'Nothing exists for one cause' : putting biology back into evolution

The opening phrase of the title is from Charles Darwin’s notebooks (Schweber 1977). It is a double reminder, firstly that mainstream evolutionary theory is not just about describing nature but is particularly looking for mechanisms or ‘causes’, and secondly, that there will usually be several causes affecting any particular outcome. The second part of the title is our concern at the almost universal rejection of the idea that biological mechanisms are sufficient for macroevolutionary changes, thus rejecting a cornerstone of Darwinian evolutionary theory. Our primary aim here is to consider ways of making it easier to develop and to test hypotheses about evolution. Formalizing hypotheses can help generate tests. In an absolute sense, some of the discussion by scientists about evolution is little better than the lack of reasoning used by those advocating intelligent design. Our discussion here is in a Popperian framework where science is defined by that area of study where it is possible, in principle, to find evidence against hypotheses – they are in principle falsifiable. However, with time, the boundaries of science keep expanding. In the past, some aspects of evolution were outside the current boundaries of falsifiable science, but increasingly new techniques and ideas are expanding the boundaries of science and it is appropriate to re-examine some topics. It often appears that over the last few decades there has been an increasingly strong assumption to look first (and only) for a physical cause. This decision is virtually never formally discussed, just an assumption is made that some physical factor ‘drives’ evolution. It is necessary to examine our assumptions much more carefully. What is meant by physical factors ‘driving’ evolution, or what is an ‘explosive radiation’. Our discussion focuses on two of the six mass extinctions, the fifth being events in the Late Cretaceous, and the sixth starting at least 50,000 years ago (and is ongoing). Cretaceous/Tertiary boundary; the rise of birds and mammals. We have had a long-term interest (Cooper and Penny 1997) in designing tests to help evaluate whether the processes of microevolution are sufficient to explain macroevolution. The real challenge is to formulate hypotheses in a testable way. For example the numbers of lineages of birds and mammals that survive from the Cretaceous to the present is one test. Our first estimate was 22 for birds, and current work is tending to increase this value. This still does not consider lineages that survived into the Tertiary, and then went extinct later. Our initial suggestion was probably too narrow in that it lumped four models from Penny and Phillips (2004) into one model. This reduction is too simplistic in that we need to know about survival and ecological and morphological divergences during the Late Cretaceous, and whether Crown groups of avian or mammalian orders may have existed back into the Cretaceous. More recently (Penny and Phillips 2004) we have formalized hypotheses about dinosaurs and pterosaurs, with the prediction that interactions between mammals (and groundfeeding birds) and dinosaurs would be most likely to affect the smallest dinosaurs, and similarly interactions between birds and pterosaurs would particularly affect the smaller pterosaurs. There is now evidence for both classes of interactions, with the smallest dinosaurs and pterosaurs declining first, as predicted. Thus, testable models are now possible. Mass extinction number six: human impacts. On a broad scale, there is a good correlation between time of human arrival, and increased extinctions (Hurles et al. 2003; Martin 2005; Figure 1). However, it is necessary to distinguish different time scales (Penny 2005) and on a finer scale there are still large numbers of possibilities. In Hurles et al. (2003) we mentioned habitat modification (including the use of Geogenes III July 2006 31 fire), introduced plants and animals (including kiore) in addition to direct predation (the ‘overkill’ hypothesis). We need also to consider prey switching that occurs in early human societies, as evidenced by the results of Wragg (1995) on the middens of different ages on Henderson Island in the Pitcairn group. In addition, the presence of human-wary or humanadapted animals will affect the distribution in the subfossil record. A better understanding of human impacts world-wide, in conjunction with pre-scientific knowledge will make it easier to discuss the issues by removing ‘blame’. While continued spontaneous generation was accepted universally, there was the expectation that animals continued to reappear. New Zealand is one of the very best locations in the world to study many of these issues. Apart from the marine fossil record, some human impact events are extremely recent and the remains less disrupted by time.

