Literature

Massimo Pigliucci goes on the offensive when he writes: "I have little patience for the pretense of a "fair and balanced view," when we all know that balance comes out of discussions and disagreements among peers, not from the point of view of a single individual". In this case, the individual is Michael Lynch, author of The Origins of Genome Architecture and Pigliucci is reviewing the book as one of his peers.
Lynch represents an 'evolved modern synthesis' position. He accepts that the modern synthesis needed developing: "One of the central theses of the book is that natural selection is not necessarily the central evolutionary mechanism, as quite a bit of the details of genomic structures and evolution can be accounted for by invoking the neutral mechanisms of mutation, recombination, and drift." With this framework, the explanatory tools are to hand and the remaining task is to use them to systematise the genetic information that we are able to gather. "Lynch's thesis [. . .] is that the theoretical apparatus of evolutionary theory is complete and that people should stop whining about missing pieces and the need for a new synthesis: just study your population genetics and everything will be all right."
Pigliucci presents this as a "rather uninspiring theme". Furthermore, "what the modern synthesis has not given us is a theory of form, and applying population genetics to genomics - as valuable an exercise as that is in its own right - isn't going to give us one either. As much as genes are fundamental to the evolutionary process, there is much more to biology than genes and their dynamics." This is interesting territory to explore, as readers of Why is a Fly not a Horse? will agree.
The review closes with this paragraph: "Ultimately, the main reason we need an expansion of the modern synthesis was pointed out by Popper several years ago: "[the Darwinian theory] is strictly a theory of genes, yet the phenomenon that has to be explained is that of the transmutation of form". Lynch's contribution in The Origins of Genome Architecture goes a long way toward completing our explanation of how genes (and genomes) change over time. Nonetheless, although indeed necessary, population genetics is not even close to sufficient for understanding how phenotypes evolve. There is much more to do, and a large undiscovered country lies out there. Let's take a look." This is the kind of emphasis that ID scientists welcome!

Postgenomic Musings
Massimo Pigliucci
Science 317, 31 August 2007, 1172-1173. DOI: 10.1126/science.1146047

Book Reviewed:
The Origins of Genome Architecture, by Michael Lynch
Sinauer Associates, Sunderland, MA, 2007. 510 pp. ISBN 9780878934843.

Everyone in biology keeps predicting that the next few years will bring answers to some of the major open questions in evolutionary biology, but there seems to be disagreement on what, exactly, those questions are. Enthusiasts of the various "-omics" (genomics, proteomics, transcriptomics, metabolomics, and even phenomics) believe, as Michael Lynch puts it in the final chapter of The Origins of Genome Architecture, that "we can be confident of two things: the basic theoretical machinery for understanding the evolutionary process is well established, and we will soon be effectively unlimited by the availability of information at the DNA level." [snip]

See also:

scordova, Michael Lynch: Darwinism is a caricature of evolutionary biology
Uncommon Descent, 1 September 2007

The cover story of today's Nature is concerned with the first unambiguous finding of fossilised orchid pollen. This is very exciting for evolutionary botanists, who have long been "fascinated by the spectacular adaptations to insect pollination exhibited by orchids".
The discovery involves an extinct worker stingless bee (Meliorchis caribea) preserved in Dominican amber that carries an orchid pollinarium (the male reproductive structure that is transferred as a single unit during pollination). The researchers have analysed the morphology of this structure and assign it to "the extant subtribe Goodyerinae (subfamily Orchidoideae)". This means that an essentially modern orchid was living at the time when the amber was formed (Miocene, considered to be 15-20 million years old). Thus far, there is little here for evolutionary biologists to work with, because the pollinarium does not reveal anything about origins - only that a modern orchid was also present in the Miocene.
In this case, evolutionary theory is imported in order to frame the find and to allow a transformist interpretation. "We use the ages of other fossil monocots and M. caribea to calibrate a molecular phylogenetic tree of the Orchidaceae. Our results indicate that the most recent common ancestor of extant orchids lived in the Late Cretaceous (76-84 Myr ago), and [. . .] support the hypothesis of an ancient origin for Orchidaceae." The report by Ledford adds: "To investigate, the team used genetic information from 55 genera of living orchids to make a family tree, determining which plants are most related to each other today and then working backwards to see when they probably split apart. By dating the amber of their new fossil find to 15-20 million years ago, they could then start to put dates onto the various branches of this tree." The Late Cretaceous age was arrived at by "assuming a relatively constant rate of orchid evolution".
It is important to realise that that these conclusions have not emerged naturally from the empirical data, but are the product of an evolutionary framework adopted by the researchers. With different assumptions and a different methodology, it should not be deemed surprising if the same data can lead to contrasting conclusions. However, on the basis that the "rate of orchid evolution" exhibited by the subtribe Goodyerinae is almost zero, the comment of the lead author is probably correct: "The dinosaurs could have walked among orchids".

