Posted: Mar 05, 2011 1:25 am
With respect to the first of those "quotes" (how propagandists for creationism love their quotes, or should that be quote mines?) ...
Let's take a look at the actual paper, shall we? Namely:
Dynamical Patterning Modules: Physico-Genetic Determinants Of Morphological Development And Evolution by Stewart A. Newman and Ramray Bhat, Physical Biology, 5: 1-15 (9th April 2008) [Full paper downloadable from here]
Oh look. What the authors of this paper are saying, is that one specific hypothesis about the origin of body plans is falsified by their results. However, even from the abstract, it is clear to me that they might not understand as much about the Modern Synthesis as they think, because last time I checked the relevant scientific papers, phenotypic diversity was considered by evolutionary biologists to be a product of genotypic change, not something that occurred "in advance" thereof. Methinks once again, that hyperbolic claims about the Modern Synthesis being "in crisis" are woefully premature.
Plus, the authors explicitly state in the above abstract, that natural selection and genetic drift, which are both integral parts of the Modern Synthesis, would have consolidated the products of their process, and consequently, they are not "casting doubt upon the Neo-Darwinian orthodoxy", rather, they are extending the remit of the Modern Synthesis by adding a new process to the mix. There is a difference, though I don't expect propagandists for mythology to understand this.
One tell tale paragraph from that paper underpins the authors' lack of understanding about what the Modern Synthesis actually says, which makes me wonder how it passed peer review without editing changes being suggested - so much for the "conspiracy to enforce Darwinism". The paragraph in question is this:
First of all, the assertion "a fairly straightforward relationship between genotypic and phenotypic change is assumed" is plain, flat wrong, as anyone who has been reading papers in evolutionary developmental biology (evo-devo for short) will readily understand. The research literature in evo-devo is littered with instances of complex chains of signal transduction mechanisms being elucidated, and workers in the field have known for at least two decades to my knowledge, and possibly even longer, that "a fairly straightforward relationship between genotypic and phenotypic change" is NOT what the hard evidence from reality is delivering. Which once again makes me wonder how this paper passed peer review.
As for the assertion "Morphological evolution should therefore be gradual [according to the Modern Synthesis], rather than abrupt", this once again smells highly suspicious, not least because instances of major evolutionary change taking place in relatively short time frames are extant and voluminous in the evolutionary biology literature. This includes experiments on incipient speciation, which in the case of Dobzhansky's 1971 paper on Drosophila pseudoobscura, took place in just five years. Now, since the Cambrian radiation is hypothesised in the literature to have taken a good deal longer than five years, indeed, one paper in my collection cites a time span of 18 to 23 million years for this process, first of all, the idea that this was an "abrupt" process is at best a naive simplification, and at worst an outright canard, one that should not be appearing in a proper scientific paper. If I had reviewed this paper, I would have sent it back with a raft of corrections just for this one paragraph alone.
Then we have the following paragraph, namely:
First of all, the part highlighted in blue above directly contradicts their assertion at the end of the abstract, which again is a sign of sloppy, non-rigorous thinking, and once again leads me to wonder how this paper passed peer review without being sent back for a serious re-write. Second, the assertion highlighted in green was never a part of the Modern Synthesis. Indeed, the Modern Synthesis never erected assertions about the relationship between genotype and phenotpye, because, wait for it, this is an active area of research for evo-devo researchers. They are in the business of determining the real mechanisms that connect genotype to phenotype, courtesy of empirical research, about which I shall say more that is relevant in a moment. Because, wait for it, the part highlighted in red cites a research paper by Walter J. Gehrig that is intimately connected with a research paper in my collection on eye evolution, that, like every other paper of the same variety, never erected the assertion highlighted in green above. Indeed, conservation of bauplan genes is one of the extant hypotheses of the Modern Synthesis, and how the authors of this paper could have failed to know this escapes me at this juncture.
So already, this paper contains some serious deficiencies that even an elementary literature search would have remedied. Perhaps they were so keen to rush their findings to print, that they failed to apply due rigour to some of their more florid speculations.
The next paragraph is also instructive, viz:
First, the part highlighted in blue testifies to the fact that the authors appear not to have read much, if any, of the extant evo-devo literature. Because, as I've stated above, that literature contains papers documenting empirical research aimed at elucidating the underlying mechanisms. What do the authors of this paper think that evo-devo biologists are doing, sitting in the rest room playing poker?