Implications of lipid biology for the pathogenesis of schizophrenia

Objective: Preclinical and clinical data suggest that lipid biology is integral to brain development and neurodegeneration. Both aspects are proposed as being important in the pathogenesis of schizophrenia. The purpose of this paper is to examine the implications of lipid biology, in particular the role of essential fatty acids (EFA), for schizophrenia. Methods: Medline databases were searched from 1966 to 2001 followed by the crosschecking of references. Results: Most studies investigating lipids in schizophrenia described reduced EFA, altered glycerophospholipids and an increased activity of a calcium-independent phospholipase A2 in blood cells and in post-mortem brain tissue. Additionally, in vivo brain phosphorus-31 Magnetic Resonance Spectroscopy (31P-MRS) demonstrated lower phosphomonoesters (implying reduced membrane precursors) in first- and multi-episode patients. In contrast, phosphodiesters were elevated mainly in first-episode patients (implying increased membrane breakdown products), whereas inconclusive results were found in chronic patients. EFA supplementation trials in chronic patient populations with residual symptoms have demonstrated conflicting results. More consistent results were observed in the early and symptomatic stages of illness, especially if EFA with a high proportion of eicosapentaenoic acid was used. Conclusion: Peripheral blood cell, brain necropsy and 31P-MRS analysis reveal a disturbed lipid biology, suggesting generalized membrane alterations in schizophrenia. 31P-MRS data suggest increased membrane turnover at illness onset and persisting membrane abnormalities in established schizophrenia. Cellular processes regulating membrane lipid metabolism are potential new targets for antipsychotic drugs and might explain the mechanism of action of treatments such as eicosapentaenoic acid.

Paradoxical roles of tumour necrosis factor-alpha in prostate cancer biology

Tumour necrosis factor (TNF) is a pleiotropic cytokine with dual roles in cancer biology including prostate cancer (PCa). On the one hand, there is evidence that it stimulates tumour angiogenesis, is involved in the initiation of PCa from an androgen-dependent to a castrate resistant state, plays a role in epithelial to mesenchymal plasiticity, and may contribute to the aberrant regulation of eicosanoid pathways. On the other hand, TNF has also been reported to inhibit neovascularisation, induce apoptosis of PCa cells, and stimulate anti-tumour immunity. Much of the confusion surrounding its seemingly paradoxical roles in cancer biology stems from the dependence of its effects on the biological model within which TNF is investigated. This review will address some of these issues, and also discuss on the therapeutic implications.

Biology or behavior : which is the strongest contributor to weight gain?

Combating unhealthy weight gain is a major public health and clinical management issue. The extent of research into the etiology and pathophysiology of obesity has produced a wealth of evidence regarding the contributing factors. While aspects of the environment are ‘obesogenic’, weight gain is not inevitable for every individual. What then explains potentially unhealthy weight gain in individuals living within an environment where others remain lean? In this paper we explore the biological compensation that acts in response to a reduced energy intake by reducing energy needs, in order to defend against weight loss. We then examine the evidence that there is only a weak biological compensation to surplus energy supply, and that this allows behavior to drive weight gain. The extent to which biology impacts behavior is also considered.

Serine protease inhibition and mitochondrial dysfunction associated with cisplatin resistance in human tumor cell lines : targets for therapy

Indicators of mitochondrial function were studied in two different cell culture models of cis-diamminedichloroplatinum-II (CDDP) resistance: the intrinsically resistant human ovarian cancer cell line CI-80-13S, and resistant clones (HeLa-S1a and HeLa-S1b) generated by stable expression of the serine protease inhibitor—plasminogen activator inhibitor type-2 (PAI-2), in the human cervical cancer cell line HeLa. In both models, CDDP resistance was associated with sensitivity to killing by adriamycin, etoposide, auranofin, bis[1,2-bis(diphenylphosphino)ethane]gold(I) chloride {[Au(DPPE)2]Cl}, CdCl2 and the mitochondrial inhibitors rhodamine-123 (Rhl23), dequalinium chloride (DeCH), tetraphenylphosphonium (TPP), and ethidium bromide (EtBr) and with lower constitutive levels of ATP. Unlike the HeLa clones, CI-80-13S cells were additionally sensitive to chloramphenicol, 1-methyl-4-phenylpyridinium ion (MPP+), rotenone, thenoyltrifluoroacetone (TTFA), and antimycin A, and showed poor reduction of 1-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT), suggesting a deficiency in NADH dehydrogenase and/or succinate dehydrogenase activities. Total platinum uptake and DNA-bound platinum were slightly lower in CI-80-13S than in sensitive cells. The HeLa-S1a and HeLa-S1b clones, on the other hand, showed poor reduction of triphenyltetrazolium chloride (TTC), indicative of low cytochrome c oxidase activity. Total platinum uptake by HeLa-S1a was similar to HeLa, but DNA-bound platinum was much lower than for the parent cell line. The mitochondria of CI-80-13S and HeLa-S1a showed altered morphology and were fewer in number than those of JAM and HeLa. In both models, CDDP resistance was associated with less platinum accumulation and with mitochondrial and membrane defects, brought about one case with expression of a protease inhibitor which is implicated in tumor progression. Such markers may identify tumors suitable for treatment with gold phosphine complexes or other mitochondrial inhibitors.