Dating the origin of the Orchidaceae from a fossil orchid with its pollinator
Santiago R. Ramirez, Barbara Gravendeel, Rodrigo B. Singer, Charles R. Marshall and Naomi E. Pierce
Nature 448, 1042-1045 (30 August 2007) | doi:10.1038/nature06039

Since the time of Darwin1, evolutionary biologists have been fascinated by the spectacular adaptations to insect pollination exhibited by orchids. However, despite being the most diverse plant family on Earth2, the Orchidaceae lack a definitive fossil record and thus many aspects of their evolutionary history remain obscure. Here we report an exquisitely preserved orchid pollinarium (of Meliorchis caribea gen. et sp. nov.) attached to the mesoscutellum of an extinct stingless bee, Proplebeia dominicana, recovered from Miocene amber in the Dominican Republic, that is 15-20 million years (Myr) old3. This discovery constitutes both the first unambiguous fossil of Orchidaceae4 and an unprecedented direct fossil observation of a plant-pollinator interaction5, 6. By applying cladistic methods to a morphological character matrix, we resolve the phylogenetic position of M. caribea within the extant subtribe Goodyerinae (subfamily Orchidoideae). We use the ages of other fossil monocots and M. caribea to calibrate a molecular phylogenetic tree of the Orchidaceae. Our results indicate that the most recent common ancestor of extant orchids lived in the Late Cretaceous (76-84 Myr ago), and also suggest that the dramatic radiation of orchids began shortly after the mass extinctions at the K/T boundary. These results further support the hypothesis of an ancient origin for Orchidaceae.

See also:

Ledford, H. Amber preserves rare orchid pollen,
news@nature.com: 29 August 2007; | doi:10.1038/news070827-4

Here's some good holiday reading - at least this proved to be the case for me!
According to some contemporary Earth scientists, "Kelvin's famous calculations, coupled with denial of observational data, impeded geoscience for ~100 yr." They are referring, of course, to Lord Kelvin"s 1863 calculations of the age of the Earth, based on mathematical modeling of Earth cooling and direct measurements of thermal gradients. As a physicist, Kelvin sought to develop quantitative, rather than qualitative, science and he found himself in conflict with geologists who wanted an Earth with "no vestige of a beginning". Kelvin"s estimate of 24-400 million years was a thorn in their side for over 40 years. The story that has been passed down to modern-day students of Earth history is that Kelvin had overlooked the possibility of another heat source - that of radioactive decay - which was not discovered until 1903. Then, Kelvin was proved wrong and the geologists claimed victory!
Describing this aa a modern myth, England et al. have provided a splendid service to the Earth science community in putting the record straight. They rework the calculations of Kelvin and demonstrate their coherence and rational basis. They also repeat the calculations to incorporate a radiogenic heat energy component, showing that Kelvin's conclusions are unaffected. "Thus, the discovery of radioactivity did not invalidate Kelvin's calculation for the age of the Earth."
How then did the myth come about and why did it persist? The authors suggest two reasons. The first is that the myth was a "good story" for the geologists, convenient for reinforcing the idea that geophysics must be the servant, not the master, of geology. (In another context, we have met the "good story" justification before). The second is the personal influence of Lord Rutherford, who had a humorous anecdote to tell of his encounters with Kelvin. The authors have an astute comment on the way established researchers can promote opinion as science: "It is hard to dissuade aging scientists, as they slip into their anecdotage, from repeating stories that they find amusing, but their younger colleagues must not mistake such stories for the history of science."
The main thrust of England et al's excellent article is that Kelvin's argument was addressed in 1895 by John Perry, who suggested a different physical model for the interior of the Earth. "Instead of focusing on Kelvin's calculations, Perry suggested, one should examine his assumptions." Perry's revised model introduced the concept of convection, which was at that time controversial, because the Earth was considered a solid. However, although Perry did have a valid response to Kelvin, which did allow the Earth to have an age of several billion years, it was not received with approval. This is because the geologists of the day, like Kelvin, also held to a solid Earth. "If Perry's analysis had been absorbed by the scientific community of the day, then the first radiometric ages for the Earth would have come as confirmation of the convective explanation for the Earth's surface heat flux, and the "fixist" view of the Earth, which exerted such a brake on geological progress in the first half of the twentieth century, would have been difficult to sustain."
In one sense, Kelvin's challenge to the geological community was successful. Whereas previously they thought they could invoke as much time as they wanted (drawing on Hutton's view of the cycle of time), the geologists were forced to come to terms with time's arrow and a beginning for Earth history. For this achievement, Kelvin ought to be held in esteem by students of geology, and not dismissed. Paradoxically, the geologists and Kelvin now emerge as both victors and losers!
This controversy illustrates very well the importance of paradigms in science. Kelvin and the geologists held to a fixist Earth; eventually, Perry's concept of convection came to be adopted; and radioactive decay brought significant changes to our understanding of the Earth. We all work with mental models or paradigms, and science can easily become an exercise in finding ways of making available data fit the particular model we are working with. Far better to operate with multiple working hypotheses, so that alternative paradigms can be tested and potentially falsified. This strategy applies just as much to biology as it does to geology. This is where ID should be seen as a stimulus to good science, facilitating the methodology of testing and falsifying paradigms. The real dangers we face today are the dogmatists in science who refuse to allow their own paradigms to be critically appraised.

