Science Literature

According to Massimo Pigliucci and Maarten Boudry, the widespread use of machine-information metaphors is unfortunate and misleading. They complain about textbooks that develop metaphors to a considerable level of detail. As an example, they cite Alberts, who is often quoted for his analogy between a cell and a "miniature factory, complete with assembly lines, messengers, transport vehicles, etc." Another machine metaphor they dislike is that of the genome as a "blueprint", notably in the hype surrounding the Human Genome Project. Whilst these analogies are widely held within the scientific community and by educators, the main target of Pigliucci and Boudry's paper appears to be intelligent design:

"The analogy between living organisms and man-made machines has proven a persuasive rhetorical tool of the ID movement. In fact, for all the technical lingo and mathematical 'demonstrations', in much of their public presentations it is clear that ID theorists actually expect the analogies to do the argumentative work for them. In Darwin's Black Box, Behe takes Alberts' machine analogy to its extreme, describing the living cell as a complicated factory containing cargo-delivery systems, scanner machines, transportation systems and a library full of blueprints."

From the Editorial of Molecular Cell (October 2010): "Looking at a textbook picture of a cell, it all seems perfectly serene within, like a bird's eye view of a beautiful city. Zooming in close, however, a much more dynamic image emerges (see the cover). It soon becomes apparent that cells encounter a wide variety of conditions, many of which can induce stresses. These insults must be carefully and appropriately dealt with to maintain the balance that is needed for cell survival and growth." (Source here)

Pigliucci and Boudry rightly trace the emergence of machine metaphors back to, at least, the Middle Ages, and a rise to prominence with the rise of science in the 17th Century. The well-known analogy made by William Harvey is mentioned: the human heart is a pump. The authors also rightly point out that the scientists of the time gave these metaphors some additional substance, because they considered human designs to be imaging designs of the Creator.

"For Newton and many of his contemporaries, the importance of the mechanical conception of nature was greater than the mere term 'metaphor' would suggest, as the development of mechanistic philosophy was itself largely inspired by religious motivations. As Shanks wrote in his account of the history of the design argument, "the very employment of machine metaphors invited theological speculation"."

The authors turn to David Hume to find arguments foreshadowing the demise of design inferences made by the science community. Hume's (1779) Dialogues concerning natural religion is said to expose "several problems with the central analogy". The key thought is that our experience of design is limited to human artifacts, and it is presumptuous to extrapolate from this and make statements about design in general and God's design in particular.

"Hume realized that, at least in some cases, appearances of intelligent design can be deceptive. [. . .] Although Hume does not deny that we can discern similarities between nature and human artifacts, he warns us that the analogy is also defective in several respects. And if the effects are not sufficiently similar, conclusions about similar causes are premature. [. . .] Aware of the fallibility and imperfections of human reasoning, Hume remains highly skeptical about the design inference and the machine analogy, even though he was not able to provide a satisfactory explanation for the appearance of design in nature."

It has always surprised me that David Hume's arguments are considered weighty. The preceding generations of scholars did have a rationale for thinking that there is a relationship between the Creator's design and human design. This was based on the concept of image-bearing, drawn from the Judeo-Christian worldview of the time. If man is made in the image of God, they reasoned, then we design because God designs, and analogies can be drawn between human design and design in nature. Science became, for Johannes Kepler as for them all, "thinking God's thoughts after him".

The real challenge came when the theistic worldview of the pioneers of science was replaced by the deistic worldview of the Enlightenment scholars and the naturalistic worldview of their heirs. Only then does Hume's argument become coherent - and even then, design inferences can still be made at the level of hypotheses that can be tested and potentially falsified.

