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

Transitional Fish-Face Fossils

Ancient fish was pivotal in evolution of face researchers find | euronews

This week sees the publication of yet another rebuttal of the creationist faith-based, evidence-denying mantra, "There are no transitional fossils". Swedish and French researches have reconstructed in three dimensions the evolving head parts of a small, primitive armoured early fish called Romundina which lived 415 million years ago and whose fossil remains were found in Arctic Canada. In doing so they have revealed the step by step evolutionary process which led to the evolution of the face.

Britain's Oldest Humans.

Oldest human footprints outside Africa found in UK - life - 07 February 2014 - New Scientist

A couple of news stories from Britain in the last few days have given creationists some more things to ignore.

First there was the news that the oldest hominin footprints outside of Africa were found on a beach in Norfolk at Happisburgh (pronounced Haze-bruh) after a severe storm last May wore away the cliff which had been covering them for the past 850,000-950,000 years. We were incredibly lucky that they were spotted and recognised almost immediately because they were washed away by the sea within a few weeks but by then they had been photographed and 12 of the 49 footprints had been analysed in forensic details. One wonders what else is being uncovered on the south and west coast of Britain as we reap the benefits of climate change in the form of massive waves, tidal storm surges and devastating coastal erosion two or three times a week, if only it was safe enough to go and look.

First Americans And Crackpot Religions

Ancestry of first Americans revealed by a boy's genome - life - 12 February 2014 - New Scientist

Two different crackpot religious beliefs took another blow recently when scientists succeeded in sequencing the genome of a three year-old boy who died and was buried, apparently with some considerable ceremony, 12,600 years ago in the Rocky Mountains, and in doing so have shown that several absurd but never-the-less firmly held religious beliefs are quite simply without foundation.

The child, known at the Anzick child after the family on whose land his grave was found, was from the 'Clovis People', almost certainly the first people to arrive in the Americas and the evidence from the DNA is that they came from Eastern Asia across a land-bridge into Alaska and then either down the coast or, less likely, through an inland gap which had opened in the North American Ice-Age ice sheet.

Intelligent Design - What A Lot Of Balls!

Posidonia oceanica balls – Kefalonia, Greece

Source: anthropogen.com

Some years ago, on our first visit to the beach in Port El Kantaoui, Tunisia, we were astonished to find it littered with suspicious-looking, slightly flattened fibrous balls, especially along the tide line. Were these washed-up camel turds, maybe? Should we complain to the hotel on whose private beach all this stuff was scattered? Was this beach fit to walk barefoot on?

Eventually, curiosity got the better of us and I gingerly picked up one. It was dry and when I sniffed it (one has to be prepared to make sacrifices for science) it was odourless save for a slightly salty sea smell. It was clearly made of tightly matted plant fibres which could be pulled apart. Maybe they were seed cases of some sort but we could find no seeds in them and what sort of seed case would be made of randomly arranged fibres? Being an inveterate collector of natural curiosities, I simply had to take some home.

I still have one in my little museum alongside fossil trilobites, a plesiosaur vertebra, pieces of fossilised wood, bits or fossilised coral, sea anemones and ammonites - the latter three picked up from a single field in Buckinghamshire, England. But still we had no idea what they were or if they really had passed through the digestive system of a camel, or a fish of some sort. And why did they come in assorted sizes from one or two inches to some six inches or more. Did they all start off the same size and get worn down by wave action? So many questions; so few answers. The only thing for sure was that they had come from the sea.

Black Holes, Science And Religion

Fiery black hole debate creates cosmological Wild West - space - 05 February 2014 - New Scientist

As the above New Scientist article shows, one of those little frissons of excitement is spreading through the worlds of theoretical physics and cosmology, just as it did a couple of years ago when the folks at CERN thought they had discovered neutrinos which could travel faster than light. Now another fundamental idea is being questioned, reassessed and reconsidered.

Harvesting the Genetic Algorithm

Antibiotic abyss: The extreme quest for new medicines - health - 27 January 2014 - New Scientist

This New Scientist article made me smile, probably because I still remember a time back in the 1990s, before they had really got to grips with the notion of 'intelligent design' when a favourite theme of creationists and other loons was how wonderful antibiotics were.

