Only Turkey lower than USA in accepting evolution

In a study in Science, Jon Miller, Eugenie Scott and Shinji Okamoto present the scary statistic that the acceptance of evolution is lower in the USA than in 31 European countries and Japan. Only in Turkey is evolution less accepted than in the USA. 80% of adults in Denmark, Sweden and France, 78% in Japan and 76% in the UK and 70% in Germany accept evolution as true, compared with 40% in the USA.

The study investigates multiple variables that contribute to this. They conclude that the reason for the low acceptance of evolution in the USA is because of widespread fundamentalism and the politicization of science in the United States. They conclude:

The politicization of science in the name of religion and political partisanship is not new to the United States, but transformation of traditional geographically and economically based political parties into religiously oriented ideological coalitions marks the beginning of a new era for science policy. The broad publicacceptance of the benefits of science and technology in the second half of the 20th century allowed science to develop a nonpartisan identification that largely protected it from overt partisanship. That era appears to have closed.

This makes depressing reading for anyone who understands how much confidence we have in the fact of evolution. Those of us who care about protecting science from political or religious meddling have a fight on our hands.

AIDS rising again in Uganda

Uganda has long been held out as a beacon in the fight against AIDS. Uniquely among African nations, where the disease is frighteningly common, the prevalence and incidence of the disease has been falling in Uganda. The disease prevalence peaked in 1992 and has been falling ever since. The success in fighting AIDS in Uganda can be traced to several things, including effective government communication, determined work at the grass roots, and the effectiveness of the ABC approach (abstain, be faithful, use condoms).

Now, however, comes the dreadful news that the decline in AIDS in Uganda has stopped and some indications that the epidemic is on the rise again. In the same period, the prevention programmes in Uganda have been de-emphasising the use of condoms, and promoting abstinence-only approaches. This is being driven partly by US aid policy, which itself is being influenced by powerful faith groups in the USA. Of course, American aid is extremely generous and very welcome, and is making a real difference in treating existing cases of HIV, but the way it is being used in the prevention programme is being seen increasingly as counter-effective.

The churches bear a heavy burden of responsibility. People, by the millions, are paying with their lives for the Catholic Church's absurd fixation with sexuality and its obsessive teaching against contraception. Under John Paul II, it painted itself into a corner by adopting an increasingly strident stance against all forms of contraception: to do the right thing now would undermine its authority and that is unthinkable in the current authoritarian climate that John Paul II created and that Benedict is maintaining. AIDS in Uganda is again, tragically, on the increase, because the Church teaches that it is immoral to separate the 'unitive and procreative' functions of intercourse. Instead, it is the teaching of the Catholic Church and other faith groups, in undermining the successful ABC programme, that is deeply immoral.

Complexity - we ain't seen nothing yet

Each of our billions of cells contains about two metres or six feet of nuclear DNA. All of this DNA has to be packed into a nucleus that is about 10 microns or one hundredth of a millimetre across. In order to fit all this DNA into this tiny space most of the DNA strand is wrapped into tiny loops called nucleosomes. This is true for all organisms that have nuclei - animals, plants and yeasts which together are called eukaryotes.

The nucleosomes are loops of DNA, 147 base pairs long, wrapped tightly around a core made of eight protein molecules called histones. Each loop or knot of DNA is connected to the next by a stretch of unwrapped DNA (called linker DNA) that can be anything between 10 and 50 base pairs long. DNA in the nucleus, therefore, resembles a string of beads, each bead representing a nucleosome. The structure of individual nucleosomes with their histone core has been known for some time. There are about 30 million nucleosomes in a human nucleus.

Now the fascinating thing about this arrangement is that its physical structure affects the cell and the organisms. It has a profound effect on the readout of the DNA sequence. The very compact structure of DNA in the nucleosomes makes it difficult to physically access the DNA. So, genes or parts of genes which are located in a nucleosome are far less easily transcribed than genes located in linker DNA. Transcription factors and other regulatory factors will bind more readily to target sites located in linker DNA than in nucleosomes. Indeed not only do individual nuclesomes hide DNA from regulators and from transcription, but complexes of nucleosomes, packed tihghtly together to physically hide the DNA do the same job, but in spades. This enables the genome to physically hide non-functional binding sites from regulatory factors and moderate the expression of genes.

