People who love the countryside and open places tend to value biodiversity and rich ecosystems. There is a perception that a high species diversity helps to stabilise ecosystems by buffering the effects of environmental change, and in addition create ecosystems with greater functionality. According to MacDougall et al. (2013), "Biodiversity can stabilize ecological systems by functional complementarity, with different species thriving under different conditions." However, scientific underpinning has lagged behind tacit knowledge and we are faced with the growth of monocultures in agricultural husbandry and commercial land use. Nevertheless, the situation is changing, and the benefits of biodiversity are being increasingly recognised. Researchers face the problem of complex patterns of human interventions.
"Human land management is often persistent, by intentional (for example, fire suppression and overfishing) or inadvertent (for example, nitrogen pollution) disturbances that homogenize both resident diversity and environmental conditions. Persistent disturbances obscure diversity-stability relationships because they can affect ecosystem function independently of diversity, as when overgrazing directly decreases production and provides opportunities for invasion. Because persistent disturbances can also drive species loss, false positives may arise between diversity and ecosystem function, in which reductions in diversity and function are correlated but have weak mechanistic connections." (MacDougall et al. (2013), page 86)
"Biodiversity is vital for our survival and is a key measure of the health of our planet." (Source here)
Two studies have been published recently that develop the themes of (1) biodiversity promoting more resilient ecosystems, and (2) biodiversity expanding the functionality of ecosystems. First, we consider the issue of resilience.
The study area is in the Pacific Northwest of North America on grasslands described as oak savannah. Human influence has resulted in a loss of plant diversity but an increased yield of grass production. The grasslands are said to remain "resilient to invasive species and climate fluctuation". The research programme involved the periodic burning of experimental plots followed by recovery. The results show that grasslands "were able to recover from burning only in areas that had a relatively high diversity of native plants". By contrast, the species-poor grasslands were rapidly invaded by tree species with the resulting collapse of the savannah ecosystem.
"Our work demonstrates how persistent human activity can homogenize the structure and function of ecological systems, while simultaneously weakening diversity-related compensatory mechanisms needed to respond to sudden disturbance. These findings are consistent with previously demonstrated connections between diversity and ecosystem function, in which a larger portfolio of functional strategies within a community provides insurance against sudden environmental change. Given that many terrestrial systems possess this signature of compositional homogenization owing to persistent human activity, there may be a similar vulnerability to sudden environmental change that will be only evident after the collapse occurs." (MacDougall et al. (2013), page 88)
The second study was concerned with trees, and particularly with the link between ecosystem diversity and ecosystem services (functions). Again, tacit knowledge has recognised the connections before being able to document them by rigorous research.
"Ecosystems provide a wealth of benefits to human society, and the provision of such ecosystem services depends fundamentally on functions performed by organisms. This has led scientists to enquire how the diversity and composition of communities may regulate ecosystem functions. A large body of evidence has established that species diversity promotes ecosystem functions under experimental conditions. There are, however, many exceptions to the positive diversity-function relationship." (Gamfeldt et al. 2013, page 2)
The need is for research designed to look at multiple functions at a regional scale, leading to a more holistic assessment of an ecosystem. The researchers studied plots in production forests. These were relatively species-poor. The maximum recorded was 10, and only 1.5% of the plots hade more than 5 species. They identified six ecosystem services, including tree biomass production.
"Our results from boreal and temperate production forests show that the relationships between tree species richness and multiple ecosystem services were positive to positively hump-shaped, and that all services attained higher levels with five tree species than with one species. Although the relatively high level of tree biomass production with five compared with one tree species may seem both impressive and surprising, we note that similar effect sizes have been found previously. [. . .] There are, unfortunately, no previous studies on the relationships between tree species richness and the other five services that allow for comparisons with our findings." (Gamfeldt et al. 2013, page 2,3)
The paper has an interesting discussion of trade-offs leading to an explanation as to why diversity should be more prominent in strategic thinking in forestry.
