Science Literature

In a recently-published book, Eric Davidson, “the world's leading expert” in the field of evo-devo, offers his perspective “on the gene regulatory networks that control animal development”. The book is significant because Davidson “proposes a scenario to explain how these distinct types of network subcircuits have emerged in animal evolution.”

The complexity of the gene networks is well known. “These networks consist of huge sets of regulatory genes that control one another's expression as well as the expression of downstream effector genes via so-called cis-regulatory elements (to which the transcription factors bind).” The reviewer comments appreciatively on the way Davidson describes the genetic control of development in living animals: “In essence, through a stepwise process, development subdivides the embryo into territories, subterritories, and "progenitor fields" that make up a given body part of the adult animal. This stepwise subdivision is accomplished by gene regulatory network subroutines called subcircuits that consist of small sets of genes and cis-regulatory elements.” Something of this complexity can be appreciated by reference to the figure that accompanies the review.

“The final chapter, on the evolution of gene regulatory networks, is the most speculative and most stimulating. Here, Davidson outlines a possible evolutionary origin of kernels …”. The reviewer refers to three stages of evolution. “In a third stage … , the animal body parts and, concomitantly, the territorial subdivision of the developing embryo became more and more elaborate until finally the underlying subcircuits were locked down into kernels that could no longer be changed without deleterious consequences. According to Davidson, this "triumph of the bilaterian versions of animal body plans" was in place sometime before the Cambrian and has persisted, constraining metazoan evolution ever since with tremendous success.”

The concept being developed here can be related to irreducible complexity (although Davidson clearly thinks these IC systems can be constructed by evolutionary processes). The “kernel” is a term drawn from information science, referring to the core of an operating system. When these kernels were in place, they could no longer be modified by evolutionary processes, because any change was deleterious and was not preserved.

We thus have the developmental architectures of animals in place sometime before the Cambrian. This is a scenario that is discussed in that much denigrated paper by Steve Meyer (“The Origin of Biological Information and the Higher Taxonomic Categories” Proceedings of the Biological Society of Washington 117(2004):213-239.). Meyer writes: “Can neo-Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion--either in the form of new genetic information or in the form of hierarchically organized systems of parts?” Davidson’s book undoubtedly puts more substance into the argument, spelling out some essential elements of the complexity that has to be in place for the Cambrian Explosion.

The reviewer continues: “The proposed link between the evolution of kernels and the evolution of bilaterian body plans is exciting, but it awaits validation through more comparative analyses of gene networks. As Davidson himself concedes, "for the identification of kernels … an overwhelming feature of the evidence thus far is its thinness."” This seems to be a realistic assessment of the state of knowledge. There is also the significant absence of ancestors of the Cambrian animals, despite continuing discoveries about the Ediacaran fauna. But it seems to me that the convergence between the thinking of Davidson and Meyer is such that it gives strength to the argument of Meyer’s 2004 paper. I wonder if others see the situation like this?

A Kernel Bears Fruit
Detlev Arendt
Science 314, 17 November 2006: 1085-1086.

A review of: "The Regulatory Genome. Gene Regulatory Networks in Development and Evolution" by Eric H. Davidson, Academic Press (Elsevier), Burlington, MA, 2006.

This review of Paul Davies’ latest book will raise a few eyebrows. Some will think that Davies has abandoned science. Others will express their puzzlement why Davies cannot make a Design Inference. Earlier this week, I was reading Alvin Plantinga on the twin pillars of Christian Scholarship. He identifies three main contestants in the contemporary intellectual world: Christianity, Perennial Naturalism and Creative Anti-realism. The latter finds expression in Kant, Wittgenstein, existentialism, relativism and post-modernism. The reviewer's description of Davies' "more interesting" idea fits neatly into this approach. How curious to find Davies avoiding ID only to end up in the Creative Anti-realist camp!

Books and Arts: Life in the universal porridge
What were the chances that the conditions in the Universe would be just right for life?
Jim Al-Khalili reviews The Goldilocks Enigma: Why Is the Universe Just Right for Life? by Paul Davies
Nature 444, 423 (23 November 2006) | doi:10.1038/444423a

Selected excerpts:
"Davies’ first suggestion is that the ‘biofriendliness' of the Universe may be due to some as yet undiscovered 'life principle: built into the laws of physics from the very beginning, that has steered and constrained the Universe towards producing life. I find this idea hard to swallow and I don't think Davies dwells on it long enough to really make a convincing case.
"He then invites us to consider a more interesting - I hesitate to endorse it with the term 'appealing' - idea originally expounded by physicist John Wheeler. It takes one of the weirdest features of quantum mechanics and pushes it to its logical conclusion: that conscious observers bring about the universe they find themselves in by the very act of observing it, thereby dragging it out of the quantum superposition of all possible paths it could have followed. Actually, I think this is related to what supporters of the Multiverse version of quantum mechanics would argue -with the difference that, for Davies, our universe is the only one.
"The main options, then, are: first, that the Universe is a fluke; second, that it is one of many and happens to be, much like Goldilocks' porridge, just right for us; and third, that conscious observers bring the universe they inhabit into existence simply by observing it, although their teleological actions would have to reach back into the past, forcing the right conditions to be selected at the Big Bang."

