Saturday 29 March 2014

If Only Noah Had Known About Evolution!

Noah's ark on the Mount Ararat, Simone de Myle 1570
Tree of bird life could solve Noah's Ark problem - life - 27 March 2014 - New Scientist

One of the many absurdities in the Noah's Ark myth, several more of which can be found in No Way Noah!, is the sheer impossibility of providing an ocean-going sea-worthy wooden boat large enough to house something like 19 million animals of all shapes and sizes, many of which require highly specialised environments, together with enough food, to last something over a year.

Creationist pseudo-scientists who make their living trying to explain away these absurdities have no option but to fall back on an almost equally absurd version of warp-speed evolution so they can reduce the numbers to mere few thousand from which all the species have evolved in the last few thousand years, apparently with no one noticing all the new species popping into existence every generation. We're expected not to notice that they also tell their credulous followers that evolution is impossible but holding two diametrically opposite views simultaneously has never been a problem for creationists.

Now scientists have suggested a way we could, should the need ever arise in the future to take the world's species into protective custody to prevent the extinction of life on Earth, whilst not needing to take a pair of every single species. What we would need to safeguard is the DNA of all different species, not in test-tubes but in living members of those species which are the most evolutionarily distinct. From these, we could, theoretically reconstruct other related species.

You could increase the amount of evolutionary diversity that is currently protected by 25 per cent by expanding the reserve system by 5 per cent.

Laura Pollock, University of Melbourne, Victoria, Australia
For example, we would not need to save a pair of every wild cat but nor would it work to save, say, lions, or tigers because these have close relatives, so most of their DNA would survive their extinction. What we need to do is to preserve the main limbs and major branches of the evolutionary tree of life rather than the terminal twigs. Losing a species which is closely related to several others, such as the lion, would merely remove a twig from the tree. Conserving an evolutionary distinct species with few living relatives however will conserve more of the DNA from further down the branch for the same effort.

The Zoological Society of London (ZSL) has been running the Edge of Existence Project since 2007. This seeks to identify key endangered and evolutionary unique species and to rank them into an order of priority for conservation. At the moment, effort tends to be concentrated on a few high-profile species, often at the expense of a higher priority species according to this ranking.

Now, Walter Jetz of Yale University has ranked the world's birds in terms of evolutionary distinctness using genetic data from 6500 of the 10,000 species combined with data on threats and population size to produce a list of just 100 priority species. He has also shown that concentrating on just 113 sites could conserve 60 percent of the most endangered evolutionary unique species.

Jetz has used the ranking to point to species that should be protected. For example, the highly distinct shore plover (Thinornis novaeseelandiae) lives only on the tiny Chatham Islands, near New Zealand. Just 250 are left. Focusing on plover habitat would preserve 14.46 million years of evolution for each 10,000 square kilometres conserved. In contrast, the ostrich is the 10th most distinct species, but as it has a large range only 0.05 million years would be preserved per unit area.

Andy Coghlan, Tree of bird life could solve Noah's Ark problem, New Scientist, 27 March 2014.

It's a beautiful irony that, had the Bible's authors had the least inkling of evolution or DNA and how it allows species to be arranged in a tree of life, they could have made their absurd tale just a little more plausible by explaining that Noah had reduced the number of species to conserve by doing just what conservationists are now doing. They would have had to explain how Noah had then reconstructed all the other species by careful bioengineering of course but at least their daft notion would have been just slightly less implausible.

Unfortunately, they had to try to force-fit the story into what little they knew and understood, and the prevailing superstition of the orthodoxy they were selling, and so ended up with a story so implausible that only children and scientifically illiterate, gullible adults could believe it.

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Ringing the Changes - Sex in Siberia

Oldest Homo sapiens Genome Pinpoints Neandertal Input

Just another little piece in the jigsaw puzzle of human evolution emerged this week when researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced the results of their sequencing of the entire genome from DNA recovered from the 45,000 year-old Homo sapiens male thigh bone, found in 2008 in an exposed banks of the Irtysh River at Ust-Ishim in western Siberia. It had been found by an ivory carver looking for mammoth tusks.

And, as with so often with science, a little piece of information has raised more questions and suggests that some of our earlier assumptions might just have been wrong.

Svante Pääbo's team have a lot more work to do but already a couple of things have been found:

  • The DNA contained unmistakable traces of Neanderthal DNA showing that the man was descended from people who had interbred with H. neanderthalensis.
  • Interbreeding had been quite recent judging by the fact that the sequences of Neanderthal DNA occurred in longer chunks than normally found in modern humans. As time progresses the chance of any chunk of DNA being chopped in half by crossover during the first stage of meiosis increases. A bit like whole fruit in a smoothy maker.