However, Pigliucci and Boudry suggest these metaphors and analogies are bad science. This needs to be examined closely. They object to the 'cell as a factory' analogy, the 'genome as blueprint' analogy, the 'bacterial flagellum as rotary motor' analogy, and the 'biochemical processes as digital characters in a machine code' analogy. Significantly, all these examples relate primarily to our understanding of how cells function. The major objections to metaphors, however, are linked to theories of development and the need for a viable theory of evolutionary transformation. This gives the clue to the real argument of this paper: Pigliucci and Boudry want to show that the neodarwinian synthesis and genetic reductionism have failed to deliver answers to the real problems of development and evolution, and the popular 'genome as blueprint' metaphor is inhibiting the critical appraisal of existing theory.

The 'blueprint' metaphor receives extensive discussion. They say that wherever it is used, it is always in the context of molecular biology research, not the organism as a whole. They claim that many biologists are concerned about the "hyper-reductionist approach brought about by the molecular revolution". With new discoveries about gene regulation and epigenetics, the blueprint metaphor is looking increasingly limited in its application.

"[N]ew ways of thinking about development and evolution are building a conceptual vocabulary that increasingly distances itself from the machine-information metaphor. [. . .] An answer that is being explored successfully is the idea that the information that makes development possible is localized and sensitive (as well as reactive) to the conditions of the immediate surroundings. In other words, there is no blueprint for the organism, but rather each cell deploys genetic information and adjusts its status to signals coming from the surrounding cellular environment, as well as from the environment external to the organism itself."

The need to move beyond classical genetics is even more pressing when we turn our attention from development to evolution. At best, neodarwinism is perceived to provide relatively few of the answers needed. The "current frontiers of theoretical evolutionary biology" have moved. Further comments on this are found here and here.

An example from Pigliucci and Boudry follows.

"Eva Jablonka and Marion Lamb have gone in some sense a step further and attempted to formalize a broader view of evolutionary change, which depends on the existence of not one but four mechanisms of inheritance: first, the standard genetic system; second, a panoply of epigenetic heritable effects, based on recently or newly discovered phenomena, such as differential methylation of genes, alterations of chromatin structure, so-called interference RNAs,7 and changes in conformation of proteins (e.g., prions), to mention a few; third, behavioral inheritance, mediated through the ability of some animal species to mimic each other's behavior without having it to be "inscribed" in their genes; and fourth cultural inheritance, which is limited to humans and perhaps a few other species of primates, but which has had an obviously disproportionate effect on the recent history of our planet."

The conclusion of all this is that education and research needs to refocus: away from the molecular revolution which is proving increasingly unproductive.

"The preceding discussion, we argue, shows that the limitations intrinsic in metaphors such as 'genes as blueprints' and the like are not just deleterious for science education - which would be bad enough. They actually misdirect or partially derail thinking about what sort of research programs biologists ought to carry out and how. While there is no question that the "molecular revolution" has been a central and positive development in biology, and indeed in science in general, throughout the second part of the 20th century, it is also becoming increasingly clear that the ultra-reductionist approach inspired and fueled by machine-information metaphors is running out of steam and needs to be replaced with more sophisticated and realistic thinking (a kind of reasonable, or non-greedy reductionism, so to speak). Is it then time to retire metaphors like blueprints and machines, and to seek an alternative way to conceptualize biological organisms, or would it perhaps be better to abandon the use of metaphors in this field altogether?"

Anyone reading the abstract of this paper would think that the "bad science" references relate to ID arguments. However, this is not the focus of their arguments! The authors are actually writing about the failure of the Modern Synthesis to understand both development and the processes of evolutionary transformation. They spend most of their critical discussion on the 'genome as blueprint' metaphor. It may surprise most readers to know that few, if any, ID scholars use the analogy outside the context of protein synthesis within the cell. They do not use this metaphor to suggest that the blueprint comprehends all aspects of reproduction and development. I am familiar with ID scholars questioning genetic-reductionism along the lines followed by Pigliucci and Boudry, and arguing that development needs some information-rich organismally-orientated thinking. Similarly, ID scientists critique the approach of the Modern Synthesis to evolutionary theory in much the same way as Pigliucci and Boudry have done. So there is much common ground here. The main complaint appears to be that ID scientists use metaphors to suggest that natural objects are actually intelligently designed. They are comfortable with the thought that the living world evidences features that bear witness to intelligent agency. They make use of analogies between human designs and natural phenomena because they infer intelligent agency for both categories. However, this has not led to bad science. Allowing that analogies are always partial, there should be no difficulty recognising the immense benefits that have come to science by pursuing this approach. Historical examples are easy to find; some recent examples are here and here and here.

