of my whole body and myself with life, with the world, with the 'All'.

64 year-old woman

... it is as if I were very, very conscious, more aware, and the sensations, everything seems bigger, overwhelming me.

53 year-old female teacher

...the most amazing feeling came over me... a feeling of complete and utter love - I felt as if I were radiating like the heat of the sun...

Middle-aged woman

You are just feeling energy and all your senses. You take in everything that is around, you get a fusion.

41 year-old architect

...a sensation of velvet, as if I were sheltered from anything negative.

37 year-old man

How Viruses Helped Us Evolve

Origin of organs: Thank viruses for your skin and bone - life - 27 February 2014 - New Scientist

It must be awful being a creationist pseudo-scientist having to keep finding ways to ignore the latest piece of scientific research which shoots creationism down in flames.

Here we see yet another example of just this sort of recent discovery.

One of the mysteries in the biology of complex multicellular organism is how cells fuse together to form some of the organs like muscle and skin. The cells don't just stick together but actually unite rather like sperm and eggs unite to form a single cell. This produces large, multinucleated cells. In muscle, for example, a single muscle fibre can consist of a single, very long cell. This makes propagation of a wave of contraction almost instantaneous, instead of needing a chain reaction to stimulate a sequence of small cells.

For cells to unite in this way, they need to be able to break down their cell walls at the point of contact and that requires an enzyme. The problem was that these protein enzymes were hard to find so we weren't really sure what they were and how they worked.

Then in 2000 Sha Mi, Xinhua Lee and colleagues of the Genetics Institute, Cambridge, Massachusetts, USA, found the protein involved in producing this cell fusion to form the cyncytia in mammalian placentae. This layer forms an effective barrier between the mother and the developing foetus which prevents material passing across which would be recognised as foreign by the mother, who would then form antibodies against the foetus, so killing it, just as we would do with any other foreign tissue invading our body.

Not only did they discover the protein but they found that the gene for producing it had come from a virus.

Abstract
Many mammalian viruses have acquired genes from their hosts during their evolution. The rationale for these acquisitions is usually quite clear: the captured genes are subverted to provide a selective advantage to the virus. Here we describe the opposite situation, where a viral gene has been sequestered to serve an important function in the physiology of a mammalian host. This gene, encoding a protein that we have called syncytin, is the envelope gene of a recently identified human endogenous defective retrovirus, HERV-W. We find that the major sites of syncytin expression are placental syncytiotrophoblasts, multinucleated cells that originate from fetal trophoblasts. We show that expression of recombinant syncytin in a wide variety of cell types induces the formation of giant syncytia, and that fusion of a human trophoblastic cell line expressing endogenous syncytin can be inhibited by an anti-syncytin antiserum. Our data indicate that syncytin may mediate placental cytotrophoblast fusion in vivo, and thus may be important in human placental morphogenesis.

Sha Mi, Xinhua Lee, et al, Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis;
Nature 403, 785-789 (17 February 2000) doi:10.1038/35001608;

So here we had evidence that infection by a retrovirus had resulted in one of its genes being captured by the genome of one of our remote, pre-placental ancestors. This gene was the gene it had used to break down the cell wall and inject itself into the cell - exactly what happens when cells fuse to form the structure we are discussing.

And without that infection, placental mammals, including us, could not have evolved.

In 2002 a team led by William A. Mohler of the Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut, USA, found a protein called EFF-1 in the roundworm Caenorhabditis elegans which it uses to make its skin.

Abstract
Multinucleate cells are widespread in nature, yet the mechanism by which cells fuse their plasma membranes is poorly understood. To identify animal fusogens, we performed new screens for mutations that abolish cell fusion within tissues of C. elegans throughout development. We identified the gene eff-1, which is expressed as cells acquire fusion competence and encodes a novel integral membrane protein. EFF-1 sequence motifs suggest physicochemical actions that could cause adjacent bilayers to fuse. Mutations in the extracellular domain of EFF-1 completely block epithelial cell membrane fusion without affecting other prefusion events such as cell generation, patterning, differentiation, and adhesion. Thus, EFF-1 is a key component in the mechanism of cell fusion, a process essential to normal animal development.

William A. Mohler, Gidi Shemer, et al; The Type I Membrane Protein EFF-1 Is Essential for Developmental Cell Fusion;
Developmental Cell, Volume 2, Issue 3, 355-362, (1 March 2002) doi:10.1016/S1534-5807(02)00129-6

By 2007, after another similar protein, AFF-1, had been found it was clear that there was a family of very similar proteins called FF proteins which all have similar rolls and without which we would not be able to make many of our organs. Some have gone so far as to suggest multicellularity and even sexual reproduction might not have been possible without them.