Second, the part highlighted in green is already being investigated in the evo-devo literature. The hilarious part being that the authors of this paper cite relevant works in the literature in their list of citations at the end of the paper, yet apparently do not recognise that these prior papers are documenting precisely the sort of research into epigenetic mechanisms that they claim here to be advancing. Anyone who thinks that research into epigenetics has nothing to do with evolutionary biology really does need to sit down with a couple of dozen papers and learn otherwise. Indeed, the authors of this paper make several references to such processes as signal transduction (which is a classic epigenetic process) and Turing morphogenesis, which again is a staple part of evo-devo research - I have enough papers on Turing morphogenesis in butterflies alone telling me this, let alone any other clade of organisms.
So, how does this paper "cast doubt" upon the Modern Synthesis again, given that it merely explores a research area that is already a part of evo-devo research?
Ramray Bhat:
...we have the first really coherent framework to explain the origination and evolution of body plans and organ forms within a short evolutionary period, known as the Cambrian explosion.
...This framework also solves the Molecular Homology-Analogy paradox - why same/similar sets of genes are employed to build functionally or structurally similar organ forms in widely divergent organisms.
All of these are inconsistent with and cannot be explained by the classical neo-Darwinian model. We accommodate the role of natural selection in our framework mainly to lock the already-emerged but immensely plastic forms into place, and to render them robust
Let's take a look at the actual paper, shall we? Namely:
Dynamical Patterning Modules: Physico-Genetic Determinants Of Morphological Development And Evolution by Stewart A. Newman and Ramray Bhat, Physical Biology, 5: 1-15 (9th April 2008) [Full paper downloadable from here]
Newman & Bhat, 2008 wrote:Abstract
The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved ‘developmental-genetic toolkit’, the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of ‘dynamical patterning modules’ (DPMs), units consisting of one or more products of the ‘toolkit’ genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a ‘pattern language’ capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent ‘molecular homology-analogy paradox’, whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo-Darwinian principle, that phenotypic disparity early in evolution occurred in advance of, rather than closely tracked, genotypic change.
Oh look. What the authors of this paper are saying, is that one specific hypothesis about the origin of body plans is falsified by their results. However, even from the abstract, it is clear to me that they might not understand as much about the Modern Synthesis as they think, because last time I checked the relevant scientific papers, phenotypic diversity was considered by evolutionary biologists to be a product of genotypic change, not something that occurred "in advance" thereof. Methinks once again, that hyperbolic claims about the Modern Synthesis being "in crisis" are woefully premature.
Plus, the authors explicitly state in the above abstract, that natural selection and genetic drift, which are both integral parts of the Modern Synthesis, would have consolidated the products of their process, and consequently, they are not "casting doubt upon the Neo-Darwinian orthodoxy", rather, they are extending the remit of the Modern Synthesis by adding a new process to the mix. There is a difference, though I don't expect propagandists for mythology to understand this.
One tell tale paragraph from that paper underpins the authors' lack of understanding about what the Modern Synthesis actually says, which makes me wonder how it passed peer review without editing changes being suggested - so much for the "conspiracy to enforce Darwinism". The paragraph in question is this:
Newman & Bhat, 2008 wrote:This is not what would have been predicted by the standard model for evolutionary change—the Neo-Darwinian synthesis. In that model, where a fairly straightforward relationship between genotypic and phenotypic change is assumed, the engine of evolution is change (under natural selection) in the populational frequency of genes with small effects on the phenotype. Morphological evolution should therefore be gradual, rather than abrupt, as seen in the early metazoa.
First of all, the assertion "a fairly straightforward relationship between genotypic and phenotypic change is assumed" is plain, flat wrong, as anyone who has been reading papers in evolutionary developmental biology (evo-devo for short) will readily understand. The research literature in evo-devo is littered with instances of complex chains of signal transduction mechanisms being elucidated, and workers in the field have known for at least two decades to my knowledge, and possibly even longer, that "a fairly straightforward relationship between genotypic and phenotypic change" is NOT what the hard evidence from reality is delivering. Which once again makes me wonder how this paper passed peer review.
As for the assertion "Morphological evolution should therefore be gradual [according to the Modern Synthesis], rather than abrupt", this once again smells highly suspicious, not least because instances of major evolutionary change taking place in relatively short time frames are extant and voluminous in the evolutionary biology literature. This includes experiments on incipient speciation, which in the case of Dobzhansky's 1971 paper on Drosophila pseudoobscura, took place in just five years. Now, since the Cambrian radiation is hypothesised in the literature to have taken a good deal longer than five years, indeed, one paper in my collection cites a time span of 18 to 23 million years for this process, first of all, the idea that this was an "abrupt" process is at best a naive simplification, and at worst an outright canard, one that should not be appearing in a proper scientific paper. If I had reviewed this paper, I would have sent it back with a raft of corrections just for this one paragraph alone.