The cancer stem-cell hypothesis : its emerging role in lung cancer biology and its relevance for future therapy

The cancer stem-cell (CSC) hypothesis suggests that there is a small subset of cancer cells that are responsible for tumor initiation and growth, possessing properties such as indefinite self-renewal, slow replication, intrinsic resistance to chemotherapy and radiotherapy, and an ability to give rise to differentiated progeny. Through the use of xenotransplantation assays, putative CSCs have been identified in many cancers, often identified by markers usually expressed in normal stem cells. This is also the case in lung cancer, and the accumulated data on side population cells, CD133, CD166, CD44 and ALDH1 are beginning to clarify the true phenotype of the lung cancer stem cell. Furthermore, it is now clear that many of the pathways of normal stem cells, which guide cellular proliferation, differentiation, and apoptosis are also prominent in CSCs; the Hedgehog (Hh), Notch, and Wnt signaling pathways being notable examples. The CSC hypothesis suggests that there is a small reservoir of cells within the tumor, which are resistant to many standard therapies, and can give rise to new tumors in the form of metastases or relapses after apparent tumor regression. Therapeutic interventions that target CSC pathways are still in their infancy and clinical data of their efficacy remain limited. However Smoothened inhibitors, gamma-secretase inhibitors, anti-DLL4 antagonists, Wnt antagonists, and CBP/β-catenin inhibitors have all shown promising anticancer effects in early studies. The evidence to support the emerging picture of a lung cancer CSC phenotype and the development of novel therapeutic strategies to target CSCs are described in this review.

Why we need a population-based approach to clinical indicators for cancer: a case study using microscopic confirmation of lung cancer in Queensland

An important function of clinical cancer registries is to provide feedback to clinicians on various performance measures. To date, most clinical cancer registries in Australia are located in tertiary academic hospitals, where adherence to guidelines is probably already high. Microscopic confirmation is an important process measure for lung cancer care. We found that the proportion of patients with lung cancer without microscopic confirmation was much higher in regional public hospitals (27.1%) than in tertiary hospitals (7.5%), and this disparity remained after adjusting for age, sex and comorbidities. The percentage was also higher in the private than in the public sector. This case study shows that we need a population-based approach to measuring clinical indicators that includes regional public hospitals as a matter of priority and should ideally include the private sector.

Systematics and biology of the iconic Australian scribbly gum moths Ogmograptis Meyrick (Lepidoptera: Bucculatricidae) and their unique insect-plant interaction

The larvae of particular Ogmograptis spp. produce distinctive scribbles on some smooth-barked Eucalyptus spp. which are a common feature on many ornamental and forest trees in Australia. However, although they are conspicuous in the environment the systematics and biology of the genus has been poorly studied. This has been addressed through detailed field and laboratory studies of their biology of three species (O. racemosa Horak sp. nov., O. fraxinoides Horak sp. nov., O. scribula Meyrick), in conjunction with a comprehensive taxonomic revision support by a molecular phylogeny utilising the mitochondrial Cox1 and nuclear 18S genes. In brief, eggs are laid in bark depressions and the first instar larvae bore into the bark to the level where the future cork cambium forms (the phellegen). Early instar larvae bore wide, arcing tracks in this layer before forming a tighter zig-zag shaped pattern. The second last instar turns and bores either closely parallel to the initial mine or doubles its width, along the zig-zag shaped mine. The final instar possesses legs and a spinneret (unlike the earlier instars) and feeds exclusively on callus tissue which forms within the zig-zag shaped mine formed by the previous instar, before emerging from the bark to pupate at the base of the tree. The scars of mines them become visible scribble following the shedding of bark. Sequence data confirm the placement of Ogmograptis within the Bucculatricidae, suggest that the larvae responsible for the ‘ghost scribbles’ (unpigmented, raised scars found on smooth-barked eucalypts) are members of the genus Tritymba, and support the morphology-based species groups proposed for Ogmograptis. The formerly monotypic genus Ogmograptis Meyrick is revised and divided into three species groups. Eleven new species are described: Ogmograptis fraxinoides Horak sp. nov., Ogmograptis racemosa Horak sp. nov. and Ogmograptis pilularis Horak sp. nov. forming the scribula group with Ogmograptis scribula Meyrick; Ogmograptis maxdayi Horak sp. nov., Ogmograptis barloworum Horak sp. nov., Ogmograptis paucidentatus Horak sp. nov., Ogmograptis rodens Horak sp. nov., Ogmograptis bignathifer Horak sp. nov. and Ogmograptis inornatus Horak sp. nov. as the maxdayi group; Ogmograptis bipunctatus Horak sp. nov., Ogmograptis pulcher Horak sp. nov., Ogmograptis triradiata (Turner) comb. nov. and Ogmograptis centrospila (Turner) comb. nov. as the triradiata group. Ogmograptis notosema (Meyrick) cannot be assigned to a species group as the holotype has not been located. Three unique synapomorphies, all derived from immatures, redefine the family Bucculatricidae, uniting Ogmograptis, Tritymba Meyrick (both Australian) and Leucoedemia Scoble & Scholtz (African) with Bucculatrix Zeller, which is the sister group of the southern hemisphere genera. The systematic history of Ogmograptis and the Bucculatricidae is discussed.