It is plausible that all cell fusion stems from viral genes slipping into our genome, but the jury is still out.

Elizabeth Chen,
Johns Hopkins University, Baltimore, Maryland, USA

Now Felix Rey of the Pasteur Institute, Paris, France, has found that the gene for the EFF-1 protein also comes from viruses. Using crystallography and X-ray diffraction to work out the 3D structure Rey's team has shown that it is very similar to virus proteins and that the active part is virtually identical. It looks almost certainly as though C. elegans got its ability to make skin by being infected with a retrovirus in its early evolutionary history.

There is still a lot of work to be done and other teams are looking for the protein responsible for muscle formation, for example, but with the first two such proteins to be found both coming from viruses, its likely that more, if not most of them will be found to have too.

Before cells can make something like skin or a digestive tract – as soon as you are thinking tissue and organs – usually you need some kind of fusion. If it's proved, it could be a Nobel prize.

Fasseli Coulibaly, Monash University, Melbourne, Australia.

Why is this a problem for creationists?

Well, notice that the proteins found have been nearly identical, but not exactly so, to those of viruses even though the active parts are almost identical. It is possible to argue, of course, that this is simply the 'Intelligent Designer' reusing the same genes he invented for viruses to do a similar job, but why not make them exactly identical in that case? On the other hand, if the genes were acquired from viruses, and only the active part is essential, then the rest is free to mutate and change in any way, so long as the active region remains active. So, the most vicarious explanation - the one which doesn't require us to account for the origins of an 'Intelligent Designer' and to incorporate magic into the explanation, in other words the one which has an entirely natural explanation, is that these organisms have evolved in the presence of viruses which 'gifted' them these proteins and so greatly expanded their 'fitness landscape' into which they were now free to evolve.

This makes me think that viruses have contributed enormously to the communication between cells, and to the appearance of multicellular organisms on Earth.

Felix Rey, The Pasteur Institute, Paris, France

It is even possible that this interaction with viruses allowed disorganised clumps of single-celled organisms to evolve sexual reproduction and to become organised into the colonies of coordinated cells we call multi-cellular organisms. We already know that it allowed placental mammals to evolve, probably from pre-placental mammals such as the monotremes or marsupials only now found in Australia and a few other places. The findings of course fit entirely comfortably within the model of animals evolving by unguided, unplanned and unintelligent Darwinian Evolution and genetic drift which does not require magic or supernatural beings.

Imagine being a professional liar for the Institute for Creation Research or the Discovery Institute and having to think up ways to mislead people over the significance of these findings, and to have to do that day after day after day as the evidence mounts up against you. It must feel at times like King Cnut trying to order the tide to turn, only faced with a tsunami.

They must consider themselves fortunate to be parasitising a bunch of people who are the least likely to be aware of this research if for no other reason than it tends to be published in science journals and pop-science magazines where the cognitive dissonance produced by reading them is far too uncomfortable, so they will be avoided like the plague.

'via Blog this'

---

The Universe's Dark Secret

Fresh hint of dark matter seen in neutrino search - space - 25 February 2014 - New Scientist

Dark Matter is something of a problem for science because it suggests our understanding of the Universe is incomplete. Not just incomplete in the detail, but incomplete at a fundamental level. The problem is, we devised our models, such as the model of fundamental particles, to explain what we could see.

This is not to say we are on the wrong track completely - the discovery of the Higgs Boson which essentially completed the theoretical collection of fundamental particles suggests quite the opposite - but that the track is much longer than we expected.

In some ways it's analogous to the state we were in when Einstein discovered the relationship between matter and energy and showed the velocity of light in a vacuum to be a universal constant independent of the velocity of an observer, and so discovered Relativity. Like just about everyone else at that time, Einstein's conceptual model of the Universe was that it consisted of the Milky Way galaxy and very little else, and that it was static - neither expanding nor shrinking.

Having realised his formula predicted that the Universe should be expanding, Einstein then made what he later called 'the biggest mistake of my life' and included a 'cosmological constant' for no other reason but to remove the expansion which he assumed must be an error. In doing so, he not only failed to be the first to predict that the Universe was expanding but also to make the logical deduction that it must therefore once have been very small, and so to discover the very small silent event mis-named the Big Bang.

The problem with dark matter is that it isn't a small problem. Some theoreticians have calculated that it, together with dark energy which is thought to be related to it, comprises some 95% of the Universe, meaning we only really have much idea about 5% of it.