Apparently, they were gifts from God which could cure just everything from the common cold to cancer and restricting their use was somehow an infringement of the First Amendment - to most creationists the world only consisted of the USA then as now.

Vatican Complains About Interference

BBC News - Vatican 'must immediately remove' child abusers - UN

Far from being open and putting the paedophile abuse scandals behind the Catholic Church, like Pope Frankie promised, the Vatican is still putting the interests of the predatory priests and the Catholic Church above the needs of the victims and the need to protect future generations from their predation.

And so the scandal which has seen church membership haemorrhage and the reputation of priests plummet from one of the most trusted members of society to being someone most people would avoid leaving their children alone with, continues to fester.

Why Didn't God Make A Better Planet For Us?

Star next door may host a 'superhabitable' world - space - 31 January 2014 - New Scientist

A traditional circular argument used by creationists is that this planet must be perfect because it was designed by their god; they know it was designed by their god because it's perfect. They call this the 'Goldilocks' argument and seem jolly pleased with it. Basically, they seem to inhabit a fantasy Panglosian world in which everything is for the best in the best of all possible worlds - if you ignore all the bad bits and imperfections.

Stirring The Human Gene-Pool

Humanity's forgotten return to Africa revealed in DNA - life - 03 February 2014 - New Scientist

A new analysis of the DNA from a distinct African population - the Khoisan of Southern Africa - has helped shed some light on why humans didn't diversify into different species as they spread out of Africa into the rest of the world, even though they developed regional varieties. It seems we were simply too mobile and didn't stay isolated for very long.

One of the 'causes' of evolution is the isolation of a population from the rest of the species for long enough for the two populations to diverge genetically

Hawking, Black Holes and Evolving Universes

Stephen Hawking: "There Are No Black Holes" - Nature

When one of the creators of the Black Hole theory questions one of the fundamental principles of black holes, people take notice.

Stephen Hawking has just published an online paper entitled Information Preservation and Weather Forecasting for Black Holes, which has yet to be peer-reviewed, in which he casts doubt on the idea that nothing can escape from a black hole and that all information about the matter which falls into one will

Eelgrass And Circular Reasoning

Mysterious rings explaines

ScienceShot: Mysterious Underwater Circles Explained | Science/AAAS | News

The thing about geometric shapes like circles is that they look designed. They look as though something intelligent made them deliberately.

A few years ago a tourist took some photographs of mysterious rings that had appeared in the sea near the chalk cliffs of the island of Møn in the Baltic Sea and a host of magical theories, conspiracy theories and other wacky notions sprang up, all claimed to be the cause of the circles and the circles to be evidence of the cause. Each theory (and I use the term in its non-scientific sense here) claimed to be the cause of the rings and claimed the rings to be proof of the theory.

Myxy Sticks, Rabbits And Rapid Evolution

When I was a child of about 10 or 11, the English countryside saw one of the most impressive cases of rapid evolution yet witnessed in a wild mammal. It took just about ten years. It was also witnessed in Australia and the rest of Europe. It was how the European rabbits (Oryctolagus cuniculus) and the myxoma virus co-evolved to accommodate one another.

I remember still how during the first onslaught of rabbit myxomatosis the countryside suddenly became full of pathetic 'myxy' rabbits staggering blindly (and deafly) about, their eyes and ears swollen and closed with hideous pustules, completely lost and disorientated to be squashed by cars, killed by dogs and cats and dispatched mercifully by us humans who carried our 'myxy sticks'. The foxes had a heyday and their population exploded for a year or two. I once killed twenty rabbits in the corner of a single field in a few minutes. You had to be careful how you handled a myxy stick as the wrong end was a gory, pusy mess. You could easily spot a distant myxy rabbit because the swelling exposed the pale under-fur making it look like they had pale bases to their ears and pale stripes over their eyes.

The Legacy Of Sex With Neanderthals

Neanderthal-human sex bred light skins and infertility - life - 29 January 2014 - New Scientist

Modern techniques of DNA recovery, sequencing and analysis are quickly adding enormously to our understanding of the human evolutionary story, at a rate which must be terrifying to the professional liars at the Discovery Institute and the Institute for Creation Research whose job it is to either rubbish the science or distort it to make it look like creationists have a rational scientific point of view.