The received wisdom that the “DNA of any two humans is 99.9% similar in content and identity” appears not to be true. "One of the real surprises of these results was just how much of our DNA varies in copy number. We estimate this to be at least 12% of the genome.” "The copy number variation that researchers had seen before was simply the tip of the iceberg, while the bulk lay submerged, undetected. We now appreciate the immense contribution of this phenomenon to genetic differences between individuals."
This raises numerous questions about methodology and those embedded assumptions that are usually completely hidden to those outside the research community. A rethink appears to be needed in two areas:
1. The much heralded claim that human genome is only 3% different from the Chimpanzee. Do we now infer that some of the human population are much closer to Chimps than others? Of course not! Something else of significance is going on here.
2. The concept that the human genome can be documented, with all the variants treated as random mutations. The indication is rather that the genome is much more dynamic than this, and that most of the variations are not random mutations at all. A design perspective has great potential to stimulate new hypotheses.

Global variation in copy number in the human genome
Richard Redon, et al.
Nature 444, 444-454 (23 November 2006) | doi:10.1038/nature05329

Abstract: Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

See also: Shianna, K.V. and Willard, H.F., Human genomics: In search of normality, Nature 444, 428 (23 November 2006) | doi:10.1038/444428a

The biodiversity of marine species since the Cambrian shows significant differences before and after the Permian extinction event. In his commentary, Kiessling writes: “The big surprise in their analysis is a major difference between Paleozoic … and younger communities. In older assemblages, complex and simple distributions are about equally common, but complexly structured assemblages are substantially more common in more recent times. With so many paleobiologists looking at local, regional, and global diversity patterns through time, how could this striking pattern have escaped our attention for so long?”

Maybe because "evolution" rather than "ecology" has been the guiding word? It is increasingly apparent that environmental factors have been a major driver in understanding the pattern of fossils in different strata. The focus needs to shift from viewing the past through “evolutionary” spectacles.

Discussion within the ID community has drawn a parallel between the Cambrian explosion and the post-Permian radiations. In the latter, huge opportunities were present for the evolution of new phyla/body plans, yet what we see are not new phyla but radiations and complex ecosystems. Why the difference with the Cambrian Explosion? Is this yet another case of Darwinism failing to correlate well with the evidence?

Abundance Distributions Imply Elevated Complexity of Post-Paleozoic Marine Ecosystems
Peter J. Wagner, Matthew A. Kosnik, and Scott Lidgard
Science 314, 24 November 2006: 1289-1292.

Abstract: Likelihood analyses of 1176 fossil assemblages of marine organisms from Phanerozoic (i.e., Cambrian to Recent) assemblages indicate a shift in typical relative-abundance distributions after the Paleozoic. Ecological theory associated with these abundance distributions implies that complex ecosystems are far more common among Meso-Cenozoic assemblages than among the Paleozoic assemblages that preceded them. This transition coincides not with any major change in the way fossils are preserved or collected but with a shift from communities dominated by sessile epifaunal suspension feeders to communities with elevated diversities of mobile and infaunal taxa. This suggests that the end-Permian extinction permanently altered prevailing marine ecosystem structure and precipitated high levels of ecological complexity and alpha diversity in the Meso-Cenozoic.

See also: Kiessling, K. Life's Complexity Cast in Stone, Science 314, 24 November 2006: 1254-1255.

The thoracic musculature of insects that enables very high wing beat frequencies is described as “striking”. At a molecular level, a series of interrelated characteristics are required, including: “the highest measured detachment rate of myosin from actin”, “an exceptionally weak affinity of MgATP for myosin” and “a unique rate-limiting step in the cross-bridge cycle at the point of inorganic phosphate release.” Although this paper is written from an evolutionary perspective, the authors are continually flagging up design issues at the molecular level. The properties of the materials used to power flight are remarkable.

An exceptionally fast actomyosin reaction powers insect flight muscle
Douglas M. Swank, Vivek K. Vishnudas and David W. Maughan
Proc. Natl. Acad. Sci. USA. November 14, 2006, vol. 103, no. 46, 17543-17547 | doi:10.1073/pnas.0604972103.