In several ways, dark matter is paradoxical to our understanding. For example, it is generally accepted that dark matter consists of weakly interactive massive particles (WIMPs) which basically means they have mass (and therefore gravity) but barely interact with the particles we know about. This means they are difficult to detect because we detect things by observing how they interact with other things. This in turn means we would expect not to be able to find much evidence for it, and that, apart from one thing, comes perilously close to arguing that absence of evidence is not only not evidence of absence but confirmation of presence.

The one thing, of course, is the reason we know about it in the first place. We can detect it's effect on other things because it has mass and so exerts a gravitational effect. In fact, it was that which led us to suspect there was a lot of dark matter about. Rotating galaxies rotate at speeds which should make them fly apart according to basic Relativity and Newtonian Laws of Motion, yet we see they don't. Therefore there must be more mass present than we can see. In fact, it's the presence of so much dark matter that causes the rate of rotation in the first place to conserve angular momentum.

The term WIMPs is merely descriptive of what we are fairly sure particles of dark matter will be like. It doesn't tell us what they are nor how they relate to other particles so we don't know what it is that has this mass and in the absence of evidence, all we have is theory and hypotheses - rather like where we were with Higgs Boson.

We tested every single scenario we could come up with and eliminated things very carefully. The upshot is we just don't know what this is. The most exciting explanation is the decay signature of sterile neutrinos.

Esra Bulbul, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA

But now we may have moved a little closer to understanding what this dark matter is, or rather confirming one of the theories about what it's made of. Two teams of researchers acting independently have both detected bursts of x-rays being emitted from crowded clusters of galaxies and their energies appear to be exactly what we would expect of a hypothetical 'sterile neutrino' decaying into x-ray photons and other neutrinos, and these 'sterile neutrinos' are one suspected culprit for the building blocks of dark matter.

Neutrinos are notoriously incapable of interacting with 'normal' matter, hence the difficulty in detecting them. Billions of neutrinos come sleeting through the cosmos to pass right through your body and right through Earth every second, yet leave no trace at all, so their form make them highly suspect as the WIMPs of dark matter. The problem is that the three neutrinos we know about don't have enough mass, hence the hypothecated 'sterile' type which is not only even less interactive that the others but is much more massive. (Incidentally, don't confuse 'massive' with volume; it relates more to weight).

It's intriguing. There's a consistent picture for it being dark matter, but I think confirming it would really require deeper observations of other things.

Kevork Abazajian, University of California, Irvine, USA

The teams were Esra Bulbul of Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts, USA and her colleagues, using observations of 73 galaxy clusters from the European Space Agency's XMM-Newton space telescope and NASA's Chandra X-ray telescope, and Alexey Boyarsky of Leiden University in the Netherlands and colleagues using XMM-Newton observations of the Perseus galaxy cluster and the Andromeda galaxy.

For a contrast with how science copes with something like dark matter and how religion copes with new information which upsets its established dogma, see The Dark Matter of Gods. Imagine, for example, authenticated documentary evidence being found that the 'Gospels' were the work of committees complete with evidence of editing and embellishment, and marginal notes such as "Will people believe this?!!!", so destroying the standard Christian theological model of how the New Testament was written and how reliable it is as history. How would established churches incorporate this into their understanding and teaching? My guess is it would be ignored completely.

'via Blog this'

---

Income from ads will be donated to charities such as moderate centre-left groups, humanist, humanitarian and wildlife protection and welfare organisations.

Evolving Bible! It All Adds Up!

I found this cartoon by Ruben Bolling on PZ Myers' Phayingula blog the other day. Apart from wickedly satirising the absurdity of Bible literalism, it illustrates another neat little point that hopefully also embarrasses Bible literalists. It shows us how the current version of the Bible came about by an evolutionary process.

The particular piece of Bible nonsense I'm referring to here is from Ezra 1:5-11.

Then rose up the chief of the fathers of Judah and Benjamin, and the priests, and the Levites, with all them whose spirit God had raised, to go up to build the house of the Lord which is in Jerusalem. And all they that were about them strengthened their hands with vessels of silver, with gold, with goods, and with beasts, and with precious things, beside all that was willingly offered.

Also Cyrus the king brought forth the vessels of the house of the Lord, which Nebuchadnezzar had brought forth out of Jerusalem, and had put them in the house of his gods; Even those did Cyrus king of Persia bring forth by the hand of Mithredath the treasurer, and numbered them unto Sheshbazzar, the prince of Judah. And this is the number of them: thirty chargers of gold, a thousand chargers of silver, nine and twenty knives, Thirty basons of gold, silver basons of a second sort four hundred and ten, and other vessels a thousand.

All the vessels of gold and of silver were five thousand and four hundred. All these did Sheshbazzar bring up with them of the captivity that were brought up from Babylon unto Jerusalem.