"[O]ur results suggest the importance of tree species mixtures for the continued provisioning of ecosystem services from the 2-billion hectares of forest in the world currently managed as production forests or used for multiple purposes (55% of all forests). [. . .] Although the trade-offs we found imply that it will be difficult to maximize all ecosystem services simultaneously at the stand scale, the positive relationships between tree diversity and individual services suggest that adjacently located monocultures would not optimize the provision of ecosystem services at the landscape scale. Instead, adjacent stands, each with multiple species but in different combinations, might be the best way to provide multiple ecosystem services at the landscape scale." (Gamfeldt et al. 2013, page 4)
Some of the deeper issues relating to diversity are explored further below. Research findings are now complementing tacit knowledge that diversity is beneficial for ecosystems and for agriculture. This means that diversity promotion should be an integral part of the different ways we interact with ecosystems - whether for husbandry or for conservation. In other words, 'diversity by design' should be the way we think about human intervention. We might also reflect on 'diversity by design' without human intervention. This means that if the ecosystems we see around us witness to an intelligent Designer, then 'diversity' is a keyword. If this avenue of thought is valid, the inference can be made that mechanisms will exist for promoting diversity. We may then envisage machinery for engineering ecosystems to match environmental constraints. This leads to a highly dynamic perspective of organisms and one that confronts some very stereotyped popular views about design thinking.
The stereotype was advanced by Charles Darwin in his On the Origin of Species. Darwin claimed that if animals and plants were created, they would not display changes. Belief in a Creator, he argued, leads to a doctrine of fixity of species. So any evidence of variation was used to argue for evolution ("my theory") rather than creation. He wrote (Chapter XIV, Page 458): "Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created", but nowhere did Darwin support this statement with quotations or references to scholars who upheld the doctrine of the fixity of species. He asserted it, and his readers soaked it all up. It has been endlessly repeated over the years, and is part of school textbooks - so the next generation of students is programmed to think like Darwin. The reality is that the fixity of species was not held by scholars contemporary with Darwin. For example, Darwin should have known that his creationist mentor, Professor John Stevens Henslow, had embarked on a research programme to probe the limits of variation of selected plants (Kohn et al. 2005).
If we start with evidence (that diversity is beneficial) and infer that mechanisms exist for promoting diversity, then we will approach the observational data quite differently from Darwin and the Darwinists. We will recognise mechanisms that deliver diversity (e.g. via recombination of DNA during sexual reproduction). We will find that the genome exhibits plasticity, so that many phenotypes can emerge from the same genotype. Scholars today are developing understanding of phenotypic plasticity - a phenomenon that owes nothing to Darwinism. For more on this topic, go here. For case studies, go here and here.
'Diversity by design' is a rational and reasonable starting point for the study of ecology. Those who set out with this perspective will find that they travel along a different path from the one taken by Darwin, and it leads to quite different conclusions. This is a Kuhnian paradigm shift. Dominant and recessive genes are the tip of the iceberg! Speciation that is rapid, rather than gradual, is an indication of diversity by design. When we find non-random mutations or mutation hot spots, these are pointers to designed mechanisms. Epigenetics has the potential for expanding our understanding of the ways for diversity to develop. The more diversity by design is probed, the more it presents itself as a viable and interesting research paradigm.
Diversity loss with persistent human disturbance increases vulnerability to ecosystem collapse
A. S. MacDougall, K. S. McCann, G. Gellner & R. Turkington
Nature, 494, 86-89 (07 February 2013) | doi:10.1038/nature11869
Long-term and persistent human disturbances have simultaneously altered the stability and diversity of ecological systems, with disturbances directly reducing functional attributes such as invasion resistance, while eliminating the buffering effects of high species diversity. Theory predicts that this combination of environmental change and diversity loss increases the risk of abrupt and potentially irreversible ecosystem collapse, but long-term empirical evidence from natural systems is lacking. Here we demonstrate this relationship in a degraded but species-rich pyrogenic grassland in which the combined effects of fire suppression, invasion and trophic collapse have created a species-poor grassland that is highly productive, resilient to yearly climatic fluctuations, and resistant to invasion, but vulnerable to rapid collapse after the re-introduction of fire. We initially show how human disturbance has created a negative relationship between diversity and function, contrary to theoretical predictions. Fire prevention since the mid-nineteenth century is associated with the loss of plant species but it has stabilized high-yield annual production and invasion resistance, comparable to a managed high-yield low-diversity agricultural system. In managing for fire suppression, however, a hidden vulnerability to sudden environmental change emerges that is explained by the elimination of the buffering effects of high species diversity. With the re-introduction of fire, grasslands only persist in areas with remnant concentrations of native species, in which a range of rare and mostly functionally redundant plants proliferate after burning and prevent extensive invasion including a rapid conversion towards woodland. This research shows how biodiversity can be crucial for ecosystem stability despite appearing functionally insignificant beforehand, a relationship probably applicable to many ecosystems given the globally prevalent combination of intensive long-term land management and species loss.
