Evolutionpages blog

Ratzinger and Dylan

2007-03-09T21:49:00.000Z

So Ratzinger is going public with his view that rock music in general, and Bob Dylan's music in particular is the work of Satan. Apparently Mozart and Bach are fine but music that includes guitars and political protest are not. Of course, Mozart and Bach wrote astonishingly beautiful music and Ratzinger is perfectly entitled to prefer Mozart and Bach to Bob. But there is a distinction between one's personal taste, and one's pronouncements as pope and spiritual leader of a billion people. (I wonder whether Ratzinger appreciates The Magic Flute and other Mozart works based on Mozart's masonic values?) But to suggest that modern music is universally immoral or valueless is simply ignorant prejudice. This about sums up the way the Roman Catholic Church is going - what was once a haven for good sense is rapidly becoming more absurdly reactionary than a fundamentalist cult in 1960s Alabama. There is nothing that I can say that will make Ratzinger appear more ridiculous than he has made himself appear.

For the countless confused, accused, misused, strung-out ones an' worse
An' for every hung-up person in the whole wide universe
An' we gazed upon the chimes of freedom flashing.
Dylan - 'Chimes of Freedom'

More evidence to acquit Tripoli Six

2006-12-13T22:39:00.000Z

More evidence that the outbreak of HIV and HCV in the Libyan children's hospital predates the arrival in Libya of the foreign healthworkers accused of deliberately causing the outbreak, is published in a peer-reviewed paper in Nature tomorrow. Go here for more information about the plight of the Tripoli Six.

Here is the abstract of the paper (de Oliveira et al, Nature 444, 836 - 837):

In 1998, outbreaks of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection were reported in children attending Al-Fateh Hospital in Benghazi, Libya. Here we use molecular phylogenetic techniques to analyse new virus sequences from these outbreaks. We find that the HIV-1 and HCV strains were already circulating and prevalent in this hospital and its environs before the arrival in March 1998 of the foreign medical staff (five Bulgarian nurses and a Palestinian doctor) who stand accused of transmitting the HIV strain to the children.

They conclude:

Our results support the existing nosocomial transmission scenario^1,¹¹ and suggest that Al-Fateh Hospital had a long-standing infection-control problem. The earlier origin and greater number of HCV clusters than HIV-1 clusters reflect the higher transmissibility of HCV compared with HIV-1 by such routes¹². Crucially, we have shown that the HIV-1 and HCV strains responsible were being spread and transmitted among individuals attending the hospital before March 1998, indicating that many of the transmissions giving rise to the infection clusters must have already occurred before the foreign medical staff arrived.

The verdict in the trial is due soon. Let us hope the Libyan authorities see sense and acquit these innocent people.

Another fish to tetrapod transitional

2006-11-16T22:12:00.000Z

Tiktaalik, found exactly where a tetrapod transitional was predicted in the fossil record, in exactly the geological formation predicted, was a spectacular find of a fish to tetrapod transitional.

Now comes another earlier find and the first of a tetrapod transitional in Australia. Dated to 380 million years ago, Gogonasus is fantastically well preserved in 3-D, and the team have used X-ray tomography and other new techniques to reveal fine detail of the skeletal anatomy. While still a fish, it shows some characters that begin to show a transition to the tetrapod form, particularly in the ears and in the limbs.

Gogonasus lies quite early in the fish to tetrapod transition. Fish that are more derived, ie closer to tetrapods are known from Europe and America (Pandericthys and Tiktaalik) but none are known from the Godwana supercontinent. However, early tetrapods are known from Godwana. The authors therefore predict that fossils of fish closer to tetrapods than Gogonasus will be found in Australia to parallel Tiktaalik from Eurasia. They have set off to test this prediction by exploring Devonian formations – who said that palaeontology makes no predictions?

Correction thirteen years on

2006-11-16T19:04:00.000Z

Scientists are rightly proud of the self-correcting and self-policing that the scientific community applies to itself. This is exemplified by the brouhaha surrounding a correction published last week by the authors (from the Oak Ridge National Laboratory in Tennessee) of a paper published thirteen years ago in Nature. The paper is widely acknowledged to represent a major contribution to the technique of very high resolution compositional analysis with a scanning electron microscope, and its claims are not in doubt, having been confirmed many times over since then.

The problem is that the authors claimed, and assured the referees, that some data had been analysed in a way which it turns out they had not, for reasons that are not now entirely clear. The authors have publicly eaten humble pie and apologised, but the paper has not been retracted and its conclusions still stand. The reason for this focus on truth and accuracy in a refereed paper, even where the errors do not affect the central claims of the paper, is that other workers often rely on reported methods and the community is as anxious to protect the integrity of subsequent work as it is to ensure that the central claims are properly supported by the evidence.