Ezra 1:5-11

I wonder just how many people will read that passage and not actually add the numbers together to see if there really were 5,400 vessels? Let's be generous and exclude the twenty-nine knives and assume we really are counting the vessels, in this case the chargers and the basons.

More Evolution Myths Debunked

In 2008, Michael Le Page wrote an article for New Scientist in which he listed 24 myths and misconceptions about evolution, 14 of which were specific to creationism and which, despite them being continually refuted by proper scientists, creationist pseud-scientist continue to promote and disseminate amongst their gullible audience, usually for money. I listed these in Creation Myths Debunked and added my own refutation of them.

Here I give the same treatment to the other 10 common misconceptions. You will, of course find these being trotted out by creationists in debates with evolutionists, not realising they are simply misconceptions about what evolution is and how it works, rather than refutations of it. No one could ever accuse a creationist of knowing what they are talking about when it comes to science, even a science so basic and easy to understand as evolution.

Everything is an adaptation produced by evolution.

It's easy to assume that because every species is essentially the product of its evolutionary history that everything about it must have evolved because it gave an advantage of some sort. However, this ignores the fact that genes coding for particular traits can be linked on the same strand of DNA, so if one gene gives an advantage, descendants which inherit that gene will also inherit the linked gene. It may be that the linked gene has no particular advantage at all. It might also be that the linked gene is actually deleterious but not enough to cancel out the benefit of the advantageous gene. The linked pair will still convey an overall advantage so they will tend to increase in the species genepool.

One of the explanation why sexual reproduction came to dominate early - even a form of it is normal in bacteria - is that it involved crossing over of sections of DNA between paired chromosomes, which increases the chance of linkages being broken so advantageous genes can be freed from the evolutionary drag of being linked to disadvantageous ones and disadvantageous ones can be eliminated without losing the advantageous genes. They may even become linked to other advantageous ones, giving both a combined advantage which might even be synergistic.

Gender differences can also mean that features which are an advantage to one sex are also inherited by the other. Male mammals have useless nipples, for instance. There is simply no evolutionary pressure for males to lose them, even if it was possible to isolate the genes for them in female DNA only and there is no particular disadvantage to males in having nipples.

Evolution is always a work in progress, so to speak. (Creationist quote-mine alert! It's a metaphor, creationists! Calm down!). Several characters such as wisdom teeth, Darwin's Tubercle and the human appendix are vestigial structures because there has not been enough time, given our relatively slow generation time, for us to lose them altogether or to adapt them to serve some other purpose.

The evolution of a trait might be an incidental consequence of evolving some other advantageous trait. It has been suggested, for example, that the short stature of pygmies was a consequence of them evolving early reproduction in conditions where early adult mortality was common.

Lastly, what is beneficial to one gender may be deleterious in the other. One suggestion for homosexuality in males is that it could be linked to increased fertility in females. Females with increased fertility will tend to have more children so the chance of passing her DNA on to the next generation may still be higher despite the occasional son being homosexual.

Evolution happens because of natural selection.

Natural selection, and especially the special form of natural selection, sex selection, is undoubtedly a major cause of changes in allele frequency in the gene pool, but it is not the only one.

Random genetic drift will also cause change and is capable of leading to a gene becoming fixed in a population (where all individuals carry it) or to a gene being eliminated altogether. This will happen where variations give no particular advantage. It could account for the variations to be seen in the modern human face, for example. Random genetic drift in small, isolated populations could have led to differences between populations which have no adaptive purpose.

The graphs on the right from the New Scientist article show the result of two computer simulations of the change in frequency of five genes all from the same starting point.

A related aspect of random genetic drift is the so-called 'founder effect'. A population moving into new territory and becoming isolated from the parent population will normally be a random selection of individuals (not always as I'll explain in a moment). This effectively resets the starting position for genetic drift and the new population will randomly drift in different direction to its parent population. Include new random variations and over many generations the two populations will gradually, and randomly, drift further apart, even without any natural selection. This change alone could be enough to make it impossible for successful interbreeding to occur if the two populations ever come into contact again. All it needs is time.

The exception to the selection of the founder population being random would be a situation where individuals in a population had an ability which allowed them to move into the new territory. The founder population would thus be a self-selecting non-random sample. It could also be that a founder population expanding further into a new territory is actively selecting for success in that new territory so the expansion itself becomes part of the selection process. This can lead to very rapid diversification from the parent population in a newly-isolated population. In terms of cultural evolution, how much of the 'pioneering spirit' of present-day Americans is due to the founder population being selected for it in the first place and then the migration west further selecting from an already pioneering population? Who ups sticks and moves into new lands if not pioneers?