So, the obvious question is: since the position of nucleosomes along the DNA sequence is so important, how is it controlled? Segal et have shown that the DNA sequence itself makes a major contribution to determining the position of nucleosomes along the DNA.

What's the interesting thing here? Well we have been fascinated by the logical code in DNA for decades. We have known for some time how proteins are coded in DNA sequences. The idea that the physical arrangement of DNA is important is more recent. But the fascinating thing that Segal et al show is that DNA encodes proteins as we expect, and that it also encodes its physical arrangemen and packaging. It's very complex - it's like a computer program that not only codes for the actions that it should perform, but also for the computer that reads itself out.

The code that Segal et al have revealed predicts that centromeres (where sister chromatids connect) and telomeres (the ends of chromosomes) should be highly occupied by nucleosomes. On the contrary, genes that code for ribosomal and transfer RNA, which need to be highly expressed are predicted to be poor in nucleosomes. Nucleosomes are not expected at the functional binding sites for regulatory factors but are expected at the non-functional sites with similar sequence. Transcription start sites, where gene transcription begins, are poor in nucleosomes and so available to the transcription machinery. So the genome itself encodes a physical packing structure that encourages regulatory factors to bind at the active functional sites. If the logical protein coding wasn't complex enough, we find it overlaid with coding for physical DNA packing which has functional consequences.

To make things even more complicated, nucleosome positions are adjusted dynamically and nucleosomes compete with factors to bind DNA; furthermore nucleosome positions are determined not just by DNA sequence but dynamically by enzymes (which are themselves produced by DNA transcription) called chromatin remodelling factors. Biology is more complex, much more complex , than we realised a couple of decades ago.

HAR1 makes us human?

Here's a cool paper pre-published in Nature on-line. Pollard, Haussler et al have analysed the human, chimpanzee, mouse and rat genomes in search of sequences that show evidence of rapid evolution in humans. They found one sequence in a region they have called HAR1 (Human Accelerated Region) which is highly conserved in other animals. For example, between chicken and chimpanzee there are only two substitutions in the 118 base pair region. Between chimpanzee and human there are 18 differences, all of which have occurred in the human lineage. The rate of evolution in HAR1 is about 70 times what would be expected from observing this region in other species. HAR1 is clearly under strong positive selection.

HAR1 is not a protein coding gene - it codes instead for RNA. But the most interesting thing about HAR1 is that it is expressed in the developing brain, specifically in the developing cortex of the embryo between nine and 17 weeks of gestation. It seems to act in conjunction with the protein reelin that is known to be implicated in the multi-layer patterning of the human cortex. No-one knows yet what the function of the HAR1 RNA is, but our understanding of the functions of non-protein-coding regions of the genome is in its infancy. However, we can reasonably infer that HAR1 influences the patterning of the mammalian and bird cortexes and that the big differences between the human sequence and that of other animals is one of the things that makes us uniquely human.

Everything about molecular biology is turning out to be more complex than anyone imagined 20 years ago. Most of the other sequences of highly accelerated evolution in the human genome seem to be in non-protein coding regions. In the last few years we have discovered that more than 60% of the conserved (and therefore probably functional) part of the mammalian genome is in non-protein coding regions. What does it all do? We don't know as yet - in fact, we've only just scratched the surface.

It was a rather humbling experience for us all when it was seen that humans and mice had about the same number of genes. Many scientists had predicted that humans, as befitted our status as the most complex beings on earth, would have many more genes than other animals. It turned out they were wrong. What's more, the human and mouse protein coding differed in regions that didn't seem to have much to do with special humanity - most of the difference was in the nose and the balls. But now, it's becoming clear that there is much more to a genome than making proteins and that makes everything much, much more complicated.

As for complications, well, in the same issue of Nature, Segal et al present data about the importance of the physical arrangement of DNA in the cell. Until recently, scientists have concentrated on the logical coding, ie the protein coding sequences - now it is turning out that the physical arrangement of DNA in the cell is important too. That also makes things much more complicated. More about this next time.