Is the process perfect? Of course not. Would Nature have forced this corrigendum if the paper was less prominent? I think probably not – errors in methods in a little cited paper in a less prestigious journal would be much less likely to be uncovered and much less likely to be publicly corrected. Nevertheless, this incident illustrates the ability and determination of the community to police itself and to ensure integrity.

Contrast the almost paranoid care demonstrated here with the appalling contempt for the truth demonstrated by creationists in their interminable repetition of false claims long after their errors have been pointed out to them.

AIDS medics - open letter to Colonel Gaddafi

2006-11-12T12:47:00.000Z

Many bloggers, the scientific community and Nature journal have all been campaigning recently for a fair trial for the six foreign medical workers accused of deliberately infecting 400 children with AIDS. If found guilty they face the firing squad. Their trial is complete and the verdict is due in mid December. The disturbing fact is the 'shocking lack of scientific evidence' to link them to their alleged crime.

Go here for more information from Nature's web focus in support of the Tripoli six.

Here is the text of the open letter signed by 114 Nobel Laureates to Colonel Gaddafi:

Dear Colonel Muammar al-Gaddafi:

We, Nobel Laureates in the sciences, are gravely concerned about the ongoing trial of five Bulgarian nurses, Valya Chervenyashka, Snezhana Dimitrova, Nasya Nenova, Valentina Siropulo, Kristiana Valcheva, and a Palestinian doctor, Ashraf Ahmad Jum'a, in Tripoli. The six face death-penalty charges of deliberately infecting 426 children with HIV at al-Fateh Children's Hospital in Benghazi in 1998. Strong scientific evidence is needed to establish the cause of this infection. However, independent science-based evidence from international experts has so far not been permitted in court.

Libya is currently making efforts to join the community of peaceful nations by renouncing weapons of mass destruction and adhering to international standards regarding the rule of law. This trial is another opportunity for Libya to demonstrate its commitment to recognized values and norms. But so far Libya has failed to follow the norms of international justice in the case of the charged medical workers.

We appreciate the agony and the sadness of the parents of these children and we sympathize with the difficult situation of the Libyan authorities in trying to deal with this matter. However, we feel that if justice is to be served it is essential that the defence should be permitted to present its case.

Among the disallowed scientific evidence is a 2003 report, which Libya requested, and which was provided by Luc Montagnier, a co-discoverer of the virus that causes AIDS, and Italian microbiologist Vittorio Colizzi. The report concluded that the infection at the hospital resulted from poor hygiene and reuse of syringes, and also that the infections began before the arrival of the nurses and doctor in 1998.

On 29 August 2006, a Libyan prosecutor reiterated the call for the six to be given the death penalty. The next, and probably last, court hearing is scheduled for the 4 November, with a verdict expected shortly thereafter. A miscarriage of justice will take place without proper consideration of scientific evidence. We urge the appropriate authorities to take the necessary steps to permit such evidence to be used in this case.

To uphold justice, and ensure a fair trial, we affirm the need for:

Defence lawyers to have the right to call and examine witnesses on the health workers' behalf under the same conditions as witnesses called against them, and
The appropriate authorities to call upon internationally recognized experts in AIDS research to examine and testify on the evidence as to the cause of the HIV infections in the children.

Yours sincerely,

Richard J. Roberts and 113 fellow Nobel Laureates

More explanations for why we believe in gods

2006-11-09T21:28:00.000Z

Todd Tremlin of Central Michigan Umiversity has written a book on why human beings are predisposed to believe in gods (Minds and Gods: The Cognitive Foundations of Religion). The recent review in Nature (by Kruger and Konner) points out that there is much to admire in the book, in particular its explanation that human minds are predisposed by evolutionary considerations to detect agents everywhere and that human minds have a Theory of Mind Module that is very adroit, and unique in the animal kingdom. I find that explanation compelling but, like the reviewers yearn for a more complex explanation that illuminates the powerful emotions that belief in god(s) elicits.

Pascal Boyer's 'Religion Explained: The Evolutionary Origins of Religious Thought' is still for me one of the most insightful books on this topic. As time passes, we will, of course, come to understand more clearly the things in human evolution history that predispose us to believe in god(s).