Some people have proposed that genetic drift alone could account for far more evolution that is generally acknowledged.

Incidentally, can anyone say where 'speciation' occurred in that process? It couldn't have been when the populations initially became isolated because they were then indistinguishable and fully capable of interbreeding. In fact, speciation is not an event but the incidental result of a process spread over time - which is why creationist charlatans prime their credulous victims to keep asking why no one has ever seen a new species come into existence. They know no-one has because they know it doesn't happen like that. It's as idiotic as arguing that you can't drive to New York because no-one has ever seen a car materialise from nowhere in New York.

Yes folks! It's that easy to fool a creationist and get them to part with their money. They are the scientific equivalent of people not knowing how cars move along a road and who refuse even to acknowledge that they do so or that roads exist.

Natural selection leads to ever greater complexity.

Natural selection leads to improved ability to reproduce in the given environment. This may or may not involve changes in complexity. In the case of internal parasites it more often than not leads to greater simplicity. Parasitic worms and flukes for example may even lose their gut and simply absorb nutrients from their host through their skin. Adult tapeworms are little more than a head with hooks for attaching themselves to their host and maturing egg cases to be excreted and ingested by a new host.

Because redundant structures tend to carry an overhead in terms of being a drain on resource, and a risk in that they can be injured or cause problems - wisdom teeth, appendix, for example - that natural selection will gradually eliminate them giving less complexity. Atrophied organs and structures are examples of reduced complexity.

It has been proposed that complexity in the genome - which is where increases in complexity will really occur - may be more likely in conditions where natural selection is weak.

Michael Le Page explains it thus:

Suppose an animal has a gene that carries out two different functions. If mutation results in some offspring getting two copies of this gene, these offspring won't be any fitter as a result. In fact, they might be slightly less fit due to a double dose of the gene. In a large population where the selective pressure is strong, such mutations are likely to be eliminated. In smaller populations, where selective pressure is much weaker, these mutations could spread as a result of random genetic drift... despite being slightly disadvantageous.

The more widely the duplicated genes spread in a population, the faster they will acquire mutations. A mutation in one copy might destroy its ability to carry out the first of the original gene's two functions. Then the other copy might lose the ability to perform the second of the two functions. As before, these mutations won't make the animals any fitter - such animals would still look and behave exactly the same - so they will not be selected for, but they could nevertheless spread by genetic drift.

In this way, a species can go from having one gene with two functions to two genes that each carry out one function. This increase in complexity occurs not because of selection but despite it.

Once the genome is more complex, however, further mutations can make a creature's body or behaviour more complex. For instance, having two separate genes means each can be switched on or off at different time or in different tissues. As soon as any beneficial mutations arise, natural selection will favour its spread.

Michael Le Page, Evolution Myths; New Scientist; 16 April 2008

Evolution produces perfectly adapted creatures.

This quite simply flies in the face of the evidence. A perfectly adapted species will always survive and, as we shall see in the next topic, most haven't.

In fact, you don't need to be perfectly adapted to be successful, you just need to be adapted well enough to be more successful than your rivals. Competition will often lead to evolutionary arms races in which two species will evolve in ways which are ultimately of no advantage to either.

A giraffe's stupidly long neck, which has necessitated it evolving ways of pumping blood up to its brain and then having to overcome that mechanism when reaching down to drink to avoid a brain haemorrhage, then accelerating it again when raising its head back up to avoid losing consciousness, is all to overcome the acacia tree's long trunk which it has had to evolve, and now needs to find the resources to grow, to avoid having its leaves eaten by giraffes. Both adaptations now mean the two species have to make a huge investment in simply growing their adapted bodies and yet neither is perfectly adapted. Acacia trees still have many of their leaves eaten and giraffes find drinking water difficult and standing up quickly from drinking even more difficult, making them vulnerable to crocodiles and other predators, but they still can't reach all the acacia leaves.

The panda's true thumb is committed to another role. So the panda must... settle for an enlarged wrist bone and a somewhat clumsy, but quite workable, solution.

Stephen Jay Gould, 1978

Humans are not perfectly adapted to living in an environment which contains malaria, trypanosomes, viruses, pathogenic bacteria, parasitic worms, alcohol, carcinogens and saturated fats, otherwise we would need fewer doctors, and we humans would not suffer from scurvy if we don't eat enough vitamin C just because a gene got broken way back in our evolutionary history so we can't make our own vitamin C anymore like most mammals do.

Whales, seals, manatees and marine turtles are not perfectly adapted to living in water because they have constantly to return to the surface to breathe. Many insects and birds in temperate zones can suffer huge population crashes in cold winters or dry summers and for most species, just as it was for most of humanity for most of our history, life can be nasty, brutish and short and a real struggle for survival. Very few wild creatures, sentient or otherwise, die peacefully of old age in their sleep.