Why Machine-Information Metaphors are Bad for Science and Science Education
Massimo Pigliucci and Maarten Boudry
Science and Education, Online October 2010 | DOI: 10.1007/s11191-010-9267-6

Abstract: Genes are often described by biologists using metaphors derived from computational science: they are thought of as carriers of information, as being the equivalent of "blueprints" for the construction of organisms. Likewise, cells are often characterized as "factories" and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Importantly, modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists' use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as "irreducible complexity" and on flawed analogies between living cells and mechanical factories. However, the living organism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume's criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume's original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public.

The earliest macrofossils of plants occur in the Silurian Period of Earth history. However, palynology (the study of plant spores, pollen and particulate organic matter in rocks) has pushed the history of plants back to the Middle Ordovician. Newly reported work has documented spores in strata that are dated 8-12 Ma earlier that the previous record holder. Both the research paper (Rubinstein et al. 2010) and the commentary (Wellman 2010) present the findings within a framework of evolutionary transformation. Press coverage puts it this way:

"As land plants matured, they evolved from liverworts into mosses, and then into plants known as hornworts and lycopods. Then ferns appeared before seed plants, of which there are many species today, finally evolved."

Liverworts are ideally suited for colonising barren ground (source here)

The concept of evolution as a 'maturing' trend is itself loaded with cultural baggage. People read into the concept all sorts of ideas that are not explicit or implied by the theory of evolution they espouse. However, landscapes mature, as do ecosystems. By employing the word in an ecological way, we can, perhaps, escape from always viewing the fossil record through evolution-tinted glasses.

The Ordovician spores are referred to as cryptospores because they have some unusual features. Wellman lists seven reasons why the spores should be associated with bryophytes in general and liverworts in particular. Interestingly, the research team found fossilised spores from five different types of liverwort, which is evidence of diversification:

"Spores of liverworts are very simple and are called cryptospores," Dr Rubinstein told the BBC. "The cryptospores that we describe are the earliest to date." These spores, dating from between 473 and 471 million years ago, come from plants belonging to five different genera - groups of species. "That shows plants had already begun to diversify, meaning they must have colonised land earlier than our dated samples," said Dr Rubinstein.

To appreciate the ecological significance of the discovery, we need to remind ourselves of the inhospitable environments that existed in the Ordovician. What land plants could conceivably have survived, let alone prosper, when faced with such arid terrains?

"Colonization of the land by plants presumably occurred in a step-wise fashion starting during the Early Paleozoic with plants at a bryophyte, most likely liverwort, grade of organization. It resulted in acceleration of weathering processes and in the formation of modern terrestrial environments, including structured soils and complex microbial communities; it also profoundly affected carbon cycling, changed the atmosphere composition and irreversibly altered climates."

In such environments, plants lacking stems and roots have significant advantages. Liverworts were able to colonise the land. The lack of a good soil is no disadvantage to a plant without roots, although they do have structures to anchor them to the ground and to absorb water. Their ability to survive both droughts (desiccation up to 90% of water content) and water-logged periods is an asset. The complex process of photosynthesis allows these plants to gain whet they needed to survive and multiply. "Bryophytes assist in the stabilisation of soil crust by colonising bare ground and rocks, and are essential in nutrient recycling, biomass production, and carbon fixing." (source here)

On ecological grounds, the plants that grew in the Ordovician were ideally suited to initiating the colonisation process. They were not there because they were primitive (because there are plenty of complexities if we look for them) but because they were pioneers in the colonisation process. Furthermore, although there is evidence of diversification, the message we need to take home is one of stasis. Having established diversity, the authors of the research paper are constrained to comment that this same diversity is apparent at higher stratigraphical levels. It would appear that diversification was accompanied by stasis. This is not a story of macroevolutionary transformation, but of variations within a basic type. Today there are over 6,000 liverwort species: there is plenty of evidence for diversification, but all of it is within the Liverwort group.