Dawkins and his legacy

There are many aspects to Richard Dawkins’ influence on the world of ideas such as his Selfish Gene hypothesis and the concept of memes, his popular writing about evolutionary biology, his robust opposition to Creationism and its slick cousin, Intelligent Design, his forthright atheism, and his championing of evidence-based reasoning in opposition to faith. It is thirty years since the publication of The Selfish Gene, and after a period where his reputation seemed to be on the wane, his immense contribution to evolutionary biology and his defence of science in the face of religious attack is again being recognised more widely. A book of essays, ‘Richard Dawkins - How a Scientist Changed the Way We Think’, celebrating the anniversary of ‘The Selfish Gene’ and Dawkins’ wide-ranging contribution to our intellectual life has recently been published and I’ve just received my copy. Many glittering names are represented; it’s edited by fellow Oxford biologists Mark Ridley and Alan Grafen and includes essays by Grafen, Daniel Dennett, Steven Pinker, Michael Ruse, Michael Shermer, A C Grayling, Marek Kohn, Matt Ridley, Philip Pullman and several others.

I’ve only had time to dip into it, but am struck by Matt Ridley’s and Pullman’s essays on Dawkins’ writing – concentrating not so much on the ideas as on his writing; comprehensible, taut, expressive, architecturally structured and entertaining.

Dawkins presented a series on UK’s Channel 4 earlier this year, challenging religious faith, called ‘The Root of All Evil?’. As much as I admire his writing, I found the TV series disappointing. It confirmed my view that he communicates best when writing – the TV series was a lost opportunity to stimulate a serious debate about the harm religion can do to society. Dawkins is unable to hide his contempt for religion and for faith as a route to belief. In the TV shows, only the bishop of Oxford represented the voice of moderate tolerant religion; otherwise Dawkins’ interviewees occupied some bizarre outposts of religious fundamentalism - to be fair to him, these fanatical views are gaining more influence both in the West and in the Middle East, a desperately worrying situation. Dawkins, however, had hardly a good word to say about any form of religion and came over as rather fanatical himself, aggressive, humourless and intense. The show revealed an image of the man that repelled many thoughtful viewers. He is not at his best on camera.

But he writes like an angel. Absurdly late nights and bleary mornings are testament to the fascinating tales they weave. It is a rare treat for a non-specialist to read and enjoy a book that simultaneously entertains, educates and lays out a major scientific concept for the first time, as he does in the 'Selfish Gene'. Science isn’t done much like that these days; scientists usually express their ideas within a closed world of technical conferences and focused journals written in impenetrable jargon. Even as he flays the perpetrators of superstition and pseudoscience, he writes wonderfully well.

Philip Pullman, who, by the way, accomplishes in ‘His Dark Materials’ the rare feat of an unremittingly anti-clerical work that is also steeped in spirituality, points out three characteristics in Dawkins’ writing that make it such a joy: his gift for creating memorable and apposite phrases; the powerful and serious personality that emerges from his writing; and his genius at communicating the flavour and texture of difficult ideas by telling stories

Dawkins’ reputation as a major contributor to biology through his selfish gene framework is growing. His influence in demolishing superstition and warning us against the increasing dangers of unreasoning faith is already immense, and will become more important as the battle between reason and darkness intensifies.

Lithium in stars supports standard Big Bang

I am, as some will know, a supporter of the standard Big Bang model of cosmology. It seems to me that the more information we receive from very different sources, such as data from WMAP’s measurement of the Cosmic Microwave Background and from galaxy surveys that independently verify the standard model, the more confident we can be that the Big Bang theory is right. I think it ios time to reject models with much poorer empirical support such as Lerner’s Plasma Universe and other steady state models (and of course the inanities of Young Earthers and others of their ilk).

This is not to say that all the issues around the standard model have been resolved – there are in fact some huge unresolved problems (for example, we can’t explain the superabundance of matter over anti-matter; we don’t know what the nature of dark matter or dark energy are, and so on). One of those problems was the fact in very old stars we expect the abundance of elements to be more or less the same as in the Big Bang nucleosynthesis, whereas the lithium in the surface of halo stars is three times less abundant than that.