Higher levels of multiple ecosystem services are found in forests with more tree species
Lars Gamfeldt, Tord Snall, Robert Bagchi, Micael Jonsson, Lena Gustafsson, Petter Kjellander, Maria C. Ruiz-Jaen, Mats Froberg, Johan Stendahl, Christopher D. Philipson, Grzegorz Mikusinski, Erik Andersson, Bertil Westerlund, Henrik Andren, Fredrik Moberg, Jon Moen & Jan Bengtsson.
Nature Communications, January 2013, 4, 1340 | doi:10.1038/ncomms2328
Abstract: Forests are of major importance to human society, contributing several crucial ecosystem services. Biodiversity is suggested to positively influence multiple services but evidence from natural systems at scales relevant to management is scarce. Here, across a scale of 400,000Ã¢â‚¬â€°km2, we report that tree species richness in production forests shows positive to positively hump-shaped relationships with multiple ecosystem services. These include production of tree biomass, soil carbon storage, berry production and game production potential. For example, biomass production was approximately 50% greater with five than with one tree species. In addition, we show positive relationships between tree species richness and proxies for other biodiversity components. Importantly, no single tree species was able to promote all services, and some services were negatively correlated to each other. Management of production forests will therefore benefit from considering multiple tree species to sustain the full range of benefits that the society obtains from forests.
A frequently heard phrase in discussions of the science of origins is "evidence-based". It is important that scientists affirm that their work has to do with evidence and that it is different from speculation. This blog is concerned with the evidence base for evolutionary innovation via gene duplication. The press release for the paper under consideration claims that the researchers have come up with answers, but it also contains a significant acknowledgement that, in the past, there have been significant unanswered questions about this topic:
"An important unanswered question in Darwin's theory of evolution is how new characteristics seem to appear out of nowhere. Such innovations appear to contradict the principle of gradual change, in which existing characteristics slowly evolve into another form. Yet we know that many "inventions" took place during the evolution of life."
"These results provide answers to an argument frequently used by opponents of the theory of evolution: the chance of the occurrence of a new characteristic - a functional new segment of DNA - from scratch is similar to the chance of a modern jumbo jet assembling spontaneously from a few pieces of scrap metal." (Sources - text and graphic)
The scientists consider that they have succeeded in rebuilding the DNA and proteins of prehistoric yeast cells. This is what they say:
Steven Maere: "We used sequence reconstruction algorithms to predict the DNA sequence of ancestral genes from dozens of present-day DNA sequences. This enabled us to rebuild the corresponding ancestral proteins."
Karin Voordeckers: "We searched very specifically for how the yeast adapted to break down various sources of sugar. We found that the primal gene that codes for the protein for the digestion of maltose - a sugar in grain - was copied a number of times during evolution. The DNA of some copies changed slightly, resulting in new proteins that could break down different sugars. By modeling these changes in the corresponding proteins, we now understand how just a few changes in the DNA can lead to the development of new activity in the corresponding proteins"
The scientists think that this type of duplication of the DNA often forms the basis of the emergence of apparently "new" proteins. In other words: the jumbo jet is gradually built from a copy of an existing airplane.
In a blog on the research, Doug Axe finds that the paper does not explain the origin of anything new. He suggests that the authors have used the word "Innovation" in their title in an "innovative" way!
"They clearly want to say that they've shown how a bunch of brand new enzyme activities can evolve from an ancestral enzyme that lacks them. I understand their passion. That's what I'd want to say if I wanted Darwinism to be true. And, truth be told, science papers do allow authors to cast their results in their own terms. But they also press them to state the facts plainly, and in this case here's the plain statement:
"The preduplication [i.e., ancestral] ancMalS enzyme was multifunctional and already contained the different activities found in the postduplication [i.e., evolved] enzymes, albeit at a lower level."
So, all we have here is a demonstration of what we already knew -- that evolution can adjust somewhat the relative preferences enzymes show for the molecules they already work on. Those aren't new activities, though, and this isn't a new result either."
Axe is reminding us that the evidence base says "complexity comes from complexity", which should be regarded as the finding of science. Those who seek to build complexity gradually from simple precursors are still presuming the answers rather than discovering them. The words quoted above: "Yet we know that many "inventions" took place during the evolution of life" is stating a 'given' of evolutionary theory and is unwilling to even consider that the evidence points elsewhere.
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
Karin Voordeckers, Chris A. Brown, Kevin Vanneste, Elisa van der Zande, Arnout Voet, Steven Maere, Kevin J. Verstrepen
PLoS Biology, 10(12): e1001446 | doi:10.1371/journal.pbio.1001446
Abstract: Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.