"The assemblage described here includes five cryptospore genera. Both from morphological and systematic points of view, this Dapingian assemblage is not different from younger cryptospore occurrences, including Aeronian (Early Silurian, c. 439-436 Ma) assemblages. This seems to indicate that the evolutionary rate of the earliest embryophytes was extremely low, or that selective pressures did not act on the morphology of propagules."

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)
C. V. Rubinstein, P. Gerrienne, G. S. De La Puente, R. A. Astini, P. Steemans.
New Phytologist (October 2010) 188(2): 365-369 | doi: 10.1111/j.1469-8137.2010.03433.x

Summary: The advent of embryophytes (land plants) is among the most important evolutionary breakthroughs in Earth history. It irreversibly changed climates and biogeochemical processes on a global scale; it allowed all eukaryotic terrestrial life to evolve and to invade nearly all continental environments. Before this work, the earliest unequivocal embryophyte traces were late Darriwilian (late Middle Ordovician; c. 463-461 million yr ago (Ma)) cryptospores from Saudi Arabia and from the Czech Republic (western Gondwana). Here, we processed Dapingian (early Middle Ordovician, c. 473-471 Ma) palynological samples from Argentina (eastern Gondwana). We discovered a diverse cryptospore assemblage, including naked and envelope-enclosed monads and tetrads, representing five genera. [snip]

See also:

Wellman, C.H. The invasion of the land by plants: when and where? New Phytologist, (October 2010) 188(2): 306-309 | DOI: 10.1111/j.1469-8137.2010.03471.x

Walker, M. Fossils of earliest land plants discovered in Argentina, BBC News, 12 October 2010.

The archetypal image of Neanderthals has been one that reinforced the Darwinian story of human evolution. A Washington Post story puts it like this: "Early study of Neanderthals described them as very hairy, brutish, unable to talk or walk like more-modern humans." Although things have changed slowly, media presentations have continued to create an impression that does not differ much from this description. However, the evidence for their humanity has accumulated rather rapidly in recent years, and the past month has seen two significant additions to the literature. A Wired Science report introduces one of these studies like this:

"For decades, Neanderthal was cultural shorthand for primitive. Our closest non-living relatives were caricatured as lumbering, slope-browed simpletons unable to keep pace with nimble, quick-witted Homo sapiens. However, anthropologists have found evidence in recent years suggesting considerable Neanderthal sophistication, and not only in tool-making and hunting, but in their ability to feel [i.e. to show compassion]."

It is time to wear the t-shirt (Source here)

The first paper is concerned with the role of emotions in social relationships and re-appraises the archaeological record of Neanderthals and other Palaeolithic peoples. A summary is provided by Penny Spikins in an interview with Wired.

"We look in the archaeological record for evidence of individuals who were sick, and not able to care for themselves. We see that in early Homo, and by the time we get to Neanderthals, that kind of record becomes much more extensive. Take the "Old Man of Shanidar". He had had degenerative deformities in the base of his legs, would have had difficulty walking, and had a crushing injury to his cranium, so he was probably blind in his left eye. The bones show those injuries occurred when he was adolescent, and he lived to 40. He was probably looked after for 25 to 30 years, which implies that it wasn't just one person looking after him, but several. Most of our Neanderthal skeletons show some evidence of having been looked after for their injuries. And in the age of Neanderthals, you also start to see evidence of deliberate burials and funerary rites. That means a shared feeling."

The other study is from Julien Riel-Salvatore, who has come to realise that the explanations given to evidences of Neanderthal technology and cultural artefacts is flawed. It has been said that Neanderthals gained 'modern' tools and ornaments through contact with groups of migrating Homo sapiens. The thinking was that Neanderthals could not have done it on their own - they lacked creativity. However, by studying a group of Neanderthals that lived separately from Homo sapiens, the picture changes dramatically.