Then we have the following paragraph, namely:
Newman & Bhat, 2008 wrote:The discrepancies of these findings from the predictions of the standard model, when probed deeper, are even more serious. ]Since evolutionary change supposedly tracks genetic change, it would be expected that the genes that mediate developmental morphogenesis and pattern formation would have changed dramatically during origination of the disparate metazoan body plans. But this is also not the case. The genes of the ‘developmental-genetic toolkit’ are highly conserved among all metazoan phyla. In fact the proteins specified by these genes have changed so little during the more than half-billion years since the common ancestor of chordates and arthropods was extant, that their coding sequences will often function in development when swapped between the embryos of mice and fruit flies (see, e.g., Gehring (2002)).
First of all, the part highlighted in blue above directly contradicts their assertion at the end of the abstract, which again is a sign of sloppy, non-rigorous thinking, and once again leads me to wonder how this paper passed peer review without being sent back for a serious re-write. Second, the assertion highlighted in green was never a part of the Modern Synthesis. Indeed, the Modern Synthesis never erected assertions about the relationship between genotype and phenotpye, because, wait for it, this is an active area of research for evo-devo researchers. They are in the business of determining the real mechanisms that connect genotype to phenotype, courtesy of empirical research, about which I shall say more that is relevant in a moment. Because, wait for it, the part highlighted in red cites a research paper by Walter J. Gehrig that is intimately connected with a research paper in my collection on eye evolution, that, like every other paper of the same variety, never erected the assertion highlighted in green above. Indeed, conservation of bauplan genes is one of the extant hypotheses of the Modern Synthesis, and how the authors of this paper could have failed to know this escapes me at this juncture.
So already, this paper contains some serious deficiencies that even an elementary literature search would have remedied. Perhaps they were so keen to rush their findings to print, that they failed to apply due rigour to some of their more florid speculations.
The next paragraph is also instructive, viz:
Newman & Bhat, 2008 wrote:These observations present the following puzzle: how did large-scale morphological evolution take place so rapidly without much change in the genes specifying the proteins that mediate development? There are two possible answers: (i) unusually intense selection on regions of DNA that do not encode proteins (e.g., the regulatory regions of the genes) led to extremely rapid, but still incremental, diversification of form during a narrow period of time at the Precambrian–Cambrian boundary; and (ii) non-genetic/epigenetic determinants were responsible for generating many different organismal forms during that period, with genetic change occurring after this rapid episode of diversification. Scenario (i) underlies the analysis of many articles in what may be called the ‘Neo-Neo-Darwinian’ mode, and is well summarized in a recent book by Carroll (2005). Scenario (ii), which we favor, proposes that early multicellular forms were subject to the action at the mesoscopic scale of physical processes characteristic of viscoelastic and chemically excitable matter, and thus assumed the three-dimensional structures and patterns generic to these materials (Newman et al 2006). We will describe this latter view in what follows. In doing so, we will present evidence in support of the idea that molecular functionalities that evolved to serve unicellular life inescapably took on new morphogenetic roles in the new physical environment and larger spatial scale entailed by the transition to multicellularity.
First, the part highlighted in blue testifies to the fact that the authors appear not to have read much, if any, of the extant evo-devo literature. Because, as I've stated above, that literature contains papers documenting empirical research aimed at elucidating the underlying mechanisms. What do the authors of this paper think that evo-devo biologists are doing, sitting in the rest room playing poker?
Second, the part highlighted in green is already being investigated in the evo-devo literature. The hilarious part being that the authors of this paper cite relevant works in the literature in their list of citations at the end of the paper, yet apparently do not recognise that these prior papers are documenting precisely the sort of research into epigenetic mechanisms that they claim here to be advancing. Anyone who thinks that research into epigenetics has nothing to do with evolutionary biology really does need to sit down with a couple of dozen papers and learn otherwise. Indeed, the authors of this paper make several references to such processes as signal transduction (which is a classic epigenetic process) and Turing morphogenesis, which again is a staple part of evo-devo research - I have enough papers on Turing morphogenesis in butterflies alone telling me this, let alone any other clade of organisms.
So, how does this paper "cast doubt" upon the Modern Synthesis again, given that it merely explores a research area that is already a part of evo-devo research?