A different kind of transitional

2006-10-24T22:46:00.000+01:00

Transitionals are usually regarded as extinct fossil species that occupy a space between major groups and which represent the process of transition between these groups. So, for example, the transition between marine and land vertebrates is represented wonderfully by a number of clear transitionals such as Acanthostega gunnari, Ichthyostega , Tulerpeton, Pederpes finneyae and Tiktaalik (see also Jennifer Clack’s superb book on the marine:land transition, Gaining Ground). Transitionals are, of course, not just represented in fossils – all species are in transition between the ancestral form from which they came and the evolved form to which they are headed.

A recent paper in Science seems to me to represent a different sort of transition in action. Lynn Margulis (whose views on other matters such as the Gaia hypothesis and her claim that there is no scientifically demonstrated link between HIV and AIDS shows just how much tolerance good science shows to those with a mixture of good and bizarre ideas) developed the now widely accepted idea that organelles (such as mitochondria which have their own DNA) in the cells of eukaryotes (animals, plants, fungi and protists) originated as bacterial endosymbionts. Endosymbionts are separate organisms that live in symbiosis with a host cell – ie they provide some benefit that the host cell needs and in turn are supported and protected by the host cell. There is strong evidence that mitochondria were originally free-living bacteria, which invaded host cells, perhaps originally as parasites. Subsequently a mutually beneficial relationship developed (there are a vast number of mutually beneficial relationships between bacteria and host organisms, with bacteria providing benefits by their action in environments as diverse as mammalian guts and the roots of plants). Endosymbionts make their living on the same principle except that they live within the cells of their host organism. Long lasting endosymbiotic relationships become very close – they get to the point where neither host nor bacterial invader can live without the other. There is good evidence that the bacterial invader over time abandons much of the basic genetic makeup that enabled it to live independently, because the host cell provides many basic functions. Indeed, there is evidence that lateral processes transfer some of the genetic material of the endosymbiont from the genome of the organelle to the nuclear genome of the cell. For example go here.

Endosymbionts are well known today. For example, endosymbionts are known to exist in many varieties of insect cells. In most cases the endosymbionts are restricted to specialised cells called bacteriocytes. They reproduce through generations of the host cells like organelles. The endosymbionts have massively reduced genome sizes and a big bias of nucleotide composition (the four nucleotides, A, T, G and C are approximately equally represented in the genomes of free living organisms but in endosymbionts and organelles the GC content is significantly reduced). Examples of endosymbiotic bacteria in insects include Buchnera, Blochmannia, Wigglesworthia and Baumannia. Nakabachi et al have just published a fascinating short paper in Science in which they report the sequencing of an endosymbiont, called Carsonella ruddii, that is found in all species of a type of insect called psyllids that feed on plant sap (Pachypsylla venusta). The characteristics of this bacterial symbiont lie way beyond that of other known insect endosymbionts.

How? Well first of all the genome of Carsonella is tiny – it consists of 160 kilobases (which is a third of the smallest previously known bacterial genome), and it contains only 182 genes most of which have some physical overlap with one another. It has a very low GC - guanine/cytosine - content at only 16.5%, way below that of other known organisms. Carsonella has lost all of its genes for many categories that free-living bacteria need such as the creation of a cell envelope and the genesis of nucleotides and lipids. Its genome lacks many genes that are necessary for biological processes of free-living bacteria. It seems that the host cell compensates for this lack of apparently critical function. On the other hand Carsonella is rich in genes to synthesise essential amino acids in which the food (plant sap) of the host insect is poor – this is evidence of the positive function of Carsonella to its insect host. Carsonella is so reduced and so utterly dependent on its host nuclear genome that it can be regarded as a transition between an obligate endosymbiont and a eukaryotic organelle. It is a genuine transitional on its way from bacterium to organelle.Never let creationists tell you that there are no transitionals.

CMB measurements grab Nobel prize

2006-10-11T22:12:00.000+01:00

Good to see that this year's Nobel prizes in physics have gone to Mather and Smoot for separate work on the cosmic microwave background. Studies of the CMB have revolutionised cosmology. Mather measured the spectrum of the CMB and showed that it was an almost perfect black body spectrum, showing beyond a reasonable doubt that it is the red-shifted glow of the early universe. Smoot first detected and measured the miniscule temperature ripples in the CMB that carry a huge amount of information about the early universe and the way the universe evolved.

The most accurate recent measurements of the CMB have been carried out by the WMAP satellite. I've just posted a summary of the findings of WMAP from three years of observations here.