Insects, as a group, have been remarkably successful in adapting to a great range of physical and biological environments, in large part because of their ability to fly. The evolution of flight in small insects was accompanied by striking adaptations of the thoracic musculature that enabled very high wing beat frequencies. At the cellular and protein filament level, a stretch activation mechanism evolved that allowed high-oscillatory work to be achieved at very high frequencies as contraction and nerve stimulus became asynchronous. At the molecular level, critical adaptations occurred within the motor protein myosin II, because its elementary interactions with actin set the speed of sarcomere contraction. Here, we show that the key myosin enzymatic adaptations required for powering the very fast flight muscles in the fruit fly Drosophila melanogaster include the highest measured detachment rate of myosin from actin (forward rate constant, 3,698 s-1), an exceptionally weak affinity of MgATP for myosin (association constant, 0.2 mM-1), and a unique rate-limiting step in the cross-bridge cycle at the point of inorganic phosphate release. The latter adaptations are constraints imposed by the overriding requirement for exceptionally fast release of the hydrolytic product MgADP. Otherwise, as in Drosophila embryonic muscle and other slow muscle types, a step associated with MgADP release limits muscle contraction speed by delaying the detachment of myosin from actin.

For further reading: Myosin's need for speed, JCB, 2006. 175(4), 519. | doi:10.1083/jcb.1754rr3
http://www.jcb.org/cgi/content/full/175/4/519b

Research into taste has not been as extensive as that for sight and hearing. This ‘state of the art’ paper provides a fascinating read, and the “emerging picture of taste coding at the periphery is one of elegant simplicity”. There are unique receptors tuned to detect each of the five basic tastes. These are linked in with other inputs to taste and fed to the brain for neural activity to provide the final orchestration of “positive hedonic value and behavioural acceptance”. All this, according to the authors, is an accommodation to an “evolutionary need.” The paper gives no evidence that this is actually the case. Unspecified hypothetial evolutionary needs are invoked as ‘context’ for the research, but ‘design’ can also provide ‘context’. What is lacking in this paper is a discussion as to why “evolutionary need” should be preferred over “design”.

The receptors and cells for mammalian taste
Jayaram Chandrashekar, Mark A. Hoon, Nicholas J. P. Ryba and Charles S. Zuker
Nature 444, 288-294 (16 November 2006) | doi:10.1038/nature05401

Abstract: The emerging picture of taste coding at the periphery is one of elegant simplicity. Contrary to what was generally believed, it is now clear that distinct cell types expressing unique receptors are tuned to detect each of the five basic tastes: sweet, sour, bitter, salty and umami. Importantly, receptor cells for each taste quality function as dedicated sensors wired to elicit stereotypic responses.

For further reading: Bradbury J (2004) Taste Perception: Cracking the Code. PLoS Biol 2(3): e64
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020064

Non-biting midges reveal not only insects that are similar to those today, but also ecosystem stability in the Caribbean from the Miocene until today. These new results are part of a less-appreciated characteristic of the fossil record: that stasis is widespread and deserves a much higher profile in our scientific thinking.

Chironomidae (Diptera) in Dominican amber as indicators for ecosystem stability in the Caribbean
Martin Grund
Palaeogeography, Palaeoclimatology, Palaeoecology, 241(3-4), 14 November 2006, 410-416.

Abstract: A first overview on fossil chironomids in Dominican amber is given. This fossil assemblage seems to represent an insular fauna, very similar to its living relatives. Stenochironomus sp. and especially the true xylophagous, neotropical/southern North American Xestochironomus spp. prove the persistence of submerged dead wood in nutrient poor mountain streams in the Greater Antilles from the Miocene until today. Their abundance indicates that the special ecological conditions in extant Caribbean tropical mountain streams already ruled the ancient ecosystem. The results arising from the fossils of these freshwater organisms do not coincide with the faunal changes shown by other groups of insects. General systematic descriptions of new fossil representatives of Xestochironomus and Stenochironomus are given.

Genetic information: Codes and enigmas
There's more than one way to read a stretch of DNA, finds Helen Pearson — and we need to understand them all.
Nature 444, 259-261 (16 November 2006) | doi:10.1038/444259a

Computer buffs interested in cracking codes have developed software routines to prise out hidden information. “We are treating DNA as we used to treat problems in intelligence” [Shepherd] says. “We want to break the code at the most fundamental level.”

This is the first point where an ID perspective will help research. “Breaking the code” cannot be reduced to an exercise in computer science. We need to recognise the biological context for the DNA operation and to treat the whole cell as a complex system. This will lead to a systems engineering methodology for analysis.

A highly significant paragraph is as follows:
“DNA seems well adapted for supporting a number of codes. For a start, only 1-2% of the human genome is occupied with protein-coding sequences, which leaves plenty of intervening DNA to hold other information. But many stretches of DNA in humans and other organisms manage to multitask: a sequence can code for a protein and still manage to guide the position of a nucleosome. This is possible because the triplet code is ‘degenerate’. Several slightly different triplets can code for the same amino acid, and many positions in a protein can be filled by different amino acids – so different sequences can effectively mean the same thing. This allows other signals to be imprinted on top of the first – especially when those other signals are themselves encoded with some slack.”