Take for example the three new studies published recently which shed more light on how Euro-Asian humans interacted with Neanderthals. Neanderthals (Homo neanderthalensis) are believed to have evolved from the close ancestors of 'modern' humans (H. sapiens), possibly H. heidelbergensis or H. erectus which migrated out of Africa and dispersed into Europe and Asia some 200,000 years ago, leaving those behind in Africa to evolve into H. sapiens, who followed them out in a second exodus, some 65,000 years ago and where they then co-existed as separate human species for some 35,000 years. It could be that we owe much of our success to our sister species who went before us.

It was once believed that there was no interbreeding between H. sapiens and H. neanderthalensis until the Neanderthal genome was successfully isolated and sequenced. It was then found that non-African H. sapiens have between 1% and 3% Neanderthal DNA showing beyond doubt that interbreeding had taken place.

Now detailed analysis of the genomes of 1004 people by Sriram Sankararaman, David Reich and colleagues of Harvard Medical School has revealed that Neanderthal DNA tends to be concentrated in regions of the genome with greatest variability, making these genes more susceptible to natural selection and so contributing more to our evolution. So, although forming a relatively small proportion of the genome, Neanderthal genes could have contributed disproportionately to our evolution, especially into a northern, temperate climate.

Meanwhile, a second study by Joshua Akey and Ben Vernot of the University of Washington in Seattle has shown that Neanderthal genes tend to be clustered around those associated with keratin production. Keratin is the structural fibrous protein found in skin, nails and hair. This finding was also supported by the Harvard study.

One of the genes involved was that producing pale skin, which is an advantage in cloudy northern climates where skin cancer is less of a problem and where Vitamin D, which is produced in the skin under the influence of sunlight and which is essential for normal bone development in children, can be deficient, especially if the sunlight is filtered out by pigmentation. So we have the possibility that Neanderthal genes provided us with paler skin.

However, this may be contradicted by a third study published in Nature by Iñigo Olalde, Morten E. Allentoft and colleagues of the genome of a single Stone Age European who lived about 7000 years ago near León, Spain had dark skin. Of course we can't project this finding onto all Europeans from 7000 years ago but it shows that pale skin was not then a universal European trait. This was some 40,000 after interbreeding between H. sapiens and Neanderthals could have taken place, so it they contributed to European pale skin, it was slow to spread throughout the European H. sapiens gene pool.

The question then is did Neanderthal keratin genes give us straighter hair than our African ancestors?

This underlines that modern humans and Neanderthals are indeed different species.

Fred Spoor, The Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

Other findings by the Harvard study show that not all Neanderthal genes were beneficial. Some seem to have made us more susceptible to autoimmune diseases such as type II diabetes, lupus and Crohn's Disease. It has previously been suggested that they could have made us more susceptible to arthritis in later life. They also found an almost complete absence of any Neanderthal genes on the sex-determinant X chromosome, suggesting that, when these were passed on they may have caused infertility and so would have been quickly eliminated. This is a common problem when related but distinct species interbreed, reinforcing the idea that Neanderthals had evolved into a distinct species, not a subspecies or merely a local variant, as had earlier been thought.

Because Neanderthal DNA is clustered in the H. sapiens genome rather than being more evenly admixed within it, this suggests that inter-breeding was a rare event. Sriram Sankararaman goes so far as to estimate that it may have happened only four times.

If this is so, it may well be that it was always H. sapiens male mating with H. neanderthalensis females since Neanderthal Y chromosomes, which are always inherited only from the father, have never been recovered from modern humans. Of course, this could also be because they are so rare that we just haven't found one yet - which doesn't square with Neanderthal DNA being found in all non-African humans. It could also indicate that a Neanderthal father and an H. sapiens mother always produced offspring with reduced fertility, or even sterile offspring.

'via Blog this'

---

Is This The Mother Of All Spiders?

A Silurian short-great-appendage arthropod

A strange new arthropod beautifully preserved in a nodule of calcite, found in rocks known to geologists as the Wenlock Series Lagerstätte in Herefordshire, UK, may be the ancestor of modern arthropods, including spiders, insects, lobsters, king crabs and scorpions. It has been given the scientific name Enalikter aphson. The arthropods get their name from the fact that they all have jointed legs and an external skeleton, features which evolved very early on. The only other group to evolve jointed limbs were the much later vertebrates with internal skeletons.