Birds : indicators of environmental repair in oil affected coastlines

Bird coastal communities were studied along Bribie Island and Moreton Island, two islands within Moreton Bay, Brisbane, Queensland, Australia, using the point counts method. A total of 128 five-hundred metre radius area surveys and 81 beach drive surveys were conducted and observations made over four seasons. Bird species were identified, counted and recorded. The data was compared between the two islands and, between sites on each island as oil-spill affected sites to non-oil spill affected sites. Species such as waders, shorebirds, terns/gulls and raptors were identified as species at most risk from an oil spill and the data was selected to look mainly at these species. The data indicated that sites affected by the oil spill contained 50% less oil-affected species than sites not affected by the oil spill. Bribie Island held on average 5 species per site in the oil affected sites compared to 12 species in non-oil affected sites. This same trend was observed on Moreton Island which held 6 species compared to 14 species. Bird data will continue to be counted over several years to determine whether the observed data is a true reflection of the affects of an oil spill on the habitat of shorebirds.

Fecal indicators and bacterial pathogens in bottled water from Dhaka, Bangladesh

Forty-six bottled water samples representing 16 brands from Dhaka, Bangladesh were tested for the numbers of total coliforms, fecal indicator bacteria (i.e., thermotolerant Escherichia coli and Enterococcus spp.) and potential bacterial pathogens (i.e., Aeromonas hydrophil, Pseudomonas aeruginos, Salmonella spp., and Shigella spp.). Among the 16 brands tested, 14 (86%), ten (63%) and seven (44%) were positive for total coliforms, E. coil and Enterococcus spp., respectively. Additionally, a further nine (56%), eight (50%), six (37%), and four (25%) brands were PCR positive for A. hydrophila lip, P. aeruginosa ETA, Salmonella spp. invA, and Shigella spp. ipaH genes, respectively. The numbers of bacterial pathogens in bottled water samples ranged from 28 ± 12 to 600 ± 45 (A. hydrophila lip gene), 180 ± 40 to 900 ± 200 (Salmonella spp. invA gene), 180 ± 40 to 1,300 ± 400 (P. aeruginosa ETA gene) genomic units per L of water. Shigella spp. ipaH gene was not quantifiable. Discrepancies were observed in terms of the occurrence of fecal indicators and bacterial pathogens. No correlations were observed between fecal indicators numbers and presence/absence of A. hydrophila lip (p = 0.245), Salmonella spp. invA (p = 0.433), Shigella spp. ipaH gene (p = 0.078), and P. aeruginosa ETA (p = 0.059) genes. Our results suggest that microbiological quality of bottled waters sold in Dhaka, Bangladesh is highly variable. To protect public health, stringent quality control is recommended for the bottled water industry in Bangladesh. Key words: bottled water, fecal indicator bacteria, quantitative PCR, bacterial pathogens, public health risk.

Profiling event logs to configure risk indicators for process delays

Risk identification is one of the most challenging stages in the risk management process. Conventional risk management approaches provide little guidance and companies often rely on the knowledge of experts for risk identification. In this paper we demonstrate how risk indicators can be used to predict process delays via a method for configuring so-called Process Risk Indicators(PRIs). The method learns suitable configurations from past process behaviour recorded in event logs. To validate the approach we have implemented it as a plug-in of the ProM process mining framework and have conducted experiments using various data sets from a major insurance company.