Belgian Waffle by Douglas Axe (Biologic Institute, 17 January 2013)
It is often said that the timescales for evolution are too long to allow speciation to be studied experimentally. Consequently, researchers look to the fossil record to provide the evidence base. However, this also has its limitations. With fossils, molecular analyses are not possible because soft tissues decay rapidly. Furthermore, the drivers of speciation are often a matter of speculation. Nevertheless, by selecting a depositional environment that provides a sequence of stratigraphical horizons that allow analysis of environmental factors, some informative studies are possible.
"Long-lived lakes are virtually predetermined for these studies, because of their duration and relative stability, being therefore often called 'islands of evolution'. Many studies have proven this fact repeatedly, including the papers on the impressive morphological developments in the Middle Miocene Lake Steinheim planorbids, the Neogene Aegean freshwater gastropods, or the Recent Lake Tanganyika gastropods." (page 117)
Geographical setting of Lake Pannon (source here)
The research considered in this blog has gathered data from Lake Pannon. In the past, this covered parts of eastern Austria, Hungary, Slovakia, Croatia, Serbia, and western Romania. At its maximum, it covered 290,000 km2; it lasted from the Late Miocene to the Early Pliocene. A stratigraphy has been developed and its diverse fauna logged. The research paper considers the changing fortunes of the gastropod genus Melanopsis over successive stages of the lake's chronological development.
"The aim of this paper is to document and discuss the phenotypic evolution in a single evolutionary lineage by modern morphometric analysis. The investigated geological interval of c. 1.6 Ma provides an excellent opportunity to study alternating modes of evolution in the fossil record, including stasis, the proposed adaptive radiation, and the final extinction of one of the emerging branches. The integration of a comprehensive set of palaeoenvironmental data taken from the literature provides the necessary link between the observed phenotypic evolution and underlying parameters, potentially allowing evaluation of the taxonomic status of the phenotypes." (pages 117-118)
"Recent Melanopsis praemorsa (Linnaeus, 1758) is a generalist, living in a great variety of habitats. These include rivers, ponds, springs, shallow lakes with inundated marshes, mud and gravel shores of estuaries, irrigation canals, and oases. It tolerates high temperatures and brackish conditions. This species feeds variably on algae, detritus and carrion." (image source here)
The authors are very cautious about affirming that any particular phenotype is a species. They are aware that taxonomists have tended to declare a novel phenotype to be a species rather too easily. This is relevant to Melanopsis, and all the phenotypes observed have been given specific names by researchers. Those appearing in this study are: Melanopsis impressa, M. pseudonarzolina, M. coaequat, M. fossilis, M. rugosa, M. handmanniana and M. vindobonensis. All are illustrated in Figure 2 in the research paper.
"Moreover, the authors act on the a priori assumptions of the distinctiveness of species within a lineage. To retain objectivity, we refrained from any predefined species/subspecies delimitations, many of which were proposed in earlier studies, and refer to the different morphologies as phenotypes." (page 117)
Morphometric analysis of gastropod shells has many challenges. The authors explain their approach, which is based on defining the curves (or outlines) that make up the shape. This gave a quantitative dimension to the observed phenotypic changes that correlated well with the descriptive morphological work of taxonomists. Environmental interpretations draw on prior research:
"Both the samples used for the morphological analysis as well as the major part of the isotope samples studied by Harzhauser et al. (2007) originate from a geographically small area at the western margin of Lake Pannon. Based on the previously published isotope data a rather detailed model of palaeoenvironmental change is available for the time interval and area studied. This model is used to correlate changes observed in gastropod morphology with palaeoclimate shifts." (p.120)
The scenario that emerges has three phases.
Phase 1. Fluvio-deltaic but arid environment. The molluscs lived in flowing water and tended to be small and slender (i.e. the streamlined shape matched these conditions). This situation was stable and stasis is reported.
Phase 2. Humid climate with increased precipitation. The lake level rose and water flows became slow and sluggish. Stabilising selection for the streamlined morphology ceased, and the molluscs experienced a radiation of phenotypes. Several different morphologies emerged, finding their niche somewhere in the lake.
Phase 3. Climatic instability. The environment fluctuated, with variable river discharges, lake level changes, lake stratification with periodic eutrophic conditions involving algal blooms. The impact was felt primarily by shallow water animals such as Melanopsis. Gastropod phenotypes reduced during this phase until only one phenotype was left: a small form that is inferred to have coped with the range of environmental stresses experienced. There is some evidence that this morphology is adapted to higher water energies.
The authors are careful to avoid claiming too much. They are aware that they are unable to identify the mode of speciation. The term "adaptive radiation" is one they use tentatively.