Using a technique known as Optical Projection Tomography the team led by Derek J. Siveter of Oxford University Department of Earth Science produced this detailed image from the only known 3D fossil of what are known as the stem-group arthropods, i.e. the group from which other arthropods evolved.

The significance of this find is that it is from rocks known to be 425 million years old, which makes it young by stem-group arthropod standards, being some 100 million years younger than previously found Megacheira (=short-great-appendage) all of which were from the Middle Cambrian era between 480 and 540 million years ago.

The taxonomic position of the Megacheira is controversial: were they stem chelicerates (a later sub-group of arthropods), or stem euarthropods? This specimen, together with another older Megacheira, Bundenbachiellus giganteus, found in Hunsrück Slate in Germany from the Devonian Era, makes it much more likely that the group this new species belonged to were stem euarthropods, in other words, that they were the ancestors of all spiders, lobsters, insects, etc.

Any creationist prepared to hazard an explanation of why an intelligent designer who made everything just the way it is today, would put this fossil of a primitive arthropod so unlike anything else we see today, in a calcite nodule in Herefordshire, UK and made it look 425 million years old?

Derek J. Siveter, Derek E. G. Briggs, David J. Siveter, Mark D. Sutton, David Legg, and Sarah Joomun, A Silurian short-great-appendage arthropod; Proc R Soc B 2014 281: 20132986

'via Blog this'

---

River Dolphins Teach Us About Evolution

Prompted by a comment by Bill The Butcher on my recent blog about the newly-discovered river dolphin in the Amazon river system, I decided to do a little reading around the subject.

The changing state of our knowledge about the evolution of these specialised dolphins, which inhabit river systems as widely separated as the Amazon and its tributaries, the Indus and Ganges rivers in northern India, the Yangtze River in China and the Rio de la Plata in South America, is a good illustration of how science modifies its theories in view of new knowledge and how any current explanation is regarded as provisional and open to revision with unsolved questions freely acknowledged.

On a technical note, the De La Plata dolphin (Pontoporia blainvillei), although in the same family as the river dolphins is actually an estuarine and coastal dolphin, not a freshwater dolphin. Sadly, the Baiji from the Yangtze River (Lipotes vexillifer) has not been seen since 2004 and is now considered extinct in the wild.

So, the first question is how did these dolphins, which were once included in the same Platanistidae family because they all shared the same anatomical features, come to be so widely separated if they were adaptive features for living in rivers? The 'solution' was to assume all these shared anatomical features evolved independently by convergent evolution in response to similar environments. The anatomical features are:

• A long thin 'beak' or rostrum
• Reduced eyes
• A large number of teeth in both upper and lower jaws
• A flexible neck

Of course, it's possible that some of these features could have convergently evolved but so many seems unlikely and this is further complicated by the fact that the De La Plata dolphin, P. blainvillei, shares these features but lives in the sea and salt-water estuaries.

But, if these features evolved independently then there is no real basis for lumping them all together in the same family in the first place. The taxonomy and the theory were inconsistent and unsatisfactory.

Cue DNA and molecular analysis.

This has shown the original taxonomic grouping to be to crude. On the basis of molecular evidence, the Ganges and Indus River dolphins are in one group which, under the rules of nomenclature, retains the Platanistidae family name, being the first to be named. The remaining ones are placed in a new Iniidae family which includes the newly-discovered species, Inia araguaiaensis.

But that still leaves the problem of explaining related species in China and South America, and on opposite sides of India with no communication between the river systems. Here fossil evidence gives us a further clue.

Fossil evidence strongly suggests that the original environment of the ancestors of the Inia, Platanista and Lipotes genuses were all marine, not riverine. It seems that the flexible neck, long rostrum and large numbers of teeth could be adaptations not for rivers but for hunting in sea water, as could the reduced eyes as the ancestors came to rely more on sonar than on sight for prey detection in turbid waters. Turbid waters are found in estuaries and inshore waters as well as in rivers. These adaptations also fitted them equally well for rivers, estuaries and coastal plains, opening up the rivers as potential new niches to move into. The only thing that has probably evolved three or four times is freshwater tolerance.