John Perry's neglected critique of Kelvin's age for the Earth: A missed opportunity in geodynamics
Philip England, Peter Molnar, Frank Richter
GSA Today, January 2007, 17(1), 4-9.

Abstract: Many readers know the tale of how William Thomson (later Lord Kelvin) calculated the age of the Earth from physical principles and adhered for over 50 years to an estimate that was far younger than geologists' estimates, despite the virtually unanimous opposition of the geological community of the time. The prevalent version of this tale alleges that the discovery of radioactivity simultaneously provided the demonstration (through radiometric dating) that Kelvin had greatly underestimated the age of the Earth and the explanation of why he was wrong (radioactivity being a source of heat that invalidated Kelvin's calculation). We show this popular story to be incorrect; introducing the known distribution of radioactivity into Kelvin's calculation does not invalidate its conclusion. In 1895, before the discovery of radioactivity, John Perry showed that convection in the Earth's interior would invalidate Kelvin's estimate for the age of the Earth, but Perry's analysis was neglected or forgotten, with the consequence that a powerful argument in favor of mobilism was overlooked during the first few decades of debate about continental drift.

See also:

COMMENT by Anne M. Hofmeister, Robert E. Criss
REPLY by Philip England, Peter Molnar, Frank Richter
GSA Today, July 2007, 17(7), 10-11.

Lord Kelvin's Core Values Defended, by David Coppedge, 2 July 2007.

The quest for a plausible scenario for tetrapod evolution continues. Contrary to much popular (and some technical) literature, we have not yet arrived. A new fossil find promises to stimulate a fresh debate about the contribution the Coelacanth makes to our thinking.
The new fossil reveals, for the first time, the pectoral fin endoskeleton. Significantly, it is not like the modern form. "The most conspicuous feature of Shoshonia is its broad, fanshaped pectoral fin supported by a central lobe [. . . This] differs from the near-symmetrical finweb common to the living coelacanth Latimeria and lungfishes and their closest extinct relatives." One of the co-authors said that the fossil's pattern is similar to the branching arrangement still embedded in the fins of paddlefishes, sturgeons and sharks. "To understand the developmental evolution of the limbs of tetrapods, we shouldn't be looking at the fins of our nearest living fish relatives - lungfishes and coelacanths - because they're far too specialized."
The find is significant for consigning an extensive discussion of coelacanth and lungfish fins to the filing cabinet of history. The main author is quoted as saying: "Our fossil shows that what we've been using to define a primitive state is actually very specialized, which means it might give a deceptive view of what evolution was like for these fins skeletons."
Previous discussion drew attention to significant similarities of coelacanth and lungfish fins, and this was considered to give confidence in the validity of the argument. The new fossil turns that upside down also. "The discovery suggests that the two living groups of close fish relatives of tetrapods (lungfish and coelacanth) are both highly specialized [. . .]. Both groups acquired many of the same specializations, but independently of one another." Convergent evolution of derived characters replaces shared primitive traits. Such is the vulnerability of the account of tetrapod evolution that many have regarded as plausible!
What can be said about the similarities with paddlefins, sturgeons and sharks? "With this fossil, we have a conservative pattern in a close relative of tetrapods that is actually conserved in other fish groups outside of this immediate group." Where this will lead is not at all clear. The words in the title of the paper, that the discovery "fills a major gap" might suggest to some that the evolutionary trajectory has been clarified. But the content of the paper says: 'back to the drawing board'!

