Ratzinger and Dylan

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

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

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

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

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

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

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

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

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'?

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.