So here we see the molecular and fossil evidence coming together to solve a previous mystery in dolphin evolution and so giving us a much more satisfactory taxonomic structure. We can also see how features evolved for use in one environment can sometimes open up potential new niches, and how when this happens, species can diversify into these new niches. Again the revealed facts fit comfortably within the Darwinian Theory of Evolution by Natural Selection, the unifying principle which makes sense of biology.

The question creationists need to address is why an intelligent designer would put dolphins in the rivers but the fossils of all their ancestors in the sea and then made the molecular evidence agree with the fossil record to make it look like the river dolphins evolved out of a marine one slowly over time, so giving a perfectly natural explanation for both their morphology and geographical distribution without needing to invoke magic and a magic creator. Any takers?

One can almost hear the groans of disappointment of a creationist pseudo-scientist as he tears up the manuscript of another book explaining to his credulous audience how the distribution of river dolphins can't be explained by evolution and so proves evolution doesn't happen, so their favourite magic god must have made them 6000 years ago by magic and put them in the rivers, therefore science is all wrong and the country should be run by self-appointed Christian fundamentalists who know what's best for everyone.

Further reading:

Wild Mammal Blogs, The Evolution of River Dolphins, 15 July 2011
Geisler JH, McGowen MR, Yang G, Gatesy J. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evol Biol. 2011 Apr 25;11:112. doi: 10.1186/1471-2148-11-112.

---

Lost Lake May Have Helped Humans Leave Africa

Long-lost lake may have helped humans out of Africa - 22 January 2014 - New Scientist

Another piece has probably just fallen into place in the jigsaw puzzle of human evolution and our diversification out of Africa into the Middle East and Euro-Asia.

Migrating populations rarely up sticks and go on a long journey to distant lands. Instead the movement can be slow, spread over many generations and involve long stops and stable populations on the way. One problem, for example, is taking enough food for the journey because fruit and vegetables go bad after a while and livestock needs food and water. Sure you can hunt and gather on the way but that presupposes there will be something to hunt and gather. For this reason, deserts and barren mountain ranges are impassable barriers to human migration, especially early, low tech people like our early human ancestors.

It had long been assumed that modern Homo sapiens didn't come out of Africa until we had developed to a certain threshold level of intelligence and technology about 70,000 years ago to enable us to adapt to new environments on the way, but this was thrown into question when remains of very early humans from about 100,000 years ago were found in Israel. The mystery was how these people managed to cross the Sahara and the expanses of desert between East Africa and the Eastern Mediterranean.

But Martin Williams of the University of Adelaide in Australia and Tim Barrows of the University of Exeter, UK, have analysed samples collected from former lake-shore deposits, and dated them to about 109,000 years ago. This lake would have been one of the largest lakes in the world if it existed today at about 450,000 square kilometers and would have been in just the right place at the right time to support a large human population north of Ethiopia and with connections to the Nile which forms a narrow fertile strip across the Sahara to the Mediterranean coast. Although the size of the lake would have varied with the seasons it would have been large enough to still be a sizeable lake even in dry periods.

A big lake like this would have been a great place to live. It would have supported a large population, probably fishing and hunting game.

Stephen Oppenheimer, University of Oxford

Then, due to climate change and loss of monsoon rains the lake began to shrink, disappearing sometime between 70,000 and 100,000 years ago. The population would have been forced to migrate, and the obvious route is via the Nile to the Mediterranean and then east to modern Israel. A lake-side people could have easily adapted to living along a river.

So, we now have an explanation of how humans reached the Eastern Mediterranean before we had reached the assumed intelligence/technological threshold. However, DNA analysis shows that the modern Euro-Asian population only came out of Africa about 71,000 years ago, presumably absorbing or exterminating any earlier migration, assuming anyone had survived.

The question is whether the newly-discovered lake played any part in this second wave. This depends on precisely when it finally disappeared and there is not enough evidence to determine that precisely. It's disappearance could have triggered the second wave but it seems more likely that by then sea levels had dropped as the last Ice-Age reached its height, so making it possible to walk across what is now the Red Sea basin into Arabia.

'via Blog this'

---