First discovery of a primitive coelacanth fin fills a major gap in the evolution of lobed fins and limbs
Matt Friedman, Michael I. Coates, Philip Anderson
Evolution & Development, 9(4), 329-337 | doi:10.1111/j.1525-142X.2007.00169.x

SUMMARY: The fossil record provides unique clues about the primitive pattern of lobed fins, the precursors of digit-bearing limbs. Such information is vital for understanding the evolutionary transition from fish fins to tetrapod limbs, and it guides the choice of model systems for investigating the developmental changes underpinning this event. However, the evolutionary preconditions for tetrapod limbs remain unclear. This uncertainty arises from an outstanding gap in our knowledge of early lobed fins: there are no fossil data that record primitive pectoral fin conditions in coelacanths, one of the three major groups of sarcopterygian (lobe-finned) fishes. A new fossil from the Middle-Late Devonian of Wyoming preserves the first and only example of a primitive coelacanth pectoral fin endoskeleton. The strongly asymmetrical skeleton of this fin corroborates the hypothesis that this is the primitive sarcopterygian pattern, and that this pattern persisted in the closest fish-like relatives of land vertebrates. The new material reveals the specializations of paired fins in the modern coelacanth, as well as in living lungfishes. Consequently, the context in which these might be used to investigate evolutionary and developmental relationships between vertebrate fins and limbs is changed. Our data suggest that primitive actinopterygians, rather than living sarcopterygian fishes and their derived appendages, are the most informative comparators for developmental studies seeking to understand the origin of tetrapod limbs.

See also:

Coelacanth Fossil Sheds Light On Fin-to-limb Evolution, Science Daily, August 1, 2007

Flagged up as an "Opinion" paper, the contribution of Forrest and Gross to Trends in Biochemical Sciences cannot be accused of sailing under false colours. Here is opinion in abundance. There is opinion about Michael Behe (notably, his "evasion of the evidential responsibilities of his profession"), William Dembski ("No Free Lunch was, and is, a failed argument"), the ID Movement (characterised by "scientific sterility" and "propelled by powerful cultural and political currents"). There is also opinion about Behe's critics (identified as "competent hands" that have provided "solid refutations"), the Kitzmiller trial (with ID's "deserved legal defeat") and the 'Teach the Controversy' campaign (a "clever marketing ploy").
Academic content of this paper is provided by citing recent objections that have been made to Behe's irreducible complexity arguments. As might be expected from this "Opinion" paper, these arguments are presented as knockdown and final - as though nothing more needs be said! It might be worth reminding ourselves that this just repeats the story of the past 10 years.
I will pick up just one point made in the following quotation. "The ID movement's antipathy to the Enlightenment is understandable: critical inquiry, the central legacy of the Enlightenment, threatens the pre-modern intellectual and religious authoritarianism that the creationists would reinstate." Let it be said that critical enquiry is not the exclusive legacy of the Enlightenment. That emphasis comes from the founders of science in the 17th Century and it is highly prized by ID advocates. This emphasis is much needed today, because Darwinism and the Modern Synthesis appear to be protected from critical scrutiny in schools and colleges. The distinctive legacy of the Enlightenment is rationalism. It is the elevation of reason to create a secular authoritarianism that has managed to establish a stranglehold on the academic community so that any dissenters are deemed to be betrayers of the cause. This paper, sad to say, epitomises the hegemony of the Enlightenment as the authors try to portray dissent from their rationalist ideology as an attack on science.

Biochemistry by design
Barbara C. Forrest and Paul R. Gross
Trends in Biochemical Sciences, Volume 32, Issue 7, July 2007, Pages 301-310

Abstract: Creationists are attempting to use biochemistry to win acceptance for their doctrine in the public mind and especially in state-funded schools. Biochemist Michael Behe is a major figure in this effort. His contention that certain cellular structures and biochemical processes - bacterial flagella, the blood-clotting cascade and the vertebrate immune system - cannot be the products of evolution has generated vigorous opposition from fellow scientists, many of whom have refuted Behe's claims. Yet, despite these refutations and a decisive defeat in a US federal court case, Behe and his associates at the Discovery Institute continue to cultivate American supporters. They are also stepping up their efforts abroad and, worryingly, have achieved some success. Should biochemists (and other scientists) be concerned? We think they should be.