Korn et al, published in last week’s Nature, have come up with a solution. The hypothesis is that complex combinations of processes such as atomic diffusion and turbulence transports lithium away from the surface of the star into its hotter core where it undergoes nuclear fusion. Good models exist for this process. Korn et al have observed stars of the same age but different stages of evolution in a globular cluster. They find that the lithium (and iron) abundance is different for different stages of evolution and thus temperatures of a star in a very good match to the model.

So it seems that the apparent shortfall of lithium in halo stars is caused by the transportation of lithium away from the surface into the interior of the star. If we extrapolate the process back to when the star was very young we can calculate the original abundance of lithium and lo and behold, it matches very accurately the abundance derived from the constraints imposed by observations of the CMB. It’s all coming together.

Intelligent Thought

‘Intelligent Thought: Science Versus the Intelligent Design Movement’ is a recently published collection of sixteen essays edited by John Brockman that includes the major part of the ruling by Judge Jones in the Kitzmiller Intelligent Design. The essays refute the ridiculous idea that Intelligent Design is an alternative to evolution as a scientific explanation for the existence and diversity of life in the universe. The ID movement’s politico-religious motivation and entire lack of scientific credentials have been fully exposed in the Kitzmiller ruling. This entertaining and informative collection of essays drives another nail in ID’s coffin. It contains excellent and scholarly rebuttals of ID’s claims from prestigious evolutionary biologists, such as Richard Dawkins and Jerry Coyne, palaeontologists such as Scott Sampson and Tim White, cognitive scientist, Steven Pinker, and philosopher Daniel Dennett.

Of course there will be howls of protest from the ID websites and from ID proponents like Dembski and Behe. Since the ID movement is a religiously motivated pressure group, its adherents are not interested in discovering the truth but in promoting a religiously prejudiced agenda. The fact that it has failed to make any impact amongst knowledgeable scientists, and that its claims to be scientific have been roundly rejected both by the scientific community and by judicial process will not stop it – the ID movement will continue to seek ways to push their agenda into education and scientific funding.

Read Brockman’s collection of essays if you can – they entertainingly unmask and demolish Intelligent Design’s upstart claims. I'll be saying more about individual essays in the days to come: starting woth Coyne's insight into 'strong' and 'weak' ID and his dismantling of the idea that either flavour, strong or weak, can be part of science; and followed by physicist Susskind's reflections on the links between the anger generated amongst extreme conservatives by their defeat in the culture wars and their current attempt to foment distrust of scientists and their views.

Exaggeration from opponents of embryonic stem cell research

The recent debates in Europe and the USA about the morality of embryonic stem cell research have pitched those who believe that science should be funded to find cures for many devastating illnesses using embryonic stem cells against the religious right who oppose the research on moral grounds.

A common argument used by the opponents of ES research is that treatments using adult stem cells and stem cells derived from umbilical cords is very successful at treating disease.

This is disingenuous at best and deceitful at worst. As Smith, Neaves and Teitelbaum point out in their letter published in Science on 28th July here, the opponents of ES research commonly claim that adult stem cell therapy is sufficiently successful that embryonic stem cell therapy is not needed. Such claims can be found here, here and here. A common claim is that adult stem cell therapy is successful in 65 illnesses. The list of claimed adult stem cell successes appears to be based on the work of David A Prentice, an employee of the Christian Family Research Council. In fact adiult stem cell therapy shows no promise for the prime disease targets for ES, including Parkinson's disease, diabetes, and Alzheimer's. As Smith, Neaves and Teitelbaum write:

"In fact, adult stem cell treatments fully tested in all required phases of clinical trials and approved by the U.S. Food and Drug Administration are available to treat only nine of the conditions on the Prentice list, not 65 ...Contrary to what Prentice implies, however, most of his cited treatments remain unproven and await clinical validation. Other claims, such as those for Parkinson's or spinal cord injury, are simply untenable...

The references Prentice cites as the basis for his list include various case reports, a meeting abstract, a newspaper article, and anecdotal testimony before a Congressional committee. A review of those references reveals that Prentice not only misrepresents existing adult stem cell treatments, but also frequently distorts the nature and content of the references he cites (5).