The God Delusion - lazy criticism

2006-10-09T20:18:00.000+01:00

For a blogger who lays claim to scholarly qualities, rmj presents depressingly superficial arguments against Dawkins's 'The God Delusion'. Here is rmj:

Neither a theologian nor a philosopher of religion, he [Dawkins] spends 80+ pages on the arguments for the existence of the God of Abraham (the Hindu pantheon and other gods of other world religions need not apply, apparently). Neither an anthropologist nor a psychiatrist, he devotes 70 pages to the "roots of religion" and a discussion of whether morality is possible outside of religion (I'll save you the money: yes. That's me. Ignore Dawkins.). Not trained as a scriptural scholar (not all of whom are either religious nor Christian), he devotes another 40 pages to scriptural criticism. The rest of the book is devoted to making clear his straw man is actually a version of Christian fundamentalism, one that exists largely in his fevered perceptions.Skimming the index, I find no reference to any philosopher of religion outside of Immanuel Kant (and he merits only a page; thus does Mr. Dawkins apparently dispose of both Kant's Idealism and Religion within the Limits of Reason Alone). The chapter on the proofs of God references Aquinas (whom Dawkins deigns to declare a thinker with an "eminent" reputation. Yeah, and Shakespeare was a pretty good writer, too.) and Pascal. The index betrays no reference anywhere in the book to St. Anselm (creator of what Kant later labelled the "ontological proof"), nor to modern philosophers like Charles Hartshorne (The Logic of Perfection, his updating of Anselm's argument) or Alvin Plantinga...Nowhere in his index, indeed, does Mr. Dawkins reference any important philosophers of religion or even of phenomenology.

What have we here? A critique based on a reading of the Table of Contents and the Index? Surely not. But yes, as we read rmj, the truth dawns. He hasn't read the Dawkins book that he so ineffectually criticises in such an appallingly innappropriate magisterial tone. He fails to address a single one of Dawkins arguments, relying instead on what he imagines Dawkins arguments must be based on his scanning of the Table of Contents and the Index. He hasn't even bothered to read the index properly, claiming that:

The index betrays no reference anywhere in the book to St. Anselm

Well, Anselm of Canterbury appears large as life in the Index and is referenced on four pages. It's quite disgraceful to critique a book based on a reading of its index, but if he is hell bent on that flummery, it behoves him to read the index properly - if he is so incompetent that he gets even that wrong, well, we need not give much credence to anything else he says about the matter. (If, against all the evidence, rmj has read the book, things are no better for him since he stands accused of egregious superficiality; his criticism is indistinguishable from that of someone who hasn't read the book. But, the evidence is that he hadn't read it at the time of his writing).

Since it's impossible to properly represent Dawkins arguments without reading the book (a task that rmj regards as an unnecessary chore), rmj sets up and knocks down strawmen with grim satisfaction and utter futility. For example, he criticises Dawkins for concentrating on Abrahamaic religion, a point that, had he only bothered to read the book, he would find Dawkins addressing head on.

Rmj is more concerned to present himself as learned than to offer any sort of properly reasoned criticism. His is the sort of pseudo-intellectualism that seeks to impress others and that is impressed by the length and complexity of arguments: "Hartshorne's argument is so complex that even Mr. Gale declines to include it in his book, saying it needs separate consideration". Well, it must be right, then. I trust that even rmj can see the fallacy of that now that it's pointed out to him. Hartshorne's argument might be telling or it might not; whether it is or not does not depend on how long or complex it is; and its utter ruin need not require more than three sentences. And rmj knows (or should know) that Hartshorne's philosophy is completely marginalised in the context of practical religion (as well as being thoroughly criticised by many other philosophers - the philosophers of religion have never been able to agree on any matter whatsoever), so it is unnecessary and inappropriate for Dawkins to spend any ink on him.

There are some valid criticisms that one might raise against Dawkins's thesis. Rmj misses them all. At one point in his dreadful critique he heaves himself up on to a pedestal, and in reference to Dawkins pronounces: "I must admit a weakness, though: I do not suffer fools gladly" I wonder, then, if he doesn't suffer fools gladly, how he manages to live with himself.

A coherent argument against the 'selfish gene'?

2006-10-04T20:38:00.000+01:00

I've received my copy of Dawkins's 'The God Delusion' and am well into it. rmj has blogged a critique of it, which I'll get to later, but in exploring his/her blog I found this imbedded in a critique of Daniel Dennett's 'Breaking the Spell'.

For some reason I had forgotten Richard Dawkins' connection to "selfish gene" theory, and I also thought that the "selfish gene" idea had found its Wittgenstein, and already been as discredited as thoroughly as Wittgenstein and Godel discredited logical positivism.