The findings by anthropologist Julien Riel-Salvatore challenge a half-century of conventional wisdom maintaining that Neanderthals were thick-skulled, primitive 'cavemen' overrun and outcompeted by more advanced modern humans arriving in Europe from Africa. "Basically, I am rehabilitating Neanderthals," said Riel-Salvatore, assistant professor of anthropology at UC Denver. "They were far more resourceful than we have given them credit for."

The research has involved an analysis of Uluzzian archaeological sites throughout southern Italy, and Riel-Salvatore has come to the conclusion that the inhabitants responsible for the artefacts were Neanderthals who developed their own unique blend of "projectile points, ochre, bone tools, ornaments".

Such innovations are not traditionally associated with Neanderthals, strongly suggesting that they evolved independently, possibly due to dramatic changes in climate. More importantly, they emerged in an area geographically separated from modern humans. "My conclusion is that if the Uluzzian is a Neanderthal culture it suggests that contacts with modern humans are not necessary to explain the origin of this new behavior. This stands in contrast to the ideas of the past 50 years that Neanderthals had to be acculturated to humans to come up with this technology," he said. "When we show Neanderthals could innovate on their own it casts them in a new light. It 'humanizes' them if you will."

The picture that is emerging, reinforced and validated by the newly reported research, is that Neanderthals are somewhat different, but nevertheless equal. The evolutionary story is misleading and it needs to be discarded. The comments of Riel-Salvatore are spot on:

"The fact that Neanderthals could adapt to new conditions and innovate shows they are culturally similar to us," he said. "Biologically they are also similar. I believe they were a subspecies of human but not a different species." [. . .] "It is likely that Neanderthals were absorbed by modern humans," he said. "My research suggests that they were a different kind of human, but humans nonetheless. We are more brothers than distant cousins."

A previous blog had the title: Neandertals are part of the human family. Other blogs in this series carried similar messages. Burying the view that Neanderthals were half-wits, Darwinist thinking on the origin of religion, The cognitive skills of Stone Age Man, Images of evolution as secular icons, Walks like a man, talks like a man - is it a man?, and Rethinking Neanderthals. If we are prepared to follow the science, we must move on in our understanding of Neanderthals!

From Homininity to Humanity: Compassion from the Earliest Archaics to Modern Humans
Spikins, P.A.; Rutherford, H.E.; Needham, A.P.
Time and Mind, 3(3), November 2010, pp. 303-325 | DOI: 10.2752/175169610X12754030955977

Abstract: We are increasingly aware of the role of emotions and emotional construction in social relationships. However, despite their significance, there are few constructs or theoretical approaches to the evolution of emotions that can be related to the prehistoric archaeological record. Whilst we frequently discuss how archaic humans might have thought, how they felt might seem to be beyond the realm of academic inquiry. In this paper we aim to open up the debate into the construction of emotion in early prehistory by proposing key stages in the emotional motivation to help others; the feeling of compassion, in human evolution. We review existing literature on compassion and highlight what appear to be particularly significant thresholds in the development of compassion for human social relationships and the evolution of the human mind.

A Niche Construction Perspective on the Middle-Upper Paleolithic Transition in Italy
Julien Riel-Salvatore
Journal of Archaeological Method and Theory, published online 19 August 2010 | DOI 10.1007/s10816-010-9093-9

Abstract: This paper presents an overview of the Middle-Upper Paleolithic transition in Italy in light of recent research on the Uluzzian technocomplex and on the paleoecological context of the transition. Drawing on the realization that human niche construction can be documented in the pre-agricultural archaeological record, niche construction theory is used as a conceptual framework to tie together facets of the behavioral, biological, and ecological dimensions of the transition interval into formal models of their interaction over time and in diverse contexts. Ultimately, this effort shows how foragers of the transitional interval in the Italian peninsula were active agents in shaping their evolutionary history, with consequences of some adaptive systems being felt only much later and directing the forces responsible for the ultimate disappearance of the Mousterian and Uluzzian technocomplexes in favor of the proto-Aurignacian industry, the exact nature of which clearly appears to vary on a regional level.