Urinary biomolecular indicators of exercise-induced over exertion injury

Poor health and injury represent major obstacles to the future economic security of Australia. The national economic cost of work-related injury is estimated at $57.5 billion p/a. Since exposure to high physical demands is a major risk factor for musculoskeletal injury, monitoring and managing such physical activity levels in workers is a potentially important injury prevention strategy. Current injury monitoring practices are inadequate for the provision of clinically valuable information about the tissue specific responses to physical exertion. Injury of various soft tissue structures can manifest over time through accumulation of micro-trauma. Such micro-trauma has a propensity to increase the risk of acute injuries to soft-tissue structures such as muscle or tendon. As such, the capacity to monitor biomarkers that result from the disruption of these tissues offers a means of assisting the pre-emptive management of subclinical injury prior to acute failure or for evaluation of recovery processes. Here we have adopted an in-vivo exercise induced muscle damage model allowing the application of laboratory controlled conditions to assist in uncovering biochemical indicators associated with soft-tissue trauma and recovery. Importantly, urine was utilised as the diagnostic medium since it is non-invasive to collect, more acceptable to workers and less costly to employers. Moreover, it is our hypothesis that exercise induced tissue degradation products enter the circulation and are subsequently filtered by the kidney and pass through to the urine. To test this hypothesis a range of metabolomic and proteomic discovery-phase techniques were used, along with targeted approaches. Several small molecules relating to tissue damage were identified along with a series of skeletal muscle-specific protein fragments resulting from exercise induced soft-tissue damage. Each of the potential biomolecular markers appeared to be temporally present within urine. Moreover, the regulation of abundance seemed to be associated with functional recovery following the injury. This discovery may have important clinical applications for monitoring of a variety of inflammatory myopathies as well as novel applications in monitoring of the musculoskeletal health status of workers, professional athletes and/or military personnel to reduce the onset of potentially debilitating musculoskeletal injuries within these professions.

Phenotypical characterisation of the isolated Norfolk Island population focusing on epidemiological indicators of cardiovascular disease

Objectives Only 193 people from Pitcairn Island, all descended from 9 ‘Bounty’ mutineers and 12 Tahitian women, moved to the uninhabited Norfolk Island in 1856. Our objective was to assess the population of Norfolk Island, several thousand km off the eastern coast of Australia, as a genetic isolate of potential use for cardiovascular disease (CVD) gene mapping. Methods A total of 602 participants, approximately two thirds of the island’s present adult population, were characterized for a panel of CVD risk factors. Statistical power and heritability were calculated. Results Norfolk Islander’s possess an increased prevalence of hypertension, obesity and multiple CVD risk factors when compared to outbred Caucasian populations. 64% of the study participants were descendents of the island’s original founder population. Triglycerides, cholesterol, and blood pressures all had heritabilities above 0.2. Conclusions The Norfolk land population is a potentially useful genetic isolate for gene mapping studies aimed at identifying CVD risk factor quantitative trait loci (QTL).

The biology of the glutamatergic system and potential role in migraine

Migraine is a common genetically linked neurovascular disorder. Approximately ~12% of the Caucasian population are affected including 18% of adult women and 6% of adult men (1, 2). A notable female bias is observed in migraine prevalence studies with females affected ~3 times more than males and is credited to differences in hormone levels arising from reproductive achievements. Migraine is extremely debilitating with wide-ranging socioeconomic impact significantly affecting people's health and quality of life. A number of neurotransmitter systems have been implicated in migraine, the most studied include the serotonergic and dopaminergic systems. Extensive genetic research has been carried out to identify genetic variants that may alter the activity of a number of genes involved in synthesis and transport of neurotransmitters of these systems. The biology of the Glutamatergic system in migraine is the least studied however there is mounting evidence that its constituents could contribute to migraine. The discovery of antagonists that selectively block glutamate receptors has enabled studies on the physiologic role of glutamate, on one hand, and opened new perspectives pertaining to the potential therapeutic applications of glutamate receptor antagonists in diverse neurologic diseases. In this brief review, we discuss the biology of the Glutamatergic system in migraine outlining recent findings that support a role for altered Glutamatergic neurotransmission from biochemical and genetic studies in the manifestation of migraine and the implications of this on migraine treatment.