Multitasking is something we typically associate with intelligence. Getting a code to convey one message is a challenge in itself, but getting the same code to carry several messages is evidence of higher level intelligent agency. ID helps here, allowing the premise that the ‘degenerate’ aspects of the triplet code are actually designed to permit sophisticated encoding.

The writer, however, goes on to make an extraordinary comment on this. “This elegance is surely the handiwork of evolution – and if the way in which that hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier.”

It is extraordinary because of the word “surely”. Why “surely”? Not because of the sophisticated design features! Not because the whole thing is “elegant”! I can only think that the word “surely” is deductive: because “we know” that Darwinism is true. The same rationale is behind this comment that appears earlier in the article: “Biology has probably figured out a way to squeeze every bit of information from that molecule it can”.

There is no empirical base for suggesting that these design features can emerge from evolutionary processes. Our recognition of them as a phenomenon comes only because we have met them before in intelligently designed digital information.

That sentence should read: “This elegance is surely the handiwork of an Intelligent Designer – and if the way in which His hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier.”

One further point on the use of anthropomorphic language. Examples already cited are:
“Biology has probably figured out a way to squeeze every bit of information from that molecule it can”.
“This elegance is surely the handiwork of evolution”
“the way in which that hand had worked to solve these problems”

In each case, we have intelligent agency attributed to the mechanistic processes of evolution. As Dembski’s design filter shows, these mechanisms give us law-like and chance-like characteristics, but these are distinct from design-like characteristics. Although the evolutionary paradigm dies not permit intelligent agency, those within its mould have to resort to anthropomorphisms to develop their ideas. Sad. That's perhaps the biggest "enigma" in this essay.

Nature 444, 243-244 (16 November 2006) | doi:10.1038/444243b; Published online 15 November 2006

Order for microbes
Abstract

Burgeoning microbial gene data require coherent efforts to make them readily usable.

Microbes don't subscribe to the single life. They are coupled with complex ecosystems of diverse, mutually dependent species. This complexity and the vast numbers of microbes in the ocean, the soil, in our gut and almost everywhere else pose a challenge to those seeking to understand microbial ecology.

In the 1980s, surveying the microbial world by sequencing the collective ribosomal RNA opened up new avenues. For the first time it was possible to get a glimpse of the make-up of complex microbial systems. It's a reasonable assumption that the more similar these sequences are, the more closely related the microbes are, and the more closely related their lifestyles must be - hence the pursuit of insights into what microbes might be doing in their environments.

But this assumption turned out to be fragile, as it emerged that microbes frequently shuffle around their genes both within and between species. A similarity in one gene does not necessarily correlate with the absence or presence of other genes in the genome.

Fortunately, the continuous decrease in sequencing costs allows today's microbiologists to sequence not only a single gene from each of the most abundant species in a microbial ecosystem, but also, at least in theory, all the genes present. These composite genomes, or 'metagenomes', provide a wealth of information that could only be dreamt of even a couple of years ago. With sequencing facilities continuing to increase their capacities by applying new technologies, and funding agencies supplying the necessary resources, sequencing the ocean or the contents of the human gut has become relatively easy. But how to extract meaningful information from a metagenome, and to gain insight into both the individual species' impact on the microbial community and the impact of this community on the ecosystem?

We can hope to unravel the function of every gene when individual species can be cultivated and genetically manipulated in the laboratory, but this is impossible when dealing with a complex community containing hundreds or thousands of species. Functional assignment of genes needs to be performed, even when the only information available is a string of nucleotide bases.

There are numerous databases and websites, public and not-so-public, some adhering to an easily understandable framework of standards and regulation, and some not so transparent. Five years ago it was a big disappointment to compare one's chosen sequence with the GenBank database and not find a 'hit'. Today there is a feeling of sheer inadequacy in the face of vast quantities of sequence and annotation information - and an acute need for a degree in bioinformatics.

Publication in most cases (including the Nature journals) requires the deposition of sequence data into the GenBank or EMBL databases. Much less effort is spent depositing unpublished data or updating information that is already published. In all probability, in the not too distant future, metagenomic studies will be done not only by the big sequencing centres, but by anybody with a reasonable research budget and university support. To make all the data more easily accessible, it would be desirable to have a collaborative effort of genome centres and funding agencies to build a universal microbial-sequence database, with a readily comprehensible framework for sequencing and annotation standards and regulations.

Microbiology has come a long way from investigating the easily cultured individual microbe from a rich microbial community and describing what is out there, and is now starting to get a grip on what they actually do. With the intrinsic difficulties of dealing with complex systems, it is good to see a field galvanized by new technologies and scientific daring. But more infrastructural order is required, to prevent the discipline getting ahead of itself.