There is so much absurdity here that it's hard to know where to start. Richard Dawkins isn't merely 'connected' to the Selfish Gene concept: in 'The Selfish Gene', he laid out, for the first time, the entire gene-centred framework that has proven to have such explanatory power. Not to know that is akin to saying 'I had forgotten that Einstein was connected to General Relativity'. We'll leave rmj's premature declaration of victory over logical positivism for another time.

For a (wo)man who claims later in this post:

My critiques of science come from my study of it, not from my blank ignorance

rmj is remarkably ignorant. The notion that the selfish gene idea has been discredited is utterly foolish given the acknowledgement that the concept is receiving in this, the 30th anniversary of its publication. He goes on:

I worked out a fairly coherent argument against the "selfish gene" theory when I first heard of it, and seem to remember reading most of my points among criticisms of the idea, which is why, I think, I considered it a dead issue. It is, by and large, premised on a reductio ad absurdum...

It is, of course, too much to hope that he/she might actually develop this argument for us, or even say something to show that he/she has the merest inkling of understanding of the selfish gene framework. We shall just have to take his/her word for it, as we would take the word of a fisherman for the size of the fish that escaped.

Dawkins and the God Delusion

2006-09-23T00:42:00.000+01:00

Richard Dawkins is about to publish his latest book which is not about biology but about religious belief (or rather about why religious belief of any flavour is no more than a delusion). He had a substantial slot on the prestigious UK 'Tonight' programme tonight where he was interviewed by 'Rottweiler' Jeremy Paxton (on a bizarre set comprised of terminally uncomfortable chairs that I can only suppose were prescribed by the BBC producer in the hope of making Dawkins squirm. He didn't, although both Dawkins and Paxman in their suits looked like ragged crows confronting one another in a doctor's waiting room).

Dawkins gave an extremely good account of himself (even though Paxman pushed him hard - I think Paxman is sympathetic to Dawkins's views but you wouldn't know it by viewing this programme).I look forward to reading the book. It is interesting that in this year of the thirtieth anniversary of the publication of his great work, 'The Selfish Gene', he is focusing more on debunking the delusion of religion than on biology.

Good for Dawkins. It's time we stopped pussy-footing around the fantasies and delusions that provide the foundation for religion, and stand up for the truth - supernatural religion is an evolutionarily developed mechanism that helps humanity to cope with the hard aspects of life and particularly with death, but that has absolutely no basis in reality. It's time for us to grow up and give up our belief in fairy tales. The universe will seem colder and lonelier, but we can live prouder and more fulfilled lives if we accept the truth.

Vatican Evolution Debate Group

2006-09-04T23:06:00.000+01:00

Ratzinger organises an annual debate for his former theology students. This weekend the topic was evolution - why anyone, including Ratzinger, would think that a group of theologians should have anything interesting or of value to say about evolution is beyond me. Still, the press had speculated that the group might come down on the side of Intelligent Design (obviously Schönborn would have liked that) which would be a tragedy for the Church, reason and scholarship. Not much is known about the detail of what the theologians had to say about biology this weekend but apparently the minutes of the meeting will be published later this year. Don't expect any important scientific insights.

The press reports here, here, here and here seem to reach a consensus that the theolgians' conclusion was that evolution is a fact and not incompatible with Catholic theology provided it doesn't seek to explain God away as the Prime Mover. Well, science as a mode of knowing has nothing formal to say about the existence or non-existence of God, which topic is beyond its competence, so we can give them that (which is not to say that scientists should not use their knowledge of nature to reach the conclusion that God is unnecessary to explain the existence of the Universe and intelligent life within it, as many, convincingly, do). Maybe Catholicism, in spite of Schönborn's ill-advised foray into the debate on the side of ID, will remain a beacon of reason and a defender of science amongst increasingly fundamentalist and anti-science Christians. Now that would be cause for celebration.

Only Turkey lower than USA in accepting evolution

2006-08-31T21:44:00.000+01:00

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

2006-08-31T19:36:00.000+01:00

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

2006-08-22T20:21:00.000+01:00

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?

2006-08-20T23:29:00.000+01:00

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

2006-08-18T22:14:00.000+01:00

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

2006-08-16T20:46:00.000+01:00

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

2006-08-15T23:43:00.000+01:00

‘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

2006-08-08T22:15:00.000+01:00

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

2006-08-08T21:18:00.000+01:00

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

2006-08-08T01:07:00.000+01:00

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.

A blog for evolutionpages.com

2006-07-22T00:23:00.000+01:00

I'm going to publish an occasional blog linked to the evolutionpages.com website, with thoughts on evolutionary biology, cosmology, anthropology, religion and politics and anything else that takes my fancy.