For example, to support the inclusion of Parkinson's disease on his list, Prentice cites congressional testimony by a patient and a physician, a meeting abstract by the same physician, and two publications that have nothing to do with stem cell therapy for Parkinson's. In fact, there is currently no FDA-approved adult stem cell treatment--and no cure of any kind--for Parkinson's disease.

For spinal cord injury, Prentice cites personal opinions expressed in Congressional testimony by one physician and two patients. There is currently no FDA-approved adult stem cell treatment or cure for spinal cord injury.

The reference Prentice cites for testicular cancer on his list does not report patient response to adult stem cell therapy; it simply evaluates different methods of adult stem cell isolation.

The reference Prentice cites on non-Hodgkin's lymphoma does not assess the treatment value of adult stem cell transplantation; rather, it describes culture conditions for the laboratory growth of stem cells from lymphoma patients.

Prentice's listing of Sandhoff disease, a rare disease that affects the central nervous system, is based on a layperson's statement in a newspaper article. There is currently no cure of any kind for Sandhoff disease.

By promoting the falsehood that adult stem cell treatments are already in general use for 65 diseases and injuries, Prentice and those who repeat his claims mislead laypeople and cruelly deceive patients."

Science in Iran; science in the West

Science journal ran an article on 21^st July 2006 by John Bohannon on science in Iran. There, the ayatollahs control everything including the science that can be done and the results that can be reported. Stepping out of line can be mortally dangerous. ‘Even the Iranian supreme leader Ayatollah Ali Khamenei has issued a fatwa, or edict, calling on researchers to secure Iran's position as the "leader in science" in the Middle East over the next 20 years. But at the same time, discussing ideas that displease the religious elite can land you in jail. As Haddad-Adel told Science, "We do not allow our scientists to make propaganda against Islam." Exactly what might constitute such propaganda is unclear, and Haddad-Adel declined to specify…Religious constraints have consequences for academia, says an Iranian philosopher of science who spoke on condition of anonymity. "Censorship, and especially self-censorship, is everywhere," he says. "In my papers and presentations, I must often change the ending to include some religious aspects, even though I am agnostic, which of course I can never admit."’ This is reminiscent of the pre-Enlightenment Christian Europe in which Galileo lived and worked.

Meanwhile, in the West, we owe the triumph of Enlightenment values for the freedom from intellectual censorship and our ability to declare our belief or lack of it without fear of persecution. We are free to report scientific results that undermine religious superstition and cant, and the religious leaders hate it. So, Cardinal Schönborn, Archbishop of Vienna, leads the Church unashamedly away from good science and towards the dark shadows of Intelligent Design. Cardinal Trujillo proposes excommunication for those working in good conscience for cures for many devastating diseases. Here is more about Trujillo's proposal.

There is a new war brewing between reason and enlightenment on the one hand, and religious authority on the other hand. We can no longer rely on intellectual and reasonable believers within the Church to moderate the urge of the religious to control not just their own, but everyone’s life. The moderates have lost the battle within the church communities and the conservatives have the whole of society in their sights.

Six months ago, I was astonished that a Catholic cardinal would lend his credibility to the absurdities of Intelligent Design, but now I understand that the Catholic Church, the largest single religious community in the world, is moving to openly oppose the fundamental scientific principles of Darwinism, in particular the contingency and randomness of evolution. There is little doubt that Ratzinger approves this enterprise and might well be its architect.

Those of us who care about the freedom of the human intellect to reach conclusions that run counter to religious beliefs and religiously inspired dogma have a fight on our hands. The battle between reason and dogma is just beginning.

The Battle to defend science and reason

The battle to defend science and reason against religious dogma is far from over.

Take, for example, Bush’s anti-science and hypocritical vetoing of the expansion of Federal funding for embryonic stem cell research – funding that is supported by a majority of the American people. Take the Roman Catholic Church’s meddling in the EU decision on European funding for embryonic stem cell research. Take the failed attempt by the Vatican to impose a Christian religious statement in the (now rejected) draft Constitution for Europe (here). The religious right is united in its desire to impose its morality and its thinking on the rest of us.

There is no doubt that the Bible Belt fundamentalists and the Vatican, in spite of their mutual hatred, are beginning to share a common objective which is to undo the freedom of the Enlightenment and to return the West to a neo-mediaeval condition of clerical control.