See also:

Neanderthals more advanced than previously thought, EurekAlert, (September 21, 2010)

Drosophila melanogaster is a model organism for the study of genetics and some laboratory populations have been bred for different life-history traits over the course of 30 years. Professor Michael Rose, of UC Irvine, began breeding flies with accelerated development in 1991 (600 generations ago). Doctoral student Molly Burke compared the experimental flies with a control group on a genome-wide basis. This is significant because it is the first time such a study of a sexually reproducing species has been done. Burke examined specific genes and also obtained "whole-genome resequencing data from Drosophila populations that have undergone 600 generations of laboratory selection for accelerated development." The results are noteworthy on several counts:

"For decades, most researchers have assumed that sexual species evolve the same way single-cell bacteria do: A genetic mutation sweeps through a population and quickly becomes "fixated" on a particular portion of DNA. But the UCI work shows that when sex is involved, it's far more complicated. "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.

Knowing the genome sequence of Drosophila has opened new avenues of research (Source here)

The researchers were looking for the fixation of positive mutations within the genome and within the whole population. This is referred to using the term "selection sweep". When it occurs, the new mutation at a base pair (a novel single nucleotide polymorphism or SNP) not only experiences replication to be transmitted to the descendants of the organism, but the gene pool of variation is effectively swept clean as the new mutation becomes dominant in the whole population. However, such sweeping was conspicuous by its absence.

"Recent research on evolutionary genetics has focused on classic selective sweeps, which are evolutionary processes involving the fixation of newly arising beneficialmutations. In a recombining region, a selected sweep is expected to reduce heterozygosity at SNPs flanking the selected site. [. . .] Notably, we observe no location in the genome where heterozygosity is reduced to anywhere near zero, and this lack of evidence for a classic sweep is a feature of the data regardless of window size."

The paper considers a range of possible explanations for the evidence obtained. First: "Classic sweeps may be occurring, but have had insufficient time to reach fixation." Second: "selection in these lines may generally act on standing variation, and not new mutations." Third, "selection coefficients associated with newly arising mutations are not static but in fact decrease over time." No conclusion is reached regarding these various options.

"Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case."

This empirical work is worth noting on two counts. First, we are here considering a mechanism that is central to Darwinian evolution. Positive natural selection of hereditable variation is the key (we are informed) to understanding how descent with modification occurs. However, the first set of empirical data relating to a sexually reproducing species does not confirm that modification works this way. This is why Long's comment is worth repeating: "This research really upends the dominant paradigm about how species evolve". Many scientists have long suspected that the Darwinian mechanisms are inadequate to account for large-scale transformation - these research findings provide empirical support for such doubts.

The other reason for taking an interest in this research is that the Darwinian paradigm has been widely used in the development of drugs for medical use. Whereas the classical view is that genes have specific functions, the new research supports the growing body of evidence that the norm is for genes to have pleiotropic effects. A novel SNP can then be expected to have not one, but many, effects. This has been underplayed by researchers of a darwinian persuasion.

"Based on that flawed paradigm, Rose noted, drugs have been developed to treat diabetes, heart disease and other maladies, some with serious side effects. He said those side effects probably occur because researchers were targeting single genes, rather than the hundreds of possible gene groups like those Burke found in the flies. Most people don't think of flies as close relatives, but the UCI team said previous research had established that humans and other mammals share 70 percent of the same genes as the tiny, banana-eating insect known as Drosophila melanogaster."

Genome-wide analysis of a long-term evolution experiment with Drosophila
Molly K. Burke, Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose and Anthony D. Long.
Nature, 467, 587-590, (30 September 2010) | doi: 10.1038/nature09352 (preprint)

Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.

See also:

Scientists Decode Genomes of Precocious Fruit Flies, ScienceDaily (September 19, 2010)