There are many ways of dying - very few of them are pleasant - but evolution can only occur if a trait can be passed on. This means evolution can only have any bearing on what happens after an organism has bred successfully if survival helps the success of its descendents. In most species, survival of the previous generation after breeding is detrimental to the survival of their offspring because they compete for resources, so mechanism for avoiding death in later life will not only not evolve but there may even be pressure to evolve mechanism to ensure it happens relatively quickly.

None of this is perfect adaptation from the point of view of the individual.

Evolution promotes the survival of species.

This also quite simply flies in the face of the evidence. Some 90% plus of all known species from history are extinct. Of course, some of these went 'extinct' by evolving into another another species - Homo heidelbergensis evolved into H. sapiens and probably H. neanderthalensis, for example - but most simply went extinct like H. neanderthalensis, most probably because it was over-specialised to ice-age conditions.

The problem with evolution is that it is unplanned and undirected. It has no prior knowledge of the future and has no ability to plan for it even if it did. Evolution by natural selection is driven by change in the environment but that change might be reversed in the future or may changed far more quickly than the species can evolve. A species can find itself specialised for living in an environment which no longer exists.

A species' environment can change quickly because a new predator has evolved or moved into the habitat - think dodo, passenger pigeon or Tasmanian wolf. Catastrophic climate change causes by, for example, a cosmological event, or continental drift leading to changes in ocean currents and weather pattern have also caused mass extinctions in Earth's history. No matter how creative the evolutionary process might be, it can't always cope with catastrophic change. The fact is there are far more ways of going extinct than there are of surviving.

Sex selection may be another way in which a species can be driven to extinction simply because it can't put a stop to an increasingly harmful process. For example, female peacocks select males with the largest, most conspicuous tails. They have no choice in the matter and males must evolve larger and ever more conspicuous tails which females can't help but choose. Yet males will become increasingly prone to predation and will find escape ever more difficult. The male population can become threatened and yet fewer males actually increases male evolution in a deleterious way. With no males, the species goes extinct. The only way this can be avoided is if males are incapable of evolving larger and more conspicuous tails for some reason, or females suddenly switch their preferences - and what would drive that switch other than possibly the random genetic drift of several genes involved in the selection behaviour?

Evolving to extinction - the eventual fate of almost all species - is surely evidence that there is no intelligence involved in the process. It can only be the result of a blind, undirected and unthinking, amoral process.

Mike Huckabee. Young Earth Creationist. Southern Baptist Preacher.
Candidate in 2008 US Republican presidential primaries.

It doesn't matter if people do not understand evolution

Well, no, on an individual level it doesn't matter if someone lives their entire life no knowing about evolution. Before 1859 almost no-one knew about it. Consequently even highly educated and intelligent sceptics like Thomas Paine and Thomas Jefferson could not see an answer to the teleological argument and settled for the idea that there must be a creator of some sort.

It's a great shame though that, because they've been lied to, or made afraid some terrible fate awaits them if they acquire some forbidden knowledge which contradicts an ancient superstition, that some people miss out on learning one of the most remarkable and fascinating processes on Earth and the process which is responsible for the huge diversity of life. I know no-one who understands evolution who isn't perpetually awestruck by what it has produced and how it makes sense of an otherwise bewildering collection of living things. Most serious biologists find the knowledge of how they are related to every other living thing, deeply spiritual and humbling.

The explanatory power of Darwin's theory of evolution which needs only three easily observable things to be true, and yet which can account for seemingly hugely unlikely things becoming inevitable through a process of accumulation of small differences over time, is immense and has application far beyond explaining the evolution of species.

All that is required is:

• Inheritance of traits.
• Imperfect replication of those traits to give variation.
• Differential selection of those variations.

Clearly, this can apply to many systems, not just biological ones. The only other thing required is sufficient time, and that depends on the generation time.

Imagine if Mike Huckabee ends up as vice-president of the US - a mere heart attack away from the top job. Would you feel comfortable if the world's biggest superpower was run by a man who rejects evolution, thanks to the support of tens of millions of people who also refuse to accept the truth?

...Any leader who thinks evolution is a matter of belief is arguably unfit for office. How can someone who dismisses the staggering amount of evidence for evolution assembled by researchers in myriad fields possibly evaluate more subtle scientific evidence for, say, climate change?