Genetically we now have a modern human that just barely postdates the Neandertal introgression into modern humans.

Bence Viola. Max Planck Institute for Evolutionary Anthropology
Now, and this might be a small crumb of comfort for those creationists who haven't simply ignored all this evidence of the hybrid origins of modern humans and must be feeling pretty depressed by all the evidence piling up against them, this has produced one of those small areas of disagreement amongst paleoanthropologists. Creationists normally enjoy these small disagreements and wave them around as evidence that, whilst science claims to be the only way to determine truth, it normally involves disagreement and changes of mind.

It's like having a time machine, to go back 45,000 years to see how the genomes of modern humans differed both from our own and also from Neanderthals and Denisovans.

Sarah Tishkoff, University of Pennsylvania, USA
It had been assumed that H. neanderthalensis had evolved in Europe or Asia, probably from H. heidelbergensis or maybe H. habilis or even H. ergaster or H. antecessor and had adapted to the colder northern climate. Later, when H. sapiens came out of Africa they did not move up into the colder north initially but skirted the southern margins into southern Europe and across Asia. The most likely place for the interbreeding with H. neanderthalensis in this scenario would have been the Middle East somewhere around northern Arabia, Asian Minor, Iraq or Iran. And this more or less tied in with the estimated dates of our expansion out of Africa and the period of cohabitation with Neanderthals.

However, this find suggests that modern humans adapted quite quickly to colder climates and were interbreeding with Neanderthals much further north. But, there is still much to be done to determine if this rapid adaptation was actually the result of the DNA we got from Neanderthals, or even to survival techniques and cold climate technologies we got from them.

One other intriguing possibility here is that, given the close proximity between Ust-Ishim and the Denisovan cave where a finger bone which yielded the DNA of a third species of humans was found, there may have been three different human species all capable of interbreeding and living in a relatively small area. All extra-African modern humans have some Neanderthal DNA and several groups of Southeast Asian and Austronesian people also have some Denisovan DNA, so it could be that this area was the point where all three came into contact and behaved very much like a ring species - just as we should expect gradually diverging species spread across a large geographical range to behave.

Researchers still think the Middle East is a likely place for the encounters. Other fossils in Israel, such as a 49,000-year-old Neandertal at Tabun Cave, might belong to people who were alive at the time of the unions or just after, says archaeologist Ofer Bar-Yosef of Harvard University, who was not a member of the team.

Ann Gibbons, Oldest Homo sapiens Genome Pinpoints Neandertal Input,
Science 28 March 2014: Vol. 343 no. 6178 p. 1417 DOI: 10.1126/science.343.6178.1417

Creationists who may be tempted to latch on to this little disagreement should bear in mind that there is no disagreement about human evolution here, or even the now established fact the modern humans coexisted with, and interbred with, related species of humans. The disagreement is simply over where the interbreeding took place.

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Sunday 23 March 2014

Evolution Has More to Crow About

Carrion crow, Corvus corone corone
A few days ago I mentioned at the end of a blog post about the evolution of crows in the presence of the great spotted cuckoo, the fact that carrion crows and hooded crows are now regarded as different species. This illustrates neatly the problem of defining a species, especially where two closely related species are at a stage in their evolution where they have not fully diverged and retain the capability of interbreeding. I'll discuss this more later, but first, the case of the Eurasian crows.

As you drive north from England across southern Scotland and up towards the Highlands, you might, if you're interested in the birds, notice that the ubiquitous glossy black crows you will have seen almost everywhere from town parks to country fields and woodlands have quite suddenly been replaced by an equally common crow with a black head, tail and wings and a grey back and underparts.

Friday 21 March 2014

Ancient Stick Insect Shows Evolutionary History

Early Cretaceous stick insect (Cretophasmomima melanogramma)
Image: Olivier Béthoux
The stripy stick insect that walked with dinosaurs - life - 19 March 2014 - New Scientist:

In my previous blog I touched on how what we see today in a species may be the result of ancient evolutionary forces which no longer apply, so it may not be immediately obvious what adaptive advantage there is to something in particular.

It's easy to overlook the fact that everything alive today is carrying the descendents of genes which survived through the Cambrian, the Devonian, the Triassic, Jurassic and the Cretaceous periods and were selected not by today's environment but maybe a very different one with different species and different ecosystems, even in the absence of orders like birds or mammals or in the presence of dinosaurs, pterodactyls, ammonites or giant tree ferns.

None of today's living species has an ancestor which did not live on an Earth where these extinct species once lived.