"Nevertheless, the correlation between the phenotypic changes and the environmental alterations strongly argues for ecologically driven natural selection. Consequently, the strong phenotypic divergence is thought to reflect reproductive isolation. The argument for directional selection is corroborated by the fact that both shape and size traits show massive changes within the interval of the proposed adaptive radiation. Hunt (2007) suggested body size to be a more common subject to directional selection than shape traits." (p.124)
So, what has this research achieved? A sequence of morphological changes has been identified and a correlation has been made with palaeoenvironmental data. The authors suggest that an adaptive radiation occurred when the climate became more humid, with higher precipitation and higher lake levels. They note that stratigraphic resolution was coarse, so that conclusions were unable to be drawn as to whether speciation was gradual or punctuated.
It should be said that the clearest examples of adaptation are in phases 1 and 3, where the phenotypes can be regarded as tuned to environmental factors. Phase 2 is more a case of lifting constraints, so that a wider range of morphologies were viable. Whether or not they are adaptive does not yet appear to be established. We have a radiation, but it may be a case of populating the larger ecospace.
The authors see their work as contributing to a greater understanding of how morphological changes are related to evolutionary mechanisms. It is worth pointing out that the data does not take us very far in this direction. The morphologies can be described as examples of micro-evolutionary change. The Melanopsis gastropods are all members of the same genus. Whilst morphologies change, there are no evolutionary novelties. Indeed, there is no evidence here for anything more than multiple phenotypes emerging from the same genotype. The situation fits well with the concept of phenotypic plasticity (discussed here and here). A relevant comment comes from Luskin, pointing out the implications of the research of Austin Hughes:
"This leads to the question: How, then, do new traits arise? Rather than relying on positive selection, Hughes claims that one prevalent mechanism in producing new traits is the relaxation of purifying selection -- i.e. random genetic drift. But genetic drift, of course, is essentially a random process where mutations not only arise without respect to the needs of the organism, but also are preserved (or lost) without regard for the needs of the organism. In other words, it would have no reason to build complex traits."
There is nothing here to support the thesis that macroevolution is but the extrapolation of microevolution. Indeed, the argument can be made that the observed phenotypes in Melanopsis occur within limits: constrained by the Melanopsis genotype. There may be no requirement for new genetic information to produce the range of observed phenotypes. If this is the case, far too much emphasis is being placed on speciation. The real question for evolutionary biologists relate to the origin of novelty, of body plans, and ultimately of biological information.
Phenotypic evolution in a fossil gastropod species lineage: Evidence for adaptive radiation?
Thomas A. Neubauer, Mathias Harzhauser, Andreas Kroh
Palaeogeography, Palaeoclimatology, Palaeoecology, 370, 15 January 2013, 117-126.
Abstract: Detecting speciation in the fossil record is a particularly challenging matter. Palaeontologists are usually confronted with poor preservation and limited knowledge on the palaeoenvironment. Even in the contrary case of adequate preservation and information, the linkage of pattern to process is often obscured by insufficient temporal resolution. Consequently, reliable documentations of speciation in fossils with discussions on underlying mechanisms are rare. Here we present a well-resolved pattern of morphological evolution in a fossil species lineage of the gastropod Melanopsis in the long-lived Lake Pannon. These developments are related to environmental changes, documented by isotope and stratigraphical data. After a long period of stasis, the ancestral species experiences a phenotypic change expressed as shift and expansion of the morphospace. The appearance of several new phenotypes along with changes in the environment is interpreted as adaptive radiation. Lake-level high stands affect distribution and availability of habitats and, as a result of varied functional demands on shell geometry, the distribution of phenotypes. The ongoing divergence of the morphospace into two branches argues for increasing reproductive isolation, consistent with the model of ecological speciation. In the latest phase, however, progressively unstable conditions restrict availability of niches, allowing survival of one branch only.
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Evolution has become a favorite topic of the news media recently, but for some reason, they never seem to get the story straight. The staff at Discovery Institute's Center for Science and Culture started this Blog to set the record straight and make sure you knew "the rest of the story".
A blogger from New England offers his intelligent reasoning.
We are a group of individuals, coming from diverse backgrounds and not speaking for any organization, who have found common ground around teleological concepts, including intelligent design. We think these concepts have real potential to generate insights about our reality that are being drowned out by political advocacy from both sides. We hope this blog will provide a small voice that helps rectify this situation.
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Most guys going through midlife crisis buy a convertible. Austrialian Stephen E. Jones went back to college to get a biology degree and is now a proponent of ID and common ancestry.
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