Michael Le Page, Op. Cit. [Written in 2008]

But be that as it may, if individuals need to imagine they are so important they must have been deliberately made by some creator of the universe and it made everything else by magic just for them, because Bronze-Age people in the infancy of our species couldn't think how else it could have happened, the pleasure of enjoying the real magic of reality is lost to them. Their need to feel super-important is preventing them knowing how they really fit in with everything else on Earth and understanding how very special and fortunate they really are to be alive, the products of this process and capable of learning and understanding it.

But why should these unfortunate individuals be allowed to prevent others from learning about it?

Because the next generation is going to provide us with the scientists, doctors and bioengineers on whom we will increasingly depend for food, medicine and technological progress. Telling them they cannot trust science and that science is worthless will lead to two things. I disagree with much of what he says, but on this, Old Earth Creationist and evolutionary scientist Francis Collins hits the nail on the head:

By attacking the fundamentals of virtually every branch of science, it [Young Earth Creationism] widens the chasm between the scientific and spiritual worldviews, just at a time where a pathway toward harmony is desperately needed. By sending a message to young people that science is dangerous, and that pursuing science may well mean rejecting religious faith, Young Earth Creationism may be depriving science of some of its most promising future talents.

But it is not science that suffers most here. Young Earth Creationism does even more damage to faith, by demanding that belief in God requires assent to fundamentally flawed claims about the natural world. Young people brought up in homes and churches that insist on Creationism sooner or later encounter the overwhelming scientific evidence in favor of an ancient universe and the relatedness of all living things through the process of evolution and natural selection. What a terrible and unnecessary choice they then face! To adhere to the faith of their childhood, they are required to reject a broad and rigorous body of scientific data, effectively committing intellectual suicide. Presented with no other alternative than Creationism, is it any wonder that many of these young people turn away from faith, concluding that they simply cannot believe in a God who would ask them to reject what science has so compellingly taught us about the natural world?

Francis Collins. The Language of God

Mit Romney. Young Earth Creationist. Mormon.
Republican candidate, 2012 US presidential election.

Of course, it's in his first paragraph above that Collins identified the real danger of Creationism. If his second paragraph were true of a wider population than those who do reject faith because science shows it to be wrong, then more power to their elbow, I say. However, it is far more likely that they will remain anti-science and superstitious as we can see from American society today where 25% of the population still believe the sun orbits a 6000 year-old Earth which is the centre of the Universe and Noah's Ark was a historic event. This in the world's largest economy where one would expect to find the highest standard of general education, instead of one of the lowest for any developed economy.

And these religious fundamentalist could be controlling the world's largest nuclear arsenal.

We need political leaders voted into office who understand how evolution informs decisions regarding fishing policies, agricultural policies, antibiotic use and research, ecology, environmental and conservation policies, virology, epidemiology and public health policies and we need political leaders who understand how to evaluate evidence and base decisions on it. The last people we need are those who not only don't understand science and evolution but actually believe it to be wrong because they know no better than Bronze-Age nomads did but can't entertain the possibility of being wrong and so turn blind eyes to the evidence they don't want to see.

Ironically, the religious right in America has created conditions in which those best fitted to lead America - the scientists and intellectuals - are effectively debarred from office because they don't have the right irrational superstitions and phobias.

'Survival of the fittest' justifies 'everyone for themselves'

Firstly, even if this were true it would be nothing more than an argument from consequences. The truth of science does not hang on whether the consequences are convenient or not but on whether the evidence supports it or not. Atomic theory is no less true because atom bombs are destructive and nuclear war would be unpleasant.

The term 'survival of the fittest' is often falsely attributed to Charles Darwin. In fact, it was coined by Herbert Spencer. It is widely quoted by creationists if for no other reason than they can disguise their straw men with it by making 'fittest' mean whatever they want it to mean. If it means anything in evolutionary terms it refers only to the last of the three stages I listed above - differential selection from amongst variations. Trying to apply this to social situation, in particular the business or political world, to justify a dog-eat-dog morality and trying to drive the competition out of business by any means available neatly ignores the replication and inheritance stages.

Strangely, those who argue against evolution on these grounds often have a close relationship with big businesses which justify their amoral business ethics by misquoting Darwin, just as the social Darwinists, also usually from the political right, do. Nothing wrong with Darwinism when it suits you, it seems.

Of course, the 'fittest' may be the most cooperative, the most conciliatory, the most loving and affectionate or the most altruistic. Fitness to reproduce, which is what evolution by natural selection actually results in, does not often mean the most aggressive. It can mean the most fertile, the cleverest, the tallest or fastest, the best able to run and hide or the best able to tolerate extremes like temperature, salinity, pH or pressure. Or it can simply mean the best able to find and use resources. The peacock butterfly did not evolve mammalian-looking eyes on its wings nor did the zebra evolve stripes by being aggressive.