So, it should be no surprise to find ancient species like this early cretaceous stick insect which had adapted to live alongside early cretaceous plants by protective mimicry. This fossil was found in Inner Mongolia, China, in the Yixian Formation which has been dated between 122-130 million years ago. This rock formation which was laid down probably as volcanic ash from a catastrophic eruption, so capturing and preserving in exquisite detail, delicate structures like this insect with its wings, feathered dinosaurs and proto-avians as well as plant leaves. This is known collectively as the Jehol biota.

The significance of this fossil of Cretophasmomima melanogramma is that it is the earliest known example of stick insect mimicry. Stick insects today are renowned for their evolved mimicry to resemble the plants on which they feed but this example mimics a plant which was common then, but is extinct today. It was a species related to the maidenhair tree or Ginkgo biloba, now the only known representative of the Ginkgophyta division of the plant kingdom. The dark straight veins in the wings seen in this fossil, when the wings were folded over the back, would have closely resembled the leaves of Ginkgophyta, Membranifolia admirabilis also found in the Jehol biota.



Fossil species that can be conclusively identified as stem-relatives of stick- and leaf-insects (Phasmatodea) are extremely rare, especially for the Mesozoic era. This dearth in the paleontological record makes assessments on the origin and age of the group problematic and impedes investigations of evolutionary key aspects, such as wing development, sexual size dimorphism and plant mimicry.

Methodology/Principal Findings
A new fossil insect species, Cretophasmomima melanogramma Wang, Béthoux and Ren sp. nov., is described on the basis of one female and two male specimens recovered from the Yixian Formation (Early Cretaceous, ca. 126±4 mya; Inner Mongolia, NE China; known as ‘Jehol biota’). The occurrence of a female abdominal operculum and of a characteristic ‘shoulder pad’ in the forewing allows for the interpretation of a true stem-Phasmatodea. In contrast to the situation in extant forms, sexual size dimorphism is only weakly female-biased in this species. The peculiar wing coloration, viz. dark longitudinal veins, suggests that the leaf-shaped plant organ from the contemporaneous ‘gymnosperm’ Membranifolia admirabilis was used as model for crypsis.

As early as in the Early Cretaceous, some stem-Phasmatodea achieved effective leaf mimicry, although additional refinements characteristic of recent forms, such as curved fore femora, were still lacking. The diversification of small-sized arboreal insectivore birds and mammals might have triggered the acquisition of such primary defenses.

Wang M, Béthoux O, Bradler S, Jacques FMB, Cui Y, et al. (2014)
Under Cover at Pre-Angiosperm Times: A Cloaked Phasmatodean Insect from the Early Cretaceous Jehol Biota.
PLoS ONE 9(3): e91290. doi:10.1371/journal.pone.009129
Copyright: © 2014 Wang et al. Published under open access permission.

C. melanogramma being hunted amongst Membranifolia admirabilis foliage
Artists impression.
It seems very likely that these stick insects would have been the prey of the same early birds and mammals which are also found in the Jehol biota and evolved mimicry as a defence against them.

Of course, we can't know for sure if any of today's stick insects evolved directly from C. melanogramma but if they had they would carry genes that were once selected by the presence of early birds and late Ginkgophytes and they might well still have wings with dark straight veins having no apparent adaptive purpose today.

Evolution can't even look forward to tomorrow but it harks back to life on Earth hundreds of millions, even billions of years ago. We all carry the results inside us embedded in our genome, some of which was shaped by species and ecosystems of which we are not yet aware.

Dismissing this as magic, as creationist frauds and pseudo-scientists do, denies those who fall for their deceptions the pleasure of finding out how they were shaped by these forces and how they are connected to every other living thing through the process of genetic evolution by descent with modification from a common ancestor. It's like denying people the wonder of looking up into a night sky and being inspired by the awesome majesty of the cosmos.

It is denying people a heritage which is literally their birthright - the right to know who they are and where they came from.

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Evolutionists Have Even More to Crow About

Great spotted cuckoo (Clamator glandarius)
Predation Favors Parasitism

The fascinating results of research into the relationship between a species of parasitic cuckoo, the great spotted cuckoo, Clamator glandarius, and one of it's host species, the carrion crow, Corvus corone corone, was published in Science this week and illustrates an interesting aspect of evolution - how competing evolutionary pressures can produce a dynamic equilibrium.

