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.