In human evolution, it was almost certainly the evolution of the ability to empathise with our fellows and to work cooperatively which led to our present level of technological development and societies bases on mutually agreed rules of interpersonal conduct. Had we adopted a dog-eat-dog strategy on the African savannah it would have been the wild dogs, cats, snakes and eagles who ate us. We 'won' by being the best at being cooperative.

Paradoxically, it's probably by being aggressive in the way they falsely accuse Darwinists of supporting that religions have gradually eliminated the opposition until we are left with two major religions now squaring up to one another and threatening the future of humanity in order to prove which one has the best imaginary friend.

Evolution is limitlessly creative.

In his book, Climbing Mount Improbable, Richard Dawkins introduced the idea of a fitness landscape - a theoretical world in which all the possible peaks of fitness existed. Looked at without any appreciation of how evolution is a slow, cumulative process, it might appear that there is no way a species could have got from the plains to the top of a peak in a single jump - the origin of the creationist straw men, "no one has ever seen a chimpanzee give birth to a human", or "the eye is too complex to have evolved spontaneously", etc.

In reality of course, the species has strolled slowly and inevitably up a gradual slope in this fitness landscape until it finds itself on the peak. There was no intent involved and no deliberate, massive and hugely unlikely jump anywhere in the process.

However, some fitness peaks may really be unclimbable and for reasons not entirely unrelated to creationist's misconceptions, feigned or otherwise. It could be that there is no gentle slope and the peak could only have been climbed using impossible jumps. Michael Le Page uses the example of evolving two-way radio communications.

The advantage of two-way radio communications would be considerable but how could any species climb to this peak? In fact, two different technologies would need to evolve independently yet each would only be an advantage in the presence of the other. There is no advantage to evolving transmitters if receivers don't exist and there is no advantage in evolving receivers because even being able to detect naturally-occurring radio waves such as those from lightning would not provide any useful information. For an intelligent designer, this would be no problem at all. If two-way radio communication was required it could be created fully formed, as creationists tell us wrongly that so many structures and processes were. The fact that nothing alive has in-built radio communication is because they were 'designed' by a mindless process with no plan and in which the required big jumps are impossible.

So, although evolution is undoubtedly hugely creative, there are limits.

Natural selection cannot explain homosexuality.

It seems to be a curious feature of evolution deniers that they are almost invariably from the extreme right politically and are obsessively homophobic. It's almost as though they are conditioned to look for reasons to hate, as though they need to feel better about themselves by denigrating others. But even homophobes who do accept evolution will use this one to try to prove that homosexuality is really just a choice of lifestyle. I wonder when they chose to be heterosexual!

In fact we know that some traits are linked because the genes coding for them are close to other genes in a chromosome. We also know that some genes have more than one function and a function which can change over the lifetime of the organism. I have already mentioned above how homosexuality in males (and it is common in many species despite the claims of religious bigots who believe their homophobic god created everything) could be a consequence of increased fertility in females, for example. The advantage of increased female fertility could out-weigh the disadvantage to the genes of producing a few homosexual males. But homosexuality is not always an exclusive process anyway. Many homosexuals are in fact bisexual and quite capable of having children.

Simple reasoning shows that evolution cannot explain homosexuality - how would a homosexuality gene get selected for? Why have the genetic traits predisposing to homosexuality not been eliminated long ago?

Any homophobic evolution denier

Any advantage of an evolved trait might not express in prolonged survival of the individual or even in an improved ability for a specific individual to reproduce, but in the survival of close relatives. After all, evolution is increasing the frequency of the 'selfish' gene in the species gene-pool, not in making specific carriers better able to produce offspring.

It has been proposed that one explanation for the increased tendency for boys with older brothers to become homosexual - something which apparently increases the more older brothers there are - is because male foetuses may leave something in the mother's blood which increases the possibility of future sons being homosexual. This trojan horse strategy would give older brothers an advantage in a future competition for mates. I don't know if this is generally accepted now, but at least it illustrates one possible mechanism for how homosexuality could evolve by natural selection.

It could also be that homosexuality is a consequence of sex selection. I have already mentioned the peacock's tail where female sex selection is pushing males to evolve traits which appear to be disadvantageous. It could be that homosexuality is also the result of females selecting traits in males which are linked to homosexuality, not necessarily in their partners but in their children. Similarly males could be selecting traits in females which increase the likelihood of her daughters being lesbian.

It would be interesting to see how creationists explain the common occurrence of homosexuality in other species in terms of creation by a magic man who allegedly abhors homosexuality and intended sex to be for procreation only, rather than simply denying that a readily observable phenomenon exists.

---

Tweet Link