The study was carried out in northern Spain where 67.7% of carrion crow nests are parasitized by the great spotted cuckoo, which also parasitizes another member of the crow family, the magpie (Pica pica), which has a broadly similar geographical range to the carrion crow. Unlike the magpie, which will often evict alien eggs from it's nest and will mob great spotted cuckoos in the vicinity, carrion crows exhibit neither of these defence mechanisms. It is normally assumed, when this is found in other cases of avian parasitism that the species has only recently begun to be parasitized, so has not yet had time to evolve these defensive behaviors. However, it is also possible that there has been no evolutionary pressure to evolve defences because there may be a degree of mutualism in the relationship. In other words, the parasitized species might be deriving some benefit.


Avian brood parasites lay eggs in the nests of other birds, which raise the unrelated chicks and typically suffer partial or complete loss of their own brood. However, carrion crows Corvus corone corone can benefit from parasitism by the great spotted cuckoo Clamator glandarius. Parasitized nests have lower rates of predation-induced failure due to production of a repellent secretion by cuckoo chicks, but among nests that are successful, those with cuckoo chicks fledge fewer crows. The outcome of these counterbalancing effects fluctuates between parasitism and mutualism each season, depending on the intensity of predation pressure.

Canestrari et al., From Parasitism to Mutualism: Unexpected Interactions Between a Cuckoo and Its Host;
Science, 343 (6177): 1350-1352; 21 March 2014:DOI: 10.1126/science.1249008

Carrion crow (Corvus corone corone)
Unlike many other avian parasites, great spotted cuckoo chicks do not evict host eggs and chicks from the nest but simply out-compete them in their demand for food from the adults. This often leads to reduced breeding success for the host species especially if food is scarce.

The difference in nest location and construction between carrion crows and magpies is also significant in explaining the different responses of these two species to cuckoo parasites. Carrion crows nest in the tops of tall trees and construct an open nest, making the brood prone to predation by predators such as falcons and buzzards. Magpies, however, build a nest in a thicker cover and construct a roof over it, making it harder for flying predators to take the chicks.

This difference in nest construction has created a different dynamic because it means the cuckoo chicks in carrion crow nests are also more liable to predation. This has produced evolutionary pressure for them to evolve a defence mechanism - they secrete a substance which repels predators. This in turn protects the host chicks in the same nest.

Magpie (Pica pica)
Magpies, which don't benefit much from the anti-predator strategy of the parasite chicks because their chicks are not so heavily predated, and therefore suffer much more from competition for resources with it, have had evolutionary pressure to evolve avoidance strategies.

Carrion crows, on the other hand, which can, in situations where predation is high, actually benefit from having a parasite chick in the nest, have had little evolutionary pressure to evolve avoidance strategies and might even be expected to evolve strategies to encourage it. However, given that predator numbers can fluctuate and there are years when predator numbers are low and so any potential benefit is not realised and loss due to competition can be the more significant effect, there may also be pressure acting in the reverse direction.

So, there is a dynamic of competing forces at work here which has probably reached an equilibrium at which the carrion crow does little or nothing to avoid parasitism because of the benefits it can get from it, but it has not evolved behaviours to encourage it because it also often suffers from it. Being dynamic of course means that it is relatively easy for a small change in one of the forces to push the dynamic in one direction or another, maybe over just a small part of the range, especially if the species involved is relatively sedentary.

And the evolution of the different strategies between magpies and carrion crows has its origins in the different nesting strategies adopted by the two species, which was itself probably produced by different responses to evolutionary pressures at some point in their evolutionary histories.

The historic forces which shaped evolution in the past may not even be present today so it can be difficult to see why something like different nesting behaviours in birds developed as related species diverged until we understand how natural selection operates. I'll be looking at this in my next blog.

As always, I'd love a creationist to come here to explain how this finding fits in with their currently fashionable 'intelligent design' notion. None have yet managed it with any other blogs on similar topics, but there is always hope that one will one day find the moral courage to defend their idea or to have the integrity to say they can't.

NB: Corvus corone corone is a three-part name to distinguish it from the Eastern subspecies, C. corone orientalis. The species formerly included the hooded crow, previously Corvus corone cornix. However, since 2002, these have been recognised as distinct species, C. corone and C. cornix respectively, and there is disagreement about the exact taxonomic status of C. corone orientalis. The reasons for this classification debate is interesting in itself and illustrates the problem of precise definition of the terms 'species' and 'subspecies' as an original species diverges and speciates, and may well be the subject of another blog here soon.

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Monday 17 March 2014

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.

Saturday 15 March 2014

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.

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?

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Thursday 13 March 2014

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.

Sunday 9 March 2014

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.

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.
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.

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Saturday 8 March 2014

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.

Friday 7 March 2014

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.

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.

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.

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Tuesday 4 March 2014

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.

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Monday 3 March 2014

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.

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Sunday 2 March 2014

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.

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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.

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.

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